WO2013066442A2 - Mammalian genes and gene products involved in infection - Google Patents

Abstract

The present disclosure relates to mammalian genes and gene products that are involved in infection or are otherwise associated with the life cycle of one or more pathogens. Disclosed herein are methods of reducing infection of a cell by a pathogen, for example to treat or prevent a pathogen infection. Exemplary pathogens include HIV-1, HIV-2, influenza A, Marburg virus and Ebola virus. The disclosure also relates to methods of identifying agents involved in pathogen infection.

Description

MAMMALIAN GENES AND GENE PRODUCTS

INVOLVED IN INFECTION

CROSS REFERENCE TO RELATED APPLICATION

This application claims the benefit of U.S. Provisional Application No.

61/513,437, filed July 29, 2011, which is incorporated by reference herein in its entirety.

FIELD

The present disclosure relates to genes and gene products as well as modulators thereof that are involved in infection or are otherwise associated with the life cycle of one or more pathogens, such as a virus, bacteria, fungus or parasite.

BACKGROUND

Infectious diseases affect the health of people and animals around the world, causing serious illness and death. Black Plague devastated the human population in Europe during the middle ages. Pandemic flu killed millions of people in the 20^th century and is a threat to reemerge.

Some of the most feared, widespread, and devastating human diseases are caused by viruses that interfere with normal cellular processes. These include influenza, poliomyelitis, smallpox, Ebola, yellow fever, measles and acquired immunodeficiency syndrome (AIDS), to name a few. Viruses are also responsible for many cases of human disease including encephalitis, meningitis, pneumonia, hepatitis, cervical cancer, warts and the common cold. Furthermore, viruses causing respiratory infections and diarrhea in young children lead to millions of deaths each year in less-developed countries. Also, a number of newly emerging human diseases such as severe acute respiratory syndrome (SARS) is caused by viruses. In addition, the threat of a bioterrorist designed pathogen is ever present.

While vaccines have been effective to prevent certain viral infections, relatively few vaccines are available or wholly effective, have inherent risks and tend to be specific for particular conditions. Vaccines are of limited value against rapidly mutating viruses and cannot anticipate emerging viruses or new bioterrorist designed viruses. Currently there is no good solution to these threats.

Traditional treatments for viral infection include pharmaceuticals aimed at specific virus-derived proteins, such as human immunodeficiency virus (HIV) protease or reverse transcriptase, or the administration of recombinant (cloned) immune modulators (host derived), such as the interferons. However, the vast majority of viruses lack an effective drug. Further, the presently available drugs have several limitations and drawbacks including limited effectiveness, toxicity, and high rates of viral mutations which render antiviral pharmaceuticals ineffective.

SUMMARY OF THE DISCLOSURE

An urgent need exists for alternative treatments for viruses and other infectious diseases, and methods of identifying new drugs to combat these threats. The present disclosure identifies genes and gene products (as set forth in Table 1 below) that are involved in infection by one or more pathogens such as a virus, a parasite, a bacteria or a fungus, or are otherwise associated with the life cycle of a pathogen. The identification of these genes and gene products permits the identification of sequences that can be targeted for therapeutic intervention. The genomics-based discovery of nucleic acids and proteins involved in, or even required for, infection provides a new paradigm for identifying and validating various aspects of infectious disease, including assessing individual or population resistance to infection and finding novel diagnostic and drug targets for infectious disease and altering the nucleotide sequence of the host nucleic acid sequence.

Based on the observation that the genes and gene products set forth in Table 1 are involved in pathogenic infection, provided herein are methods of decreasing infection in a cell by a pathogen by decreasing expression or activity of one or more genes or gene products set forth in Table 1 or modulators thereof. In particular examples, decreasing infection does not require a 100% decrease in infection. For example, a decrease of at least 50%, at least 75%, at least 90%, or at least 98% (for example as compared to an amount of infection in the absence of the therapeutic agent) can be sufficient. The methods disclosed herein for decreasing the activity or expression of one or more genes or gene products provided in Table 1 can also be used to treat or prevent infection by a pathogen, such as a viral, fungal, parasitic, or bacterial pathogen. Further, the present disclosure also provides methods of decreasing the toxicity of a toxin in a cell including decreasing expression or activity of a gene or gene product set forth in Table 1 associated with generating a toxin, thereby reducing or inhibiting the toxicity of a toxin in a cell.

Moreover, methods of identifying an agent that decreases pathogenicity of a pathogen are disclosed. For example, the method includes contacting a test agent with a cell expressing a gene or gene product set forth in Table 1 or a modulator thereof; and determining whether the test agent decreases expression or activity of the gene or gene product set forth in Table 1, wherein a decrease in expression or activity of the gene or gene product of Table 1 as compared to a control, indicates the agent decreases pathogenicity of the pathogen.

Also provided are methods of determining resistance or susceptibility to pathogen infection in a subject, including comparing a first nucleic acid sequence of a subject to a second nucleic acid sequence comprising a sequence of a gene or gene product set forth in Table 1, wherein a higher similarity between the first and second nucleic acid sequence indicates the subject is more susceptible to pathogen infection, and wherein a lesser similarity between the first and second nucleic acid sequence indicates the subject is more resistant to pathogen infection.

In any of the disclosed methods, expression and/or activity of a gene or gene product set forth in Table 1 can be decreased by contacting the cell with an agent that decreases expression and/or activity of one or more genes or gene products listed in Table 1 or modulators thereof. As such, disclosed herein are compositions for decreasing, inhibiting, preventing or treating a pathogenic infection.

Cells and non-human mammals are also provided that have decreased susceptibility to infection by pathogens. For example, a disclosed cell can include a functional deletion of a gene set forth in Table 1, wherein the cell has a decreased susceptibility to infection by a pathogen. Further, a disclosed non-human transgenic mammal can include a functional deletion of a gene set forth in Table 1 or a modulator gene thereof that increases activity of a gene set forth in Table 1 , wherein the mammal has decreased susceptibility to infection by a pathogen is also provided.

The foregoing and other features of the disclosure will become more apparent from the following detailed description of a several embodiments.

DETAILED DESCRIPTION

/. Terms

The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure. The singular forms "a," "an," and "the" refer to one or more than one, unless the context clearly dictates otherwise. For example, the term "comprising a nucleic acid molecule" includes single or plural nucleic acid molecules and is considered equivalent to the phrase "comprising at least one nucleic acid molecule." The term "or" refers to a single element of stated alternative elements or a combination of two or more elements, unless the context clearly indicates otherwise. As used herein, "comprises" means "includes." Thus,

"comprising A or B," means "including A, B, or A and B," without excluding additional elements.

Unless explained otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes IX, published by Jones and Bartlett Publishers, 2007 (ISBN 0763740632); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Inc., 1998; and Robert A.

Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and not intended to be limiting. All sequences provided in the disclosed ENTREZ® and GENBANK® Accession numbers are incorporated herein by reference as available on July 29, 2011. In order to facilitate review of the various embodiments of the disclosure, the following explanations of specific terms are provided:

Activity: Refers to the native biological activity of a molecule, such as a gene or a gene product, such as those listed in Table 1 or a modulator thereof.

Methods of interfering with the biological activity of a molecule are known in the art, and include, but are not limited to, decreasing expression of a protein or nucleic acid sequence (such as decreasing transcription or translation), as well as decreasing the interaction between a desired molecule and its target (such as a pathogen, for example a pathogen protein). Methods of increasing the biological activity of a molecule are also known in the art, and include, but are not limited to, increasing expression of a protein or nucleic acid sequence (such as increasing transcription or translation), as well as increasing the interaction between a desired molecule and its target. An "activity of a gene product" can be an activity that is involved in pathogenicity, for example, interacting directly or indirectly, with pathogen, e.g., viral protein or viral nucleic acids, or an activity that the gene product performs in a normal cell, such as in a non-infected cell.

Administration: To provide or give a subject an agent, such as a therapeutic agent, by any effective route. Exemplary routes of administration include, but are not limited to, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), oral, intraductal, sublingual, rectal, transdermal, intranasal, and inhalation routes.

Agent: Any protein, nucleic acid molecule (including chemically modified nucleic acids), compound, antibody, small molecule, organic compound, inorganic compound, or other molecule of interest. Agent can include a therapeutic agent, a diagnostic agent or a pharmaceutical agent. A therapeutic or pharmaceutical agent is one that alone or together with an additional compound induces the desired response (such as inducing a therapeutic or prophylactic effect when administered to a subject, including inhibiting or treating an infection, such as inhibiting or treating a pathogen infection). For example, a "therapeutic agent" is a chemical compound, small molecule, or other composition, such as an antisense compound, antibody, protease inhibitor, hormone, chemokine or cytokine, capable of inducing a desired therapeutic or prophylactic effect when properly administered to a subject. In some examples, the therapeutic agent includes an isolated gene, gene product or modulator thereof is an inhibitor of a gene, gene product or modulator thereof that is up- regulated in a subject with a pathogenic infection.

An example of a therapeutic agent is one that can decrease the activity of a gene or gene product listed in Table 1 involved in pathogen infection, for example as measured by clinical response (such as a decrease in infection by a pathogen, such as an inhibition of infection). Therapeutically agents also include organic or other chemical compounds that mimic the effects of the therapeutically effective peptide, antibody, or nucleic acid molecule.

A "pharmaceutical agent" is a chemical compound or composition capable of inducing a desired therapeutic or prophylactic effect when administered to a subject, alone or in combination with another therapeutic agent(s) or

pharmaceutically acceptable carriers. In a particular example, a pharmaceutical agent decreases or even inhibits infection of a cell, such as the cell of a subject, by a pathogen, such as a virus.

Alteration in expression: An alteration in expression of a gene, gene product or modulator thereof, such as one or more disclosed in Table 1 refers to a change or difference, such as an increase or decrease, in the level of the gene, gene product, or modulators thereof that is detectable in a biological sample (such as a sample from a subject at risk or having an infection) relative to a control (such as a sample from a subject without an infection) or a reference value known to be indicative of the level of the gene, gene product or modulator thereof in the absence of infection. An "alteration" in expression includes an increase in expression (up- regulation) or a decrease in expression (down-regulation).

Antisense, Sense, and Antigene molecules: Antisense molecules are nucleic acid molecules that are at least partially complementary to the region of a larger nucleic acid molecule to which it hybridizes. An antisense compound that is "specific for" a target nucleic acid molecule is one which specifically hybridizes with and modulates expression of the target nucleic acid molecule. A "target" nucleic acid is a nucleic acid molecule to which an antisense compound is designed to specifically hybridize and modulate expression. In some examples, the target nucleic acid molecule is a gene or gene product provided in Table 1.

Nonlimiting examples of antisense molecules/compounds include primers, probes, antisense oligonucleotides, siRNAs, miRNAs, shRNAs and ribozymes. As such, these compounds can be introduced as single-stranded, double-stranded, circular, branched or hairpin compounds and can contain structural elements such as internal or terminal bulges or loops. Double- stranded antisense compounds can be two strands hybridized to form double-stranded compounds or a single strand with sufficient self complementarity to allow for hybridization and formation of a fully or partially double-stranded compound. In particular examples herein, the antisense compound is an antisense oligonucleotide, siRNA or ribozyme.

In some examples, an antisense compound is an "antisense

oligonucleotide." An antisense oligonucleotide is a single-stranded antisense compound that is a nucleic acid-based oligomer. An antisense oligonucleotide can include one or more chemical modifications to the sugar, base, and/or

internucleoside linkages. Generally, antisense oligonucleotides are "DNA-like" such that when the antisense oligonucleotide hybridizes to a target RNA molecule, the duplex is recognized by RNase H (an enzyme that recognizes DNA:RNA duplexes), resulting in cleavage of the RNA.

Contacting: Placement in direct physical association, including both a solid and liquid form. Contacting an agent with a cell can occur in vitro by adding the agent to isolated cells or in vivo by administering the agent to a subject, such as for administering an agent to inhibit or decrease infection of pathogen.

Control: A "control" refers to a sample or standard used for comparison with a test sample, such as a biological sample obtained from a patient (or plurality of patients) without an infection, such as a pathogenic infection. In some embodiments, the control is a sample obtained from a healthy patient (or plurality of patients) (also referred to herein as a "normal" control), such as a normal biological sample. In some embodiments, the control is a historical control or standard value (e.g., a previously tested control sample or group of samples that represent baseline or normal values (e.g., expression values), such as baseline or normal values of a particular gene, gene product or modulator thereof provided in Table 1 in a subject without an infection). In some examples, the control is a standard value

representing the average value (or average range of values) obtained from a plurality of patient samples (such as an average value or range of values of gene, gene products or modulators thereof expression for those listed in Table 1).

Decrease: To reduce the quality, amount, strength or activity of something, for example as compared to a control. In on example, an agent decreases or reduces a pathogenic infection, such as a viral, fungal, bacterial or parasitic infection by altering the expression of one or more genes, gene products or modulators thereof provided in Table 1. When the term "decrease" or "reduction" is used herein, a 100% decrease or reduction is not required. Therefore, the term can refer to decreases of at least 20%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100%, such as between 30% and 90%, 40% and 80%, 50% and 70%, including 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 93%, 95%, 98% or 100% decrease. In some examples, the amount of decrease is compared to a control, such as a sample or subject not receiving a therapeutic agent or a reference value known to be indicative of the amount or activity of something in the absence of treatment.

In some examples, a reduction or downregulation refers to any process which results in a decrease in production of a gene product, such as a primary transcript microRNA (pri-miRNA), precursor microRNA (pre-miRNA), mature microRNA, mRNA or protein. In certain examples, production of a gene product decreases by at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6- fold, at least 8-fold, at least 10-fold, at least 15-fold, at least 20-fold, at least 30-fold or at least 40-fold, as compared to a control.

Diagnosis: The process of identifying a disease by its signs, symptoms and/or results of various tests. The conclusion reached through that process is also called "a diagnosis." Forms of testing commonly performed include blood tests, medical imaging, genetic analysis, urinalysis, and biopsy. Ebola virus: A highly contagious hemorrhagic virus named after a river in the Democratic Republic of the Congo (formerly Zaire) in Africa, where it was first recognized. Ebola is one of two members of a family of RNA viruses called Filoviridae. There are four identified subtypes of Ebola virus. Ebola-Zaire, Ebola- Sudan, and Ebola- Ivory Coast have caused disease in humans. Ebola- Reston has caused disease in nonhuman primates, but not in humans.

Ebola hemorrhagic fever (Ebola HF) is a severe, often fatal disease in humans and nonhuman primates (for example, monkeys, gorillas, and chimpanzees) that is caused by Ebola virus infection. Early symptoms of Ebola infection can include red eyes and a skin rash. Antigen-capture enzyme- linked immunosorbent assay (ELISA) testing, IgM ELISA, PCR, and virus isolation can be used to diagnose a case of Ebola HF within a few days after the onset of symptoms.

Subjects tested later in the course of the disease, or after recovery, can be tested for IgM and IgG antibodies. The disease also can be diagnosed by using

immunohistochemistry testing, virus isolation, or PCR.

Effective amount: An amount of agent that is sufficient to generate a desired response, such as reducing or inhibiting one or more signs or symptoms associated with a condition or disease. When administered to a subject, a dosage will generally be used that will achieve target tissue/cell concentrations. In some examples, an "effective amount" is one that treats one or more symptoms and/or underlying causes of any of a disorder or disease. In some examples, an "effective amount" is a therapeutically effective amount in which the agent alone with an additional therapeutic agent(s) (for example anti-pathogenic agents), induces the desired response such as treatment of a pathogenic infection, such as a viral, fungal, parasitic, or bacterial infection.

In particular examples, it is an amount of an agent capable of modulating one or more of the disclosed genes, gene products or modulators thereof associated with a pathogenic infection (such as one or more genes, gene products or modulators thereof provided in Table 1) by least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100%

(elimination of detectable infection) by the agent. In some examples, an effective amount is an amount of a pharmaceutical preparation that alone, or together with a pharmaceutically acceptable carrier or one or more additional therapeutic agents, induces the desired response.

In one example, a desired response is to decrease or inhibit infection of a cell by a pathogen, such as a cell of a subject. Infection does not need to be completely inhibited for the pharmaceutical preparation to be effective. For example, a pharmaceutical preparation can decrease infection by a desired amount, for example by at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100%, as compared to an amount of infection in the absence of the pharmaceutical preparation. This decrease or inhibition can result in halting or slowing the progression of, or inducing a regression of a pathological condition caused by the pathogen infection, or which is capable of relieving signs or symptoms caused by the condition.

In another or additional example, it is an amount sufficient to partially or completely alleviate symptoms of pathogen infection within a host subject.

Treatment can involve only slowing the progression of the infection temporarily, but can also include halting or reversing the progression of the infection permanently.

Effective amounts of the agents described herein can be determined in many different ways, such as assaying for a reduction in the rate of infection of cells or subjects, a reduction in the viral load within a host, improvement of physiological condition of an infected subject, or increased resistance to infection following exposure to the virus. Effective amounts also can be determined through various in vitro, in vivo or in situ assays, including the assays described herein.

The disclosed therapeutic agents can be administered in a single dose, or in several doses, for example daily, during a course of treatment. However, the effective amount of can be dependent on the source applied (for example a nucleic acid molecule isolated from a cellular extract versus a chemically synthesized and purified nucleic acid), the subject being treated, the severity and type of the condition being treated, and the manner of administration.

Enveloped RNA virus: A virus whose genome includes RNA (such as a plus or minus RNA strand), and can derive an envelope from the host. The viral envelope contains the lipid and protein constituents of the membrane from which it is derived. In particular examples, the envelope is derived from the host cell plasma membrane (as in the case of HIV), from the host nuclear membrane (as in the case of herpesviruses), or from the host Golgi body (as in the case of vaccinia).

Particular examples of positive-strand RNA viruses that have an envelope include, but are not limited to: Togaviruses (examples of which include rubella); alphaviruses (such as Western equine encephalitis virus, Eastern equine encephalitis virus, and Venezuelan equine encephalitis virus); Flavi viruses (examples of which include Dengue virus, West Nile virus, Japanese encephalitis virus, and hepatitis C virus); and Coronaviruses (such as SARS).

A specific example of a positive-strand RNA virus is a retrovirus.

Retroviruses genomes consist of two molecules of RNA, which are single stranded, (+) sense and have 5' cap and 3' poly-(A) (equivalent to mRNA). Particular examples of retroviruses include, but are not limited to: human immunodeficiency virus type 1 (HIV-1), HIV-2; equine infectious anemia virus; feline

immunodeficiency virus (FIV); feline leukemia viruses (FeLV); simian

immunodeficiency virus (SIN); and avian sarcoma virus.

Exemplary negative-strand RNA viruses that have an envelope include, but are not limited to: Orthomyxoviruses (such as influenza virus), Rhabdoviruses (such as Rabies virus), Paramyxoviruses (examples of which include measles virus, mumps virus, respiratory syncytial virus), and Filoviruses such as Marburg and Ebola.

Gene: A nucleic acid sequence that encodes a peptide under the control of a regulatory sequence, such as a promoter or operator. A gene includes an open reading frame encoding a peptide, as well as exon and (optionally) intron sequences. An intron is a DNA sequence present in a given gene that is not translated into protein and is generally found between exons. The coding sequence of the gene is the portion transcribed and translated into a peptide (in vivo, in vitro or in situ) when placed under the control of an appropriate regulatory sequence. The boundaries of the coding sequence can be determined by a start codon at the 5' (amino) terminus and a stop codon at the 3' (carboxyl) terminus. If the coding sequence is to be expressed in a eukaryotic cell, a polyadenylation signal and transcription termination sequence can be included 3' to the coding sequence. Transcriptional and translational control sequences include, but are not limited to, DNA regulatory sequences such as promoters, enhancers, and terminators that provide for the expression of the coding sequence, such as expression in a host cell. A polyadenylation signal is an exemplary eukaryotic control sequence. A promoter is a regulatory region capable of binding RNA polymerase and initiating transcription of a downstream (3' direction) coding sequence. Additionally, a gene can include a signal sequence at the beginning of the coding sequence of a protein to be secreted or expressed on the surface of a cell. This sequence can encode a signal peptide, N-terminal to the mature polypeptide, which directs the host cell to translocate the polypeptide.

A "gene nonessential for cellular survival" is a gene for which disruption of one or both alleles results in a cell viable for at least a period of time which allows viral replication to be decreased or inhibited in a cell. Such a decrease can be utilized for preventative or therapeutic uses or used in research. A "gene required for pathogenic infection or growth" means the gene product of this gene, either protein or RNA, secreted or not, is necessary, either directly or indirectly in some way for the pathogen to grow.

As utilized herein, when referring to any one of the genes in Table 1, what is meant is any gene, any gene product, or any nucleic acid (DNA or RNA) associated with that gene name or a pseudonym thereof, as well as any protein, or any protein from any organism that retains at least one activity of the protein associated with the gene name or any pseudonym thereof which can function as a nucleic acid or protein utilized by a pathogen. By way of example, Table 1 refers to AHDC1. Therefore, this is intended to include, but not be limited to, any AHDC1 gene, AHDC1 gene product, for example, an AHDC1 nucleic acid (DNA or RNA) or AHDC1 protein, from any organism that retains at least one activity of AHDC1 and can function as a AHDC1 nucleic acid or protein utilized by a pathogen.

As utilized throughout, "gene product" is the primary transcript microRNA (pri-miRNA), precursor microRNA (pre-miRNA), mature microRNA, mRNA or protein resulting from the expression of a gene listed in Table 1.

Host Cell: Any cell that can be infected with a pathogen, such as a virus. A host cell can be prokaryotic or eukaryotic, such as a cell from an insect, crustacean, mammal, bird, reptile, yeast, or a bacterium such as E. coli. Exemplary host cells include, but are not limited to, mammalian B-lymphocyte cells.

The host cell can be part of an organism (such as a human or veterinary subject), or part of a cell culture, such as a culture of mammalian cells or a bacterial culture. A host nucleic acid molecule is a nucleic acid molecule present in a host cell that expresses a host protein.

Human Immunodeficiency Virus (HIV): A retrovirus that causes immunosuppression in humans and leads to a disease complex known as acquired immunodeficiency syndrome (AIDS). This immunosuppression results from a progressive depletion and functional impairment of T lymphocytes expressing the CD4 cell surface glycoprotein. Depletion of CD4 T cells results from the ability of HIV to selectively infect, replicate in, and ultimately destroy these T cells (for example see Klatzmann et al., Science 225:59, 1984). CD4 itself is an important component of the cellular receptor for HIV.

HIV subtypes can be identified by particular number, such as HIV-1 and

HIV-2. In the HIV life cycle, the virus enters a host cell in at least three stages: receptor docking, viral-cell membrane fusion, and particle uptake (D'Souza et al., JAMA 284:215, 2000). More detailed information about HIV can be found in Coffin et al., Retroviruses (Cold Spring Harbor Laboratory Press, 1997).

HIV can be diagnosed in a subject using routine methods, such as quantitative PCR methods to measure the amount of HIV virus present in an infected individual, and antibody assays (such as an ELISA assay or Western blot) to determine whether HIV antibodies are present in a subject's blood.

Early symptoms of HIV infection are usually what would be observed for any viral infection, such as one or more of the following: fever, headache, tiredness, and enlarged lymph nodes. Later symptoms of HIV infection, including

development of AIDS, can include one or more of the following: lack of energy, weight loss, frequent fevers and sweats, persistent or frequent yeast infections (oral or vaginal), persistent skin rashes or flaky skin, pelvic inflammatory disease in women that does not respond to treatment, and short-term memory loss.

Hybridization: Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (such as the Na⁺ concentration) of the hybridization buffer will determine the stringency of hybridization.

Calculations regarding hybridization conditions for attaining particular degrees of stringency are discussed in Sambrook et al., (1989) Molecular Cloning, second edition, Cold Spring Harbor Laboratory, Plain view, NY (Chapters 9 and 11). The following is an exemplary set of hybridization conditions and is not limiting:

Very High Stringency (detects sequences that share at least 90% identity)

Hybridization: 5x SSC at 65°C for 16 hours

Wash twice: 2x SSC at room temperature (RT) for 15 minutes each

Wash twice: 0.5x SSC at 65°C for 20 minutes each

High Stringency (detects sequences that share at least 80% identity)

Hybridization: 5x-6x SSC at 65°C-70°C for 16-20 hours

Wash twice: 2x SSC at RT for 5-20 minutes each

Wash twice: lx SSC at 55°C-70°C for 30 minutes each

Low Stringency (detects sequences that share at least 50% identity)

Hybridization: 6x SSC at RT to 55°C for 16-20 hours

Wash at least twice: 2x-3x SSC at RT to 55°C for 20-30 minutes each.

Infection: The entry, replication, insertion, lysis or other event or process involved with the pathogenesis of a virus or other infectious pathogen into a host cell. For example, the term "infection" can encompass one or more phases of a pathogenic life cycle including, but not limited to, attachment to cellular receptors, entry, internalization, disassembly, replication, genomic integration of pathogenic sequences, transcription of viral RNA, translation of viral RNA, transcription of host cell mRNA, translation of host cell mRNA, proteolytic cleavage of pathogenic proteins or cellular proteins, assembly of particles, endocytosis, cell lysis, budding, and egress of the pathogen from the cells. Thus, decreasing infection includes decreasing entry, replication, insertion, lysis, or other pathogenesis of a virus or other pathogen into a cell or subject, or combinations thereof.

Infection also includes the introduction of an infectious agent, such as a non- recombinant virus, recombinant virus, plasmid, bacteria, prion, eukaryotic microbe, bacterium, fungus, protozoa, or other agent capable of infecting a host, such as the cell of a subject.

In another example, infection is the introduction of a recombinant vector into a host cell, for example, via transduction, transformation, or transfection. For example, a recombinant vector can include an antisense molecule or siRNA that recognizes one or more genes listed in Table 1.

Isolated or purified: An "isolated" or "purified" biological component (such as a nucleic acid molecule or protein) has been substantially separated, produced apart from, or purified away from other biological components in the cell of the organism in which the component naturally occurs, such as other

chromosomal and extrachromosomal DNA and RNA, and proteins. Nucleic acid molecules and proteins which have been "isolated" or "purified" include, but are not limited to, nucleic acid molecules and proteins purified by standard purification methods, those prepared by recombinant expression in a host cell, as well as chemically synthesized nucleic acid molecules and proteins. Examples of methods that can be used to purify proteins, include, but are not limited to the methods disclosed in Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, New York, 1989, Ch. 17). Protein purity can be determined by, for example, polyacrylamide gel electrophoresis of a protein sample, followed by visualization of a single polypeptide band upon staining the polyacrylamide gel; high-pressure liquid chromatography; sequencing; or other conventional methods.

The term "purified" or "isolated" does not require absolute purity; rather, it is a relative term. Thus, an isolated or purified protein preparation is one in which the protein is more enriched than the protein is in its environment within a cell, such that the protein is substantially separated from cellular components (nucleic acids, lipids, carbohydrates, and other proteins) that may accompany it. For example, an isolated or purified polypeptide is a polypeptide that is substantially free from the materials with which the polypeptide is normally associated in nature or in culture. In another example, a purified protein preparation is one in which the protein is substantially-free from contaminants, such as those that might be present following chemical synthesis of the protein. In one example, a protein is purified when at least 60% by weight of a sample is composed of the protein, for example when at least 75%, at least 95%, or at least 99% or more of a sample is composed of the protein.

Marburg virus (MBGV): A highly contagious hemorrhagic virus named after Marburg, Germany where the first outbreak occurred in 1967. Marburg is one of two members of Filovirus in the family of RNA viruses called Filoviridae. There is little genetic variability among viruses belonging to the Marburg type.

Symptoms of Marburg infection can include one or more of the following: sudden onset of fever (typically lasting 7 days), maculopapular petechial rash, and hemorrhaging.

Marburg can be diagnosed using methods known in the art. Particular examples include, but are not limited to, Taqman-RT-PCR (for example see

Weidmann et al., J. Clin. Virol. 30:94-9, 2004), real-time reverse transcription-PCR (for example see Drosten et al., J. Clin. Microbiol. 40:2323-30, 2002), as well as detecting Marburg antibodies in a sample obtained from a subject.

Measles virus (MV): Measles is a Morbillivirus in the family of viruses called Paramyxoviridae. Measles is one of the most highly contagious infectious diseases. The virus is transmitted by airborne droplets, and is easily spread from person to person. The virus enters the body through the upper respiratory tract.

Symptoms of measles infection can include one or more of the following: fever, runny nose, cough, and red, watery eyes, often with sensitivity to light.

Measles can be diagnosed using methods known in the art. Particular examples include, but are not limited to: detecting measles virus or measles antibodies in a sample obtained from a subject, such as isolating the virus from the throat, or by a blood test for antibodies.

Measuring or detecting the level of expression: As used herein, measuring the level of expression of a particular gene, gene product or modulator refers to quantifying the amount of the gene, gene product or modulator thereof present in a sample. Quantification can be either numerical or relative. Detecting expression of the gene, gene product or modulators thereof can be achieved using any method known in the art or described herein, such as by measuring nucleic acids by PCR (such as RT-PCR) and proteins by ELISA. In primary embodiments, the change detected is an increase or decrease in expression as compared to a control, such as a reference value or a healthy control subject. In some examples, the detected increase or decrease is an increase or decrease of at least two-fold compared with the control or standard. Controls or standards for comparison to a sample, for the determination of differential expression, include samples believed to be normal (in that they are not altered for the desired characteristic, for example a sample from a subject who does not have an infection, such as a pathogenic infection) as well as laboratory values (e.g. , range of values), even though possibly arbitrarily set, keeping in mind that such values can vary from laboratory to laboratory.

