WO2021247682A1

WO2021247682A1 - Methods for mitigating or diminishing spread of pathogenic infections

Info

Publication number: WO2021247682A1
Application number: PCT/US2021/035421
Authority: WO
Inventors: Peter M. Ross
Original assignee: Ross Peter M
Priority date: 2020-06-02
Filing date: 2021-06-02
Publication date: 2021-12-09

Abstract

The present methods comprise initial administration of a first rapid test, such as rapid antigen test, that has a low likelihood of false positive results and a known likelihood of false negative results, alone or in conjunction with other rapid tests, to identify a first subpopulation of positives, to which an infection mitigation protocol (such as quarantine or the administration of a therapeutic treatment) is administered. Negatives are recorded and provisionally released from further study. A diagnostic test is then administered to this subpopulation, to identify the portion of this first subpopulation that were false positives in the first test. Ideally, a positive result for the diagnostic test is pathognomonic for the infection. Any infection mitigation protocol (such as quarantine) may then be discontinued for those testing negative in the first population and intensified for those testing positive, such as with contact tracing or other protocols, to identify all true positives and those they may have infected within the population.

Description

METHODS FOR MITIGATING OR DIMINISHING SPREAD OF

PATHOGENIC INFECTIONS

TECHNICAL FIELD

This disclosure relates to methods for controlling spread of pathogenic infection within populations, and more particularly to a two-step diagnostic protocol for mitigating the spread of such infections.

BACKGROUND

The spread of pathogens is still a significant problem within modern society, as especially demonstrated by the economic impacts and human suffering caused by the rapid spread of severe acute respiratory syndrome coronavirus 2, or SARS-CoV-2 (and the disease it causes in humans known as COVID-19). In order to limit the spread of a viral infection, rapid identification of those individuals who are currently infected is necessary to allow proper treatment and/or isolation of those individuals to slow or stop further spread. Most testing protocols for determining viral infection involve administration of a single diagnostic test. Many of the laboratory tests used to determine currently-infected individuals within a population are too slow, too expensive, too cumbersome, detect parameters that only appear late in infection (such as the antibody response of the infected individual), or may be otherwise unsuited for rapid screening of city, state, or country-sized populations as needed to control pathogen spread. There is a clear need for a viral testing protocol that allows rapid identification of infected individuals in a population so that treatment may be effectively applied, while being cheap enough that cost does not become a limiting factor in its broad administration across a total population.

SUMMARY

The present disclosure provides methods for mitigating the spread of infections by pathogens within a testable population, such as a population of stock animals or humans. The present methods comprise initial administration of a first rapid test, such as rapid antigen test, that has a low likelihood of false positive results and a known likelihood of false negative results, alone or in conjunction with other rapid tests, to identify a first subpopulation of positives, to which an infection mitigation protocol (such as quarantine or the administration of a therapeutic treatment) is administered. Negatives are recorded and provisionally released from further study. In some embodiments, the first test may be administered one or more additional times to the first subpopulation (positives), with or without skilled supervision, to confirm and refine the results of the first rapid test, or other tests may be used to narrow the first subpopulation. A diagnostic test is then administered to this subpopulation, for example a polymerase chain reaction (PCR) test, to identify the portion of this first subpopulation that were false positives in the first test. Ideally, a positive result for the diagnostic test is pathognomonic for the infection. Any infection mitigation protocol (such as quarantine) may then be discontinued for those testing negative in the first population and intensified for those testing positive, such as with contact tracing or other protocols, to identify all true positives and those they may have infected within the population.

The methods presently described herein allow for initial rapid identification within a population of infected individuals due to the nature of the first administered rapid test and allows for quick administration of mitigation protocols to prevent further spread in the population.