Laboratory standards and values can be set based on a known or determined population value and can be supplied in the format of a graph or table that permits comparison of measured, experimentally determined values.

In other examples, the detected increase or decrease is a change rounded down to the nearest whole number (so that both 2.05 and 2.67 are rounded down to 2) of the fold change shown for a gene, gene product or modulator thereof in the Example Section, or is rounded to the nearest whole number (so that 2.05 would be rounded to 2 and 2.67 would be rounded to 3). In other embodiments of the methods, the increase or decrease is of a diagnostically significant amount, which refers to a change of a sufficient magnitude to provide a statistical probability of the diagnosis.

Nucleic acid: A deoxyribonucleotide or ribonucleotide polymer in either single (ss) or double stranded (ds) form, and can include analogues of natural nucleotides that hybridize to nucleic acids in a manner similar to naturally occurring nucleotides. In some examples, a nucleic acid is a nucleotide analog.

Unless otherwise specified, any reference to a nucleic acid molecule includes the reverse complement of nucleic acid. Except where single- strandedness is required by the text herein (for example, a ssRNA molecule), any nucleic acid written to depict only a single strand encompasses both strands of a corresponding double-stranded nucleic acid. For example, depiction of a plus-strand of a dsDNA also encompasses the complementary minus-strand of that dsDNA. Additionally, reference to the nucleic acid molecule that encodes a specific protein, or a fragment thereof, encompasses both the sense strand and its reverse complement.

A fragment of a nucleic acid molecule includes at least 5 contiguous bases from a nucleic acid sequence, such as at least 5 contiguous bases from a nucleic acid sequence of a gene set forth in Table 1. In particular examples, a fragment of a nucleic acid molecule corresponds to at least 10 contiguous bases, at least 20 contiguous bases, at least 25 contiguous bases, at least 50 contiguous bases, at least 100 contiguous bases, at least 250 contiguous bases, or even at least 500 contiguous bases of a desired nucleic acid sequences. Fragments of the nucleic acids described herein can be used to generate siRNA, ribozyme, triple helix, microRNA and antisense molecules.

Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in the same reading frame.

Optional (or optionally): The subsequently described event or

circumstance may or may not occur, and that the description includes instances where the event or circumstance occurs and instances where it does not. For example, the phrase "optionally obtained prior to treatment" means obtained before treatment, after treatment, or not at all.

Pathogen: A disease-producing agent. Examples include, but are not limited to viruses, bacteria, protozoa, parasites, and fungi.

Subject: Living multi-cellular vertebrate organisms, including human and non-human mammals. Particular examples of veterinary subjects include domesticated animals (such as cats and dogs), livestock (for example, cattle, horses, pigs, sheep, and goats), laboratory animals (for example, mice, rabbits, rats, gerbils, guinea pigs, and non-human primates), as well as birds, reptiles, and fish (zebrafish, goldfish, tilapia, salmon and trout). In some example, a subject is a primate, such as a human. In some examples, a subject is a non-human primate including a marmoset, monkey, chimpanzee, gorilla, orangutan, or gibbon.

Transduce, Transform, or Transfect: To introduce a nucleic acid molecule into a cell. These terms encompass all techniques by which a nucleic acid molecule can be introduced into a cell, including but not limited to, transfection with viral vectors, transformation with plasmid vectors, and introduction of naked DNA by electroporation, lipofection, and particle gun acceleration. A transfected or transformed cell is a cell into which has been introduced a nucleic acid molecule by molecular biology techniques. In particular examples, the nucleic acid molecule becomes stably replicated by the cell, for example by incorporation of the nucleic acid molecule into the cellular genome, or by episomal replication.

Transgene: An exogenous nucleic acid sequence, for example supplied by a vector. In one example, a transgene includes a nucleic acid that encodes or specifically hybridizes to one or more genes listed in Table 1.

Treating a disease: A therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition related to a pathogen infection, such as inhibiting or decreasing pathogen infection. Treating a disease in some instances can include inhibiting the full development of a disease, for example preventing development of a pathogen infection.

Variants, fragments or fusions: The disclosed nucleic acid sequences, such as sequences for the genes listed in Table 1, and the proteins encoded thereby, can include variants, fragments, and fusions thereof that retain the native biological activity (such as playing a role in pathogen infection). DNA sequences which encode for a protein or fusion thereof, or a fragment or variant of thereof can be engineered to allow the protein to be expressed in eukaryotic cells or organisms, bacteria, insects, or plants. To obtain expression, the DNA sequence can be altered and operably linked to other regulatory sequences. The final product, which contains the regulatory sequences and the therapeutic protein, is referred to as a vector. This vector can be introduced into a cell. Once inside the cell the vector allows the protein to be produced.

One of ordinary skill in the art will appreciate that the DNA can be altered in numerous ways without affecting the biological activity of the encoded protein. For example, PCR can be used to produce variations in the DNA sequence which encodes a protein. Such variants can be variants optimized for codon preference in a host cell used to express the protein, or other sequence changes that facilitate expression.

Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. A vector can include nucleic acid sequences that permit it to replicate in a host cell, such as an origin of replication, and can also include one or more selectable marker genes and other genetic elements. An insertional vector is capable of inserting itself into a host nucleic acid. Vectors include, but are not limited to, viral, plasmid, cosmid, and artificial chromosome vectors.

//. Methods of Decreasing Infection

Table 1 lists a number of genes that the inventors identified as being involved in viral infection using gene trap methods; each of the nucleic acid and protein sequences available on ENTREZ® or GENBANK® as of July 29, 2011 by the accession numbers provided in Table 1 are each incorporated by reference in their entirety. It is demonstrated herein that in addition to these genes being involved in viral infection, their gene products and modulators thereof are involved in viral infection. The role of the disclosed genes, gene products as well as modulators of thereof, are not limited to viral infection, as such proteins (and their corresponding nucleic acid sequences) are involved generally in infection by pathogens (such as viruses, bacteria (for example, members of the genus

Pseudomonas), protozoa, parasites, and fungi), such as those pathogens that use similar pathways for infection. TABLE 1

ENTREZ® Human

Gene GENBANK® Human

Number mRNA accession GENBANK® protein

incorporated number accession number

by reference incorporated by incorporated by

HUGO Gene as of July 29, reference as of reference as of July

Name 2011 July 29, 2011 29, 2011 Aliases

AHDC1 27245 NM_001029882.2 NP_001025053.1 CL23945;

DJ159A19.3; RP1- 159A19.1

BCL6 604 NM_001130845.1 NP_001124317 BCL5; LAZ3;

BCL6A; ZNF51 ;

ZBTB27

CYP8B 1 1582 NM_004391.2 NP_004382.2 CP8B; CYP12;

FLJ 17826

E2F7 144455 NM_203394.2 NP_976328.2 FLJ 12981

FAM198A 729085 NM_001129908.2 NP_001123380.2 C3orf41 ; FLJ33682;

DKFZp434B 172

FLT3LG 2323 NM_001459.2 NP_001450.2 FL

GLRB 2743 NM_000824.4 NP_000815.1 GLRB

GPR125 166647 NM_145290.2 NP_660333.2 PGR21 ; TEM5L

GRAP 10750 NM_006613.3 NP_006604.1 MGC64880 hCG_2038586 646329 NR_034120.1 FLJ38230

(LOC646329)

HDAC9 9734 NM_058176.2 NP_478056.1 HD7; HD9; HD7b;

HDAC; HDRP; MITR; HDAC7; HDAC7B;

HDAC9B;

HDAC9FL;

KIAA0744;

DKFZp779K1053

IRS 1 3667 NM_005544.2 NP_005535.1 HIRS-1

KCNIP4 80333 NM_025221.5 NP_079497.2 CALP; KCHIP4;

MGC44947

LOCI 00128239 100128239 NR_027276.1

LOC100131512 100131512 XM_001722836.2 XP_001722888.1

LOC454497 454497 XM_529825.1 XP_529825.1 (Pan

(Pan troglodytes) troglodytes)

LOC646022 146880 NR_026899.1 FLJ30780;

(LOC146880) FLJ40381 ;

MGC40489

LOC740399 740399 XM_001142404.1 XP_001142404.1

(Pan troglodytes) (Pan troglodytes)

LOC741049 741049 XM_001156563.1 XP_001156563.1

(Pan troglodytes) (Pan troglodytes)

LOC741551 741551 XM_001144203.1 XP_001144203.1

(Pan troglodytes) (Pan troglodytes) MACROD2 140733 NM_080676.5 NP_542407.2 C20orfl33

MBNL3 55796 NM_018388.3 NP_060858.2 CHCR; MBLX;

MB XL; MBLX39; FLJ11316;

FLJ97142

NADK 65220 NM_023018.3 NP_075394.3 FLJ 13052;

FLJ37724;

(U283E3.1 ; RP1- 283E3.6

NME2P1 283458 NR_001577.1

PCDH9 5101 NM_203487.2 NP_982354.1

PLD5 200150 NM_152666.1 NP_689879.1 PLDC; FLJ40773;

MGC 120565; MGC 120566; MGC 120567

PPP1R2P3 153743 NR_002168.1 MGC87149

PROM1 8842 NM_006017.2 NP_006008.1 RP41 ; AC133;

CD133; MCDR2; STGD4; CORD 12; PROML1 ;

MSTP061

RAP2A 5911 NM_021033.6 NP_066361.1 KREV; RAP2; K- REV; RbBP-30

RAP2C 57826 NM_021183.3 NP_067006.3 DKFZp313B211

RPS 11 6205 NM_001015.3 NP_001006.1

RSL24D1 51187 NM_016304.2 NP_057388.1 L30; RLP24;

RPL24; TV AS 3; RPL24L; C15orfl5; HRP-L30-iso

SCN11A 11280 NM_014139.2 NP_054858.2 NaN; SNS-2;

NAV1.9; SCN12A

SH3GL2 6456 NM_003026.2 NP_003017.1 CNSA2; SH3P4;

EEN-B l ; SH3D2A; FLJ20276;

FLJ25015

SLC35E2 9906 NM_182838.1 NP_878258.1 FLJ34996;

FLJ44537;

KIAA0447;

MGC 104754; MGC 117254; MGC126715; MGC 138494; DKFZp686M0869

SLC44A3 126969 NM_001114106.1 NP_001107578.1 CTL3; MGC45474

SLC5A7 60482 NM_021815.2 NP_068587.1 CHT; CHT1 ;

hCHT;

MGC126299; MGC 126300

STX5 6811 NM_003164.3 NP_003155.2 SED5; STX5A TAPT1 202018 NM_153365.2 NP_699196.2 CMVFR; FLJ90013

UBE2E3 10477 NM_006357.2 NP_006348.1 UBCH9; UbcM2

WASF2 10163 NM_006990.2 NP_008921.1 SCAR2; WAVE2;

(U393P12.2

WDR48 57599 NM_020839.2 NP_065890.1 P80; UAF1 ;

KIAA1449;

DKFZp686G1794

Based on this disclosure, methods are provided for decreasing or inhibiting infection in a host cell, such as a mammalian cell, by a pathogen by decreasing expression or activity of one or more gene(s) or gene product(s) set forth in Table 1. Decreased infection can occur, in vitro, ex vivo or in vivo. In some examples, the method includes decreasing, and in some examples inhibiting, the biological activity of at least one, such as at least two, at least three, at least four, at least five, at least ten, at least twenty, such as between one to twenty, one to ten, one to five of the Table 1 genes, gene products or combinations thereof. Decreasing or inhibiting the activity of a Table 1 gene, gene product, or modulator thereof can block a

component of the life cycle of a pathogen, such as blocking a signal transduction pathway leading to transcription or translation of the viral genome, or assembly of viral sub-parts.

Methods of decreasing the activity or expression of a nucleic acid or protein sequence are known in the art. Although particular examples of such methods are provided herein for illustrative purposes, the disclosure is not limited to such methods. In some examples, decreasing expression and/or activity of a gene or gene product set forth in Table 1 includes contacting the cell with a composition, such as an agent, that can decrease expression or activity of the gene, gene product or a modulator thereof. Decreasing the activity or expression of one or more Table 1 genes, gene products, or modulators thereof, does not require a 100% reduction. For example, decreases of at least 20%, at least 40%, at least 50%, at least 60%, at least 75%, at least 80%, at least 90%, at least 95%, or at least 99%, such as between a 20% to 80%, a 30% to 60% or a 40% or 50% decrease, including a 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% decrease as compared to a control (such as an amount of activity or expression in a cell not treated with a therapeutic agent), can be sufficient. i. Gene( s) or Gene product( s )

The disclosed methods of decreasing infection involve decreasing expression or activity of one or more gene(s) or gene product(s) set forth in Table 1. The genes listed in Table 1 are host genes involved in viral infection. All of the host genes involved in viral infection, set forth in Table 1, were identified using gene trap methods that were designed to identify host genes that are necessary for viral infection or growth, but nonessential for cellular survival. These gene trap methods are set forth in the Example provided below as well as in U.S. Patent No. 6,448,000 and U. S. Patent No. 6,777,177 each of which is hereby incorporated by reference in its entirety.

In some examples, the disclosed methods can be used to decrease the expression or activity of one or more genes listed in Table 1 which is a gene nonessential for cellular survival. This disruption of one or both alleles results in a cell viable for at least a period of time which allows viral replication to be decreased or inhibited in a cell. Such a decrease can be utilized for preventative or therapeutic uses or used in research. In some examples, the disclosed methods can be used to decrease or inhibit the expression or activity of one or more genes listed in Table 1 which is required for pathogenic infection or growth. Such a decrease or inhibition results in a reduction in the gene product of this gene, either protein or RNA

(secreted or not), thereby reducing or inhibiting pathogenic infection or growth.

The nucleic acids of the genes listed in Table 1 and their encoded proteins can be involved in all phases of the viral life cycle including, but not limited to, viral attachment to cellular receptors, viral infection, viral entry, internalization, disassembly of the virus, viral replication, genomic integration of viral sequences, transcription of viral RNA, translation of viral mRNA, transcription of cellular proteins, translation of cellular proteins, trafficking, proteolytic cleavage of viral proteins or cellular proteins, assembly of viral particles, budding, cell lysis and egress of virus from the cells.

Although the genes set forth herein were identified as cellular genes involved in viral infection, as discussed throughout, the present disclosure is not limited to viral infection. Therefore, any of these nucleic acid sequences and the proteins encoded by these sequences can be involved in infection by any infectious pathogen such as bacterial, fungal or parasitic infection which includes involvement in any phase of the infectious pathogen's life cycle.

Table 1 provides the ENTREZ® Gene numbers for the human genes set forth herein. The information provided under the ENTREZ® Gene numbers listed in Table 1 is hereby incorporated by reference in their entirety as available on July 29, 2011. One of skill in the art can readily obtain this information from the

National Center for Biotechnology Information at the National Library of Medicine (at the World Wide Web address ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene). By accessing ENTREZ® Gene, one of skill in the art can readily obtain information about every gene listed in Table 1, such as the genomic location of the gene, a summary of the properties of the protein encoded by the gene, expression patterns, function, information on homologs of the gene as well as numerous reference sequences, such as the genomic, mRNA and protein sequences for each gene.

Therefore, one of skill in the art can readily obtain sequences, such as genomic, mRNA and protein sequences by accessing information available under the

ENTREZ® Gene number provided for each gene. Thus, all of the information readily obtained from the ENTREZ® Gene Nos. set forth herein is also hereby incorporated by reference in its entirety as available on July 29, 2011.

Also provided in Table 1 are the ® Accession Nos. for at least one example of the human mRNA sequence and the GENBANK® Accession Nos. for the human protein sequence, if available. It is noted that there may be multiple isoforms or variants of a gene or protein, and these are also contemplated herein by reference to the gene, even when the specific Accession Number for that isoform or variant is not given. For certain non-protein coding genes, a non-coding RNA is provided. The nucleic acid sequences and protein sequences provided under the GENBANK® Accession Nos. mentioned herein are hereby incorporated in their entireties by this reference. One of skill in the art would know that the nucleotide sequences provided under the GENBANK® Accession Nos. set forth herein can be readily obtained from the National Center for Biotechnology Information at the National Library of Medicine (on the World Wide Web at

ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide). Similarly, the protein sequences set forth herein can be readily obtained from the National Center for Biotechnology Information at the National Library of Medicine (on the World Wide Web at ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein). The nucleic acid sequences and protein sequences provided under the GENBANK® Accession Nos. mentioned herein are hereby incorporated by reference in their entireties as available on July 29, 2011.

These examples are not meant to be limiting as one of skill in the art would know how to obtain additional sequences for the genes and gene products listed in Table 1 from other species by accessing GENBANK® (Benson et al. Nucleic Acids Res., 32: D23-D26, 2004), the EMBL Database (Stoesser et al. Nucleic Acids Res., 28: 19-23, 2000) or other sequence databases. One of skill in the art would also know how to align the sequences disclosed herein with sequences from other species in order to determine similarities and differences between the sequences set forth in Table 1 and related sequences, for example, by utilizing BLAST. As set forth herein, a nucleic acid sequence for any of the genes set forth in Table 1 can be a full- length wild-type (or native) sequence, a genomic sequence, a variant (for example, an allelic variant or a splice variant), a nucleic acid fragment, a homolog or a fusion sequence that retains the activity of the gene utilized by the pathogen or its encoded gene product.

The nucleic acid may represent a coding strand or its complement, or any combination thereof. Nucleic acids may be identical in sequence to the sequences which are naturally occurring for any of the moieties discussed herein or may include alternative codons which encode the same amino acid as that which is found in the naturally occurring sequence. These nucleic acids can also be modified from their typical structure. Such modifications include, but are not limited to, methylated nucleic acids, the substitution of a non-bridging oxygen on the phosphate residue with either a sulfur (yielding phosphorothioate deoxynucleotides), selenium (yielding phosphorselenoate deoxynucleotides), or methyl groups (yielding methylphosphonate deoxynucleotides), a reduction in the AT content of AT rich regions, or replacement of non-preferred codon usage of the expression system to preferred codon usage of the expression system. The nucleic acid can be directly cloned into an appropriate vector, or if desired, can be modified to facilitate the subsequent cloning steps. Such modification steps are routine, an example of which is the addition of oligonucleotide linkers which contain restriction sites to the termini of the nucleic acid. General methods are set forth in in Sambrook et al. (2001) Molecular Cloning - A Laboratory Manual (3rd ed.) Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor Press, NY, (Sambrook).

Once the nucleic acid sequence is obtained, the sequence encoding the specific amino acids can be modified or changed at any particular amino acid position by techniques well known in the art. For example, PCR primers can be designed which span the amino acid position or positions and which can substitute any amino acid for another amino acid. Alternatively, one skilled in the art can introduce specific mutations at any point in a particular nucleic acid sequence through techniques for point mutagenesis. General methods are set forth in Smith, M. "In vitro mutagenesis" Am. Rev. Gen., 19:423-462 (1985) and Zoller, M.J. "New molecular biology methods for protein engineering" Curr. Opin. Struct. Biol., 1:605-610 (1991), which are incorporated herein by reference in their entireties for the methods. These techniques can be used to alter the coding sequence without altering the amino acid sequence that is encoded.

The sequences contemplated herein include full-length wild-type (or native) sequences, as well as allelic variants, variants, fragments, homologs or fusion sequences that retain the ability to function as the cellular nucleic acid or protein involved in viral infection. In certain examples, a protein or nucleic acid sequence has at least 50% sequence identity, for example at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 98%, such as between 50% to 70%, between 80% to 95%, between 90% to 98%, between 90% to 95%, between 95% to 98%, including 50%, 53%, 55%, 57%, 60%, 62%, 65%, 67%, 70%, 73%, 75%, 78%, 80%, 83%, 85%, 87%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a native sequence of the genes set forth in Table 1. In other examples, a nucleic acid sequence involved in viral infection has a sequence that hybridizes to a sequence of a gene set forth in Table 1 and retains the activity of the sequence of the gene set forth in Table 1. For example, and not to be limiting, a nucleic acid that hybridizes to a AT-hook DNA-binding motif-containing protein 1 (AHDCl) nucleic acid sequence and encodes a protein that retains AHDC1 activity is contemplated by the present disclosure. Such sequences include the genomic sequence for the genes set forth in Table 1. The examples set forth above for AHDC1 are merely illustrative and should not be limited to AHDC1 as the analysis set forth in this example applies to every nucleic acid and protein for the genes listed in Table 1.

Unless otherwise specified, any reference to a nucleic acid molecule includes the reverse complement of the nucleic acid. Except where single-strandedness is required by the text herein (for example, a ssRNA molecule), any nucleic acid written to depict only a single strand encompasses both strands of a corresponding double-stranded nucleic acid. Fragments of the nucleic acids for the genes set forth in Table 1 and throughout the specification are also contemplated. These fragments can be utilized as primers and probes to amplify, inhibit or detect any of the nucleic acids or genes set forth in Table 1.

The present disclosure provides isolated polypeptides comprising the polypeptide or protein sequences set forth under the GENBANK® Accession Nos. set forth in Table 1. The present disclosure also provides fragments of these polypeptides. These fragments can be of sufficient length to serve as antigenic peptides for the generation of antibodies. The present disclosure also contemplates functional fragments that possess at least one activity of a gene or gene product listed in Table 1, for example, involved in viral infection. It will be known to one of skill in the art that each of the proteins set forth herein possess other properties, such as for example, E2F7 is an E2F transcription factor, and GLRB is the beta subunit of the glycine receptor. Fragments and variants of the proteins set forth herein can include one or more conservative amino acid residues as compared to the amino acid sequence listed under their respective GENBANK® Accession Nos.

The polypeptides of the disclosure can be obtained by methods known to those of skill in the art including, for example, by extraction from a natural source if available (for example, a mammalian cell), by expression of a recombinant nucleic acid encoding the polypeptide (for example, in a cell or in a cell-free translation system), or by chemically synthesizing the polypeptide. In addition, a polypeptide can be obtained by cleaving full-length polypeptides. When the polypeptide is a fragment of a larger naturally occurring polypeptide, the isolated polypeptide is shorter than and excludes the full-length, naturally occurring polypeptide of which it is a fragment.

Also provided by the present disclosure is a polypeptide comprising an amino acid sequence at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, such as between 80% and 95%, between 90% and 98%, between 93% and 95%, between 95% and 98%, including 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the native polypeptide sequence for any gene set forth in Table 1.

It is understood that as discussed herein the use of the terms "homology" and

"identity" mean the same thing as similarity. Thus, for example, if the use of the word homology is used to refer to two non-natural sequences, it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related.

In general, it is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed nucleic acids and polypeptides herein, is through defining the variants and derivatives in terms of homology to specific known sequences. In general, variants of nucleic acids and polypeptides herein disclosed typically have at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, such as between 80% and 95%, between 90% and 98%, between 93% and 95%, between 95% and 98%, including 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% homology to the stated sequence or the native sequence. Those of skill in the art readily understand how to determine the homology of two polypeptides or nucleic acids. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.

Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison can be conducted by the local homology algorithm of Smith and Waterman, Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI; the BLAST algorithm of Tatusova and Madden, FEMS Microbiol. Lett. 174: 247-250 (1999) available from the National Center for Biotechnology Information (World Wide Web at domain name ncbi.nlm.nih.gov/blast/bl2seq/bl2.html), or by inspection.

The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al, Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al, Methods Enzymol. 183:281-306, 1989, which are herein incorporated by, reference for at least material related to nucleic acid alignment. It is understood that any of the methods typically can be used and that in certain instances the results of these various methods may differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity.

For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).

Also provided by the present disclosure are polypeptides set forth under the GENBANK® Accession Nos. disclosed herein, or fragments thereof, with one or more conservative amino acid substitutions. These conservative substitutions are such that an amino acid having similar properties replaces a naturally occurring one. Such conservative substitutions do not alter the function of the polypeptide. For example, conservative substitutions can be made as follows: Arg can be replaced with Lys, Asn can be replace with Gin, Asn can be replaced with Glu, Cys can be replaced with Ser, Gin can be replaced with Asn, Glu can be replaced with Asp, Gly can be replaced with Pro, His can be replaced with Gin, lie can be replaced with Leu or Val, Gly can be replaced with Pro, His can be replaced with Gin, He can be replaced with He or Val, Leu can be replaced with He or Val, Lys can be replaced with Arg or Gin, Met can be replaced with Leu or He, Phe can be replaced with Met, Leu or Tyr, Ser can be replaced with Thr, Thr can be replaced with Ser, Trp can be replaced with Tyr, Tyr can be replaced with Trp or Phe; and Val can be replaced with He or Leu.

Thus, it is understood that, where desired, modifications and changes may be made in the nucleic acid encoding the polypeptides of this disclosure and/or amino acid sequence of the polypeptides of the present disclosure and still obtain a polypeptide having like or otherwise desirable characteristics. Such changes may occur in natural isolates or may be synthetically introduced using site-specific mutagenesis, the procedures for which, such as mismatch polymerase chain reaction (PCR), are well known in the art. For example, certain amino acids may be substituted for other amino acids in a polypeptide without appreciable loss of functional activity. It is thus contemplated that various changes may be made in the amino acid sequence of the polypeptides of the present disclosure (or underlying nucleic acid sequence) without appreciable loss of biological utility or activity and possibly with an increase in such utility or activity. Thus, it is clear that naturally occurring variations in the polypeptide sequences set forth herein as well as genetically engineered variations in the polypeptide sequences set forth herein are contemplated by the present disclosure. Cells expressing variant polypeptides, whether naturally occurring or genetically engineered can be utilized in the methods of the present disclosure. By providing the genomic location of genes that are involved in viral infection, the present disclosure has also provided the genomic location of any variant sequences of these genes. Thus, based on the information provided herein, it would be routine for one of skill in the art to identify and sequence the genomic region identified by applicants and identify variant sequences of the genes set forth herein. It would also be routine for one of skill in the art to utilize comparison tools and bioinformatics techniques to identify sequences from other species that are homologs of the genes set forth herein and are also necessary for infection, but not necessary for survival of the cell.

ii. Cell Types

The disclosed methods can be used to decrease or inhibit infection in a variety of cells. For example, the cells of the present disclosure can be prokaryotic or eukaryotic, such as a cell from an insect, fish, crustacean, mammal, bird, reptile, yeast or a bacterium, such as E. coli. The cell can be part of an organism, or part of a cell culture, such as a culture of mammalian cells or a bacterial culture. The cell can also be part of a population of cells. The cell(s) can also be in a subject, such as a human or a veterinary animal.

Hi. Types of Infection and Pathogens

The disclosed methods can treat various infections, including a viral infection, bacterial infection, fungal infection or a parasitic infection. Exemplary pathogens include, but are not limited to, viruses, bacteria, protozoa, parasites, and fungi. Examples of viral infections include but are not limited to, infections caused by or associated with pathogens including RNA viruses (including negative stranded RNA viruses, positive stranded RNA viruses, double stranded RNA viruses and retroviruses), or DNA viruses. All strains, types, and subtypes of RNA viruses and DNA viruses are contemplated herein.

Examples of RNA viruses include, but are not limited to picornaviruses, which include aphthoviruses (for example, foot and mouth disease virus O, A, C, Asia 1, SAT1, SAT2 and SAT3), cardioviruses (for example, encephalomycarditis virus and Theiller's murine encephalomyelitis virus), enteroviruses (for example polioviruses 1, 2 and 3, human enteroviruses A-D, bovine enteroviruses 1 and 2, human coxsackieviruses A1-A22 and A24, human coxsackieviruses B1-B5, human echoviruses 1-7, 9, 11-12, 24, 27, 29-33, human enteroviruses 68-71, porcine enteroviruses 8-10 and simian enteroviruses 1-18), erboviruses (for example, equine rhinitis virus), hepato virus (for example human hepatitis A virus and simian hepatitis A virus), kobuviruses (for example, bovine kobuvirus and Aichi virus), parechoviruses (for example, human parechovirus 1 and human parechovirus 2), rhinovirus (for example, rhinovirus A, rhinovirus B, rhinovirus C, HRV^, HRV₁₆ (VR-11757), HRV₁₄ (VR-284), or HRV_1A (VR-1559), human rhinovirus 1-100 and bovine rhinoviruses 1-3) and teschoviruses (for example, porcine teschovirus).

Additional examples of RNA viruses include caliciviruses, which include noroviruses (for example, Norwalk virus), sapoviruses (for example, Sapporo virus), lagoviruses (for example, rabbit hemorrhagic disease virus and European brown hare syndrome) and vesiviruses (for example vesicular exanthema of swine virus and feline calicivirus).

Other RNA viruses include astroviruses, which include mamastorviruses and avastro viruses. Togaviruses are also RNA viruses. Togaviruses include

alphaviruses (for example, Chikungunya virus, Sindbis virus, Semliki Forest virus, Western equine encephalitis, Getah virus, Everglades virus, Venezuelan equine encephalitis virus and Aura virus) and rubella viruses. Additional examples of RNA viruses include the the flavi viruses (for example, tick-borne encephalitis virus, Tyuleniy virus, Aroa virus, Dengue virus (types 1 to 4), Kedougou virus, Japanese encephalitis virus (JEV), West Nile virus (WNV), Kokobera virus, Ntaya virus, Spondweni virus, Yellow fever virus, Entebbe bat virus, Modoc virus, Rio Bravo virus, Cell fusing agent virus, pestivirus, GB virus A, GBV-A like viruses, GB virus C, Hepatitis G virus, hepacivirus (hepatitis C virus (HCV)) all six genotypes), bovine viral diarrhea virus (BVDV) types 1 and 2, and GB virus B).