The present disclosure overcomes a central problem in use of diagnostic PCR testing to detect infected individuals and so halt rapidly spreading infections, namely that PCR is not suited to rapid screening of large populations. PCR is expensive and cumbersome and requires specialized equipment and often specialized personnel in a appropriately equipped lab, and samples must be prepared and delivered for testing. Tests take several days to more than a week to obtain results. Numbers of samples may exceed the throughput of available in testing labs, as they invariably do when attempting to create a snapshot of who is infected in a large population. This kind of snapshot is needed to apply uniform public health measures to infected individuals and so, in a few cycles, to stop the spread of the pathogen.

In sharp contrast to PCR, rapid assays, such as RATs, can be used to identify a sample that identifies true negatives for exemption from further study. However, rapid assays are prone to false negatives.

The system disclosed here for the rapid removal of a pathogen from a population in which it is spreading uses rapid tests alone, in combination, or with reiteration to generate a sample with minimal false negatives for diagnostic testing. Further iterations or added tests may be used to identify presumptive false negatives in this sample, who will be treated as positives in the next step. In addition, they confirm a diagnosis of the infection in true positives. The infection status of positives from the first test is then confirmed by administering a slower, more expensive diagnostic test such as PCR. Diagnostic test results identify more false positives from the first test to be released from the limitations imposed by the administered mitigation protocols. The numbers of PCR tests required will be manifold lower than without pretesting and so will be within capacity for PCR testing that is available. As many diagnostic methods (such as PCR) require longer timescales (typically from days to weeks), this approach allows for rapid containment of infections in the population while diminishing the number of slower and more expensive diagnostic tests that must be administered by instead only administering them to a small subset of the total population.

Thus in one aspect, a method is provided for mitigating the spread of an infection with a pathogen in a population, the method comprising: administering a rapid test (e.g., a rapid antigen test or RAT) to the population; identifying a first subpopulation within the population which tests positive for the presence of a pathogen according to the rapid test; administering to the first subpopulation a protocol to mitigate or diminish the spread of the infection with the pathogen; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of the pathogen.

In some embodiments, the pathogen may comprise a virus, a bacterium, a fungus, or an amoeba. In some embodiments, the population comprises an animal population, for example a human population.

In some embodiments, the protocol comprises quarantining the first population. In other embodiments, the protocol comprises administering a therapeutic treatment, for example an antiviral therapeutic if the pathogen is a virus.

In some embodiments, the rapid test may comprise a rapid antigen test (RAT). In some embodiments, the RAT comprises an assay, for example an enzyme-linked immunosorbent assay (ELISA), a dipstick immunoassay, or a fluorescence immunoassay. In some embodiments, the RAT tests for the present of an antigen of the pathogen, for example a viral or bacterial protein. In other embodiments, the assay may comprise a competitive binding assay or a hemagglutinin/esterase/sialidase assay.

In some alternative embodiments, the rapid test may comprise odorant or sniff testing. In other alternative embodiments, the rapid test may comprise a breathalyzer test. In yet other alternative embodiments, the rapid test comprises wastewater testing. The above rapid tests may be combined or supplemented by any other or the same of the above rapid tests. In some embodiments, the first subpopulation identified by the rapid test may be tested again by the same or a different rapid test to further delineate the first subpopulation.

In some embodiments, the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a polynucleotide of the pathogen, such as viral RNA or viral DNA if the pathogen is a virus.

In some embodiments, the pathogen is a virus comprising SARS-CoV-2. In other embodiments, the pathogen is a virus comprising the influenza virus.

This invention disclosed herein shortens testing enough to provide a static picture of infection status within a single generation of a pathogen, for example a virus such as SARS- CoV-2 or influenza. This permits elimination of the virus from the community in which it is spreading by standard public health measured applied to identified positives and their contacts as determined by contact tracing.

Other systems, methods, features, and advantages of the present disclosure will be or become apparent to one of skill in the art upon examination of the following detailed description. It is intended that all such additional systems, methods, features, and advantages be included within this description, be within the scope of the present disclosure, and be protected by the accompanying claims. In addition, all optional and preferred features and modifications of the described embodiments are usable in all aspects of the disclosure taught herein. Furthermore, the individual features of the dependent claims, as well as all optional and preferred features and modification of the described embodiments are combinable and interchangeable with one another.