Other examples of RNA viruses are the coronaviruses, which include, human respiratory coronaviruses such as SARS-CoV, HCoV-229E, HCoV-NL63 and HCoV-OC43. Coronaviruses also include bat SARS-like CoV, turkey coronavirus, chicken coronavirus, feline coronavirus and canine coronavirus. Additional RNA viruses include arteriviruses (for example, equine arterivirus, porcine reproductive and respiratory syndrome virus, lactate dehyrogenase elevating virus of mice and simian hemorraghic fever virus). Other RNA viruses include the rhabdoviruses, which include lyssaviruses (for example, rabies, Lagos bat virus, Mokola virus,

Duvenhage virus and European bat lyssavirus), vesiculoviruses (for example, VSV- Indiana, VSV-New Jersey, VSV-Alagoas, Piry virus, Cocal virus, Maraba virus, Isfahan virus and Chandipura virus), and ephemero viruses (for example, bovine ephemeral fever virus, Adelaide River virus and Berrimah virus). Additional examples of RNA viruses include the filoviruses. These include the Marburg and Ebola viruses (for example, EBOV-Z, EBOV-S, EBOV-IC and EBOV-R.

Additional examples of RNA viruses are the paramyxoviruses. Examples of these viruses are the rubulaviruses (for example, mumps, parainfluenza virus 5, human parainfluenza virus type 2, Mapuera virus and porcine rubulavirus), avulaviruses (for example, Newcastle disease virus), respoviruses (for example, Sendai virus, human parainfluenza virus type 1 and type 3, bovine parainfluenza virus type 3), henipaviruses (for example, Hendra virus and Nipah virus), morbilloviruses (for example, measles, Cetacean morvilliirus, Canine distemper virus, Peste-des-petits-ruminants virus, Phocine distemper virus and Rinderpest virus), pneumoviruses (for example, human respiratory syncytial virus A2, B l and S2, bovine respiratory syncytial virus and pneumonia virus of mice),

metapneumo viruses (for example, human metapneumovirus and avian

metapneumovirus). Additional paramyxoviruses include Fer-de-Lance virus, Tupaia paramyxovirus, Menangle virus, Tioman virus, Beilong virus, J virus, Mossman virus, Salem virus and Nariva virus.

Additional RNA viruses include the orthomyxoviruses. These viruses include influenza viruses and strains (e.g., influenza A, influenza A strain

A/Victoria/3/75, influenza A strain A/Puerto Rico/8/34, influenza A H1N1

(including but not limited to A/WS/33, A/NWS/33 and A/California/04/2009 strains) influenza B, influenza B strain Lee, and influenza C viruses) H2N2, H3N2, H5N1, H7N7, H1N2, H9N2, H7N2, H7N3 and H10N7), as well as avian influenza (for example, strains H5N1, H5N1 Duck/MN/ 1525/81, H5N2, H7N1, H7N7 and H9N2) thogoto viruses and isaviruses. Orthobunyaviruses (for example, Akabane virus, California encephalitis, Cache Valley virus, Snowshoe hare virus,) nairo viruses (for example, Nairobi sheep virus, Crimean-Congo hemorrhagic fever virus Group and Hughes virus), phleboviruses (for example, Candiru, Punta Toro, Rift Valley Fever, Sandfly Fever, Naples, Toscana, Sicilian and Chagres), and hantaviruses (for example, Hantaan, Dobrava, Seoul, Puumala, Sin Nombre, Bayou, Black Creek Canal, Andes and Thottapalayam) are also RNA viruses. Arenaviruses such as lymphocytic choriomeningitis virus, Lujo virus, Lassa fever virus, Argentine hemorrhagic fever virus, Bolivian hemorrhagic fever virus, Venezuelan hemorrhagic fever virus, SABV and WWAV are also RNA viruses. Borna disease virus is also an RNA virus. Hepatitis D (Delta) virus and hepatitis E are also RNA viruses.

Additional RNA viruses include reoviruses, rotaviruses, birnaviruses, chrysoviruses, cystoviruses, hypoviruses partitiviruses and totoviruses. Orbiviruses such as African horse sickness virus, Blue tongue virus, Changuinola virus, Chenuda virus, Chobar Gorge Corriparta virus, epizootic hemorraghic disease virus, equine encephalosis virus, Eubenangee virus, Ieri virus, Great Island virus,

Lebombo virus, Orungo virus, Palyam virus, Peruvian Horse Sickness virus, St. Croix River virus, Umatilla virus, Wad Medani virus, Wallal virus, Warrego virus and Wongorr virus are also RNA viruses.

Retroviruses include alpharetroviruses (for example, Rous sarcoma virus and avian leukemia virus), betaretroviruses (for example, mouse mammary tumor virus, Mason-Pfizer monkey virus and Jaagsiekte sheep retrovirus), gammaretroviruses (for example, murine leukemia virus and feline leukemia virus, deltraretro viruses (for example, human T cell leukemia viruses (HTLV-1, HTLV-2), bovine leukemia virus, STLV-1 and STLV-2), epsilonretriviruses (for example, Walleye dermal sarcoma virus and Walleye epidermal hyperplasia virus 1), reticuloendotheliosis virus (for example, chicken syncytial virus, lenti viruses (for example, human immunodeficiency virus (HIV) type 1, human immunodeficiency virus (HIV) type 2, human immunodeficiency virus (HIV) type 3, simian immunodeficiency virus, equine infectious anemia virus, feline immunodeficiency virus, caprine arthritis encephalitis virus and Visna maedi virus) and spumaviruses (for example, human foamy virus and feline syncytia-forming virus).

Examples of DNA viruses include polyomaviruses (for example, simian virus 40, simian agent 12, BK virus, JC virus, Merkel Cell polyoma virus, bovine polyoma virus and lymphotrophic papovavirus), papillomaviruses (for example, human papillomavirus, bovine papillomavirus, adenoviruses (for example, adenoviruses A-F, canine adenovirus type I, canined adeovirus type 2), circoviruses (for example, porcine circovirus and beak and feather disease virus (BFDV)), parvoviruses (for example, canine parvovirus), erythroviruses (for example, adeno- associated virus types 1-8), betaparvoviruses, amdoviruses, densoviruses, iteraviruses, brevidensoviruses, pefudensoviruses, herpes viruses 1,2, 3, 4, 5, 6, 7 and 8 (for example, herpes simplex virus 1, herpes simplex virus 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, Kaposi's sarcoma associated herpes virus, human herpes virus-6 variant A, human herpes virus-6 variant B and cercophithecine herpes virus 1 (B virus)), poxviruses (for example, smallpox (variola), cowpox, monkeypox, vaccinia, Uasin Gishu, camelpox, psuedocowpox, pigeonpox, horsepox, fowlpox, turkeypox and swinepox), and hepadnaviruses (for example, hepatitis B and hepatitis B-like viruses). Chimeric viruses comprising portions of more than one viral genome are also contemplated herein.

For animals, in addition to the animal viruses listed above, viruses include, but are not limited to, the animal counterpart to any of the above listed human viruses.

Examples of bacterial infections include, but are not limited to infections caused by the following bacterial pathogens: Listeria (sp.), Franscicella tularensis, Mycobacterium tuberculosis, Rickettsia (all types), Ehrlichia, and Chlamydia. Further examples of bacteria that can be targeted by the present methods include M. tuberculosis, M. bovis, M. bovis strain BCG, BCG substrains, M. avium, M.

intracellular e, M. africanum, M. kansasii, M. marinum, M. ulcerans, M. avium subspecies paratuberculosis, Nocardia asteroides, other Nocardia species,

Legionella pneumophila, other Legionella species, Salmonella typhi, other

Salmonella species, Shigella species, Yersinia pestis, Pasteurella haemolytica, Pasteurella multocida, other Pasteurella species, Actinobacillus pleuropneumoniae, Listeria monocytogenes, Listeria ivanovii, Brucella abortus, other Brucella species, Cowdria ruminantium, Chlamydia pneumoniae, Chlamydia trachomatis, Chlamydia psittaci, Coxiella burnetii, other Rickettsial species, Ehrlichia species,

Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, Bacillus anthracis, Escherichia coli, Vibrio cholerae, Kingella kingae, Campylobacter species, Neiserria meningitidis, Neiserria gonorrhea, Pseudomonas aeruginosa, other Pseudomonas species, Haemophilus influenzae, Haemophilus ducreyi, other Hemophilus species, Clostridium tetani, other Clostridium species, Yersinia enterolitica, and other Yersinia species. Examples of parasitic infections include, but are not limited to infections caused by the following parasitic pathogens: Cryptosporidium, Plasmodium (all species), American trypanosomes (T. cruzi), African trypanosomes, Acanthamoeba, Entaoeba histolytica, Angiostrongylus, Anisakis, Ascaris, Babesia, Balantidium, Baylisascaris, lice, ticks, mites, fleas, Capillaria, Clonorchis, Chilomastix mesnili, Cyclspora, Diphyllobothrium, Dipylidium caninum, Fasciola, Giardia,

Gnathostoma, Hetetophyes, Hymenolepsis, Isospora, Loa loa, Microsporidia, Naegleria, Toxocara, Onchocerca, Opisthorchis, Paragonimus, Baylisascaris, Strongyloides, Taenia, Trichomonas and Trichuris.

Furthermore, examples of protozoan and fungal species contemplated within the present methods include, but are not limited to, Plasmodium falciparum, other Plasmodium species, Toxoplasma gondii, Pneumocystis carinii, Trypanosoma cruzi, other trypanosomal species, Leishmania donovani, other Leishmania species, Theileria annulata, other Theileria species, Eimeria tenella, other Eimeria species, Histoplasma capsulatum, Cryptococcus neoformans, Blastomyces dermatitidis, Coccidioides immitis, Paracoccidioides brasiliensis, Penicillium marnejfei, and Candida species.

The present disclosure also provides a method of inhibiting infection in a cell by a pathogen including decreasing expression or activity of a gene or gene product set forth in Table 1, wherein the pathogen is a pox virus, BVDV, a herpes virus, HIV, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus.

Further provided by the present disclosure is a method of inhibiting infection in a cell by a pathogen including decreasing expression or activity of a gene or gene product set forth in Table 1, wherein the pathogen is a respiratory virus.

Respiratory viruses include, but are not limited to, picornaviruses, orthomyxoviruses, paramyxoviruses, coronaviruses and adenoviruses. More specifically, and not to be limiting, the respiratory virus can be an influenza virus, a parainfluenza virus, an adenovirus, a rhinovirus or a respiratory syncytial virus (RSV) or any strain thereof.

Also provided by the present disclosure is a method of inhibiting infection in a cell by a pathogen including decreasing expression or activity of a gene or gene product set forth in Table 1, wherein the pathogen is a gastrointestinal virus.

Gastrointestinal viruses include, but are not limited to, picornaviruses, filoviruses, flaviviruses, calciviruses and reoviruses. More specifically, and not to be limiting, the gastrointestinal virus can be a reovirus, a Norwalk virus, an Ebola virus, a Marburg virus, a rotavirus, an enterovirus, an adenovirus, a Dengue fever virus, a yellow fever virus, or a West Nile virus.

Also provided is a method of inhibiting infection in a cell by a pathogen comprising decreasing expression or activity of a gene or gene product set forth in Table 1, wherein the pathogen is a pox virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, hantavirus, Rift Valley Fever virus Ebola virus, Marburg virus or Dengue Fever virus.

The present disclosure also provides a method of inhibiting infection in a cell by a pathogen including decreasing expression or activity of a gene or gene product set forth in Table 1, wherein the pathogen is a hemorraghic fever virus.

Exemplary hemorraghic fever viruses include, but are not limited to, flaviviruses, bunyaviruses, arenaviruses, filoviruses and hantaviruses. More specifically and not to be limiting, the hemorraghic fever virus can be an Ebola virus, a Marburg virus, a Dengue fever virus (types 1-4), a yellow fever virus, a Sin Nombre virus, a Junin virus, a Machupo virus, a Lassa virus, a Rift Valley fever virus, or a Kyasanur forest disease virus.

In a certain examples, the pathogen is human immunodeficiency virus (HIV)-l, HIV-2, Ebola virus, Marburg virus, RSV, or measles virus.

iv. Decrease or inhibition of infection

A decrease or inhibition of infection can occur in a cell, in vitro, ex vivo or in vivo. A decrease in infection can include modulation of one or more phases of a pathogenic life cycle including, but not limited to, attachment to cellular receptors, entry, internalization, disassembly, replication, genomic integration of pathogenic sequences, transcription of viral RNA, translation of viral RNA, transcription of host cell mRNA, translation of host cell mRNA, proteolytic cleavage of pathogenic proteins or cellular proteins, assembly of particles, endocytosis, cell lysis, budding, or egress of the pathogen from the cells. In some examples, a decrease in infection can be a decrease in attachment to cellular receptors, a decrease in entry, a decrease in internalization, a decrease in disassembly, a decrease in replication, a decrease in genomic integration of pathogenic sequences, a decrease in translation of mRNA, a decrease in proteolytic cleavage of pathogenic proteins or cellular proteins, a decrease in assembly of particles, a decrease in endocytosis, a decrease in cell lysis, a decrease in budding, or a decrease in egress of the pathogen from the cells. This decrease does not have to be complete as this can range from a slight decrease to complete ablation of the infection. A decrease in infection can be at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 100%, about 200%, such as between a 10% to 150%, a 20% to 100%, a 30% to 80%, 40% to 60%, or any other percentage decrease as compared to the level of infection in a cell wherein expression or activity of a gene or gene product set forth in Table 1 has not been decreased.

In the methods set forth herein, expression of any gene or gene product listed in Table 1 can be inhibited, for example, by inhibiting transcription of the gene, or inhibiting translation of its gene product. Similarly, the activity of a gene product (for example, an mRNA, a polypeptide or a protein) can be inhibited, either directly or indirectly. Inhibition or a decrease in expression does not have to be complete as this can range from a slight decrease in expression to complete ablation of expression. For example, expression can be inhibited by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, such as between 10% to 150%, 20% to 100%, 30% to 80%, 50% to 70%, including 50%, 53%, 55%, 57%, 60%, 62%, 65%, 67%, 70%, 73%, 75%, 78%, 80%, 83%, 85%, 87%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 125%, 150%, 200% or any other percentage decrease as compared to a control cell wherein the expression of a gene or gene product set forth in Table 1 has not been decreased or inhibited. Similarly, inhibition or decrease in the activity of a gene product does not have to be complete as this can range from a slight decrease to complete ablation of the activity of the gene product. For example, the activity of a gene product can be inhibited by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, such as between 10% to 150%, 20% to 100%, 30% to 80%, 50% to 70%, including 50%, 53%, 55%, 57%, 60%, 62%, 65%, 67%, 70%, 73%, 75%, 78%, 80%, 83%, 85%, 87%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%, 125%, 150%, 200% or any other percentage decrease as compared to a control cell wherein activity of a gene or gene product set forth in Table 1 has not been decreased or inhibited. An activity of a gene product is an activity that is involved in

pathogenicity, for example, interacting directly or indirectly, with pathogen, e.g., viral protein or viral nucleic acids, or an activity that the gene product performs in a normal cell, such as in a non-infected cell. Depending on the gene product, one of skill in the art would know how to assay for an activity that is involved in pathogenicity, an activity that is involved in normal cellular function, or both.

In some examples, a method of decreasing infection includes inhibiting or decreasing the interaction between any of the gene products, including proteins encoded by the genes listed in Table 1 and other cellular proteins, such as, for example, receptors, enzymes, nucleic acids and hormones, provided that such inhibition correlates with decreasing infection by the pathogen. Also provided is a method of decreasing infection by inhibiting or decreasing the interaction between any of the gene products, such as proteins of the genes listed in Table 1 and a viral, bacterial, parasitic or fungal protein (such as a non-host protein).

Furthermore, a decrease of expression or activity of a gene provided herein can result in a decrease in infection for two or more pathogens selected from the group consisting of the viruses, bacteria, pathogen and fungi described herein. For example, and not to be limiting, this includes two or more viruses, two or more bacteria, two or more parasites, two or more fungi, or combinations thereof.

One particular method that can be used to decrease the biological activity of one or more genes or gene products (for example by decreasing the activity of a modulator that increases the activity of a gene or gene product) is to decrease or disrupt transcription or translation of an mRNA encoding a gene product (or a modulator thereof) of a gene listed in Table 1, or combinations thereof, in the cell.

In one example, transcription or translation of at least one (such as at least 2, at least 3, or at least 4) of the genes, gene products or modulators thereof provided in Table 1 is decreased. Based on publicly available nucleic acid sequences, including variants, fusions and fragments of such sequences, provided in Table 1, methods that can be used to interrupt or alter transcription of such nucleic acid molecules include, but are not limited to, site-directed mutagenesis (including mutations caused by a transposon or an insertional vector), providing a DNA-binding protein that binds to the coding region of the protein (thus blocking or interfering with RNA polymerase or another protein involved in transcription), disrupting expression of one or more genes or gene products coding sequence (for example by functionally deleting the coding sequence, such as by a mutation, insertion, or deletion), altering the amino acid sequence or overall shape of the gene product, degrading the gene product, or combinations thereof.

Various inactive and recombinant DNA-binding proteins, and their effects on transcription, are discussed in Lewin, Genes VII. Methods that can be used to interrupt or alter translation of a nucleic acid molecule include, but are not limited to, using an antisense RNA, ribozyme or an siRNA that binds to a messenger RNA transcribed by the nucleic acid encoding the gene products. Such methods can be used to decrease or inhibit expression of a nucleic acid molecule involved in pathogenic infection, thereby reducing pathogen infection.

For example, the amount mRNA can be decreased in the cell by contacting the mRNA with a molecule that binds to a messenger RNA of a gene listed in Table 1, such as an antisense RNA, ribozyme, triple helix molecule, miR, or siRNA that is specific for the mRNA, for example by administering to the cell the antisense RNA, ribozyme, triple helix molecule, miR, or siRNA. In one example, antisense RNA, triple helix molecule, ribozyme, miR, or siRNA molecules are contacted with the cell under conditions that permit the molecule to be introduced into the cell. In a particular example, an expression vector that transcribes one or more antisense RNA, ribozyme, triple helix molecule, miR, or siRNA sequences that recognize a mRNA sequence for one of the genes listed in Table 1 is used to transform cells.

In particular examples, decreasing the biological activity of a gene or gene product involved in pathogenic infection, such as a gene or gene product listed in Table 1, includes decreasing the interaction between the disclosed gene or gene product involved in pathogenic infection or replication, and a pathogen protein. Methods for decreasing or inhibiting the interaction between a pathogen protein and a disclosed protein or nucleic acid sequence involved in pathogenic infection or replication are known. The pathogen and specific proteins or nucleic acid molecules can be part of an in vitro solution, an in vivo expression system, or in situ with a host tissue or subject. The pathogen protein can be part of a larger molecule or complex, such as an envelope protein on the envelope of a mature virus or a fragment of a viral envelope. The disclosed gene products, such as proteins, also can be part of a larger molecule or complex, such as a peptide expressed as part of a fusion protein or contained as one subunit of a larger protein, such as a transport protein, cell receptor, structural protein, or an enzyme. A nucleic acid molecule for one of the disclosed genes can be part of a larger molecule, complex, organism or

microorganism such as a nucleic acid sequence contained within a host genome, a recombinant vector, or a transgenic organism or microorganism (including both extrachromosomal molecules or genomic insertions).

In one example, the pathogen protein is a virus (such as an enveloped RNA virus) and decreasing the interaction of the virus and disclosed gene product which is a protein decreases or inhibits infection of a host cell by the virus. In particular example, decreasing such an interaction includes decreasing the integration of the viral nucleic acid (such as a viral genome) into the host nucleic acid (such as a host genome).

In one example, interaction is decreased or inhibited between one or more pathogen proteins and at least one (such as at least 2, at least 3, or at least 4) gene or gene product provided in Table 1. Decreasing or inhibiting the interactions of one or more of the disclosed genes or gene products with one or more pathogen proteins can have additive or exponentially increasing effects. Methods that can be used to disrupt or decrease such an interaction include those described above for decreasing expression of a disclosed gene or gene product. Even if expression of the gene or gene product is not completely disrupted, pathogen infection can still be reduced or even inhibited. Decreased expression of a disclosed gene or gene product results in a decreased amount of nucleic acid molecule or protein available for interacting with the pathogen protein. For example, the methods for described above for decreasing an amount of gene product, such as mRNA of a gene provided in Table 1 in the cell can be used. Such methods will decrease or even inhibit transcription of an mRNA encoding the protein. In particular examples, mRNA transcription is decreased or inhibited by inserting a transposon or insertional vector into a coding region of gene provided in Table 1.

Another example of a method that can be used to decrease the interaction between a disclosed gene and gene product, and a pathogen protein, is to administer an agent that decreases, inhibits, or disrupts the interaction (for example, a binding interaction) between a disclosed gene or gene product, and a pathogen protein.

Agents that recognize a gene product, such as a protein encoded by one of the genes provided in Table 1 can prevent a pathogen or portion thereof, such as a pathogen protein (such as a viral protein) from binding to such proteins, thereby decreasing or inhibiting infection by the pathogen. For example, a monoclonal or polyclonal antibody that binds to a protein encoded by one of the genes listed in Table 1 can block the binding of HIV, Ebola, RSV, Marburg, or measles virus to such proteins, thus blocking infection of that cell.

IV. Methods of Treating or Preventing Infection

The methods disclosed herein for decreasing the biological activity of one or more genes or gene products provided in Table 1 can also be used to treat or prevent infection by a pathogen, such as a viral, fungal, or bacterial pathogen. By "treat," "treating," or "treatment" is meant a method of reducing the effects of an existing infection. Treatment can also refer to a method of reducing the disease or condition itself rather than just the symptoms. The treatment can be any reduction from native levels and can be, but is not limited to, the complete ablation of the disease or the symptoms of the disease. Treatment can range from a reduction in a symptom or symptoms of viral infection to complete amelioration of the viral infection as detected by art-known techniques. For example, a disclosed method is considered to be an effective treatment if there is about a 10% reduction in one or more symptoms of the disease in a subject with the disease when compared to native levels in the same subject or control subjects. Thus, the reduction can be about a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any amount of reduction in biological activity or expression in one or more genes or gene products provided in Table 1 as compared to native or control levels. It is understood that in this method, the method is not limited to the decrease in expression and/or activity of one gene or gene product, as more than one gene or gene product, for example, two, three, four, five, six, etc. can be inhibited in order to inhibit infection by a pathogen.

As utilized herein, "prevent," "preventing," or "prevention" is meant a method of precluding, delaying, averting, obviating, forestalling, stopping, or hindering the onset, incidence, severity, or recurrence of infection. For example, the disclosed method is considered to be a prevention if there is about a 10% reduction in onset, incidence, severity, or recurrence of infection, or symptoms of infection (e.g. , inflammation, fever, lesions, weight loss, etc.) in a subject exposed to an infection when compared to control subjects exposed to an infection that did not receive a composition for decreasing infection. Thus, the reduction in onset, incidence, severity, or recurrence of infection can be about a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 500% or any amount of reduction as compared to control subjects. For example, and not to be limiting, if about 10% of the subjects in a population do not become infected as compared to subjects that did not receive preventive treatment, this is considered prevention.

In one example, a functional deletion in a cell of a gene or gene product provided in Table 1, results in a cell, such as a cell in a subject, having a decreased amount of pathogen (such as pathogen nucleic acid sequences, peptide or entire peptides). Such a decrease can be used to provide a therapeutic effect in the subject, thereby reducing or even eliminating one or more symptoms of infection in the subject.

Methods for treating an existing pathogen infection in a subject, or for providing a prophylactic effect to a subject who is susceptible to a pathogen infection, are disclosed. In particular examples, the method includes administering to the subject an effective amount of an agent that decreases the expression or biological activity of a gene or gene product provided in Table 1 (for example by decreasing the expression or activity of a modulator that increases the gene or gene product activity or by increasing the activity of a modulator that decreases the gene or gene product activity). In some examples, the methods of treatment include selecting a subject afflicted with a pathogen infection or at risk of acquiring a pathogen infection. In some examples, the methods include diagnosing a subject with a pathogen infection.

In some examples, once a subject's diagnosis is determined, an indication of that diagnosis can be displayed and/or conveyed to a clinician or other caregiver. For example, the results of the test are provided to a user (such as a clinician or other health care worker, laboratory personnel, or patient) in a perceivable output that provides information about the results of the test. In some examples, the output is a paper output (for example, a written or printed output), a display on a screen, a graphical output (for example, a graph, chart, voltammetric trace, or other diagram), or an audible output.

In other examples, the output is a numerical value, such as an amount of expression or biological activity of a gene or gene product in the sample as compared to a control. In additional examples, the output is a graphical

representation, for example, a graph that indicates the value (such as amount or relative amount) of gene or gene product activity or expression in the sample from the subject on a standard curve. In a particular example, the output (such as a graphical output) shows or provides a cut-off value or level that indicates the presence of an infection. In some examples, the output is communicated to the user, for example by providing an output via physical, audible, or electronic means (for example by mail, telephone, facsimile transmission, email, or communication to an electronic medical record).

The output can provide quantitative information (for example, an amount of gene or gene product expression or activity relative to a control sample or value) or can provide qualitative information (for example, a diagnosis of an infection). In some examples, the output is accompanied by guidelines for interpreting the data, for example, numerical or other limits that indicate the presence or absence of infection. The guidelines need not specify whether infection is present or absent, although it may include such a diagnosis. The indicia in the output can, for example, include normal or abnormal ranges or a cutoff, which the recipient of the output may then use to interpret the results, for example, to arrive at a diagnosis, prognosis, or treatment plan. In other examples, the output can provide a recommended therapeutic regimen. In some examples, the test may include determination of other clinical information (such as determining the amount of one or more additional indicators for infection or a particular type of infection in the sample).

In some embodiments, the disclosed methods of diagnosis include one or more of the following depending on the patient's diagnosis: a) prescribing a treatment regimen for the patient if the patient's determined diagnosis is considered to be positive for an infection; b) not prescribing a treatment regimen for the patient if the patient's determined diagnosis is considered to be negative for an infection; c) administering a treatment to the patient if the patient's determined diagnosis is considered to be positive for an infection; and d) not administering a treatment regimen to the patient if the patient's determined diagnosis is considered to be negative for an infection. In an alternative embodiment, the method can include recommending one or more of a)-d).

In some examples, the disclosed methods of treatment result in a decrease in the amount of time that it normally takes to see improvement in a subject. For example, a reduced infection time can be a decrease of hours, a day, two days, three days, four days, five days, six days, seven days, eight days, nine days, ten days, eleven days, twelve days, thirteen days, fourteen days, fifteen days or any time in between that it takes to see improvement in the symptoms, viral load or any other parameter utilized to measure improvement in a subject. For example, if it normally takes 7 days to see improvement in a subject not taking the agent, and after administration of the agent, improvement is seen at 6 days, the composition is effective in decreasing infection.

Any mode of administration can be used. The agent that decreases the expression or biological activity of the gene or gene product (or modulator thereof that increases the gene or gene product activity) is administered at a dose capable of generating the desired effect (treating the infection or providing a prophylactic effect). However, multiple administrations may be required to achieve the therapeutically effective dose. The agent that decreases the gene or gene product (or a modulator thereof) can be administered to the subject alone or in combination with other agents. Effective amounts of such agents can be administered to a subject for the treatment of a pathogen infection or as a prophylactic measure prior to exposure of the subject to the pathogen. After the agent has taken effect, the subject can be monitored for one or more symptoms associated with infection.

In one example, the agent interferes with the interaction between a pathogen and a gene or gene product provided in Table 1, such as a protein or nucleic acid sequence involved in pathogenic infection. For example, decreasing or even inhibiting the interaction between a pathogen and gene or gene product involved in pathogenic infection can decrease, inhibit, or even prevent infection of a subject the pathogen, or otherwise decrease or inhibit the progression or clinical manifestation of the infection. In addition, decreasing the interaction of a pathogen and a gene or gene product can reduce or alleviate one or more symptoms associated with infection, such as a fever.

In one example, an agent that decreases or disrupts expression of the gene or gene product is contacted with a cell, for example by administration to a subject. Such an agent can be used for prophylactic or therapeutic purposes. For example, antisense oligonucleotides, ribozymes, triple helix molecules, miRs, and siRNA molecules that recognize a gene product of the genes listed in Table 1, can be administered to the subject to disrupt expression of the gene product. In a particular example, an expression vector including antisense RNA, ribozyme, triple helix molecule, miR, or siRNA molecules that target the pathogenic infection gene product is introduced into the bone marrow of a subject. Uptake of the vector and expression of the antisense RNA, ribozyme, triple helix molecule, miR, or siRNA within cells infected by a pathogen (such as HIV-1, HIV-2, Marburg virus, Ebola or influenza virus), offers a prophylactic or therapeutic effect by decreasing expression of the gene product, within those cells, thus decreasing or even inhibiting infection by the pathogen. In particular examples, expression of the antisense RNA, ribozyme, triple helix molecule, miR, or siRNA is under control of a promoter, such as an inducible promoter. The vector, or other nucleic acid molecule, can be introduced into a subject by any standard molecular biology method and can be included in a composition that includes a pharmaceutically acceptable carrier.

Examples of other molecules which can be used to treat or prevent an infection by decreasing the interaction between a pathogen and a gene or gene product listed in Table 1 (such as binding between such sequences) include, but are not limited to specific binding agent, such as such as an antibody, peptide, or other compound that recognizes a protein encoded by a gene provided in Table 1. For example, an agent that interferes with the interaction between a protein encoded by a gene listed in Table 1 and a pathogen or pathogen protein (such as an HIV-protein) provides a prophylactic or therapeutic effect against infection by a pathogen (such as HIV) when provided to a cell or administered to a subject.