DETAILED DESCRIPTION

Many modification and other embodiments disclosed herein will come to mind to one skilled in the art to which the disclosed methods pertain having the benefit of the teaching presented in the foregoing description. Therefore, it is to be understood that the disclosures are not to be limited to the specific embodiments disclosed and that modification and other embodiments are intended to be included within the scope of the appended claims. The skilled artisan will recognize many variants and adaptations of the aspects described herein. These variants and adaptations are intended to be included in the teaching of this disclosure and to be encompassed by the claims herein.

Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with features of any of the other several embodiments without departing from the scope or spirit of the present disclosure.

Any recited method can be carried out in the order of events recited or in any other order that is logically possible. That is, unless otherwise expressly stated, it is in no way intended that any method or aspect set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not specifically state in the claims or description that the steps are to be limited to a specific order, it is no way intended that an order be inferred, in any respect. This holds for any possible non-express basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, or the number or types of aspects described in the specification.

It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as common understood by one of ordinary skill in the art to which the disclosed compositions and methods below. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the specification and relevant art and should not be interpreted in an idealized or overly formal sense unless expressly defined herein.

Prior to describing the various aspects of the present disclosure, the following definitions are provided and should be used unless otherwise indicated. Additional terms may be defined elsewhere in the present disclosure.

As used herein, “comprising” is to be interpreted as specifying the presence of the stated features, integers, steps, or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps or components, or groups thereof. Moreover, each of the terms “by”, “comprising”, “comprising”, “comprised of’, “including”, “includes”, “included”, “involving”, “involves”, “involved”, and “such as” are used in their open, non limiting sense and may be used interchangeably. Further, the term “comprising” is intended to include examples and aspects encompassed by the terms “consisting essentially of’ and “consisting of’. Similarly, the term “consisting essentially of’ is intended to include examples encompassed by the term “consisting of’. As used in the specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a virus”, “a population”, or “a rapid antigen test”, includes, but is not limited to, two or more viruses, two or more populations, two or more rapid antigen tests, and the like.

As used herein, the terms “optional” or “optionally” means that the subsequently described event or circumstance can or cannot occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.

As used herein, a “population” can refer to a group of organisms, including but not limited to a group of animals (e.g., a group of humans or non-human animals such as a mammal, primate, cow, sheep, goat, horse, dog, cat, rabbit, fish, bird, and the like) or a group of plants (such as crop plants). A “subpopulation” refers to a group within a population or a larger subpopulation who have been selected based on some criteria, for example but not limited to, a positive or negative result of a rapid test or a diagnostic test. The population may be selected from any identified stable group of organisms of interest, and may include the inhabitants of an identified area such as a city, state, or country, individuals that are considered to be at-risk for infection, or individuals who are believed to have already been infected with the virus.

The presently disclosure provides methods to mitigate the spread of an infection with a pathogen in a population. The presently disclosed methods are useful for pathogens whose infection natural history creates shedders, that is, infected individuals who are contagious, for example individuals who shed infective pathogen, particularly before symptoms are evident. In the case of Covid-19, for example, SARS-CoV-2 shedding profiles vary between patients, but shedding is thought to be greatest in the days preceding symptoms. By the time symptoms are pronounced, most patients are past the peak of shedding. Indeed, about 30% or more of the those infected with SARS-CoV-2 possibly include super shedders, i.e., infected individuals who, in enclosed spaces and possibly due to the amount or the infectivity of virus they shed, may infect dozens of previously naive individuals regardless of whether they ever experience any characteristic symptoms of infection.