In particular examples, peptides or peptide analogs having a structure that mimics a protein encoded by a gene listed in Table 1, can be used for prophylactic or therapeutic uses. For example, such peptides or peptide analogs recognized by a pathogen can be administered to a subject as a pharmaceutical composition. These polypeptides interact with a pathogen already infecting that subject, or provide a prophylactic defense mechanism against infection if the subject is at risk of exposure to a pathogen. For example, peptides structurally similar to protein encoded by a gene listed in Table 1 are recognized by HIV. If such polypeptides are administered to an HIV-positive subject, the viruses already present in the subject interact with those peptides in addition to that subject's T-cell receptors, thus inhibiting the rate at which HIV infects T-cells. The administered peptides act as "decoys" to block HIV from interacting with T-cell receptors.

In some examples, the infection is a viral infection, a parasitic infection, a bacterial infection or a fungal infection. As utilized herein, "an unspecified infection" is an infection that presents symptoms associated with an infection, but is not identified as specific infection. One of skill in the art, for example, a physician, a nurse, a physician's assistant, a medic or any other health practitioner would know how to diagnose the symptoms of infection even though the actual pathogen may not be known. For example, the patient can present one or more symptoms, including, but not limited to, a fever, fatigue, lesions, weight loss, inflammation, a rash, pain (for example, muscle ache, headache, ear ache, joint pain, etc.), urinary difficulties, respiratory symptoms (for example, coughing, bronchitis, lung failure, breathing difficulties, bronchiolitis, airway obstruction, wheezing, runny nose, sinusitis, congestion, etc.), gastrointestinal symptoms (for example, nausea, diarrhea, vomiting, dehydration, abdominal pain, intestinal cramps, rectal bleeding, etc.). This can occur in the event of a bioterrorist attack or a pandemic. In this event, one of skill in the art would know to administer an agent that inhibits infection by decreasing the expression or activity of a gene or gene product set forth in Table 1 that is involved in the pathogenesis of several pathogens. Similarly, if there is a threat of an unspecified infection, for example, a threat of a bioterrorist attack, an agent that decreases the expression or activity of a gene or gene product set forth in Table 1 can be administered prophylactically to a subject to prevent an unspecified infection in a subject.

In some examples, the method is used prophylactically in response to a lethal outbreak of an infection. For example, the infection can be a pandemic or a bioterrorist created infection. If there is a threat of an unspecified infection, such as a viral infection, a bacterial infection, a parasitic infection or an infection by a chimeric pathogenic agent, to name a few, an agent can be administered

prophylactically to a subject to prevent an unspecified infection in a subject. The threat can also come in the form of a toxin. One of skill in the art would know to administer an agent that inhibits infection by decreasing the expression or activity of any gene or gene product set forth in Table 1 that is involved in the pathogenesis of two or more, three or more, four or more; or five or more pathogens.

Such prophylactic use can decrease the number of people in a population that are infected, thus preventing further spread of a pandemic or decreasing the effects of a bioterrorist attack.

In some examples, a method of treating an infection in a subject includes administering an agent that decreases the expression or activity of a gene or gene product set forth in Table 1 in a subject with an unspecified infection; diagnosing the type of infection in the subject and; administering an agent that decreases the expression or activity of a gene or a gene product set forth in Table 1 for the diagnosed infection. In one specific example, a method of treating viral infection includes diagnosing a subject with a viral infection; and removing a drug from the subject that decreases the expression or activity of a gene or gene product set forth in Table 1, if the viral infection is not a viral infection that is inhibited by the agent that decreases the expression or activity of a gene or gene product set forth in Table 1. As disclosed herein, upon recognizing that a subject has an infection or the symptoms of an infection, for example, in the case of a bioterrorist attack or a pandemic, given that a gene or gene product set forth in Table 1 can be involved in the pathogenesis of several pathogens, an agent is administered or prescribed that decreases the expression or activity of the gene or gene product. After

administration, the type of infection in a subject is identified, such as by a clinical healthcare worker. This diagnosis can be a differential diagnosis where infections are distinguished from one another, such as by comparing signs or symptoms and certain types of infection are eliminated before arriving at the diagnosis for a specific infection, or a diagnosis based on a test that is specific for a particular infection. Once a specific infection is diagnosed, if the gene or gene product is involved in the pathogenesis of this infection, an agent can be prescribed or administer that decreases the expression or activity of that gene or gene product. This can be the same agent administered prior to diagnosis of the specific infection or a different composition that decreases expression or activity of target involved in the specific infection.

i. Treatment and/or Prevention of Respiratory Virus

As described herein, the genes set forth in Tables 1 can be involved in the pathogenesis of one or more respiratory viruses. Therefore, the present disclosure provides methods of treating or preventing a respiratory infection in a subject by administering a composition that decreases activity or expression of a gene involved in the pathogenesis of one or more respiratory viruses.

In some examples, a method of treating an infection in a subject caused by one or more respiratory viruses is provided. For example, the method includes administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agents inhibits infection by one or more, such as two, three, four, five or more respiratory viruses. Exemplary respiratory viruses include, but are not limited to, a picomavirus, an orthomyxovirus, a paramyxovirus, a coronavirus and an adenovirus. Since picornaviruses, orthomyxoviruses, paramyxoviruses, coronaviruses and adenoviruses are families of viruses, two or more, three or more, four or more, or five or more respiratory viruses can be from the same or from different families. For example, the composition can inhibit infection by two or more

orthomyxoviruses; two or more picornaviruses; an orthomyxovirus, an adenovirus, and a picomavirus; an orthomyxovirus, a paramyxovirus and an adenovirus; an orthomyxovirus, two picornaviruses and a paramyxovirus; three orthomyxoviruses, a picomavirus and an adenovirus, etc. More particularly, the composition can inhibit infection by two or more, three or more or four or more respiratory viruses selected from the group consisting of an influenza vims, a parainfluenza vims, an adenovims, a rhinovims and an RSV vims.

In some examples, a method of treating an unspecified respiratory infection in a subject is provided. For example, the method includes diagnosing a subject with an unspecified respiratory infection; and administering to the subject an effective amount of a composition that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the composition inhibits infection by one or more respiratory vimses (such as one or more of picomavimses,

orthomyxoviruses, paramyxovimses, coronavimses, or adenovimses). As set forth above, in the methods of the present disclosure, more than one respiratory vims can be treated. For example, two or more respiratory vimses can be from the same family or from a different family of respiratory vimses. More specifically, the respiratory vims can be any strain of influenza, rhinovims, adenovims,

parainfluenza vims or RSV.

ii. Treatment and/or Prevention of Gastrointestinal Virus

The present disclosure also provides a method of preventing or treating a gastrointestinal vims in a subject. In some examples, the method includes administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent inhibits infection by one or more, such as two, three, four, five or more gastrointestinal vimses. Exemplary gastrointestinal vimses, include, but are not limited to, a filovirus, a picornavirus, a calcivirus, a flavivirus, an adenovirus or a reovirus. Since filoviruses, picornaviruses, calciviruses, flaviviruses, adenoviruses and reoviruses are families of viruses, the agent can inhibit infection by two or more, three or more, four or more, or five or more gastrointestinal viruses from the same or from different families. More particularly, the agent can inhibit infection by two or more, three or more, four or more, or five or more gastrointestinal viruses selected from the group consisting of a reovirus, a Norwalk virus, an Ebola virus, a Marburg virus, a Dengue fever virus, a West Nile virus, a yellow fever virus, a rotavirus and an enterovirus.

As described herein, the genes set forth in Table 1 can be involved in the pathogenesis of one or more gastrointestinal viruses. Therefore, the present disclosure provides methods of treating or preventing an unspecified gastrointestinal infection in a subject by administering an agent that decreases activity or expression of a gene involved in the pathogenesis of one or more gastrointestinal viruses. More particularly, the present disclosure provides a method of decreasing an unspecified gastrointestinal infection in a subject including diagnosing a subject with an unspecified gastrointestinal infection and administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent inhibits infection by one or more

gastrointestinal viruses (such as a flavivirus, a filovirus, a calcivirus or a reovirus). As set forth above, in the methods of the present disclosure, the two or more gastrointestinal viruses can be from the same family or from a different family of gastrointestinal viruses. More particularly, and not to be limiting, the

gastrointestinal virus can be any strain of reovirus, a Norwalk virus, an Ebola virus, a Marburg virus, a rotavirus, an enterovirus, a Dengue fever virus, a yellow fever virus, or a West Nile virus. In some examples, the method inhibits infection by three or more, four or more, five or more; or six or more gastrointestinal viruses selected from the group consisting of a flavivirus, a filovirus, a calcivirus and a reovirus.

Hi. Treatment of various combinations of pathogens

The present disclosure also provides a method of decreasing infection in a subject including administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent inhibits infection by one or more pathogens selected from the group consisting of: a picornavirus, an orthomyxovirus, a paramyxovirus, a coronavirus, an adenovirus, and inhibits infection by one or more pathogens selected from the group consisting of: a flavivirus, a filovirus, a calcivirus or a reovirus.

The present disclosure also provides a method of decreasing infection in a subject including administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent inhibits infection by two or more pathogens selected from the group consisting of HIV, a pox virus, a herpes virus, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus,

Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus.

The present disclosure also provides a method of decreasing infection in a subject including administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1 wherein the agent inhibits infection by two or more pathogens selected from the group consisting of: influenza, a pox virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, hantavirus, Rift Valley Fever virus Ebola virus, Marburg virus or Dengue Fever virus.

The present disclosure also provides a method of decreasing infection in a subject including administering to the subject an effective amount of a composition that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the composition inhibits infection by three or more, such as 4, 5, 6, 7 or more pathogens. The three or more pathogens can be selected from the viruses, bacteria, parasites and fungi set forth herein. More particularly, the three or more pathogens can be selected from the group consisting of: an HIV virus, a pox virus, a herpes virus, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse,

California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus.

The present disclosure also provides a method of decreasing infection in a subject including administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the composition inhibits co-infection by HIV and one or more viruses, bacteria, parasites or fungi. For example, decreasing co-infection of HIV and any of the viruses, including for example any families, genus, species, or group of viruses. As a further example, co-infection of HIV and a respiratory virus is provided herein. Respiratory viruses include picornaviruses, orthomyxoviruses, paramyxoviruses, coronaviruses, and adenoviruses. More specifically, the respiratory virus can be any strain of influenza, rhinovirus, adenovirus, parainfluenza virus or RSV. Also provided is decreasing co-infection of HIV and a gastrointestinal virus.

Gastrointestinal viruses include picornaviruses, filoviruses, flaviviruses, calciviruses and reoviruses. More specifically, and not to be limiting, the gastrointestinal virus can be any strain of reovirus, a Norwalk virus, an Ebola virus, a Marburg virus, a rotavirus, an enterovirus, a Dengue fever virus, a yellow fever virus, or a West Nile virus. Further provided is a method of decreasing co-infection of HIV with a pox virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, hantavirus, Rift Valley Fever virus Ebola virus, Marburg virus or Dengue Fever virus. More particularly, decreasing co-infection of HIV and a hepatitis virus, such as Hepatitis A, Hepatitis B or Hepatitis C is provided. Also provided is decreasing co-infection of HIV and a herpes virus, for example, HSV-1 or HSV-2. In addition decreasing co-infection of HIV and tuberculosis is also provided. Further provided is decreasing co-infection of HIV and CMV, as well as decreasing co-infection of HIV and HPV.

Also provided by the present disclosure is a method of managing, such as treating or preventing, secondary infections in a patient including administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent can inhibit infection by a primary infection, such as HIV and one or more, two or more, three or more, four or more; or five or more secondary infections, such as other viral, bacterial and/or fungal infections associated with the primary infection (such as tuberculosis, CMV, Hepatitis A, Hepatitis B, Hepatitis C, HSV-1 or HSV-2).

iv. Prevention of infection in response to pandemic or bioterror threat The present disclosure also provides a method of preventing or decreasing an unspecified pandemic or bioterror threat in a subject including: a) diagnosing a subject with an unspecified pandemic or bioterrorist inflicted infection; and b) administering to the subject an effective amount of an agent that decreases expression or activity of a gene or a gene product set forth in Table 1, wherein the agent inhibits infection by two or more, three or more, four or more; or five or more viruses selected from the group consisting of a pox virus, an influenza virus, West Nile virus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus,

LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus and a Dengue fever virus.

Combinations of gene products can be inhibited in a cell or in a subject to achieve inhibition of two or more, three or more, four or more, five or more, six or more, seven or more viruses etc. Any combination of agents that decrease expression and/or activity of two or more, three or more, four or more, five or more, six or more gene products set forth in Table 1 can be administered to inhibit infection by two or more, three or more, four or more, five or more or six or more viruses.

V. Methods of De creasing the Toxicity of a Toxin in a Cell

The present disclosure also provides a method of decreasing the toxicity of a toxin in a cell including decreasing expression or activity of a gene or gene product set forth in Table 1 associated with generating a toxin, thereby reducing or inhibiting the toxicity of a toxin in a cell. The cell can be in vitro, ex vivo or in vivo. Toxins can include, but are not limited to, a bacterial toxin, neurotoxins, such as botulinum neurotoxins, mycotoxins, ricin, Clostridium perfringens toxins, Clostridium difficile toxins, saxitoxins, tetrodo toxins, abrin, conotoxins, Staphlococcal toxins, E. coli toxins, streptococcal toxins, shigatoxins, T-2 toxins, anthrax toxins, chimeric forms of the toxins listed herein, and the like. The decrease in toxicity can be at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 100%, about 200%, such as between a 10% to a 150%, a 20% to a 100%, a 30% to a 80%, 40% to 60% or any other percentage decrease as compared to the level of toxicity in a cell wherein expression or activity of a gene or gene product set forth in Table 1 has not been decreased.

Toxicity can be measured, for example, via a cell viability, apopotosis assay, LDH release assay or cytotoxicity assay (See, for example, Kehl-Fie and St. Geme "Identification and characterization of an RTX toxin in the emerging pathogen Kingella kingae " J. Bacteriol. 189(2):430-6 (2006) and Kirby "Anthrax Lethal Toxin Induces Human Endothelial cell Apoptosis," Infection and Immunity 72: 430- 439 (2004), both of which are incorporated herein in their entireties by this reference.)

VI. Compositions

In any of the disclosed methods, expression and/or activity of a gene or gene product set forth in Table 1 can be decreased by contacting the cell with a composition that decreases expression and/or activity of one or more genes or gene products listed in Table 1 or modulators thereof. As such, disclosed herein are compositions for decreasing, inhibiting, preventing or treating a pathogenic infection. In some examples, a disclosed composition includes a chemical, a small or large molecule (organic or inorganic), a drug, a protein, a peptide, a cDNA, an antibody, a morpholino, a triple helix molecule, an aptamer, an LNA, an siRNA, a shRNA, an miRNA, an antisense RNA, or a ribozyme that decreases the expression and/or activity of a gene or gene product set forth in Table 1. A decrease in expression or activity can occur by decreasing transcription of mRNA or decreasing translation of RNA. A decrease in expression and/or activity can also occur by inhibiting the interaction between any of the proteins set forth in Table 1 and other cellular proteins, such as, for example, transcription factors, receptors, nuclear proteins, transporters, microtubules, membrane proteins, enzymes (for example, ATPases, phosphorylases, oxidoreductases, kinases, phosphatases, synthases, lyases, aromatases, helicases, hydrolases, proteases, transferases, nucleases, ligases, reductases and polymerases) and hormones. A decrease in expression and/or activity can also occur by inhibiting or decreasing the interaction between any of the proteins of the present disclosure and a cellular nucleic acid or a viral nucleic acid. A decrease can also occur by inhibiting or decreasing the interaction, either direct or indirect, between any of the proteins of the present disclosure and a viral, bacterial, parasitic or fungal protein (e.g. , a non-host protein) as described above.

In some examples, a composition is a single composition or a mixture, cocktail or combination of two or more compositions, for example, two or more compositions selected from the group consisting of chemical, a compound, a small molecule, an inorganic molecule, an organic molecule, an aptamer, a drug, a protein, a cDNA, an antibody, a morpholino, a triple helix molecule, an LNA, an siRNA, an shRNAs, an antisense nucleic acid, or a ribozyme. The two or more compositions can be the same or different types of compositions. The two or more compositions can decrease expression or activity of the same target or different targets, as one or more genes or gene products set forth in Table 1 can be modulated to decrease infection. It is understood that two or more compositions includes three or more, four or more, five or more etc. For example, and not to be limiting two or more compositions can be two or more compositions comprising an antisense and a small molecule; or two or more antisense molecules; or two or more small molecules; or two or more compositions comprising an siRNA and a small molecule, etc. It is understood that any combination of the types of compositions set forth herein can be utilized in the methods set forth herein.

The disclosed compositions can be used alone or in combination with other therapeutic agents such as antiviral compounds, antibacterial agents, antifungal agents, antiparasitic agents, anti-inflammatory agents, anti-cancer agents, etc. All of the compounds described herein can be contacted with a cell in vitro, ex vivo or in vivo.

Antibodies

The present disclosure also provides antibodies that specifically bind to the gene products, proteins and fragments thereof set forth in Table 1. The antibody of the present disclosure can be a polyclonal antibody or a monoclonal antibody. The antibody of the disclosure selectively binds a polypeptide. By "selectively binds" or "specifically binds" is meant an antibody binding reaction that is determinative of the presence of the antigen (in the present case, a polypeptide set forth in Table 1 or antigenic fragment thereof among a heterogeneous population of proteins and other biologies). Thus, under designated immunoassay conditions, the specified antibodies bind preferentially to a particular peptide and do not bind in a significant amount to other proteins in the sample. Preferably, selective binding includes binding at about or above 1.5 times assay background and the absence of significant binding is less than 1.5 times assay background.

This disclosure also contemplates antibodies that compete for binding to natural interactors or ligands to the proteins set forth in Table 1. In other words, the present disclosure provides antibodies that disrupt interactions between the proteins set forth in Table 1 and their binding partners. For example, an antibody of the present disclosure can compete with a protein for a binding site (e.g., a receptor) on a cell or the antibody can compete with a protein for binding to another protein or biological molecule, such as a nucleic acid that is under the transcriptional control of a transcription factor set forth in Table 1. An antibody can also disrupt the interaction between a protein set forth in Table 1 and a pathogen, or the product of a pathogen. For example, an antibody can disrupt the interaction between a protein set forth in Table 1 and a viral protein, a bacterial protein, a parasitic protein, a fungal protein or a toxin. The antibody optionally can have either an antagonistic or agonistic function as compared to the antigen. Antibodies that antagonize pathogenic infection are utilized to decrease infection.

Preferably, the antibody binds a polypeptide in vitro, ex vivo or in vivo.

Optionally, the antibody of the disclosure is labeled with a detectable moiety. For example, the detectable moiety can be selected from the group consisting of a fluorescent moiety, an enzyme-linked moiety, a biotin moiety and a radiolabeled moiety. The antibody can be used in techniques or procedures such as diagnostics, screening, or imaging. Anti-idiotypic antibodies and affinity matured antibodies are also considered to be part of the disclosure.

As used herein, the term "antibody" encompasses chimeric antibodies and hybrid antibodies, with dual or multiple antigen or epitope specificities, and fragments, such as F(ab')2, Fab' , Fab and the like, including hybrid fragments. Thus, fragments of the antibodies that retain the ability to bind their specific antigens are provided. Such antibodies and fragments can be made by techniques known in the art and can be screened for specificity and activity according to the methods set forth in the Examples and in general methods for producing antibodies and screening antibodies for specificity and activity (See Harlow and Lane.

Antibodies, A Laboratory Manual. Cold Spring Harbor Publications, New York, (1988)).

Also included within the meaning of "antibody" are conjugates of antibody fragments and antigen binding proteins (single chain antibodies) as described, for example, in U.S. Pat. No. 4,704,692, the contents of which are hereby incorporated by reference in its entirety.

Optionally, the antibodies are generated in other species and "humanized" for administration in humans. In one embodiment of the disclosure, the

"humanized" antibody is a human version of the antibody produced by a germ line mutant animal. Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2, or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a CDR of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity. In one embodiment, the present disclosure provides a humanized version of an antibody, comprising at least one, two, three, four, or up to all CDRs of a monoclonal antibody that specifically binds to a protein or fragment thereof set forth in Table 1. In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will include substantially all of or at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an

immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et ah, Nature, 321:522-525 (1986); Riechmann et ah, Nature, 332:323-327 (1988); and Presta, Curr. Op. Struct. Biol, 2:593-596 (1992)).

Methods for humanizing non-human antibodies are well known in the art. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import" variable domain. Humanization can be essentially performed following the method of Winter and co-workers (Jones et ah, Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al, Science, 239: 1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non- human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

Peptides

Peptides that inhibit expression or activity of a gene or a gene product set forth in Table 1 are also provided herein. Peptide libraries can be screened utilizing the screening methods set forth herein to identify peptides that inhibit activity of any of the genes or gene products set forth in Table 1. These peptides can be derived from a protein that binds to any of the genes or gene products set forth in Table 1. These peptides can be any peptide in a purified or non-purified form, such as peptides made of D-and/or L-configuration amino acids (in, for example, the form of random peptide libraries; see Lam et al., Nature 354:82-4, 1991),

phosphopeptides (such as in the form of random or partially degenerate, directed phosphopeptide libraries; see, for example, Songyang et al., Cell 72:767-78, 1993). siRNAs

Short interfering RNAs (siRNAs), also known as small interfering RNAs, are double- stranded RNAs that can induce sequence- specific post-transcriptional gene silencing, thereby decreasing gene expression (See, for example, U.S. Patent Nos. 6,506,559, 7,056,704, 7,078,196, 6,107,094, 5,898,221, 6,573,099, and European Patent No. 1.144,623, all of which are hereby incorporated by reference in their entireties). siRNAs can be of various lengths as long as they maintain their function. In some examples, siRNA molecules are about 19-23 nucleotides in length, such as at least 21 nucleotides, for example at least 23 nucleotides. In one example, siRNA triggers the specific degradation of homologous RNA molecules, such as mRNAs, within the region of sequence identity between both the siRNA and the target RNA. For example, WO 02/44321 discloses siRNAs capable of sequence-specific degradation of target mRNAs when base-paired with 3' overhanging ends. The direction of dsRNA processing determines whether a sense or an antisense target RNA can be cleaved by the produced siRNA endonuclease complex. Thus, siRNAs can be used to modulate transcription or translation, for example, by decreasing expression of a gene set forth in Table 1. The effects of siRNAs have been demonstrated in cells from a variety of organisms, including Drosophila, C. elegans, insects, frogs, plants, fungi, mice and humans (for example, WO 02/44321; Gitlin et al., Nature 418:430-4, 2002; Caplen et al., Proc. Natl. Acad. Sci. 98:9742-9747, 2001; and Elbashir et al, Nature 411:494-8, 2001).

Utilizing sequence analysis tools, one of skill in the art can design siRNAs to specifically target one or more of the genes set forth in Table 1 for decreased gene expression. siRNAs that inhibit or silence gene expression can be obtained from numerous commercial entities that synthesize siRNAs, for example, Ambion Inc. (2130 Woodward Austin, TX 78744-1832, USA), Qiagen Inc. (27220 Turnberry Lane, Valencia, CA USA) and Dharmacon Inc. (650 Crescent Drive, #100

Lafayette, CO 80026, USA). The siRNAs synthesized by Ambion Inc., Qiagen Inc. or Dharmacon Inc, can be readily obtained from these and other entities by providing a GENBANK® Accession No. for the mRNA of any gene set forth in Table 1. In addition, siRNAs can be generated by utilizing Invitrogen's BLOCK- IT™ RNAi Designer (available at web address

rnaidesigner.invitrogen.com/rnaiexpress). siRNA sequences can comprise a 3'TT overhang and/or additional sequences that allow efficient cloning and expression of the siRNA sequences. siRNA sequences can be cloned into vectors and utilized in vitro, ex vivo or in vivo to decrease gene expression. One of skill in the art would know that it is routine to utilize publicly available algorithms for the design of siRNA to target mRNA sequences. These sequences can then be assayed for inhibition of gene expression in vitro, ex vivo or in vivo.

shRNA

shRNA (short hairpin RNA) is a DNA molecule that can be cloned into expression vectors to express siRNA (typically 19-29 nt RNA duplex) for RNAi interference studies. shRNA has the following structural features: a short nucleotide sequence ranging from about 19-29 nucleotides derived from the target gene, followed by a short spacer of about 4-15 nucleotides (i.e. loop) and about a 19-29 nucleotide sequence that is the reverse complement of the initial target sequence.

Antisense Nucleic Acids

The antisense nucleic acids disclosed herein can be oligonucleotides that are double-stranded or single-stranded, RNA or DNA or a modification or derivative thereof, which can be directly administered to a cell (for example by administering the antisense molecule to the subject), or which can be produced intracellularly by transcription of exogenous, introduced sequences (for example by administering to the subject a vector that includes the antisense molecule under control of a promoter).

Antisense nucleic acids are polynucleotides, for example nucleic acid molecules that are at least 6 nucleotides in length, at least 10 nucleotides, at least 15 nucleotides, at least 20 nucleotides, at least 25 nucleotides, at least 50 nucleotides, at least 75 nucleotides, at least 100 nucleotides, at least 200 nucleotides, such as including about 6 to 100 nucleotides, 10 to 80 nucleotides, 20 to 70 nucleotides, 30 to 60 nucleotides, including 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 ,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100 nucleotides. However, antisense molecules can be much longer. In particular examples, the nucleotide is modified at one or more base moiety, sugar moiety, or phosphate backbone (or combinations thereof), and can include other appending groups such as peptides, or agents facilitating transport across the cell membrane (Letsinger et ah, Proc. Natl. Acad. Sci. USA 1989, 86:6553-6; Lemaitre et al., Proc. Natl. Acad. Sci. USA 1987, 84:648- 52; WO 88/09810) or blood-brain barrier (WO 89/10134), hybridization triggered cleavage agents (Krol et ah, BioTechniques 1988, 6:958-76) or intercalating agents (Zon, Pharm. Res. 5:539-49, 1988). Additional modifications include those set forth in U.S. Patent Nos. 7,176,296; 7,329,648; 7,262,489, 7,115,579; and 7,105,495 each of which is herein incorporated by reference in its entirety.

Examples of modified base moieties include, but are not limited to: 5- fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2- thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D- galactosylqueosine, inosine, N~6-sopentenyladenine, 1 -methyl guanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3- methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5- methylaminomethyluracil, methoxyarninomethyl-2-thiouracil, beta-D- mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio- N6-isopentenyladenine, uracil-5-oxyacetic acid, pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil- 5-oxyacetic acid methylester, uracil-S-oxyacetic acid, 5-methyl-2-thiouracil, 3-(3- amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.

Examples of modified sugar moieties include, but are not limited to:

arabinose, 2-fluoroarabinose, xylose, and hexose, or a modified component of the phosphate backbone, such as phosphorothioate, a phosphorodithioate, a

phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a

methylphosphonate, an alkyl phosphotriester, or a formacetal or analog thereof. In a particular example, an antisense molecule is an cc-anomeric

oligonucleotide. An cc-anomeric oligonucleotide forms specific double- stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gautier et al., Nucl. Acids Res. 15:6625-41, 1987). The oligonucleotide can be conjugated to another molecule, such as a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization- triggered cleavage agent. Oligonucleotides can include a targeting moiety that enhances uptake of the molecule by host cells. The targeting moiety can be a specific binding molecule, such as an antibody or fragment thereof that recognizes a molecule present on the surface of the host cell.

In a specific example, antisense molecules that recognize a nucleic acid set forth herein, include a catalytic RNA or a ribozyme (for example see WO 90/11364; WO 95/06764; and Sarver et al, Science 247: 1222-5, 1990). Conjugates of antisense with a metal complex, such as terpyridylCu (II), capable of mediating mRNA hydrolysis, are described in Bashkin et al. (Appl. Biochem Biotechnol.

54:43-56, 1995). In one example, the antisense nucleotide is a 2'-0- methylribonucleotide (Inoue et al., Nucl. Acids Res. 15:6131-48, 1987), or a chimeric RNA-DNA analogue (Inoue et al, FEBS Lett. 215:327-30, 1987).

Antisense molecules can be generated by utilizing the Antisense Design algorithm of Integrated DNA Technologies, Inc. (1710 Commercial Park, CoralviUe, IA 52241 USA; as available at the world wide web address

idtdna.com/Scitools/Applications/AntiSense/Antisense.aspx.

Any antisense sequence that is not the full length mRNA for any of the genes listed in Table 1 can be used as antisense sequences. It is known to those of skill in the art that once an mRNA sequence is routinely obtained for any of the genes set forth in Table 1, it is routine to walk along the mRNA sequence to generate antisense sequences that decrease expression of the gene. Therefore, the methods of the present disclosure can utilize any antisense sequence that decreases the expression of a gene set forth in Table 1.

Antisense molecules can be generated by utilizing the Antisense Design algorithm of Integrated DNA Technologies, Inc. (1710 Commercial Park, CoralviUe, IA 52241 USA; available at the world wide web address

idtdna.com/Scitools/Applications/AntiSense/Antisense.aspx/).

Morpholinos

Morpholinos are synthetic antisense oligos that can block access of other molecules to small (about 25 base) regions of ribonucleic acid (RNA). Morpholinos are often used to determine gene function using reverse genetics methods by blocking access to mRNA. Morpholinos, usually about 25 bases in length, bind to complementary sequences of RNA by standard nucleic acid base-pairing.

Morpholinos do not degrade their target RNA molecules. Instead, Morpholinos act by "steric hindrance", binding to a target sequence within an RNA and simply interfering with molecules which might otherwise interact with the RNA.

Morpholinos have been used in mammals, ranging from mice to humans.

Bound to the 5 '-untranslated region of messenger RNA (mRNA),

Morpholinos can interfere with progression of the ribosomal initiation complex from the 5' cap to the start codon. This prevents translation of the coding region of the targeted transcript (called "knocking down" gene expression). Morpholinos can also interfere with pre-mRNA processing steps, usually by preventing the splice- directing snRNP complexes from binding to their targets at the borders of introns on a strand of pre-RNA. Preventing Ul (at the donor site) or U2/U5 (at the

polypyrimidine moiety & acceptor site) from binding can cause modified splicing, commonly leading to exclusions of exons from the mature mRNA. Targeting some splice targets results in intron inclusions, while activation of cryptic splice sites can lead to partial inclusions or exclusions. Targets of Ul 1/U12 snRNPs can also be blocked. Splice modification can be conveniently assayed by reverse-transcriptase polymerase chain reaction (RT-PCR) and is seen as a band shift after gel electrophoresis of RT-PCR products. Methods of designing, making and utilizing morpholinos are disclosed in U.S. Patent No. 6,867,349, which is incorporated herein by reference in its entirety.

Small Molecules

Any small molecule that inhibits activity of a gene or a gene product set forth in Table 1 can be utilized in the methods of the present disclosure to decrease infection. These molecules are available in the scientific literature, in the StarLite/CHEMBL database available from the European Bioinformatics Institute, in DrugBank (Wishart et al. Nucleic Acids Res. 2006 Jan 1;34 (Database

issue):D668-72), package inserts, brochures, chemical suppliers (for example, Sigma, Tocris, Aurora Fine Chemicals, to name a few), or by any other means, such that one of skill in the art makes the association between a gene or gene product of Table 1 and inhibition of this gene or gene product by a molecule. In some examples, small molecules are molecules that have half maximal inhibitory concentration (IC₅₀) values of less than about ImM, less than about 100 micromolar, less than about 75 micromolar, less than about 50 micromolar, less than about 25 micromolar, less than about 10 micromolar, less than about 5 micromolar or less than about 1 micromolar. The IC₅₀ is a measure of the effectiveness of a compound in inhibiting biological or biochemical function. This quantitative measure indicates how much of a particular compound or other substance (inhibitor) is needed to inhibit a given biological process (or component of a process, e.g., an enzyme, cell, cell receptor or microorganism) by half. In other words, it is the half maximal (50%) inhibitory concentration (IC) of a substance (50% IC, or IC50). It is commonly used as a measure of antagonist drug potency in pharmacological research. Sometimes, it is also converted to the pIC₅o scale (-log IC₅₀), in which higher values indicate exponentially greater potency. According to the Food and Drug Administration (FDA), IC₅₀ represents the concentration of a drug that is required for 50% inhibition in vitro. It is comparable to an EC₅₀ for agonist drugs. EC₅₀ also represents the plasma concentration required for obtaining 50% of a maximum effect in vivo.

The present disclosure also provides methods of synthesis of small molecules that inhibit activity of a gene product set forth in Table 1. The present disclosure describes gene products for which three-dimensional structures are well known and can be obtained from the RCSB Protein Databank available at the World Wide Web address rcsb.org/pdb/home/home.do or rcsb.org for available three- dimensional structures. The structures and coordinates provided under the unique RCSB identifiers are hereby incorporated in their entireties by this reference. All of the structural information about the gene products set forth herein, for example, crystal structures and their corresponding coordinates, are readily available to one of skill in the art from the references cited herein, from the RCSB Protein Databank or elsewhere in the scientific literature.

Crystal structures can also be generated. Alternatively, one of skill in the art can obtain crystal structures for proteins, or domains of proteins, which are homologous to the proteins set forth in Table 1 from the RCSB Protein Databank or elsewhere in the scientific literature for use in homology modeling studies.

Routine high throughput in silico or in vitro screening of compound libraries for the identification of small molecules is also provided by the present disclosure. Compound libraries are commercially available. With an available crystal structure, it is routine for one of skill in the art to screen a library in silico and identify compounds with desirable properties, for example, binding affinity. For example, one of skill in the art can utilize the crystal structure(s) of a protein in a computer program to identify compounds that bind to a site on the crystal structure with a desirable binding affinity. This can be performed in an analogous way for any protein set forth herein to identify compounds that bind with a desirable binding affinity. Numerous computer programs are available and suitable for rational drug design and the processes of computer modeling, model building, and

computationally identifying, selecting and evaluating potential compounds. These include, for example, SYBYL (available from TRIPOS, St. Louis Mo.), DOCK (available from University of California, San Francisco), GRID (available form Oxford University, UK), MCSS (available from Molecular Simulations Inc., Burlington, Mass.), AUTODOCK (available from Oxford Molecular Group), FLEX X (available from TRIPOS, St. Louis Mo.), CAVEAT (available from University of California, Berkeley), HOOK (available from Molecular Simulations Inc.,

Burlington, Mass.), and 3-D database systems such as MACCS-3D (available from MDL Information Systems, San Leandro, Calif.), UNITY (available from TRIPOS, St. Louis Mo.), and CATALYST (available from Molecular Simulations Inc., Burlington, Mass.). Compounds can also be computationally modified using such software packages as LUDI (available from Biosym TechMA), and LEAPFROG (TRIPOS Associates, St. Louis, Mo.). These computer-modeling techniques can be performed on any suitable hardware including for example, workstations available from Silicon Graphics, Sun Microsystems, and the like. These techniques, methods, hardware and software packages are representative and are not intended to be comprehensive listing. Other modeling techniques known in the art can also be employed in accordance with this disclosure.

A filter can be applied to the results to yield one or more compounds with a binding affinity in a particular range, for example, and not to be limiting, from about 100 micromolar to about 100 nanomolar, from about 10 micromolar to about 10 nanomolar, from about 1 micromolar to about 1 nanomolar, or from about 0.5 micromolar to about 0.5 nanomolar. Another filter can provide compounds with a certain binding affinity and size, for example, less than 1000 daltons, less than 500 daltons, less than 400 daltons, less than 300 daltons, less than 200 daltons, less than 100 daltons or less than 50 daltons or any size in between. The ranges and properties can be modified depending on the protein being studied. The compounds identified via this screening method can be further studied in silico, in vitro or in vivo. For example, the compounds can be modified in silico and rescreened in silico to determine the effects of chemical modifications on binding affinity or other properties being assessed in silico. The compounds identified in silico can be synthesized for in vitro or in vivo analysis.

All of the screening leading up to in vivo testing can be done in silico or in combination with in vitro assays. The initial compounds identified in silico and the resulting modified compounds can be screened in vitro, for example, in cellular assays to determine the effect of the compound on the cellular host protein as well as in viral assays, to determine antiviral activity. IC₅₀ values can be obtained from the cellular assays, which may or may not be similar to the concentration necessary to effect 50% inhibition of viral infection in a viral assay. However, although not required, it is desirable to have a compound that has an IC₅₀ value of less than about ImM, less than about 100 micromolar, less than about 75 micromolar, less than about 50 micromolar, less than about 25 micromolar, less than about 10 micromolar, less than about 5 micromolar or less than about 1 micromolar. Similarly, although not required, it is desirable to have a compound that effects 50% inhibition of viral infection at a concentration of less than about ImM, less than about 100 micromolar, less than about 75 micromolar, less than about 50 micromolar, less than about 25 micromolar, less than about 10 micromolar, less than about 5 micromolar or less than about 1 micromolar or any concentration in between.

Further modifications of the compounds can be done after in vitro screening, either in silico or via chemical synthesis, for further evaluation, prior to additional in vitro screening or in vivo studies. It is understood that this process can be iterative, involving a combination of in silico and wet chemistry techniques, but routine in drug development.

Other filters can be applied to the in silico screening process, for example, a filter that takes ADMET (adsorption, distribution, metabolism, excretion, toxicity) properties into consideration can be applied. ADMET modeling can be used during compound optimization to define an acceptable property space that contains compounds likely to have the desired properties. These filters can be applied sequentially or simultaneously depending.

Libraries for virtual or in vitro screening are available for the skilled artisan, for example from ChemBridge Corporation (San Diego, CA), such as a GPCR library, a kinase targeted library (KINACore), or an ion channel library (Ion

Channel Set), to name a few. Compound libraries can also be obtained from the National Institutes of Health. For example, the NIH Clinical Collection of compounds that have been used in clinical trials can also be screened. Biofocus DPI (Essex, United Kingdom) also maintains and designs compound libraries that can be purchased for screening. One of skill in the art can select a library based on the protein of interest. For example, a kinase library can be screened to identify a compound that binds to and/or modulates a kinase. Other libraries that target enzyme families, for example, ATPases, hydrolases, isomerases, polymerases, transferases, phosphatases, etc., can also be screened, depending on the type of enzyme.

Compound libraries can also be screened in order to identify a compound that disrupts or inhibits specific interactions. Co-immunoprecipiation studies can be utilized. Similarly, FRET analysis can be utilized, to identify compounds that disrupt the interaction between a two proteins.

Additional inhibitors include compositions comprising carbon and hydrogen, and optionally comprising one or more of -S, -N, -O, -CI, -Br, or -Fl, appropriately bonded as a structure, with a size of less than about 1000 daltons, less than about 500 daltons, less than about 300 daltons, less than about 200 daltons, or less than about 100 daltons, that fits into a binding pocket or an active site of a gene product set forth herein. In particular, inhibitors that have the properties described in Lipinsky's Rule of Five are included herein. Lipinski's rule of five states that a drug/inhibitor has a weight under 500 Daltons, a limited lipophilicity or octanol- water partition coefficient (expressed by Log P < 5, with P = [drug]org./[drug]aq.), a maximum of 5 H-bond donors (expressed as the sum of OHs and NHs), and a maximum of 10 H-bond acceptors (expressed as the sum of oxygen and nitrogen atoms). Inhibitors that violate no more than one of the above-listed five rules are also included herein.

Other methods of decreasing expression and/or activity include methods of interrupting or altering transcription of mRNA molecules by site-directed mutagenesis (including mutations caused by a transposon or an insertional vector). Chemical mutagenesis can also be performed in which a cell is contacted with a chemical (for example ENU) that mutagenizes nucleic acids by introducing mutations into a gene set forth in Table 1. Transcription of mRNA molecules can also be decreased by modulating a transcription factor that regulates expression of any of the genes set forth in Table 1. Radiation can also be utilized to effect mutagenesis.

The present disclosure also provides decreasing expression and/or activity of a gene or a gene product set forth in Table 1 via modulation of other genes and gene products in pathways associated with the targets set forth in Table 1. Pathways include, but are not limited to ubiquitination pathways, trafficking pathways, cell signaling pathways, apoptotic pathways, TNF receptor pathways, GPCR pathways etc. Thus, other genes either upstream or downstream of the genes set forth in Table 1 are also provided herein as targets for inhibition of infection.

Additional Therapeutic Agents

Additional therapeutic agents can be administered prior to, following or simultaneously (either in the same or different composition) with any of the disclosed compositions. Examples of antiviral compounds useful in the treatment of flu and its associated symptoms include, but are not limited to, amantadine, rimantadine, ribavirin, zanamivir (Relenza®) and oseltamivir (Tamiflu®). Antiviral compounds useful in the treatment of rhinovirus infection include pleconaril and BTA-798. Antiviral compounds useful in the treatment of HIV include, but are not limited to, Combivir® (lamivudine-zidovudine), maraviroc, Crixivan® (indinavir), Emtriva® (emtricitabine), Epivir® (lamivudine), Fortovase® (saquinavir-sg), Hivid® (zalcitabine), Invirase® (saquinavir-hg), Kaletra® (lopinavir-ritonavir), LexivaTM (fosamprenavir), Norvir® (ritonavir), Retrovir® (zidovudine), Sustiva® (efavirenz), Videx EC® (didanosine), Videx® (didanosine), Viracept® (nelfinavir), Viramune® (nevirapine), Zerit® (stavudine), Ziagen® (abacavir), Fuzeon®

(enfuvirtide), Rescriptor® (delavirdine), Reyataz® (atazanavir), Trizivir®

(abacavir-lamivudine-zidovudine), Viread® (tenofovir disoproxil fumarate), Truvada® (tenofovir-emtricitabine), Atripla® (tenofovir-emtricitabine-efavirenz), Epzicom® (abacavir-lamivudine) and Agenerase® (amprenavir). Other antiviral compounds useful in the treatment of Ebola and other filoviruses include ribavirin and cyanovirin-N (CV-N). For the treatment of herpes viruses,

Zovirax®(acyclovir), Valtrex® (valacyclovir), Cytovene® (ganciclovir) and Valcyte® (valganciclovir) are available.

Antibacterial agents include, but are not limited to, antibiotics (for example, penicillin and ampicillin), sulfa Drugs and folic acid Analogs, Beta-Lactams, aminoglycosides, tetracyclines, macrolides, lincosamides, streptogramins, fluoroquinolones, rifampin, mupirocin, cycloserine, aminocyclitol and

oxazolidinones.

Antifungal agents include, but are not limited to, amphotericin, nystatin, terbinafine, itraconazole, fluconazole, ketoconazole, and griselfulvin.

Antiparasitic agents include, but are not limited to, antihelmintics, antinematodal agents, antiplatyhelmintic agents, antiprotozoal agents, amebicides, antimalarials, antitrichomonal agents, aoccidiostats and trypanocidal agents.

VII. Pharmaceutical Compositions and Modes of Administration

Pharmaceutical compositions for treating, inhibiting or preventing a pathogenic infection are disclosed herein. The pharmaceutical composition can include one or more of, a chemical, a compound, a small molecule, an inorganic molecule, an organic molecule, a drug, a protein, a cDNA, a peptide, an antibody, a morpholino, a triple helix molecule, an siRNA, an LNA, an shRNA, an miRNA, an antisense nucleic acid or a ribozyme that decreases the expression or activity of one or more of the genes or gene products of Table 1 and a pharmaceutically acceptable carrier.

A pharmaceutical composition can also be a mixture, cocktail or

combination of two or more compositions, for example, two or more compositions selected from the group consisting of chemical, a compound, a small molecule, an inorganic molecule, an organic molecule, an aptamer, a drug, a protein, a cDNA, an antibody, a morpholino, a triple helix molecule, an siRNA, an LNA, an shRNA, an antisense nucleic acid or a ribozyme. The two or more pharmaceutical compositions can be the same or different types of pharmaceutical compositions. For example, the two or more compositions can be an antisense and a small molecule, two antisense molecules, two small molecules or an siRNA and small molecule, etc. It is understood that any combination of the types of compositions set forth herein can be utilized in the methods provided herein.

The pharmaceutical composition(s) can be administered before or after infection. The decrease in infection in a subject need not be complete as this decrease can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or any other percentage decrease in between as long as a decrease occurs. This decrease can be correlated with amelioration of symptoms associated with infection. These compositions can be administered to a subject alone or in combination with other therapeutic agents described herein, such as anti-viral compounds, antibacterial agents, antifungal agents, antiparasitic agents, anti-inflammatory agents, anti-cancer agents, etc. Examples of viral infections, bacterial infections, fungal infections parasitic infections are set forth above. The compounds set forth herein or identified by the screening methods set forth herein can be administered to a subject to decrease infection by any pathogen or infectious agent set forth herein.

Various delivery systems for administering the therapies disclosed herein are known, and include encapsulation in liposomes, microparticles, microcapsules, expression by recombinant cells, receptor-mediated endocytosis (Wu and Wu, J. Biol. Chem. 1987, 262:4429-32), and construction of therapeutic nucleic acids as part of a retroviral or other vector. Methods of introduction include, but are not limited to, mucosal, topical, intradermal, intrathecal, intranasal, intratracheal, via nebulizer, via inhalation, intramuscular, otic delivery (ear), eye delivery (for example, eye drops), intraperitoneal, vaginal, rectal, intravenous, subcutaneous, intranasal, and oral routes. The compounds can be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (for example, oral mucosa, rectal, vaginal and intestinal mucosa, etc.) and can be administered together with other biologically active agents. Administration can be systemic or local. Pharmaceutical compositions can be delivered locally to the area in need of treatment, for example by topical application or local injection.

Pharmaceutical compositions are disclosed that include a therapeutically effective amount of an RNA, DNA, antisense molecule, ribozyme, siRNA, shRNA molecule, miRNA molecule, aptamer, drug, protein, small molecule, peptide inorganic molecule, organic molecule, antibody or other therapeutic agent, alone or with a pharmaceutically acceptable carrier. Furthermore, the pharmaceutical compositions or methods of treatment can be administered in combination with (such as before, during, or following) other therapeutic treatments, such as other antiviral agents, antibacterial agents, antifungal agents and antiparasitic agents.

For all of the administration methods disclosed herein, each method can optionally comprise the step of diagnosing a subject with an infection or diagnosing a subject in need of prophylaxis or prevention of infection,

i. Delivery systems

The pharmaceutically acceptable carriers useful herein are conventional. Remington's Pharmaceutical Sciences, by Martin, Mack Publishing Co., Easton, PA, 19th Edition (1995), describes compositions and formulations suitable for pharmaceutical delivery of the therapeutic agents herein disclosed. In general, the nature of the carrier will depend on the mode of administration being employed. For instance, parenteral formulations usually include injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, sesame oil, glycerol, ethanol, combinations thereof, or the like, as a vehicle. The carrier and composition can be sterile, and the formulation suits the mode of administration. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.

The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. For solid compositions (for example powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, sodium saccharine, cellulose, magnesium carbonate, or magnesium stearate. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides.

Embodiments of the disclosure including medicaments can be prepared with conventional pharmaceutically acceptable carriers, adjuvants and counterions as would be known to those of skill in the art.

The amount of the agent effective in decreasing or inhibiting infection can depend on the nature of the pathogen and its associated disorder or condition, and can be determined by standard clinical techniques. Therefore, these amounts will vary depending on the type of virus, bacteria, fungus, parasite or other pathogen. For example, the dosage can be anywhere from 0.01 mg/kg to 100 mg/kg. Multiple dosages can also be administered depending on the type of pathogen, and the subject's condition. In addition, in vitro assays can be employed to identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the seriousness of the disease or disorder, and should be decided according to the judgment of the practitioner and each subject's circumstances. Effective doses can be extrapolated from dose-response curves derived from in vitro or animal model test systems.

The disclosure also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration. Instructions for use of the composition can also be included.

In an example in which a nucleic acid is employed to reduce infection, such as an antisense or siRNA molecule, the nucleic acid can be delivered intracellularly (for example by expression from a nucleic acid vector or by receptor-mediated mechanisms), or by an appropriate nucleic acid expression vector which is administered so that it becomes intracellular, for example by use of a retroviral vector (see U.S. Patent No. 4,980,286), or by direct injection, or by use of microparticle bombardment (such as a gene gun; Biolistic, Dupont), or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (for example Joliot et al, Proc. Natl. Acad. Sci. USA 1991, 88: 1864-8). siRNA carriers also include, polyethylene glycol (PEG), PEG-liposomes, branched carriers composed of histidine and lysine (HK polymers), chitosan-thiamine pyrophosphate carriers, surfactants (for example, Survanta and Infasurf), nanochitosan carriers, and D5W solution. The present disclosure includes all forms of nucleic acid delivery, including synthetic oligos, naked DNA, plasmid and viral delivery, integrated into the genome or not.

Vector delivery can be via a viral system, such as a retroviral vector system which can package a recombinant retroviral genome (see e.g., Pastan et al., Proc. Natl. Acad. Sci. U.S.A. 85:4486, 1988; Miller et al., Mol. Cell. Biol. 6:2895, 1986). The recombinant retrovirus can then be used to infect and thereby deliver to the infected cells a nucleic acid, for example an antisense molecule or siRNA. The exact method of introducing the altered nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors. Other techniques are widely available for this procedure including the use of adenoviral vectors (Mitani et al., Hum. Gene Ther. 5:941-948, 1994), adeno-associated viral (AAV) vectors

(Goodman et al., Blood 84: 1492-1500, 1994), lentiviral vectors (Naidini et al., Science 272:263-267, 1996), and pseudotyped retroviral vectors (Agrawal et al., Exper. Hematol. 24:738-747, 1996). Other nonpathogenic vector systems such as the foamy virus vector can also be utilized (Park et al. "Inhibition of simian immunodeficiency virus by foamy virus vectors expressing siRNAs." Virology. 2005 Sep 20). It is also possible to deliver short hairpin RNAs (shRNAs) via vector delivery systems in order to inhibit gene expression (See Pichler et al. "In vivo RNA interference-mediated ablation of MDR1 P-glycoprotein." Clin Cancer Res. 2005 Jun 15;l l(12):4487-94; Lee et al. "Specific inhibition of HIV-1 replication by short hairpin RNAs targeting human cyclin Tl without inducing apoptosis." FEBS Lett. 2005 Jun 6;579(14):3100-6.).

Physical transduction techniques can also be used, such as liposome delivery and receptor-mediated and other endocytosis mechanisms (see, for example, Schwartzenberger et al., Blood 87:472-478, 1996) to name a few examples. This disclosure can be used in conjunction with any of these or other commonly used gene transfer methods.

VIII. Screening Methods

The present disclosure provides methods of identifying an agent that decreases pathogenicity of a pathogen. In some examples, the method includes contacting a test agent with a cell expressing a gene or gene product set forth in Table 1 or a modulator thereof; and determining whether the test agent decreases expression or activity of the gene or gene product set forth in Table 1 or modulator thereof, wherein a decrease in expression or activity of the gene or gene product of Table 1 or modulator thereof (which increases the gene or gene product of Table 1 in the absence of the test agent) as compared to a control, indicates the test agent decreases pathogenicity (such as decreasing the pathogen's ability to produce toxins, its ability to enter tissue and colonize and/or its ability to spread from host to host) of the pathogen.

In some examples, these methods includes contacting a test agent with a cell expressing a gene or gene product set forth in Table 1; detecting binding of the test agent to the gene product; and associating the binding with a decrease in infection by the pathogen, for example, a decrease in expression or activity of the gene or gene product of Table 1 as compared to a control, indicates the test agent decreases infection of the pathogen. This method can further include optimizing an agent that binds the gene or gene product in an assay, for example, a cell based assay or an in vivo assay that determines the functional ability to decrease infection. The binding assay can be a cellular assay or a non-cellular assay in which the gene or gene product and the test agent are brought into contact, for example, via immobilization of the gene product on a column, and subsequently contacting the immobilized gene product with the agent, or vice versa. Standard yeast two hybrid screens are also suitable for identifying a protein-protein interaction between a gene product set forth herein and another protein.

In the methods of the present disclosure, if the test agent has previously been identified as an agent that decreases or inhibits the level and/or activity of a gene product set forth in Table 1, either via information in the literature or from in vitro or in vivo results, this can indicate a decrease in infection. A decrease in infection as compared to infection in a cell that was not contacted with the agent known to decrease or inhibit the level and/or activity of the gene product can be sufficient to identify the agent as an agent that decreases or inhibits infection.

The methods described herein can be utilized to identify any agent with an activity that decreases infection, prevents infection, or promotes cellular survival after infection with a pathogen(s). Therefore, the cell can be contacted with a pathogen before, or after being contacted with the agent. The cell can also be contacted concurrently with the pathogen and the agent. The agents identified utilizing these methods can be used to inhibit infection in cells either in vitro, in vivo, or ex vivo.

The present disclosure also provides a method of identifying an agent that binds to a gene or gene product set forth in Table 1 and can decrease infection by three or more pathogens including: a) contacting a test agent with a cell expressing a gene or gene product set forth in Table 1; b) detecting binding of the compound to the gene or gene product; and c) associating binding with a decrease in infection by three or more pathogens. This method can further comprise optimizing an agent that binds the gene or gene product in an assay that determines the functional ability to decrease infection by three or more pathogens. This method can be cell based or an in vivo assay. The three or more pathogens can be any three or more pathogens set forth herein. For example, the three or more pathogens can be respiratory pathogens selected from the group consisting of picornaviruses, orthomyxoviruses,

paramyxoviruses, coronaviruses or adenoviruses. In another example, the three or more pathogens can be gastrointestinal pathogens selected from filoviruses, flavi viruses, calciviruses and reoviruses. The three or more pathogens can also be a combination of respiratory and gastrointestinal viruses. In another example, the three or more pathogens can be selected from the group consisting of: an HIV virus, a pox virus, a herpes virus, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus. The cell population used in the method can be the same cell population for each pathogen or can be different cell populations. Typically, the agent would be administered to a different cell population for each pathogen assayed. For example, and not to be limiting, if the pathogens are viruses, a cell population is contacted with the agent and a first virus, another cell population is contacted with the agent and second virus, a third cell population is contacted with the agent and a third virus etc. in order to determine whether the agent inhibits infection by three or more viruses. Since the cell type will vary depending on whether or not a given virus can infect the cell, one of skill in the art would know how to pair the cell type with the virus in order to perform the assay.

This method can further comprise measuring the level of expression and/or activity of the gene or gene product set forth in Table 1. This method can further comprise associating the level of infection with the level of expression and/or activity of the gene or gene product set forth in Table 1. In the screening methods disclosed herein, the level of infection can be measured, for example, by measuring viral replication.

In the methods of the present disclosure, if the agent has previously been identified as an agent that decreases or inhibits the level and/or activity of a gene or gene product set forth in Table 1, this can indicate a decrease in infection. A decrease in infection as compared to infection in a cell that was not contacted with the agent known to decrease or inhibit the level and/or activity of the gene or gene product can be sufficient to identify the agent as an agent that decreases or inhibits infection.

The methods described above can be utilized to identify any agent with an activity that decreases infection, prevents infection or promotes cellular survival after infection with a pathogen(s). Therefore, the cell can be contacted with a pathogen before, or after being contacted with the agent. The cell can also be contacted concurrently with the pathogen and the agent. The agents identified utilizing these methods can be used to inhibit infection in cells either in vitro, ex vivo or in vivo.

In the methods of the present disclosure any cell that can be infected with a pathogen can be utilized. The cell can be prokaryotic or eukaryotic, such as a cell from an insect, fish, crustacean, mammal, bird, reptile, yeast or a bacterium, such as E. coli. The cell can be part of an organism, or part of a cell culture, such as a culture of mammalian cells or a bacterial culture. The cell can also be in a nonhuman subject thus providing in vivo screening of agents that decrease infection by a pathogen. Cells susceptible to infection are well known and can be selected based on the pathogen of interest.

The test agents or compounds used in the methods described herein can be, but are not limited to, chemicals, small molecules, inorganic molecules, organic molecules, drugs, proteins, cDNAs, large molecules, antibodies, morpholinos, triple helix molecule, peptides, LNAs, siRNAs, shRNAs, miRNAs, antisense RNAs, ribozymes or any other compound. The compound can be random or from a library optimized to bind to a gene or gene product set forth in Table 1. Drug libraries optimized for the proteins in the class of proteins provided herein can also be screened or tested for binding or activity. Compositions identified with the disclosed approaches can be used as lead compositions to identify other

compositions having even greater antipathogenic activity. For example, chemical analogs of identified chemical entities, or variants, fragments or fusions of peptide agents, can be tested for their ability to decrease infection using the disclosed assays. Candidate agents can also be tested for safety in animals and then used for clinical trials in animals or humans. In the methods described herein, once the cell containing a cellular gene encoding a gene product set forth in Table 1 has been contacted with an agent, the level of infection can be assessed by measuring an antigen or other product associated with a particular infection. For example, the level of viral infection can be measured by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) assay (See for example, Payungporn et al. "Single step multiplex real-time RT-PCR for H5N1 influenza A virus detection." J Virol Methods. Sep 22, 2005; Landolt et al. "Use of real-time reverse transcriptase polymerase chain reaction assay and cell culture methods for detection of swine influenza A viruses" Am J Vet Res. 2005 Jan;66(l): 119-24). If there is a decrease in infection then the composition is an effective agent that decreases infection. This decrease does not have to be complete as the decrease can be a 10%, 20%, 30%, 40%, 50%, 60%. 70%, 80%, 90%, 100% decrease or any percentage decrease in between.

In the methods set forth herein, the level of the gene product can be measured by any standard means, such as by detection with an antibody specific for the protein. The nucleic acids set forth herein and fragments thereof can be utilized as primers to amplify nucleic acid sequences, such as a gene transcript of a gene set forth in Table 1 by standard amplification techniques. For example, expression of a gene transcript can be quantified by real time PCR using RNA isolated from cells. A variety of PCR techniques are familiar to those skilled in the art. For a review of PCR technology, see White (1997) and the publication entitled "PCR Methods and Applications" (1991, Cold Spring Harbor Laboratory Press), which is incorporated herein by reference in its entirety for amplification methods. In each of these PCR procedures, PCR primers on either side of the nucleic acid sequences to be amplified are added to a suitably prepared nucleic acid sample along with dNTPs and a thermostable polymerase such as Taq polymerase, Pfu polymerase, or Vent polymerase. The nucleic acid in the sample is denatured and the PCR primers are specifically hybridized to complementary nucleic acid sequences in the sample. The hybridized primers are extended. Thereafter, another cycle of denaturation, hybridization, and extension is initiated. The cycles are repeated multiple times to produce an amplified fragment containing the nucleic acid sequence between the primer sites. PCR has further been described in several patents including U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,965,188. Each of these publications is incorporated herein by reference in its entirety for PCR methods. One of skill in the art would know how to design and synthesize primers that amplify any of the nucleic acid sequences set forth herein or a fragment thereof. A detectable label may be included in an amplification reaction. Suitable labels include fluorochromes, e.g. , fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2',7'- dimethoxy-4',5'-dichloro-6-carboxyfluorescein (JOE), 6-carboxy-X -rhodamine (ROX), 6-carboxy-2',4',7',4,7-hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA), radioactive

32 35 3

labels, e.g. , ^{^} P, ^JJ S, ^J H; etc. The label may be a two stage system, where the amplified DNA is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. , avidin, specific antibodies, etc., where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product.