The presently disclosed methods are especially useful for use on pathogens which: may spread rapidly; may be shed at infectious levels prior to the development of symptoms in those who become symptomatic; may be shed by individuals who never develop symptoms; may be shed by individual who are exceptionally contagious (i.e., super spreaders); and/or may cause death or extreme debility in sufferers. The presently disclosed methods may also prove useful for mitigating pathogens for which no or inadequate preventative therapy, such as a vaccination, or no or inadequate number of therapeutic treatments are available.

The presently disclosed methods are useful in controlling infections in human populations, but may also prove useful in other animal populations such as flocks or herds of livestock. Often, culling is used to control infections in livestock populations, a technique that comes with significant costs for the farmer or rancher. A major difficulty with controlling infections in livestock populations is that the individual animals within the population often have virtually unrestricted exposure to one another. The present method, which uses a first rapid test to quickly identify potential infected individuals within the population, allows for quick isolation of the individuals within the population before confirmatory diagnostic testing and can therefore be repeated in enough cycles to allow for the pathogen to be fully eliminated from the population within weeks to months.

The present disclosure teaches use of a cheaper, faster rapid test to screen a large population for likely shedders of pathogen and to then apply a more expensive, slower, and exquisitely sensitive and specific diagnostic test only to those who test positive for the first test, which allows for implementation of pathogen mitigation protocols that separate and isolate true shedders from the main population until at least they are no longer shedding pathogen. Those who then test negative for the subsequent diagnostic test are then considered provisionally free from infection at the time of the test and can then be relaxed from pathogen mitigation protocols. To typically confirm that the individual is free from infection, multiple consecutive runs of the diagnostic test, along with other accepted evidence (for example, the present of a neutralizing antibody titer against the pathogen), may be required.

Depending on the incidence and type of false negatives which are expected, a second round of testing with the first rapid test (such as a RAT) may be applied to the first subpopulation and its contacts or a subpopulation thereof to further limit the frequency of false negatives. For example, if the known false negative incidence for the rapid test due to testing error is .3, one retest reduces that to .09 and a second retest to 0.081, or less than 1% per tested individual. Similarly, retesting after education or under supervision can be targeted to the first subpopulation and optionally its contacts, thereby improving the false negative rate from 30% to less than 5%. Most rapid test errors are due to poor administration of the test; a second round of rapid testing can be performed on suspected populations (such as individuals who has associated with known positives or by activity history such as presence at a given time in a specific venue or passively from such tracking as cell phone tracing). In some embodiments, identifying the first subpopulation may also comprise contact tracing of those who have been in social contact or close physical proximity of those who tested positive to the rapid test performed.

Rapid Tests

In one aspect, the present methods comprise administering a rapid test to a population. As used herein, a “rapid test” is defined as a test which identifies infection with the pathogen and provides a positive and/or negative result in less than a day.

In some embodiments, the rapid test comprises a rapid antigen test. A “rapid antigen test” comprises a rapid point-of-care test that directly detects the presence or absence of an antigen, for example a viral antigen. The rapid antigen test as used in the present disclosure may comprise any number of appropriate assays as would be readily understood by one of skill in the art.

In some embodiments, the rapid antigen test may comprise an enzyme-linked immunosorbent assay (ELISA). ELISA is a commonly used analytical biochemistry assay to detect the presence of a ligand (for example, an antigen such as a viral protein) in a liquid sample using antibodies directed against the protein to be measured. In its most simple representative form, antigens from the sample are attached to a surface. Then, a matching antibody is applied over the surface so it can bind to the antigen. This antibody is linked to an enzyme, and in the final step, a substance containing the enzyme’s substrate is added. The subsequent reaction produces a detectable signal, most commonly a color change. In some embodiments, the ELISA test may be administered as a dipstick test, allowing for ease of use in point-of-care testing.