The sample nucleic acid, for example amplified fragment, can be analyzed by one of a number of methods known in the art. The nucleic acid can be sequenced by dideoxy or other methods. Hybridization with the sequence can also be used to determine its presence, by Southern blots, dot blots, or other like methods known to one ordinary skill in the art.

In the methods of the present disclosure, the level of gene product can be compared to the level of the gene product in a control cell not contacted with the compound. The level of gene product can be compared to the level of the gene product in the same cell prior to addition of the compound. Activity or function, can be measured by any standard means, such as by enzymatic assays that measure the conversion of a substrate to a product or binding assays that measure the binding of a gene product set forth in Table 1 to another protein, for example.

Moreover, the regulatory region of a gene set forth in Table 1 can be functionally linked to a reporter gene and compounds can be screened for inhibition of reporter gene expression. Such regulatory regions can be isolated from genomic sequences and identified by any characteristics observed that are characteristic for regulatory regions of the species and by their relation to the start codon for the coding region of the gene. As used herein, a reporter gene encodes a reporter protein. A reporter protein is any protein that can be specifically detected when expressed. Reporter proteins are useful for detecting or quantitating expression from expression sequences. Many reporter proteins are known to one of skill in the art. These include, but are not limited to, β-galactosidase, luciferase, and alkaline phosphatase that produce specific detectable products. Fluorescent reporter proteins can also be used, such as green fluorescent protein (GFP), cyan fluorescent protein (CFP), red fluorescent protein (RFP) and yellow fluorescent protein (YFP).

Viral infection can also be measured via cell-based assays. Briefly, cells

(20,000 to 2,500,000) are infected with the desired pathogen, and the incubation continued for 3-7 days. The antiviral agent can be applied to the cells before, during, or after infection with the pathogen. The amount of virus and agent administered can be determined by skilled practitioners. In some examples, several different doses of the potential therapeutic agent can be administered, to identify optimal dose ranges. Following transfection, assays are conducted to determine the resistance of the cells to infection by various agents.

For example, if analyzing viral infection, the presence of a viral antigen can be determined by using antibody specific for the viral protein then detecting the antibody. In one example, the antibody that specifically binds to the viral protein is labeled, for example with a detectable marker such as a fluorophore. In another example, the antibody is detected by using a secondary antibody containing a label. The presence of bound antibody is then detected, for example using microscopy, flow cytometry and ELISA. Similar methods can be used to monitor bacterial, protozoal, or fungal infection (except that the antibody would recognize a bacterial, protozoal, or fungal protein, respectively).

Alternatively, or in addition, the ability of the cells to survive viral infection is determined, for example, by performing a cell viability assay, such as trypan blue exclusion. Plaque assays can be utilized as well.

The amount of protein in a cell, can be determined by methods standard in the art for quantitating proteins in a cell, such as Western blotting, ELISA,

ELISPOT, immunoprecipitation, immunofluorescence (e.g. , FACS), immunohistochemistry, immunocytochemistry, etc., as well as any other method now known or later developed for quantitating protein in or produced by a cell.

The amount of a nucleic acid in a cell can be determined by methods standard in the art for quantitating nucleic acid in a cell, such as in situ

hybridization, quantitative PCR, RT-PCR, Taqman assay, Northern blotting, ELISPOT, dot blotting, etc., as well as any other method now known or later developed for quantitating the amount of a nucleic acid in a cell.

Any of the screening methods set forth herein can optionally include the step of assessing toxicity of a composition via any of the toxicity measurement methods described herein, or via any of the toxicity measurement methods known to one of skill in the art, such as, for example, the CytoTox-Glo assay (see Niles, A. et al. (2007) Anal. Biochem., 366: 197-206) or the Cell-Titer-Glo assay from Promega.

The ability of an antiviral agent to prevent or decrease infection by a virus, for example, any of the viruses listed above, can be assessed in an animal model. Several animal models for viral infection are known in the art. For example, mouse ΗΓ models are disclosed in Sutton et al. (Res. Initiat Treat. Action, 8: 22-24, 2003) and Pincus et al. (AIDS Res. Hum. Retroviruses 19:901-908, 2003); guinea pig models for Ebola infection are disclosed in Parren et al. (J. Virol. 76:6408-6412, 2002) and Xu et al. (Nat. Med. 4:37-42, 1998); cynomolgus monkey (Macaca fascicularis) models for influenza infection are disclosed in Kuiken et al. (Vet.

Pathol. 40:304-310, 2003); mouse models for herpes are disclosed in Wu et al. (Cell Host Microbe 22:5(l):84-94. 2009); pox models are disclosed in Smee et al.

(Nucleosides Nucleotides Nucleic Acids 23(l-2):375-83, 2004) and in Bray et al. (J. Infect. Dis. 181(1): 10-19); and Franciscella tularensis models are disclosed in Klimpel et al. (Vaccine 26(52): 6874-82, 2008).

Other animal models for influenza infection are also available. These include, but are not limited to, a cotton rat model disclosed by Ottolini et al. (J. Gen. Virol., 86(Pt 10): 2823-2830, 2005), as well as ferret and mouse models disclosed by Maines et al. (J. Virol. 79(18): 11788-11800, 2005). One of skill in the art would know how to select an animal model for assessing the in vivo activity of an agent for its ability to decrease infection by viruses, bacteria, fungi and parasites. Such animal models can also be used to test agents for the ability to ameliorate symptoms associated with viral infection. In addition, such animal models can be used to determine the LD₅₀ and the ED₅₀ in animal subjects, and such data can be used to determine the in vivo efficacy of potential agents. Animal models can also be used to assess antibacterial, antifungal and antiparasitic agents.

Animals of any species, including, but not limited to, birds, ferrets, cats, mice, rats, rabbits, fish (for example, zebrafish) guinea pigs, pigs, micro-pigs, goats, and non-human primates, e.g., baboons, monkeys, and chimpanzees, can be used to generate an animal model of viral infection, bacterial infection, fungal infection or parasitic infection if needed.

For example, for a model of viral infection, the appropriate animal is inoculated with the desired virus, in the presence or absence of the antiviral agent. The amount of virus and agent administered can be determined by skilled practitioners. In some examples, several different doses of the potential therapeutic agent (for example, an antiviral agent) can be administered to different test subjects, to identify optimal dose ranges. The therapeutic agent can be administered before, during, or after infection with the virus. Subsequent to the treatment, animals are observed for the development of the appropriate viral infection and symptoms associated therewith. A decrease in the development of the appropriate viral infection, or symptoms associated therewith, in the presence of the agent provides evidence that the agent is a therapeutic agent that can be used to decrease or even inhibit viral infection in a subject. For example, a virus can be tested which is lethal to the animal and survival is assessed. In other examples, the weight of the animal or viral titer in the animal can be measured. Similar models and approaches can be used for bacterial, fungal and parasitic infections.

In the methods of the present disclosure, the level of infection can be associated with the level of gene expression and/or activity, such that a decrease or elimination of infection associated with a decrease or elimination of gene expression and/or activity indicates that the agent is effective against the pathogen. For example, the level of infection can be measured in a cell after administration of siRNA that is known to inhibit a gene product set forth in Table 1. If there is a decrease in infection then the siRNA is an effective agent that decreases infection. This decrease does not have to be complete as the decrease can be at least a 10%, such as at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, including a 10% to 100%, a 20% to 80%, a 30% to 70%, a 40% to 60%, such as about a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 500% decrease or any percentage decrease in between. In the event that the compound is not known to decrease expression and/or activity of a gene product set forth in Table 1, the level of expression and/or activity of can be measured utilizing the methods set forth above and associated with the level of infection. By correlating a decrease in expression and/or activity with a decrease in infection, one of skill in the art can confirm that a decrease in infection is affected by a decrease in expression and/or activity of a gene or gene product set forth in Table 1. Similarly, the level of infection can be measured in a cell, utilizing the methods set forth above and known in the art, after administration of a chemical, small molecule, drug, protein, cDNA, antibody, aptamer, LNA, siRNA, shRNA, miRNA, morpholino, antisense RNA, ribozyme or any other compound. If there is a decrease in infection, then the chemical, small molecule, drug, protein, cDNA, antibody, aptamer, LNA, siRNA, shRNA, miRNA, morpholino, antisense RNA, ribozyme or any other compound is an effective antipathogenic agent.

The present disclosure provides a method of identifying an agent that can decrease infection by two or more pathogens including: a) administering the agent to two or more cell populations containing a cellular gene encoding a gene product set forth in Table 1 ; b) contacting the two or more cell populations with a pathogen, wherein each population is contacted with a different pathogen; and c) determining the level of infection, a decrease or elimination of infection by two or more pathogens indicating that the agent is an agent that decreases infection by three or more pathogens.

The present disclosure provides a method of identifying an agent that can decrease infection by three or more pathogens including: a) administering the agent to three or more cell populations containing a cellular gene encoding a gene product set forth in Table 1 ; b) contacting the three or more cell populations with a pathogen, wherein each population is contacted with a different pathogen; and c) determining the level of infection, a decrease or elimination of infection by three or more pathogens indicating that the agent is an agent that decreases infection by three or more pathogens.

It is understood that two or more, also means three or more, four or more, five or more, six or more, seven or more, etc. Therefore, the screening methods set forth above can be utilized to identify agents that decrease infection by three or more, four or more, five or more, six or more, seven or more pathogens set forth herein.

More particularly, the two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can be selected from the group consisting of a picomavirus, an orthomyxovirus, a paramyxovirus, a coronavirus and an adenovirus. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of a filovirus, an adenovirus, a picomavirus, a calicivirus, a flavivirus and a reovirus. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of a picomavirus, an orthomyxovirus, a paramyxovirus, a coronavirus, an adenovirus, a filovirus, a picomavirus, a calicivirus, a flavivirus and a reovirus.

The two or more, three or more, four or more, five or more pathogens can also be selected from the group consisting of influenza, rhinovirus, parainfluenza virus, measles, a pox virus and RSV. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of a reovirus, an adenovirus, a Norwalk vims, an Ebola vims, a Marburg vims, a Dengue fever vims, a West Nile vims, a yellow fever vims, a rotavims and an enterovims. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of HIV, a pox vims, a herpes vims, an RSV vims, an influenza vims, a hepatitis C vims, a hepatitis B vims, Epstein Barr Vims, Human Papilloma Vims, CMV, West Nile vims, a rhinovims, an adenovims, measles vims, Marburg vims, Ebola vims, a reovims, Rift Valley Fever Vims, LCM, Junin vims, Machupo vims, Guanarito vims, Lassa Fever vims, Hantavims, SARS vims, Nipah vims,

Calicivimses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of influenza, a pox virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, hantavirus, Rift Valley Fever virus Ebola virus, Marburg virus or Dengue Fever virus. The two or more, three or more, four or more, five or more, six or more, or seven or more pathogens can also be selected from the group consisting of Franscicella tularensis, an HIV, a pox virus, a herpes virus, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, tuberculosis, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus.

The cell population used in the assay can be the same cell population for each virus strain or can be different cell populations. Typically, the agent would be administered to a different cell population for each viral strain assayed. For example, and not to be limiting, a cell population is contacted with the agent and a first virus, another cell population is contacted with the agent and second virus, a third cell population is contacted with the agent and a third virus etc. in order to determine whether the agent inhibits infection by three or more pathogens. Since the cell type will vary depending on whether or not a given virus can infect the cell, one of skill in the art would know how to pair the cell type with the virus in order to perform the assay.

This method can further comprise measuring the level of expression and/or activity of a gene product set forth in Table 1. This method can further comprise associating the level of infection with the level of expression and/or activity of a gene product set forth in Table 1. In the screening methods disclosed herein, the level of infection can be measured, for example, by measuring viral load as described in the Examples. In any of the screening methods described throughout this application, one of skill in the art can compare the level of infection in a cell contacted with a test agent with a cell contacted with an agent that is known to decrease infection in a cell, for example, an agent that targets a viral protein, in order to compare the level of infection with a positive control.

Further provided by the present disclosure is a method of identifying an agent that can decrease infection by three or more pathogens including: a) administering the agent to three or more cell populations containing a cellular gene encoding a gene product set forth in Table 1 ; b) contacting the three or more cell populations with a pathogen, wherein each population is contacted with a different pathogen; and c) determining the level of expression and/or activity of the gene product, a decrease or elimination of gene product expression or activity in cells indicating that the agent is an agent that decreases infection by three or more pathogens.

In the methods of the present disclosure, if the compound has previously been identified as an agent that decreases or inhibits the level and/or activity of the gene product, for example, via the scientific literature, in vitro studies or in vivo studies, it is not necessary to associate a decrease in infection with the level/and or activity of the gene product. A decrease in infection as compared to infection in a cell that was not contacted with the agent known to decrease or inhibit the level and/or activity of the gene product is sufficient to identify the agent as an agent that decreases or inhibits infection.

The methods described above can be utilized to identify any compound with an activity that decreases infection, prevents infection or promotes cellular survival after infection with a pathogen(s). Therefore, the cell can be contacted with a bacterium or a virus before, or after being contacted with the agent. The cell can also be contacted concurrently with the bacterium or the virus and the agent. The compounds identified utilizing these methods can be used to inhibit infection in cells either in vitro, ex vivo or in vivo.

In the methods of the present disclosure any cell that can be infected with a bacterium or a virus can be utilized. The cell can be prokaryotic or eukaryotic, such as a cell from an insect, fish, crustacean, mammal, bird, reptile, yeast or a bacterium, such as E. coli. The cell can be part of an organism, or part of a cell culture, such as a culture of mammalian cells or a bacterial culture. The cell can also be in a nonhuman subject thus providing in vivo screening of agents that decrease infection by a pathogen. Cells susceptible to viral infection are well known and would be selected based on the pathogen of interest.

Compositions identified with the disclosed approaches can be used as lead compositions to identify other compositions having even greater antipathogenic activity. For example, chemical analogs of identified chemical entities, or variants, fragments or fusions of peptide agents, can be tested for their ability to decrease infection using the disclosed assays. Candidate agents can also be tested for safety in animals and then used for clinical trials in animals or humans. It is understood that any of the screening methods described herein can be performed in any tissue culture dish, including but not limited to 6 well, 12 well, 24 well, 96 well or 384 well plates. The assays can also be automated by utilizing robotics and other instrumentation standard in the art of drug screening.

The genes and nucleic acids of the disclosure can also be used in

polynucleotide arrays. Polynucleotide arrays provide a high throughput technique that can assay a large number of polynucleotide sequences in a single sample. This technology can be used, for example, to identify samples with reduced expression of as compared to a control sample. This technology can also be utilized to determine the effects of reduced expression of a gene set forth in Table 1 on other genes. In this way, one of skill in the art can identify genes that are upregulated or

downregulated upon reducing expression of a gene set forth in Table 1. Similarly, one of skill in the art can identify genes that are upregulated or downregulated upon increased expression of a gene set forth in Table 1. This allows identification of other genes that are upregulated or downregulated upon modulation of expression that can be targets for therapy, such as antiviral therapy, antibacterial therapy, antiparasitic therapy or antifungal therapy.

To create arrays, single-stranded polynucleotide probes can be spotted onto a substrate in a two-dimensional matrix or array. Each single-stranded polynucleotide probe can comprise at least 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, or 30 or more contiguous nucleotides selected from nucleotide sequences set forth under GENBANK® Accession Nos. herein and other nucleic acid sequences that would be selected by one of skill in the art depending on what genes, in addition to one ore more of the genes set forth in Table 1 are being analyzed.

The array can also be a microarray that includes probes to different polymorphic alleles of these genes. A polymorphism exists when two or more versions of a nucleic acid sequence exist within a population of subjects. For example, a polymorphic nucleic acid can be one where the most common allele has a frequency of 99% or less. Different alleles can be identified according to differences in nucleic acid sequences, and genetic variations occurring in more than 1% of a population (which is the commonly accepted frequency for defining polymorphism) are useful polymorphisms for certain applications. The allelic frequency (the proportion of all allele nucleic acids within a population that are of a specified type) can be determined by directly counting or estimating the number and type of alleles within a population. Polymorphisms and methods of determining allelic frequencies are discussed in Hartl, D.L. and Clark, A.G., Principles of Population Genetics, Third Edition (Sinauer Associates, Inc., Sunderland

Massachusetts, 1997), particularly in chapters 1 and 2.

These microarrays can be utilized to detect polymorphic alleles in samples from subjects. Such alleles may indicate that a subject is more susceptible to infection or less susceptible to infection. For example, microarrays can be utilized to detect polymorphic versions of genes set forth in Table 1 that result in decreased gene expression and/or decreased activity of the gene product to identify subjects that are less susceptible to viral infection. In addition, the existence of an allele associated with decreased expression in a healthy individual can be used to determine which genes are likely to have the least side effects if the gene product is inhibited or bound or may be selected for in commercial animals and bred into the population.

The substrate can be any substrate to which polynucleotide probes can be attached, including but not limited to glass, nitrocellulose, silicon, and nylon.

Polynucleotide probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions. Techniques for constructing arrays and methods of using these arrays are described in EP No. 0 799 897; PCT No. WO 97/29212; PCT No. WO 97/27317; EP No. 0 785 280; PCT No. WO 97/02357; U.S. Pat. Nos. 5,593,839; 5,578,832; EP No. 0 728 520; U.S. Pat. No. 5,599,695; EP No. 0 721 016; U.S. Pat. No. 5,556,752; PCT No. WO 95/22058; and U.S. Pat. No. 5,631,734. Commercially available polynucleotide arrays, such as Affymetrix GeneChip.TM., can also be used. Use of the GeneChip.™. to detect gene expression is described, for example, in Lockhart et al., Nature Biotechnology 14: 1675 (1996); Chee et al, Science 274:610 (1996); Hacia et al, Nature Genetics 14:441, 1996; and Kozal et al, Nature Medicine 2:753, 1996.

IX. Methods of making compounds

The present disclosure provides a method of making an agent that decreases infection of a cell by a pathogen, including: a) synthesizing an agent; b)

administering the compound to a cell containing a cellular gene encoding a gene product set forth in Table 1; c) contacting the cell with an infectious pathogen; d) determining the level of infection, a decrease or elimination of infection indicating that the agent is an agent that decreases infection; and e) associating the agent with decreasing expression or activity of the gene product.

This method can further include making the association by measuring the level of expression and/or activity of a protein from Table 1.

Further provided is a method of making an agent that decreases infection in a cell by a pathogen, including: a) optimizing an agent to bind a gene product set forth in Table 1 ; b) administering the compound to a cell containing a cellular gene encoding the gene product; c) contacting the cell with an infectious pathogen; d) determining the level of infection, a decrease or elimination of infection indicating the making of an agent that decreases infection in a cell by a pathogen. This method can further include synthesizing therapeutic quantities of the compound.

The present disclosure also provides a method of synthesizing an agent that binds to a gene product set forth in Table 1 and decreases infection by a pathogen including: a) contacting a library of compounds with a gene product set forth in Table 1; b) associating binding with a decrease in infection; and c) synthesizing derivatives of the compounds from the library that bind to the gene product. X. Transgenic Cells and Non-Human Mammals

The present disclosure also provides a non-human transgenic mammal comprising a functional deletion of a gene set forth in Table 1, wherein the mammal has decreased susceptibility to infection by a pathogen, such as a virus, a bacterium, a fungus or a parasite. Exemplary transgenic non-human mammals include, but are not limited to, ferrets, fish, guinea pigs, chinchilla, mice, monkeys, rabbits, rats, chickens, cows, and pigs. Such knock-out animals are useful for reducing the transmission of viruses from animals to humans and for further validating a target. In the transgenic animals of the present disclosure one or both alleles of a gene set forth in Table 1 can be functionally deleted.

The present disclosure also provides a non-human transgenic mammal comprising a functional deletion of a gene set forth in Table 1 wherein the mammal has decreased susceptibility to infection by two or more, three or more, four or more, or five or more pathogens selected from the group consisting of a

picornavirus, an orthomyxovirus, a paramyxovirus, a coronavirus, an adenovirus, a flavivirus, a filovirus, a calicivirus or a reovirus. The two or more, three or more, four or more; or five or more pathogens can be respiratory viruses selected from the group consisting of influenza, RSV, rhinovirus, parainfluenza virus, pox virus, and measles. The two or more, three or more, four or more; or five or more pathogens can be gastrointestinal viruses selected from the group consisting of a reovirus, a Norwalk virus, an Ebola virus, a Marburg virus, a Dengue fever virus, a West Nile virus, a yellow fever virus, an adenovirus, a rotavirus and an enterovirus. The two or more, three or more, four or more; or five or more pathogens can be selected from the group consisting of Franciscella tularensis, HIV, a pox virus, a herpes virus, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A, LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, BVDV, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus. By "decreased susceptibility" is meant that the animal is less susceptible to infection or experiences decreased infection by a pathogen as compared to an animal that does not have one or both alleles of a gene set forth in Table 1 functionally deleted. The animal does not have to be completely resistant to the pathogen. For example, the animal can be 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% or any percentage in between less susceptible to infection by a pathogen as compared to an animal that does not have a functional deletion of a gene set forth in Table 1. Furthermore, decreasing infection or decreasing susceptibility to infection includes decreasing entry, replication, pathogenesis, insertion, lysis, or other steps in the replication strategy of a virus or other pathogen into a cell or subject, or combinations thereof.

Therefore, the present disclosure provides a non-human transgenic mammal comprising a functional deletion of a gene set forth in Table 1, wherein the mammal has decreased susceptibility to infection by a pathogen, such as a virus, a bacterium, a parasite or a fungus. A functional deletion is a mutation, partial or complete deletion, insertion, or other variation made to a gene sequence that inhibits production of the gene product or renders a gene product that is not completely functional or non-functional. Thus, a gene that is "functionally deleted" or

"inactivated" means that the gene has been mutated such that the mutation substantially reduces (and in some cases abolishes) expression or biological activity of the encoded gene product. Functional deletions can be made by insertional mutagenesis (for example via insertion of a transposon or insertional vector), by site directed mutagenesis, via chemical mutagenesis, via radiation or any other method now known or developed in the future that results in a transgenic animal with a functional deletion of a gene set forth in Table 1.

Alternatively, a nucleic acid sequence such as siRNA, a morpholino or another agent that interferes with a gene set forth in Table 1 can be delivered. The expression of the sequence used to knockout or functionally delete the desired gene can be regulated by an appropriate promoter sequence. For example, constitutive promoters can be used to ensure that the functionally deleted gene is not expressed by the animal. In contrast, an inducible promoter can be used to control when the transgenic animal does or does not express the gene of interest. Exemplary inducible promoters include tissue- specific promoters and promoters responsive or unresponsive to a particular stimulus (such as light, oxygen, chemical concentration, such as a tetracycline inducible promoter).

The transgenic animals of the present disclosure that comprise a functionally deleted a gene set forth in Table 1 can be examined during exposure to various pathogens. Comparison data can provide insight into the life cycles of pathogens. Moreover, knock-out animals or functionally deleted (such as birds or pigs) that are otherwise susceptible to an infection (for example influenza) can be made to resist infection, conferred by disruption of the gene. If disruption of the gene in the transgenic animal results in an increased resistance to infection, these transgenic animals can be bred to establish flocks or herds that are less susceptible to infection.

Transgenic animals, including methods of making and using transgenic animals, are described in various patents and publications, such as WO 01/43540; WO 02/19811; U.S. Pub. Nos: 2001-0044937 and 2002-0066117; and U.S. Pat. Nos: 5,859,308; 6,281,408; and 6,376,743; and the references cited therein.

The transgenic animals of this disclosure also include conditional gene knockdown animals produced, for example, by utilizing the SIRIUS-Cre system that combines siRNA for specific gene-knockdown, Cre-loxP for tissue- specific expression and tetracycline-on for inducible expression. These animals can be generated by mating two parental lines that contain a specific siRNA of interest gene and tissue- specific recombinase under tetracycline control. See Chang et al. "Using siRNA Technique to Generate Transgenic Animals with Spatiotemporal and

Conditional Gene Knockdown." American Journal of Pathology 165: 1535-1541 (2004) which is hereby incorporated in its entirety by this reference regarding production of conditional gene knockdown animals.

The present disclosure also provides cells including an altered or disrupted gene set forth in Table 1 that are resistant to infection by a pathogen. These cells can be in vitro, ex vivo or in vivo cells and can have one or both alleles altered.

These cells can also be obtained from the transgenic animals of the present disclosure. Such cells therefore include cells having decreased susceptibility to a virus or any of the other pathogens described herein, including bacteria, parasites and fungi. Since the genes set forth herein are involved in viral infection, also provided herein are methods of overexpressing any of the genes set forth in Table 1 in host cells. Overexpression of these genes can provide cells that increase the amount of virus produced by the cell, thus allowing more efficient production of viruses. Also provided is the overexpression of the genes set forth herein in avian eggs, for example, in chicken eggs.

Methods of screening agents, such as a chemical, a compound, a small or large molecule, an organic molecule, an inorganic molecule, a peptide, a drug, a protein, a cDNA, an antibody, a morpholino, a triple helix molecule, an siRNA, an LNA, an shRNAs, an miRNA, an antisense nucleic acid or a ribozyme set forth using the transgenic animals described herein are also provided.

XL Screening for Resistance to Infection

Also provided herein are methods of screening host subjects for resistance to infection by characterizing a nucleotide sequence or amino acid sequence of a host gene set forth in Table 1. The nucleic acid or amino acid sequence of a subject can be isolated, sequenced, and compared to the wildtype sequence of a gene set forth in Table 1. The greater the similarity between that subject's nucleic acid sequence or amino acid sequence and the wildtype sequence, the more susceptible that person is to infection, while a decrease in similarity between that subject's nucleic acid sequence or amino acid sequence and the wildtype sequence, the more resistant that subject can be to infection. Such screens can be performed for any gene set forth in Table lfor any species.

Assessing the genetic characteristics of a population can provide information about the susceptibility or resistance of that population to viral infection. For example, polymorphic analysis of alleles in a particular human population, such as the population of a particular city or geographic area, can indicate how susceptible that population is to infection. A higher percentage of alleles substantially similar to a wildtype gene set forth in Table 1 can indicate that the population is more susceptible to infection, while a large number of polymorphic alleles that are substantially different than a wildtype gene sequence can indicate that a population is more resistant to infection. Such information can be used, for example, in making public health decisions about vaccinating susceptible populations.

The present disclosure also provides a method of screening a cell for a variant form of a gene set forth in Table 1. A variant can be a gene with a functional deletion, mutation or alteration in the gene such that the amount or activity of the gene product is altered. These cells containing a variant form of a gene can be contacted with a pathogen to determine if cells including a naturally occurring variant of a gene set forth in Table 1 differ in their resistance to infection. For example, cells from an animal, for example, a chicken, can be screened for a variant form of a gene set forth in Table 1. If a naturally occurring variant is found and chickens possessing a variant form of the gene in their genome are less susceptible to infection, these chickens can be selectively bred to establish flocks that are resistant to infection. By utilizing these methods, flocks of chickens that are resistant to avian flu or other pathogens can be established. Similarly, other animals can be screened for a variant form of a gene set forth in Table 1. If a naturally occurring variant is found and animals possessing a variant form of the gene in their genome are less susceptible to infection, these animals can be selectively bred to establish populations that are resistant to infection. These animals include, but are not limited to, cats, dogs, livestock (for example, cattle, horses, pigs, sheep, goats, etc.), laboratory animals (for example, mouse, monkey, rabbit, rat, gerbil, guinea pig, etc.) and avian species (for example, flocks of chickens, geese, turkeys, ducks, pheasants, pigeons, doves etc.). Therefore, the present application provides populations of animals that comprise a naturally occurring variant of a gene set forth in Table 1 that results in decreased susceptibility to viral infection, thus providing populations of animals that are less susceptible to viral infection. Similarly, if a naturally occurring variant is found and animals possessing a variant form of the gene in their genome are less susceptible to bacterial, parasitic or fungal infection, these animals can be selectively bred to establish populations that are resistant to bacterial, parasitic or fungal infection.

The following examples are provided to illustrate particular features of certain embodiments. However, the particular features described below should not be construed as limitations on the scope of the disclosure, but rather as examples from which equivalents will be recognized by those of ordinary skill in the art.

EXAMPLES Example 1

Identification of genes and gene products involved in pathogenic infection

This example describes methods used to identify genes and gene products involved in pathogenic infection, including HIV-1, HIV-2, influenza A and Ebola virus.

Following infection with the U3NeoSVl retrovirus gene trap shuttle vector, libraries of mutagenized cells were isolated in which each clone contained a single gene disrupted by provirus integration. Gene entrapment was performed essentially as described in U.S. Patent No. 6,448,000 and U. S. Patent No. 6,777,177. The entrapment libraries were infected with HIV-1, HIV-2, influenza A, and Ebola virus and virus-resistant clones were selected as described below. Methods for infection and analysis are provided below. Genes and gene products identified by gene entrapment to be involved in pathogenic infection are provided in Table 1.

i. Infection with HIV-1 or HIV-2

Sup-Tl gene trap library cells were thawed at room temperature, and allowed to grow at 37°C under 5% C0₂ in RPMI- 1640, supplemented with 10% heat inactivated fetal calf serum, penicillin, streptomycin and Fungisome.

Approximately 3 x10 actively growing Sup-Tl library cells were infected with the CXCR4 cytopathic HIV-1 strain LAI at an MOI of 10, approximately 100 fold greater than that normally used for spreading infection in culture. The cells were incubated with the virus for four hours in 2 ml of medium, then grown in bulk at 10⁶ cells/ml for two weeks, at which time G418 was added to a final concentration of 1 mg/ml and the cultures continued for an additional two weeks. The surviving cells were exposed to two further rounds of HIV-1 infection. Following HIV-1 infection, surviving cells were incubated 1: 100 with BC7 T cells constitutively expressing the HrV-2 strain 3BX, which was modified to infect regardless of CD4 status, solely using the CXCR4 receptor. Cells were conincubated for two weeks followed by selection with 1 mg/ml G418. The surviving cells were exposed to two further rounds of HIV-2 infection as described above. The final cell culture was selected using anti-CD4 magnetic microbeads and divided into 2.0 ml cultures containing 1000 cells each. These were then infected with LAI at an MOI of 10. Surviving cells from each culture were subjected to limit dilution, or growth on

methylcellulose, and expanded in selection medium. The isolated clones were identified as being CD4 and CXCR4 positive following flow cytometry analysis using standard protocols. Several cells isolated were resistant to further HIV infection with unique expression of CD4 cell surface antigen.

ii. Identification of genes disrupted in HIV-resistant clones

The U3NeoSVl gene trap vector contained a plasmid origin of replication and ampicillin resistance gene; thus, regions of genomic DNA adjacent to the targeting vector were readily cloned by plasmid rescue and sequenced. The flanking sequences were compared to the nucleic acid databases to identify candidate cellular genes that confer resistance to lytic infection by HIV when altered by gene entrapment.

iii. Infection with Influenza

MDCK gene trap library cells were thawed at room temperature, and allowed to grow at 37°C under 5% C0₂ in DMEM, supplemented with 10% fetal bovine serum, penicillin, and streptomycin. Approximately 10 actively growing MDCK library cells were washed with phosphate buffered saline and infected with the A/PR/8/34 influenza virus reassortant having A/Johannesburg/82/96

glycoproteins (H1N1) at and MOI of 20-30 in 250 μΐ DME in a T-25 flask. The cells were incubated with the virus for two hours, and the inoculum was

subsequently placed with DMEM, supplemented with 2% FBS and 1 μg/ml TPCK trypsin (to cleavage-activate HA of new progeny virus). The cells were incubated for 18 hours to provide 2-3 rounds of infection. The maintenance medium was removed and replaced with selection medium (DMEM with 10% FBS and 1 mg/ml neomycin) and survivors allowed to expand. The surviving cells were exposed to one additional round of infection as described. Cells surviving influenza infection were cloned by either limiting dilution or growth on methylcellulose. The isolates were characterized phenotypically by flow cytometry. iv. Identification of genes disrupted in Influenza-resistant clones

The U3NeoSVl gene trap vector contains a plasmid origin of replication and ampicillin resistance gene; thus, regions of genomic DNA adjacent to the targeting vector were readily cloned by plasmid rescue and sequenced. The flanking sequences were compared to the nucleic acid databases to identify cellular genes that confer resistance to lytic infection by influenza virus when altered by gene entrapment.

v. Infection with Ebola

Vero gene trap library cells were thawed at room temperature, and allowed to grow at 37°C under 5% C0₂ in DMEM, supplemented with 10% FBS, amphotericin B, streptomycin and Glutamine. Vero library cells were infected with either the Gulu 2000 or Zaire 1976 Ebola strains, of the Voege 1967 strain of Marburg at an MOI of greater than one in T-75 flasks in medium supplemented with 500 mg/ml G418. After a cytopathic effect of 4+ was attained (greater than one week), survivors were harvested and reseeded and undiluted and at 1: 16 and 1:256 dilutions in selection medium. Wells with growth after 10 or more days were reinoculated into T-12.5 flasks in selection medium and allowed to expand. Cells surviving Ebola or Marburg infection were cloned by either limiting dilution or growth on methylcellulose. The isolates were characterized phenotypically by flow cytometry.

vi. Identification of genes disrupted in Ebola-resistant clones

The U3NeoSVl gene trap vector contains a plasmid origin of replication and ampicillin resistance gene; thus, regions of genomic DNA adjacent to the targeting vector were readily cloned by plasmid rescue and sequenced. The flanking sequences were compared to the nucleic acid databases to identify candidate cellular genes that confer resistance to lytic infection by Ebola virus or Marburg virus when altered by gene entrapment.

Example 2

Methods of decreasing pathogenic infection and/or replication

This example describes methods used to express siRNAs or other small molecules targeting one or more genes set forth in Table 1, to determine if such expression can decrease pathogenic replication and/or infection. Any of the genes set forth in Table 1 is further analyzed by contacting cells comprising a gene set forth in Table 1 with siRNA or small molecule that targets the gene product of the gene, and any pathogen set forth herein to identify the gene as a gene involved in pathogenic infection (for example, and not to be limiting, a pox virus, BVDV, a herpes virus, HIV, an RSV virus, an influenza virus, a hepatitis C virus, a hepatitis B virus, Epstein Barr Virus, Human Papilloma Virus, CMV, West Nile virus, a rhinovirus, an adenovirus, measles virus, Marburg virus, Ebola virus, Rift Valley Fever Virus, LCM, Junin virus, Machupo virus, Guanarito virus, Lassa Fever virus, Hantavirus, SARS virus, Nipah virus, Caliciviruses, Hepatitis A,

LaCrosse, California encephalitis, VEE, EEE,WEE, Japanese Encephalitis Virus, Kyasanur Forest Virus, Yellow Fever, Rabies, Chikungunya virus or a Dengue fever virus). A 20% decrease in viral infection indicates that the gene is a gene that is involved in pathogenic infection. This process can be performed for all of the genes set forth herein with any of the viruses, bacteria, parasites or fungi set forth herein.

siRNA Transfections: Pools of 4 duplexed siRNA molecules targeting a gene of interest are reconstituted to a final working concentration of 50uM as directed by the manufacturer (Qiagen). Twenty-four hours prior to transfection, cells are plated in 6- well dishes at 3xl0⁵ cells per well, such that at the time of transfection, the cells are approximately 30% confluent. Prior to transfection, the cells are washed once with IX phosphate buffered saline, and the medium replaced with approximately 1.8ml antibiotic-free medium. siRNA aliquots are diluted with Opti-MEM and RNAseOUT (Invitrogen), lOOul and lul per transfection, respectively. In a separate tube, transfection reagent Lipofectamine2000

(Invitrogen) or Oligofectamine (Invitrogen) are diluted in Opti-MEM as directed by the manufacturer. Following a 5 minute incubation at room temperature, the diluted siRNA is added to the transfection reagent mixture, and incubated for an additional 20 minutes prior to adding to independent wells of the 6- well dishes. Transfections are incubated at 37 °C for 48 hours without changing the medium.

Virus Infections: Following 48-hour transfection, medium is aspirated from

6-well plates. Viruses are diluted in the appropriate medium and 500ul of either virus-free medium or virus dilution is added to each well, and adsorption is allowed to occur at the appropriate temperature for 1 hour. Following adsorption, inoculum is aspirated off the cells, cells are washed once with IX phosphate buffered saline, and 2ml growth medium is added to the cells. The infected cells are incubated for 72 hours at the appropriate temperature prior to harvesting samples for viral titration.

Viral Genomic Extractions: Seventy-hours after inoculating cells, medium is harvested from 6- well dishes and centrifuged for 2 minutes at 10,000 rpm to remove any cellular debris. 200ul of clarified medium is added to 25ul Proteinase K, to which 200ul PureLink96 Viral RNA/DNA lysis buffer (Invitrogen) is added according to the manufacturer. Samples were processed and viral genomic RNA or DNA is extracted using an epMotion 5075 robotics station (Eppendorf) and the PureLink96 Viral RNA/DNA kit (Invitrogen).

cDNA and Quantitative Real-Time PCR Reactions: 3ul of extracted viral RNA is converted to cDNA using M-MLV reverse transcriptase (Invitrogen) and AmpliTaq Gold PCR buffer (Applied Biosystems). MgCl₂, dNTPs and RNAseOUT (Invitrogen) are added to achieve a final concentration of 5mM, ImM and 2U/ul, respectively. Random hexamers (Applied Biosystems) are added to obtain 2.5mM final concentration. Reactions are incubated at 42°C for 1 hour, followed by heat inactivation of the reverse transcriptase at 92°C for 10 minutes. Quantitative real- time PCR reactions are set up in lOul volumes using lul of template cDNA or extracted viral DNA using virus-specific TaqMan probes (Applied Biosystems) and RealMasterMix (Eppendorf). 2- step reactions are allowed to proceed through 40 to 50 cycles on an ep RealPlex thermocycler (Eppendorf). Quantitative standards for real-time PCR are constructed by cloning purified amplicons into pCR2-TOPO (Invitrogen) and sequenced as necessary.

The amount of viral replication in the cells contacted with siRNA to the gene of interest is calculated and compared to the amount of viral replication in control cells that did not receive siRNA targeting the gene of interest. A 20% decrease in viral replication as compared to the control indicates the treatment is effective. Example 3

Treatment of an RSV infected animal with siRNA

This example describes methods that can be used to treat an animal having a pathogen infection or to protect the animal from protection in the future

(prophylaxis).

RSV is an enveloped RNA virus in which rodent models are available. RSV infection causes bronchiolitis in infants and children, which can be fatal, especially in immunocompromised patients. Mouse models for RSV include the BALB/c mouse, as well as a BALB/c mouse by pretreated with cyclophosphamide (for example see Kong et ah, Virol J. 2:3, 2005). The cotton rat (Sigmodon hispidus) is also a host model for RSV (Harlan Sprague Dawley, Indianapolis, IN).

To inhibit (including prevent) RSV infection in a mouse, the following methods can be used. An siRNA (1-5 mg/kg) specific for a gene associated with RSV and listed in Table 1 is administered to the lungs of a mouse via intranasal administration (such as 6 to 16 week old BALB/c mice; Jackson Laboratory, Bar Harbor, ME), and the mouse infected subsequently (or at the same time as siRNA administration) intranasally with 10 5 - 107 PFU/mouse (such s 5 x 105 PFU) in a volume of 50 μΐ. To treat RSV infection in a mouse, the following methods can be used. The mouse is first infected intranasally with RSV and subsequently, the specific siRNA is administered to the lungs intranasally (however, systemic administration could also be used). If desired, the BALB/c mice can be

administered cyclophosphamide (Sigma, St. Louis, MO) intraperitoneally (i.p.) at a single dose of 100 mg per kg five days prior to RSV infection. The A2 strain of human RSV (American Type Culture Collection, Manassas, VA) can be propagated in HEp-2, Vero E6, A549 or primary epithelial cell lines. Alternatively, the RSV strain Bl can be used. Animal subjects can be anesthetized prior to such treatments. Similar methods can be used to infect a cotton rat (such as 2 x 10⁵ PFU of RSV in 100 μΐ).

In a particular example, the following method is used. Female 6-8 week old BALB/c mice (Harlan Sprague) are anesthetized by intraperitoneal administration of 2,2,2-tribromoethanol (Avertin) and intranasally administered 5-100 μg siRNA in a total volume of 50 μΐ at time 4 hours prior to infection for prophylaxis, or at 12, 24, 48, or 72 hours post-infection for treatment. Anesthetized mice are intranasally infected with 10⁶ plaque forming units of RSV strain A2 or Bl. Prior to removal of lungs at desired time points (such as 1-7 days post-infection), mice are anesthetized with Avertin and exsanguinated by severing the right caudal artery. Blood is collected and sera isolated. Lungs are removed and collected in 1.0 ml of

Dulbecco's phosphate buffered saline (D-PBS, Invitrogen) and stored at -70°C for simultaneous analysis of virus titers. Virus titers/gram lung tissue are assayed by standard immunostaining plaque assay (for example see J. Immunol. 164:5913-21, 2000).

Example of Prophylaxis Method:

siRNA 4 _hrs Virus (RSV/A₂)

i.n. (5 or 50ug) * i.n. (10⁶ pfu)

Example of Treatment Method:

Virus (RSV/A2) P^ siRNA

i.n. (10⁶ pfu) ^ ^l * i-n. (50 ug)

Day 3

Day 4

The animals are subsequently examined for viral titers and pathology of RSV infection, such as weight, lung condition, serum antibody titers, interferon levels, and so forth. Reduction of viral titer or one or more symptoms of RSV infection, as compared to a control (such as a mouse or other subject infected with RSV but did not receive the therapeutic molecules), indicates that the siRNA molecules can prevent or treat an RSV infection.

For example, animals can be monitored for weight loss 0, 5, 10 and 17 days after RSV infection. Mice can be sacrificed five days after infection and their lungs removed for determination of RSV titers, cytokine levels and histopathology.

To determine RSV titers, an RSV plaque assay can be used. For example, HEp-2 cells (5 x 10⁵/well) in 6- well plates are infected with 5 x 10⁵ pfu RSV per well for 2 hours at 37°C. The RSV is removed and the wells overlaid with 1.5 ml of growth medium containing 0.8% methylcellulose. The cells are then incubated at 37 °C for 72 hours, after which the overlay is removed. Following incubation, the cells are fixed in cold 80% methanol for 3 hours, blocked with 1% horse serum in PBS at 37°C for 30 min, then incubated with anti-RSV monoclonal antibody (NCL- RSV 3, Vector Laboratories, Burlingame, CA) diluted 1:400 for 1 hour at 37°C. Secondary antibody staining and substrate reactions can be performed using the Vectastain ABC Kit (Vector Laboratories) and diaminobenzidine in H₂0₂ (Pierce, Rockford, IL) used as a chromagen. The plaques can be enumerated by microscopy.

To determine airway hyperresponsiveness (AHR), the following methods can be used. AHR can be measured in unrestrained mice using a whole body plethysmograph (Buxco, Troy, NY) and expressed as enhanced pause (Penh). Mice are exposed for 5 minutes to nebulized PBS and subsequently to increasing concentrations (6, 12, 25 and 50 mg/ml) of nebulized methacholine (MCh; Sigma, St, Louis, MO) in PBS using an ultrasonic nebulizer. After nebulization, recordings are taken for 5 minutes. Penh values can be averaged and expressed as a percentage of baseline Penh values obtained following PBS exposure.

Immunohistochemical analysis of the lungs can be performed as follows. Briefly, lungs are rinsed with intratracheal injections of PBS then perfused with 10 % neutral buffered formalin. Lungs are removed, paraffin-embedded, sectioned at 20 μιη and stained with hematoxylin and eosin. A semi-quantitative evaluation of inflammatory cells in the lung sections can be determined. Whole lung

homogenates can be prepared using a TissueMizer and assayed for cytokines IL-10, IL-12 and IFN-γ by ELISA (R & D Systems, Minneapolis MN), following the manufacturer's directions. Results can be expressed as cytokine amount in picograms per gram of lung (pg/g).

RSV and cytokines in the lungs can be detected using RT-PCR. Briefly, total cellular RNA can be isolated from lung tissue using TRIZOL reagent (Life Technologies, Gaithersburg, MD). Reactions are denatured at 95°C for 1 min, annealed at 56°C for 30 sec, and extended at 72°C for 1 min for 25-35 cycles. The PCR amplicon products can be separated by agarose gel electrophoresis and quantified.

Cell enumeration of bronchoalveolar lavage (BAL) fluid can be performed as follows. Briefly, BAL is centrifuged and the cell pellet suspended in 200 μΐ of PBS and counted using a hemocytometer. The cell suspensions are then centrifuged onto glass slides, for example by using a cytospin centrifuge at 1000 rpm for 5 minutes at room temperature. Cytocentrifuged cells are air dried and stained with a modified Wright's stain (Leukostat, Fisher Scientific, Atlanta, GA) which allows differential counting of monocytes and lymphocytes.

Example 4

Molecules for Disruption of Gene Expression

This example describes siRNA, antisense, ribozyme, microRNA, and triple helix molecules, that can be used to reduce or disrupt expression of gene products of Table 1 or one or more modulators thereof that increase gene product activity, or combinations thereof, thereby decreasing the biological activity of such products (or in some examples a modulator thereof). Such agents are useful for decreasing infection by a pathogen, treating a pathogen infection, or preventing future infection by a pathogen. For example, the agents can be used to treat a subject having a pathogen infection, or susceptible to a pathogen infection. Techniques for the production and use of such molecules are well known to those of skill in the art. For example, nucleic acid sequences can synthesized by use of an automated DNA synthesizer. Methods for using these molecules are described in Example 5.

The amount of siRNA, antisense, ribozyme, microRNA, or triple helix molecule that is effective in the treatment of a particular disease or condition (the therapeutically effective amount) depends on the nature of the disease or condition, and can be determined by standard clinical techniques. For example, it can be useful to use compositions to achieve sustained release of such nucleic acid molecules. In another example, liposomes containing the desired therapeutic molecule are targeted via antibodies to specific cells.

In one example, the amount of disclosed siRNA, antisense, or ribozyme RNA administered (for example in a single dose) is 1-10 mg nucleic acid molecule/kg of subject, such as 1-5 mg/kg, or 3-7 mg/kg. siRNA Molecules

Based on publicly available sequences for the genes and gene products provided in Table 1, one skilled in the art can generate other siRNA molecules using known methods. For example, siRNA sequences that such sequences can be designed and prepared by commercial entities, such as Sequitur, Inc. (Natick, MA).

A siRNA molecule can be any length, such as at least 19 nucleotides, at least 20 nucleotides, at least 21 nucleotides, at least 22 nucleotides, at least 23

nucleotides, at least 24 nucleotides, at least 25 nucleotides, at least 26 nucleotides, at least 27 nucleotides, or at least 30 nucleotides.

Using the methods described herein, siRNA compounds can be used to decrease infection of a cell by a pathogen, treat an existing infection, prevent future infection, or combinations thereof. For example, an siRNA compound is incubated with its reverse complement, allowing hybridization of the two molecules. In particular examples, two or more, such as three or more, or four or more, siRNA compounds are introduced into a cell. For example, the duplex molecule is contacted with a cell, such as a cell of a subject in whom decreased viral infection is desired, under conditions that allow the duplex to enter the cell. In particular examples, the duplex is administered ex vivo or in vitro to a cell, or administered directly to a subject. In another example, an siRNA is part of a vector, and the vector administered ex vivo or in vitro to a cell, or administered directly to a subject. In one example, the vector is the pSilencer™ 4.1-CMV vector (Ambion, Austin, TX).

Antisense Methods

Antisense oligonucleotides can be designed and generated using methods known in the art. Regions of the sequence containing multiple repeats are not as desirable because they will lack specificity. Several different regions can be chosen. Of those, antisense oligonucleotides are selected by the following characteristics: those having the best conformation in solution; those optimized for hybridization characteristics; and those having less potential to form secondary structures.

Antisense molecules having a propensity to generate secondary structures are less desirable. An antisense molecule specific for a gene or gene product listed in Table 1 or a modulator thereof includes a sequence complementary to at least a portion of the transcript of the specific gene. However, absolute complementarity is not required. An antisense sequence can be complementary to at least a portion of an RNA, meaning a sequence having sufficient complementarily to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation can be assayed. The ability to hybridize depends on the degree of complementarity and the length of the antisense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA it may contain and still form a stable duplex (or triplex, as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

In a particular example, an antisense molecule that includes at least 80% sequence identity, such as at least 90% sequence identity, to at least a fragment of the specific gene sequence, such as an mRNA sequence. In one example, the relative ability of an antisense molecule to bind to its complementary nucleic acid sequence is compared by determining the T_m of a hybridization complex of the antisense molecule and its complementary strand. The higher the T_m the greater the strength of the binding of the hybridized strands.

Plasmids or vectors including antisense sequences that recognize the gene or gene product listed in Table 1 or modulator thereof can be generated using standard methods. For example, cDNA fragments or variants coding for a protein involved in infection are PCR amplified, for example using Pfu DNA polymerase (Stratagene). The resulting sequence is cloned in antisense orientation a vector, such as pcDNA vectors (Invitrogen, Carlsbad, CA). The nucleotide sequence and orientation of the insert can be confirmed by sequencing using a Sequenase kit (Amersham Pharmacia Biotech). Such vectors can be administered to a cell in a therapeutic amount, such as administered to a subject, to decrease pathogen infection.

The antisense nucleic acids disclosed herein can be oligonucleotides that are double-stranded or single-stranded, RNA or DNA or a modification or derivative thereof, which can be directly administered to a cell (for example by administering the antisense molecule to the subject), or which can be produced intracellularly by transcription of exogenous, introduced sequences (for example by administering to the subject a vector that includes the antisense molecule under control of a promoter).

Antisense nucleic acids are polynucleotides, for example nucleic acid molecules that are at least 6 nucleotides in length, at least 10 nucleotides, at least 15 nucleotides, at least 20 nucleotides, at least 40 nucleotides, at least 100 nucleotides, at least 200 nucleotides, such as 6 to 100 nucleotides. However, antisense molecules can be much longer. In particular examples, the nucleotide is modified at one or more base moiety, sugar moiety, or phosphate backbone (or combinations thereof), and can include other appending groups such as peptides, or agents facilitating transport across the cell membrane (Letsinger et ah, Proc. Natl. Acad. Sci. USA 1989, 86:6553-6; Lemaitre et al., Pwc. Natl. Acad. Sci. USA 1987, 84:648- 52; WO 88/09810) or blood-brain barrier (WO 89/10134), hybridization triggered cleavage agents (Krol et ah, BioTechniques 1988, 6:958-76) or intercalating agents (Zon, Pharm. Res. 5:539-49, 1988).

Examples of modified base moieties include, but are not limited to: 5- fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2- thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D- galactosylqueosine, inosine, N~6-sopentenyladenine, 1 -methyl guanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3- methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5- methylaminomethyluracil, methoxyarninomethyl-2-thiouracil, beta-D- mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio- N6-isopentenyladenine, uracil-5-oxyacetic acid, pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil- 5-oxyacetic acid methylester, uracil-S-oxyacetic acid, 5-methyl-2-thiouracil, 3-(3- amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.

Examples of modified sugar moieties include, but are not limited to:

arabinose, 2-fluoroarabinose, xylose, and hexose, or a modified component of the phosphate backbone, such as phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a

methylphosphonate, an alkyl phosphotriester, or a formacetal or analog thereof.

In a particular example, an antisense molecule is an cc-anomeric

oligonucleotide. An cc-anomeric oligonucleotide forms specific double- stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gautier et al., Nucl. Acids Res. 15:6625-41, 1987). The oligonucleotide can be conjugated to another molecule, such as a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization- triggered cleavage agent. Oligonucleotides can include a targeting moiety that enhances uptake of the molecule by host cells. The targeting moiety can be a specific binding molecule, such as an antibody or fragment thereof that recognizes a molecule present on the surface of the host cell.

In a specific example, antisense molecules that recognize a nucleic acid molecule provided in Table 1, include a catalytic RNA or a ribozyme (for example see WO 90/11364; WO 95/06764; and Sarver et al, Science 247: 1222-5, 1990).

Conjugates of antisense with a metal complex, such as terpyridylCu (II), capable of mediating mRNA hydrolysis, are described in Bashkin et al. (Appl. Biochem

Biotechnol. 54:43-56, 1995). In one example, the antisense nucleotide is a 2'-0- methylribonucleotide (Inoue et al., Nucl. Acids Res. 15:6131-48, 1987), or a chimeric RNA-DNA analogue (Inoue et al. , FEBS Lett. 215:327-30, 1987).

Ribozymes

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by a endonucleolytic cleavage. Methods of using ribozymes to decrease or inhibit RNA expression are known in the art (for example see Kashani-Sabet, J. Investig. Dermatol. Symp. Proc, 7:76-78, 2002).

Ribozyme molecules include one or more sequences complementary to a mRNA of a gene product listed in Table 1 and include the well-known catalytic sequence responsible for mRNA cleavage (see U.S. Pat. No. 5,093,246, herein incorporated by reference). Methods of designing and generating ribozyme molecules are known in the art. Briefly, specific ribozyme cleavage sites within a RNA target are identified by scanning the RNA sequence for ribozyme cleavage sites that include: GUA, GUU and GUC. Once identified, RNA sequences of between 15 and 50 ribonucleotides (such as at least 20 ribonucleotides, at least 40 ribonucleotides, or at least 46 ribonucleotides) corresponding to the region of the target gene containing the cleavage site can be evaluated for predicted structural features, such as secondary structure, that may render the oligonucleotide sequence unsuitable. The suitability of candidate targets cam also be evaluated by testing their accessibility to

hybridization with complementary oligonucleotides, using ribonuclease protection assays.

In particular examples, ribozymes are administered directly to a subject. In another example, a ribozyme is encoded on an expression vector, from which the ribozyme is synthesized in a cell (as in WO 9523225, and Beigelman et al. Nucl. Acids Res. 1995, 23:4434-42). Such a cell or the vector can be administered to a subject.

In a specific example, a vector that contains a riboyzme gene directed against pathogen gene listed in Table 1 or modulator thereof is placed behind a promoter (such as an inducible promoter), is transfected into the cells of a subject, for example a subject susceptible to infection by a pathogen, such as HIV-1, HIV-2, Ebola, Marburg virus, or influenza virus. Expression of this vector in a cell will decrease or inhibit RNA expression in the cell. In one example, the vector is the pSilencer™ 4.1-CMV vector (Ambion).

In a particular example, a vector includes self-cleaving tandem ribozymes (for example, 5 ribozymes encoded on a single RNA transcript). Once the tandem hammerhead transcript is synthesized, it recognizes ribozyme cleavage sites in cis within the newly synthesized transcript identical to the ribozyme target site on the cell's endogenously expressed mRNA. The tandem ribozyme then cleaves itself, liberating free ribozymes to cleave the target mRNA in the cell. microRNAs

MicroRNAs (miRs) that recognize a gene product of Table 1 or modulator thereof can be used to decrease the amount of such mRNAs in a cell. miRNAs silence at the post-transcriptional level by virtue of their sequence complementarity to target mRNAs. In particular examples, miRs are about 18-26 nucleotides in length, such as 21-26 nucleotides, such as at least 18 nucleotides. Animal miRNAs are generally thought to recognize their mRNA targets by incomplete base-pairing, leading to translational inhibition of the target.

Methods of generating or identifying microRNAs are known in the art (for example see Lagos-Quintana et al., Science, 294:853-8, 2001; Lagos-Quintana et al, Curr. Biol. 12:735-9, 2002; and Lagos-Quintana et al, RNA 9: 175-9, 2003).

Triple helix molecules

Nucleic acid molecules used in triplex helix formation for are ideally single stranded and composed of deoxynucleotides. The base composition of these oligonucleotides is designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex. Nucleotide sequences can be pyrimidine-based, which will result in TAT and CGC+ triplets across the three associated strands of the resulting triple helix. The pyrimidine-rich molecules provide base complementarity to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand. In addition, nucleic acid molecules can be chosen that are purine-rich, for example contain a stretch of guanidine residues. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex.

Alternatively, sequences targeted for triple helix formation are increased by creating "switchback" nucleic acid molecule. Switchback molecules are synthesized in an alternating 5'-3', 3'-5' manner, such that they base pair with one strand of a duplex first and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.

I l l Example 5

Methods of Treatment and Prophylaxis

This example provides methods that can be used to treat a subject having a pathogen infection, or to prevent or reduce the incidence of a future infection.

Methods of treatment include methods that reduce one or more symptoms in the subject due to the infection, such as fever or increased white blood cell count.

However, a complete elimination of symptoms is not required. Treatment methods can also include reducing the presence of the pathogen, such as reducing viral titer in a subject. Prophylactic methods include reducing the incidence of a future pathogen infection, for example in a subject who is susceptible to infection by the pathogen (such as children, the elderly, and medical workers).

In particular examples, the method includes administering to the subject a therapeutically effective amount of an agent that decreases the biological activity of a gene or gene product listed in Table 1 or a modulator thereof (for example by decreasing the activity of a modulator thereof that increases the activity of a gene or gene product listed in Table 1, respectively). When the activity of the gene or gene product listed in Table 1, is decreased, for example by prematurely downregulating their protein or nucleic acid molecule levels, a reduction in pathogen infection is achieved. The disclosed antisense, ribozyme, triple helix, miRs, and siRNA molecules (for example at a concentration of 1-10 mg nucleic acid molecule/kg of subject, such as 1-5 mg/kg, or 3-7 mg/kg) can be administered to a subject alone, or in combination with other agents, such as a pharmaceutical carrier, other therapeutic agents (such as anti-viral compounds), or combinations thereof. In on example, the subject is a mammal, such as mice, non-human primates, and humans.

In one example, a siRNA, ribozyme, triple helix, miR, or antisense molecule is part of a vector, and the vector administered ex vivo or in vitro to a cell, or administered directly to a subject. For example, a U6 promotor that controls the expression of 21 nucleotides, followed by a stem-loop of 8 bp, followed by an additional complementary 21 bp that anneals to the first 21 nucleotides transcribed. The 21 nucleotide sequences are siRNAs that recognize the specific molecules listed in Table 1, or a modulator thereof. Transcription is halted using a stretch of 5 T's in the plasmid immediately downstream of the last desired transcribed nucleotide. In another example, the vector is the pSilencer™ 4.1-CMV vector (Ambion).