In some embodiments, the rapid antigen test may comprise a lateral flow immunochromatographic assay (i.e., a lateral flow test). Lateral flow tests operate on the same principles as ELISA tests. These tests run the liquid sample along the surface of a pad with reactive molecules that show a visual positive or negative result for the particular antigen. These pads are based on a series of capillary beds, such as pieces of porous paper, microstructure polymer, or sintered polymer. The pads used have the capacity to transport the fluid sample (such as saliva) spontaneously. The sample pad acts as a sponge and holds an excess of fluid sample. Once soaked, the fluid sample flows to a second conjugate pad in which the manufacturer has stored freeze-dried conjugate particles in a salt-sugar matrix. The conjugate pad contains all the reagents required for an optimized chemical reaction between the antigen and its chemical partner (i.e., an antibody) that has been immobilized on the particle surface. This marks target particles as they pass through the pad and continue across to the test and control lines. The test line shows a signal, often a color. The control line contains affinity ligands which show whether the sample has flowed through and the biomolecules in the conjugate pad are active. Active passing these reaction zones, the fluid enters the final porous material, the wick, that simple acts as a waste container. In principal, any colored particle can be used, however latex (blue color) or nanoparticles of gold (red color) are used. Fluorescent or magnetically labeled particles can be used, but require the use of an electronic reader to assess the test result.

Lateral flow tests can either be used as sandwich or competitive assays. Sandwich assays are generally used for larger analytes because they tend to have multiple binding sites. As the sample migrates through the assay, it first encounters a conjugate, which is an antibody specific to the target analyte labeled with a visual tag, usually colloidal gold. The antibodies bind to the target analyte within the sample and migrate until they reach the test line. The test line also contained immobilized antibodies specific to the target analyte, which bind to the migrated analyte-bound conjugate molecules. The test line then presents a visual change due to the concentrated visual tag, hence confirming the presence of the target molecules. The majority of sandwich assays also have a control line which will appear whether or not the target analyte is present to ensure proper function of the lateral flow pad. Competitive assays are generally used for smaller analytes since smaller analytes have fewer binding sites. The sample first encounters the target analyte labeled with a visual tag (colored particles). The test line contains antibodies to the target analyte. Unbound analyte will block the binding of these molecules, meaning that a visual marker will show. This differs from sandwich assays in that no band means the analyte is present.

In some embodiments, the viral antigen tested for by the rapid antigen test comprises a viral protein. In some embodiments, the viral antigen may comprise a capsid protein. In some embodiments, the viral antigen may comprise a protein of the viral envelope (such as a viral glycoprotein). In some embodiments, the viral antigen may comprise a viral membrane fusion protein. In some embodiments, the viral antigen may comprise a protein involved in replicon formation.

In some embodiments, the viral antigen may comprise a protein for SARS-CoV-2 selected from the group consisting of the orflab protein (encoded by GenBank QHD43415.1), the SARS-CoV-2 surface glycoprotein (encoded by GenBank QHD43416.1), the ORF3a protein (encoded by GenBank QHD43417.1), the SARS-CoV-2 envelope protein (encoded by GenBank QHD43418.1), the SARS-CoV-2 membrane glycoprotein (encoded by GenBank QHD43419.1), the ORF6 protein (encoded by GenBank QHD43420.1), the ORF7a protein (encoded by GenBank QHD43421.1), the ORF8 protein (encoded by GenBank QHD43422.1), the SARS- CoV-2 nucleocapsid phosphoprotein (encoded by GenBank QHD43423.2), or the ORF10 protein (encoded by GenBank QHI42199.1). In some embodiments, the viral antigen may comprise the SARS-CoV-2 viral spike (S) glycoprotein.

In preferred embodiments, the rapid antigen test is maximally sensitive (i.e., produces a low number of false negative results) but may lack specificity for the specific viral antigen (i.e., produces some false positive results). Often, circumstances of testing determine sensitivity or specificity. A person of ordinary skill in the art can readily establish optimal conditions based on existing materials and methods.