In particular examples, a subject susceptible to or suffering from an infection, wherein decreased amounts of infection by the pathogen is desired, is treated with a therapeutically effective amount of antisense, ribozyme, triple helix, miR, or siRNA molecule (or combinations thereof) that recognizes a nucleic acid sequence of a molecule listed in Table 1. Similarly, other agents, such as an agent that specifically recognizes and interacts with (such as binds to) a protein listed in Table 1 or a modulator thereof, thereby decreasing the ability of the protein to interact with a pathogen, can also be used to decrease or inhibit infection. Other exemplary agents are those identified using the methods described in the Examples below. These agents, such as antibodies, peptides, nucleic acid molecules, organic or inorganic compounds, can be administered to a subject in a therapeutically effective amount. After the agent has produced an effect (a decreased level of pathogen infection is observed, or symptoms associated with infection decrease), for example after 24-48 hours, the subject can be monitored for diseases associated with the infection.

In particular examples, the subject is first screened to determine the type of pathogen infection present. If the pathogen is one that can be decreased by the disclosed therapies, the subject is then administered the therapy.

The treatments disclosed herein can also be used prophylactically, for example to inhibit or prevent infection by a pathogen. Such administration is indicated where the treatment is shown to have utility for treatment or prevention of the disorder. The prophylactic use is indicated in conditions known or suspected of progressing to disorders associated with a pathogen infection. Example 6

in vitro Screening Assay for Agents that Decrease Infection

This example describes in vitro methods that can be used to screen test agents for their ability to interfere with or even inhibit infection of a host cell by a pathogen. As disclosed in the Examples above, genes and gene products listed in Table 1, and modulators thereof, are involved in pathogen infection (such as HIV-1, HIV-2, Ebola, Marburg, influenza virus) and the interaction of the specific gene product listed in Table 1 or modulator thereof /pathogen protein interaction is a component in the ability of a pathogen to infect a cell. Therefore, screening assays can be used to identify and analyze agents that decrease or interfere with this interaction. For example, the following assays can be used to identify agents that interfere with the interaction of gene and/or gene product listed in Table 1 or a modulator thereof, with a pathogen protein sequence. However, the present disclosure is not limited to the particular methods disclosed herein.

Agents identified via the disclosed assays can be useful, for example, in decreasing or even inhibiting pathogen infection by more than an amount of infection in the absence of the agent, such as a decrease of at least about 10%, at least about 20%, at least about 50%, or even at least about 90%. This decrease in infection can serve to ameliorate symptoms associated with infection, such as fever. Assays for testing the effectiveness of the identified agents, are discussed below.

Exemplary test agents include, but are not limited to, any peptide or non- peptide composition in a purified or non-purified form, such as peptides made of D- and/or L-configuration amino acids (in, for example, the form of random peptide libraries; see Lam et al., Nature 354:82-4, 1991), phosphopeptides (such as in the form of random or partially degenerate, directed phosphopeptide libraries; see, for example, Songyang et al., Cell 72:767-78, 1993), antibodies, and small or large organic or inorganic molecules. A test agent can also include a complex mixture or "cocktail" of molecules.

The basic principle of the assay systems used to identify agents that interfere with the interaction between the gene products listed in Table 1 or modulator protein thereof, and a pathogen protein binding partner or partners, involves preparing a reaction mixture containing the gene product listed in Table 1 or modulator protein thereof and one or more pathogen proteins under conditions and for a time sufficient to allow the proteins to interact and bind, thus forming a complex. To test an agent for inhibitory activity, the reaction is conducted in the presence and absence of the test agent. The test agent can be initially included in the reaction mixture, or added at a time subsequent to the addition of the gene products listed in Table 1 or modulator protein thereof and a pathogen protein. Controls can be are incubated without the test agent or with a placebo. Exemplary controls include agents known not to bind to pathogen proteins, the gene products listed in Table 1 or modulator proteins thereof. The formation of any complexes between the gene products listed in Table 1 or modulator protein thereof and the pathogen protein is then detected. The formation of a complex in the control reaction, but not in the reaction mixture containing the test agent, indicates that the agent interferes with the interaction of the gene products listed in Table 1 or modulator protein thereof and the pathogen protein, and is therefore possibly an agent that can be used to decrease infection by a pathogen, for example to treat a subject having an infection or to prevent an infection in the future.

The assay for agents that interfere with the interaction of a gene product listed in Table 1 or modulator protein thereof and pathogen proteins can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring a gene products listed in Table 1 or modulator protein thereof or the pathogen protein onto a solid phase and detecting complexes anchored on the solid phase at the end of the reaction. In some examples, the method further involves quantitating the amount of complex formation or inhibition. Exemplary methods that can be used to detect the presence of complexes, when one of the proteins is labeled, include ELISA, spectrophotometry, flow cytometry, and microscopy. In homogeneous assays, the entire reaction is performed in a liquid phase. In either method, the order of addition of reactants can be varied to obtain different information about the agents being tested. For example, test agents that interfere with the interaction between the proteins, such as by competition, can be identified by conducting the reaction in the presence of the test agent, for example by adding the test agent to the reaction mixture prior to or simultaneously with a gene product listed in Table 1 or modulator protein thereof and pathogen protein. On the other hand, test agents that disrupt preformed complexes, such as agents with higher binding constants that displace one of the proteins from the complex, can be tested by adding the test agent to the reaction mixture after complexes have been formed. The various formats are described briefly below.

Once identified, test agents found to inhibit or decrease the interaction between a gene product listed in Table 1 or modulator protein thereof and a pathogen protein can be formulated in therapeutic products (or prophylactic products) in pharmaceutically acceptable formulations, and used for specific treatment or prevention of a disease associated with a pathogen, such as HIV, Ebola, Marburg, RSV, or measles.

Heterogeneous assay system

In a heterogeneous assay system, one binding partner, either the gene product listed in Table 1 or modulator protein thereof, or the pathogen protein (such as an HIV, Ebola, Marburg, RSV, or measles virus preparation) is anchored onto a solid surface (such as a microtiter plate), and its binding partner, which is not anchored, is labeled, either directly or indirectly. Exemplary labels include, but are not limited to, enzymes, fluorophores, ligands, and radioactive isotopes. The anchored protein can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished simply by coating the solid surface with a solution of the protein and drying. Alternatively, an immobilized antibody (such as a monoclonal antibody) specific for the protein can be used to anchor the protein to the solid surface. The surfaces can be prepared in advance and stored.

To conduct the assay, the binding partner of the immobilized species is added to the coated surface with or without the test agent. After the reaction is complete, unreacted components are removed (such as by washing) and any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the binding partner was pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the binding partner is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; for example by using a labeled antibody specific for the binding partner (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody). Depending upon the order of addition of reaction components, test compounds which inhibit complex formation or which disrupt preformed complexes can be detected.

Alternatively, the reaction can be conducted in a liquid phase in the presence or absence of the test agent, the reaction products separated from unreacted components, and complexes detected; for example by using an immobilized antibody specific for one binding partner to anchor any complexes formed in solution, and a labeled antibody specific for the other binding partner to detect anchored complexes. Again, depending upon the order of addition of reactants to the liquid phase, test agents which inhibit complex or which disrupt preformed complexes can be identified.

Homogenous assays

In an alternate example, a homogeneous assay can be used. In this method, a preformed complex of the gene product listed in Table 1 or modulator protein thereof and the pathogen protein is prepared in which one of the proteins is labeled, but the signal generated by the label is quenched due to complex formation (for example, see U.S. Pat. No. 4,109,496 by Rubenstein which utilizes this approach for immunoassays). The addition of a test substance that competes with and displaces one of the binding partners from the preformed complex will result in the generation of a signal above background. In this way, test agents that disrupt gene product listed in Table 1 or modulator protein thereof -pathogen protein interactions are identified.

Immobilization of Proteins

In a particular example, a gene product listed in Table 1 or modulator protein thereof can be prepared for immobilization using recombinant DNA techniques. For example, a coding region of a gene product listed in Table 1 or modulator protein thereof can be fused to a glutathione-S-transferase (GST) gene using the fusion vector pGEX-5X-l, in such a manner that its binding activity is maintained in the resulting fusion protein. In a heterogeneous assay, for example, the GST-gene product listed in Table 1 or modulator thereof fusion protein can be anchored to glutathione-agarose beads. The pathogen protein preparation can then be added in the presence or absence of the test agent in a manner that allows interaction and binding to occur. At the end of the reaction period, unbound material can be washed away, and a labeled antibody

(such as labeled with the radioactive isotope 125 I) that is specific for gene product listed in Table 1 or modulator protein thereof (or for the pathogen protein) can be added to the system and allowed to bind to the complexed binding partners. The interaction between the gene product listed in Table 1 or modulator protein thereof and the pathogen protein can be detected by measuring the amount of label that remains associated with the glutathione-agarose beads. A successful reduction or inhibition of the interaction by the test compound will result in a decrease in detectable label.

Alternatively, the GST-gene product listed in Table 1 or modulator protein thereof fusion protein, and the pathogen protein can be mixed together in liquid in the absence of the solid glutathione agarose beads. The test agent can be added either during or after the binding partners are allowed to interact. This mixture can then be added to the glutathione-agarose beads and unbound material is washed away. Again, the extent of inhibition of the binding partner interaction can be detected by adding the labeled antibody and measuring the label (such as the radioactivity) associated with the beads.

In another example, these same techniques can be employed using peptide fragments that correspond to the binding domain of the gene product listed in Table 1 or modulator protein thereof, or the pathogen protein, in place of one or more of the full length proteins. Any number of methods routinely practiced in the art can be used to identify and isolate a protein's binding site. These methods include, but are not limited to, mutagenesis of one of the genes encoding the proteins and screening for disruption of binding in a co-immunoprecipitation assay.

Compensating mutations in a host gene can be selected. Sequence analysis of the genes encoding the respective proteins will reveal the mutations that correspond to the region of the protein involved in interactive binding. Alternatively, one protein can be anchored to a solid surface using methods described in above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide including the binding domain may remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the for the protein is obtained, short gene segments can be engineered to express peptide fragments of the protein, which can then be tested for binding activity and purified or synthesized.

For example, a gene product listed in Table 1 or modulator protein thereof can be anchored to a solid material as described above by making a GST- gene product listed in Table 1 or modulator protein thereof fusion protein and allowing it to bind to glutathione agarose beads. The pathogen protein can be labeled with a radioactive isotope, such as 35 S, and cleaved with a proteolytic enzyme such as trypsin. Cleavage products can then be added to the anchored GST-fusion protein and allowed to bind. After washing away unbound peptides, labeled bound material, representing the cellular or extracellular protein binding domain, can be eluted, purified, and analyzed for amino acid sequence. Peptides so identified can be produced synthetically or fused to appropriate facilitative proteins using

recombinant DNA technology. Example 7

Cell-Based Screening Assay for Agents that Decrease Infection

This example describes methods using intact cells that can be used to screen test agents for their ability to interfere with or even inhibit infection of a host cell by a pathogen. For example, a yeast two-hybrid assay or the inverse two-hybrid assay method of Schreiber and coworkers {Proc. Natl. Acad. ScL, USA 94:13396, 1977) can be used to screen for an agent that disrupts the association between a gene product listed in Table 1 or modulator protein thereof and a pathogen protein.

Similar to Example 10, therapeutic agents identified by these approaches are tested for their ability to decrease or inhibit infection of a host cell, such as a human cell, by a pathogen.

In one example, the yeast two-hybrid system is used to identify anti-viral agents. One version of this system has been described (Chien et ah, Proc. Natl. Acad. Sci. USA, 88:9578-82, 1991) and is commercially available from Clontech (Palo Alto, CA). Briefly, utilizing such a system, plasmids are constructed that encode two hybrid proteins: one includes the DNA-binding domain of a

transcription activator protein fused to one test protein "X" and the other includes the activator protein's activation domain fused to another test protein "Y". Thus, either "X" or "Y" in this system can be a gene product listed in Table 1 or modulator protein thereof, while the other can be a test protein. The plasmids are transformed into a strain of S. cerevisiae that contains a reporter gene (such as lacZ) whose regulatory region contains the activator's binding sites. Either hybrid protein alone cannot activate transcription of the reporter gene, the DNA-binding domain hybrid because it does not provide activation function and the activation domain hybrid because it cannot localize to the activator's binding sites. Interaction of the two proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product.

The two-hybrid system or related methodology can be used to screen activation domain libraries for proteins that interact with a gene product listed in Table 1 or modulator protein thereof involved in pathogen infection. Total genomic or cDNA sequences are fused to the DNA encoding an activation domain. This library and a plasmid encoding a hybrid of the host protein involved in viral infection fused to the DNA-binding domain are cotransformed into a yeast reporter strain, and the resulting transformants are screened for those that express the reporter gene. These colonies are purified and the plasmids responsible for reporter gene expression are isolated. DNA sequencing is then used to identify the proteins encoded by the library plasmids.

For example, and not by way of limitation, a host gene encoding a gene product listed in Table 1 or modulator protein thereof, can be cloned into a vector such that it is translationally fused to the DNA encoding the DNA-binding domain of the GAL4 protein. A cDNA library of the cell line from which proteins that interact with the gene product listed in Table 1 or modulator protein thereof are to be detected can be made using methods routinely practiced in the art. In this particular system, the cDNA fragments can be inserted into a vector such that they are translationally fused to the activation domain of GAL4. This library can be co- transformed along with the host-GAL4 DNA binding domain fusion plasmid into a yeast strain which contains a lacZ gene driven by a promoter which contains GAL4 activation sequences. A cDNA encoded protein, fused to GAL4 activation domain, that interacts with the gene product listed in Table 1 or modulator protein thereof will reconstitute an active GAL4 protein and thereby drive expression of the lacZ gene. Colonies which express lacZ can be detected by their blue color in the presence of X-gal. The cDNA can then be extracted from strains derived from these and used to produce and isolate the gene product listed in Table 1 or modulator protein thereof-interacting protein using techniques routinely practiced in the art.

Example 8

Rapid Screening Assays

Prior to performing any assays to detect interference with the association of a gene product listed in Table 1 or modulator protein thereof and a pathogen protein, rapid screening assays can be used to screen a large number of agents to determine if they bind to a gene product listed in Table 1 or modulator protein thereof or a pathogen protein. Rapid screening assays for detecting binding to HIV proteins have been disclosed, for example in U.S. Patent No. 5,230,998, which is

incorporated by reference. In that assay, a gene product listed in Table 1 or modulator protein thereof, or a pathogen protein, such as an HIV protein, is incubated with a first antibody capable of binding to a gene product listed in Table 1 or modulator protein thereof, or a pathogen protein, and the agent to be screened. Excess unbound first antibody is washed and removed, and antibody bound to the gene product listed in Table 1 or modulator protein thereof, or pathogen protein, is detected by adding a second labeled antibody which binds the first antibody. Excess unbound second antibody is then removed, and the amount of the label is quantitated. The effect of the binding effect is then determined in percentages by the formula: (quantity of the label in the absence of the test agent) - (quantity of the label in the presence of the test agent /quantity of the label in the absence of the test agent) x 100.

Agents that are found to have a high binding affinity to the gene product listed in Table 1 or modulator protein thereof, or pathogen protein can then be used in other assays more specifically designed to test inhibition of the gene product listed in Table 1 or modulator protein thereof/pathogen protein interaction, or inhibition of pathogen infection. Example 9

Assays for Measuring Inhibition of Infection

Any of the test agents identified in the foregoing assay systems can be tested for their ability to decrease or inhibit infection by a pathogen. Cell-based assays

Exemplary methods are provided known to those of skill in the art including those described herein. Briefly, cells (20,000 to 250,000) are infected with the desired pathogen (such as HIV-1, HIV-2, influenza virus, Ebola or Marburg virus), and the incubation continued for 3-7 days. The test agent can be applied to the cells before, during, or after infection with the pathogen. The amount of pathogen and agent administered can be determined by skilled practitioners. In some examples, several different doses of the potential therapeutic agent can be administered, to identify optimal dose ranges. Following administration of the test agent, assays are conducted to determine the resistance of the cells to infection.

For example, if analyzing viral infection, the presence of a viral antigen can be determined by using antibody specific for the viral protein then detecting the antibody. In one example, the antibody that specifically binds to the viral protein is labeled, for example with a detectable marker such as a flurophore. In another example, the antibody is detected by using a secondary antibody containing a label. The presence of bound antibody is then detected, for example using microscopy, flow cytometry, or ELISA. Similar methods can be used to monitor bacterial, protozoal, or fungal infection (except that the antibody would recognize a bacterial, protozoal, or fungal protein, respectively).

The ability of the cells to survive in the presence of a pathogen can also be used as a measure of pathogen infection. For example, a cell viability assay, such as trypan blue exclusion, can be performed, wherein a decrease in cell viability indicates the presence of pathogen infection, and an increase in cell viability indicates a decrease in viral infection. Animal model assays

The ability of an agent, such as those identified using the methods provided above, to prevent or decrease infection by a pathogen, can be assessed in animal models. Several animal models for pathogen infection are known in the art. For example, mouse HIV models are disclosed in Sutton et al. (Res. Initiat Treat.

Action, 8:22-4, 2003) and Pincus et al. (AIDS Res. Hum. Retroviruses 19:901-8,

2003); guinea pig models for Ebola infection are disclosed in Parren et al. (J. Virol.

76:6408-12, 2002) and Xu et al. (Nat. Med. 4:37-42, 1998); mouse models for Marburg infection are disclosed in (Ruchko et al., Vopr Virusol. 46: 21-4, 2001); and macaque models for measles infection are disclosed in Premenko-Lanier et al.

(J. Infect. Dis. 189:2064-71, 2004). Such animal models can also be used to test agents for the ability to ameliorate symptoms associated with a pathogen infection.

In addition, such animal models can be used to determine the LD50 and the ED50 in animal subjects, and such data can be used to determine the in vivo efficacy of potential agents.

Animals of any species, including, but not limited to, mice, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates, such as baboons, monkeys, and chimpanzees, can be used to generate an animal model of pathogen infection if needed.

The appropriate animal is inoculated with the desired pathogen, in the presence or absence of the test agents identified in the examples above. The amount of pathogen and agent administered can be determined by skilled practitioners. In some examples, several different doses of the potential therapeutic agent can be administered to different test subjects, to identify optimal dose ranges. The therapeutic agent can be administered before, during, or after infection with the pathogen. Subsequent to the treatment, animals are observed for the development of the appropriate pathogen infection and symptoms associated therewith. A decrease in the development of the appropriate pathogen infection, or symptoms associated therewith, in the presence of the test agent provides evidence that the test agent is a therapeutic agent that can be used to decrease or even inhibit pathogen infection in a subject. In view of the many possible embodiments to which the principles of the disclosed invention may be applied, it should be recognized that the illustrated embodiments are only preferred examples of the invention and should not be taken as limiting the scope of the invention. Rather, the scope of the invention is defined by the following claims. We therefore claim as our invention all that comes within the scope and spirit of these claims.

Claims

We claim:

1. A method of decreasing infection in a cell by a pathogen comprising decreasing expression or activity of a gene or gene product set forth in Table 1 in the cell,

TABLE 1

LOC740399 740399 XM_001142404.1 XP_001142404.1

(Pan troglodytes) (Pan troglodytes)

LOC741049 741049 XM_001156563.1 XP_001156563.1

(Pan troglodytes) (Pan troglodytes)

LOC741551 741551 XM_001144203.1 XP_001144203.1

(Pan troglodytes) (Pan troglodytes)

MACROD2 140733 NM_080676.5 NP_542407.2 C20orfl33

MBNL3 55796 NM_018388.3 NP_060858.2 CHCR; MBLX;

MB XL; MBLX39; FLJ11316;

FLJ97142

NADK 65220 NM_023018.3 NP_075394.3 FLJ 13052;

FLJ37724;

(U283E3.1 ; RP1- 283E3.6

NME2P1 283458 NR_001577.1

PCDH9 5101 NM_203487.2 NP_982354.1

PLD5 200150 NM_152666.1 NP_689879.1 PLDC; FLJ40773;

MGC 120565; MGC 120566; MGC 120567

PPP1R2P3 153743 NR_002168.1 MGC87149

PROM1 8842 NM_006017.2 NP_006008.1 RP41 ; AC133;

CD133; MCDR2; STGD4; CORD 12; PROML1 ;

MSTP061

RAP2A 5911 NM_021033.6 NP_066361.1 KREV; RAP2; K- REV; RbBP-30

RAP2C 57826 NM_021183.3 NP_067006.3 DKFZp313B211

RPS 11 6205 NM_001015.3 NP_001006.1

RSL24D1 51187 NM_016304.2 NP_057388.1 L30; RLP24;

RPL24; TV AS 3; RPL24L; C15orfl5; HRP-L30-iso

SCN11A 11280 NM_014139.2 NP_054858.2 NaN; SNS-2;

NAV1.9; SCN12A

SH3GL2 6456 NM_003026.2 NP_003017.1 CNSA2; SH3P4;

EEN-B l ; SH3D2A; FLJ20276;

FLJ25015

SLC35E2 9906 NM_182838.1 NP_878258.1 FLJ34996;

FLJ44537;

KIAA0447;

MGC 104754; MGC 117254; MGC126715; MGC 138494; DKFZp686M0869

SLC44A3 126969 NM_001114106.1 NP_001107578.1 CTL3; MGC45474 SLC5A7 60482 NM_021815.2 NP_068587.1 CHT; CHT1 ;

hCHT;

MGC126299; MGC 126300

STX5 6811 NM_003164.3 NP_003155.2 SED5; STX5A

TAPT1 202018 NM_153365.2 NP_699196.2 CMVFR; FLJ90013

UBE2E3 10477 NM_006357.2 NP_006348.1 UBCH9; UbcM2

WASF2 10163 NM_006990.2 NP_008921.1 SCAR2; WAVE2;

(U393P12.2

WDR48 57599 NM_020839.2 NP_065890.1 P80; UAF1 ;

KIAA1449;

DKFZp686G1794 wherein decreasing expression or activity of the gene or gene product set forth in Table 1 in the cell as compared to a control decreases infection in the cell by the pathogen.

2. The method of claim 1, wherein decreasing activity of a gene or gene product set forth in Table 1 comprises decreasing expression or activity of a modulator that increases expression or activity of a gene product set forth in Table 1 or increasing activity of a modulator that decreases expression or activity of a gene product set forth in Table 1.

3. The method of claim lor 2, wherein the pathogen is Campylobacter jujuni, Vibrio cholerae, SV40, Legionella pneumophila, Aeromonas hydrophilia, Echovirus 1, Echovirus 11, Brucella spp, Clostridium spp., Avian sarcoma and leukosis virus, Escherichia coli, Streptcoccus pyogenes, Semiliki forest virus, Salmonella typhimurium, Bacillus anthracis, Ecotropic mouse leukaemia virus, Shigella flexneri, Bacillus thuringiensis, HTLV-1, Chlamydia spp., Helicobacter pylori, human immunodeficiency virus (HIV-1), Mycobacterium spp., hysteria monocytogenes, Ebola, Marburg, Measles, Herpes Simplex virus, influenza virus, respiratory syncytia virus (RSV ), or Epstein-Barr virus.

4. The method of claim 1 or 2, wherein the pathogen comprises an

enveloped RNA virus.

5. The method of claim 1 or 2, wherein the pathogen is human

immunodeficiency virus (HIV)-l, HIV-2, Ebola virus, Marburg virus, or influenza virus.

6. The method of any one of claims 1-5, wherein decreasing expression or activity of a gene or gene product set forth in Table 1 comprises decreasing an amount of mRNA encoding a gene product set forth in Table 1.

7. The method of claim 1, wherein decreasing the expression or activity of the gene or gene product set forth in Table 1 comprises decreasing an interaction of a pathogen protein and a protein encoded by a gene of Table 1, by decreasing expression of the protein encoded by a gene set forth in Table 1 as compared to expression in a control.

8. The method of claim 7, wherein the pathogen protein comprises a virus and decreasing the interaction of the virus and the protein encoded by a gene of Table 1, decreases infection in the cell by the virus.

9. The method of claim 7 or 8, wherein decreasing expression of the protein encoded by a gene set forth in Table 1, comprises decreasing transcription of an mRNA encoding the protein encoded by a gene set forth in Table 1.

10. The method of claim 9, wherein decreasing transcription of the mRNA comprises inserting a transposon or insertional vector into a coding region of a nucleic acid sequence encoding the protein encoded by the gene set forth in Table 1.

11. The method of claim 9, wherein decreasing the transcription of the mRNA comprises contacting the mRNA with an antisense RNA, triple helix molecule, ribozyme, microRNA, or siRNA that recognizes the mRNA.

12. The method of claim 11, wherein the cell is present in a subject, and contacting the mRNA with an antisense RNA, triple helix molecule, ribozyme, microRNA, or siRNA that recognizes the mRNA comprises administering the antisense RNA, triple helix molecule, ribozyme, microRNA, or siRNA to the subject.

13. The method of claim 7, wherein decreasing an interaction of a pathogen protein and the protein encoded by a gene set forth in Table 1, comprises contacting the cell with an agent that decreases the activity of the protein or a modulator thereof.

14. The method of claim 13, wherein the cell is present in a subject and wherein contacting the cell with the agent comprises administering the agent to the subject.

15. The method of claim 13, wherein the agent is an anti-protein binding agent that specifically binds to the protein encoded by a gene set forth in Table 1, wherein the anti-protein binding agent decreases an interaction between the protein encoded by the gene set forth in Table 1 or modulator protein thereof, and the pathogen.

16. The method of claim 15, wherein the anti-protein binding agent is an antibody or chemical compound.

17. The method of any one of claims 1-16, wherein the cell is a mammalian cell.

18. A method of treating a pathogen infection in a subject, comprising: administering to a subject having a pathogen infection an effective amount of an agent that interferes with the interaction of a pathogen and a gene product set forth in Table 1 or a modulator thereof, thereby decreasing a sign or symptom associated with in the pathogen infection as compared to the sign or symptom in the absence of treatment, thereby treating the pathogen infection in the subject.

19. The method of claim 18, wherein the agent is an antisense, triple helix molecule, ribozyme, microRNA, or siRNA molecule that recognizes a nucleic acid sequence encoding a gene product set forth in Table 1 or a modulator that enhances activity of such gene product.

20. The method of claim 18 or 19, wherein the effective amount induces a prophylactic effect in the subject, which decreases infection in the subject by the pathogen.

21. The method of claim 18 or 19, wherein the subject was previously infected by a pathogen and the effective amount induces a therapeutic effect in the host.

22. A method of identifying an agent that decreases pathogenicity of a pathogen, comprising:

contacting a test agent with a cell expressing a gene or gene product set forth in Table 1 or a modulator thereof; and

determining whether the test agent decreases expression or activity of the gene or gene product set forth in Table 1, wherein a decrease in expression or activity of the gene or gene product of Table 1 as compared to a control, indicates the agent decreases pathogenicity of the pathogen.

23. The method of claim 22, wherein the pathogen comprises

Campylobacter jujuni, Vibrio cholerae, SV40, Legionella pneumophila, Aeromonas hydrophilia, Echovirus 1, Echovirus 11, Brucella spp, Clostridium spp., Avian sarcoma and leukosis virus, Escherichia coli, Streptcoccus pyogenes, Semiliki forest virus, Salmonella typhimurium, Bacillus anthracis, Ecotropic mouse leukaemia virus, Shigella flexneri, Bacillus thuringiensis, HTLV-1, Chlamydia spp.,

Helicobacter pylori, human immunodeficiency virus- 1 (HIV-1), HIV-2,

Mycobacterium spp., Lysteria monocytogenes, Ebola, Marburg, Measles, Herpes Simplex virus, influenza virus, respiratory syncytia virus (RSV), or Epstein-Barr virus.

24. The method of claim 22 or 23, wherein determining whether the test agent decreases a gene or gene product of Table 1 activity comprises determining whether the test agent decreases expression in a cell of the gene or gene product of Table 1 as compared to expression in the absence of the test agent.

25. The method of claim 24, wherein determining whether the test agent decreases expression of a gene or gene product of Table 1 comprises determining whether the test agent decreases a level of mRNA of a gene set forth in Table 1 or a modulator thereof that affects activity of the gene set forth in Table 1 in the cell.

26. The method of claim 22, wherein the pathogen comprises a virus, bacterium, parasite, or protozoa.

27. The method of claim 26, wherein the pathogen comprises a virus.

28. The method of claim 27, wherein the virus comprises a viral envelope protein.

29. The method of claim 27, wherein the virus comprises an enveloped

RNA virus.

30. A cell comprising a functional deletion of a gene set forth in Table 1, wherein the cell has a decreased susceptibility to infection by a pathogen.

31. A non-human transgenic mammal comprising a functional deletion of a gene set forth in Table 1 or a modulator gene thereof that increases activity of a gene set forth in Table 1, wherein the mammal has decreased susceptibility to infection by a pathogen.

32. A method of determining resistance or susceptibility to pathogen infection in a subject, comprising comparing a first nucleic acid sequence of a subject to a second nucleic acid sequence comprising a sequence of a gene or gene product set forth in Table 1, wherein a higher similarity between the first and second nucleic acid sequence indicates the subject is more susceptible to pathogen infection, and wherein a lesser similarity between the first and second nucleic acid sequence indicates the subject is more resistant to pathogen infection.

33. The method of claim 32, wherein the first nucleic acid sequence is obtained from a biological sample of the subject.

34. The method of claim 32, wherein the first nucleic acid sequence comprises a plurality of nucleic acid sequences, wherein each nucleic acid sequence is obtained from a different subject.

35. The method of claim 34, further comprising determining a polymorphic variation within a population.