In alternative embodiments, other rapid testing methods may be used instead of, or in addition to, a rapid antigen test as described herein. Representative examples of additional testing modalities which can be used in the presently disclosed methods include, but are not limited to, wastewater testing, odorant or sniff testing, breathalyzer tests, or antibody testing. Other suitable rapid testing methods which are suitable for the methods described herein may be readily identified by those skilled in the art.

In one alternative embodiment, the rapid test may comprise wastewater testing. In such embodiments, one or more wastewater streams for the population are tested for the presence of genetic material (such as DNA or RNA) for the pathogen or other chemical signature. When specific wastewater streams are determined to be positive with testing, the portions of the population which are associated with those streams are identified in order to determine the first subpopulation.

In one alternative embodiment, the rapid test may comprise odorant or sniff testing. Certain pathogenic infections, such as COVID-19, are associated with anosmia (loss of smell) as a characteristic symptom. Therefore, the population may be administered a test which examines the ability for members of the population to smell an odorant (such as for example a mixture of 25% ethanol in water). Those who present with anosmia are those which are identified as members of the first subpopulation.

In one alternative embodiment, the rapid test may comprise a breathalyzer test. Certain pathogenic infections may be associated with the presence of particular volatile organic compounds (VOCs) in the breath of infected individuals. Breathalyzer systems are available which are able to detect such associated VOCs. Those who test positive within the population for the presence of such VOCs on the breath are identified as members of the first subpopulation. In another alternative embodiment, the rapid test may comprise a chemical sensor which detects one or more chemical signatures for the pathogen. Such a chemical sensor may detect compounds or biomolecules (such as a protein, DNA, or RNA) associated with the pathogen or with infection thereof. In other embodiments, the rapid test may comprise an antibody test. An antibody test may be appropriate for particular infections where the presence of an antibody response is detected before the presence of antigens from the pathogen and the presentation of symptoms. Representative examples of such infections include infection with human immunodeficiency virus (HIV). In another alternative embodiment, the rapid test may comprise odorant detection using scent dogs or other organisms which detect a scent imprint associated with the infection. Use of scent dogs in the detection of SARS-CoV-2, for example, is described in: Jendrny, R, Schulz, C., Twele, F. et al. Scent dog identification of samples from COVID-19 patients - a pilot study. BMC Infect Dis 20, 536 (2020). https://doi.org/10.1186/sl2879-020-05281-3 and Eskandari, E., Ahmadi Marzaleh, M., Roudgari, H. et al. Sniffer dogs as a screening/diagnostic tool for COVID-19: a proof of concept study. BMC Infect Dis 21, 243 (2021). https://doi.org/10.1186/sl2879-021-05939-6, each of which is incorporated herein by reference in its entirety for all purposes.

Virus Mitigation Protocols Upon identification of a first subpopulation by the rapid test (such as a RAT), one or more pathogen mitigation protocols are administered to the first population. Representative examples of such mitigation protocols may include separating (i.e., quarantining) the first subpopulation from the total population to diminish spread of the infection or requiring the first subpopulation practice behaviors that minimize the spread of the pathogen, such as handwashing, application of disinfectants or antimicrobials within places they inhabit, or wearing personal protective equipment when in contact with the total population. In some embodiments, the virus mitigative protocol may comprise administering a therapeutic agent to the population, such as for example an anti-viral agent.

Diagnostic Tests The diagnostic test as used in the present disclosure may comprise any test which is used to confirm infection with a virus, e.g., which provides a result confirming an infection with >95% accuracy (i.e., less than about 5% of the results are false negatives for infection). In some embodiments, the diagnostic test may comprise a polymerase chain reaction (PCR) test. PCT is a method widely used in molecular biology to rapidly make millions to billions of copies of a specific polynucleotide sample (typically DNA), allowing a very small sample of the polynucleotide to be amplified into large enough of an amount to be studied in detail. The majority of PCR methods rely on thermal cycling, exposing reactants to repeated cycles of heating and cooling to permit different temperature-dependent reactions - specifically, DNA melting and enzyme-driven DNA replication. PCR employs two main reagents - primers (which are short single strand DNA fragments that are complementary to the target DNA region) and a DNA polymerase. In the first step of PCR, the two strands of the DNA double helix are physically separated at a high temperature in a process called nucleic acid denaturation. In the second step, the temperature is lowered and the primers bind to the complementary sequences of DNA. The two DNA strands then become templates for DNA polymerase to enzymatically assemble a new DNA strand from free nucleotides. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the original DNA template is exponentially amplified. Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase.

In some embodiments, a revere transcription polymerase chain reaction (RT-PCR) test is used. RT-PCR is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using PCR. In RT-PCR, the RNA template is first converted into a complementary DNA (cDNA) using a reverse transcriptase. The cDNA is then used as a template for exponential amplification using PCR.

Pathogens

The methods of the present disclosure may be used to mitigate or diminish the spread of an infection with a pathogen within a population. The pathogen may comprise any organism which may lead to infection within a member of the population (such as an animal or a human). The pathogen may comprise a virus, a bacterium, a mycobacterium a fungus, or an amoeba.

In particular embodiments, the pathogen comprises an organism which is contagious during periods when an infected subject does not symptoms or only presents minimal symptoms.

In some embodiments, the infection with the pathogen is emergent and not presently described herein because it has not yet been identified, cannot yet be identified, or has not yet cause any outbreaks within a population. In some embodiments, the pathogen may comprise a virus. Exemplary viruses whose spread may be mitigated by the methods described herein include viruses which belong to the following none exclusive list of families: Adenoviridae, Arenaviridae, Astroviridae, Baculoviridae, Bamaviridae, Betaherpesvirinae, Birnaviridae, Bromoviridae, Bunyaviridae, Caliciviridae, Chordopoxvirinae, Circoviridae, Comoviridae, Coronaviridae, Cystoviridae,

Corticoviridae, Entomopoxvirinae, Filoviridae, Flaviviridae, Fuselloviridae, Geminiviridae, Hepadnaviridae, Herpesviridae, Gammaherpesvirinae, Inoviridae, Iridoviridae, Leviviridae, Lipothrixviridae, Microviridae, Myoviridae, Nodaviridae, Orthomyxoviridae, Papovaviridae, Paramyxoviridae, Paramyxovirinae, Partitiviridae, Parvoviridae, Phycodnaviridae, Picornaviridae, Plasmaviridae, Pneumovirinae, Podoviridae, Polydnaviridae, Potyviridae,

Poxviridae, Reoviridae, Retroviridae, Rhabdoviridae, Sequiviridae, Siphoviridae, Tectiviridae, Tetraviridae, Togaviridae, Tombusviridae, and Totiviridae.

Specific examples of suitable viruses whose spread may be mitigated by the methods described herein include, but are not limited to, Mastadenovirus, Human adenovirus 2, Aviadenovirus, African swine fever virus, arenavirus, Lymphocytic choriomeningitis virus, Ippy virus, Lassa virus, Arterivirus, Human astrovirus 1, Nucleopolyhedrovirus, Autographa califomica nucleopolyhedrovirus, Granulovirus, Plodia interpunctella granulovirus, Badnavirus, Commelina yellow mottle virus, Rice tungro bacilliform, Bamavirus, Mushroom bacilliform virus, Aquabimavirus, Infectious pancreatic necrosis virus, Avibimavirus, Infectious bursal disease virus, Entomobirnavirus, Drosophila X virus, Alfamovirus, Alfalfa mosaic virus, Ilarvirus, Ilarvirus Subgroups 1-10, Tobacco streak virus, Bromovirus, Brome mosaic virus, Cucumovirus, Cucumber mosaic virus, Bhanja virus Group, Kaisodi virus, Mapputta virus, Okola virus, Resistencia virus, Upolu virus, Yogue virus, Bunyavirus, Anopheles A virus, Anopheles B virus, Bakau virus, Bunyamwera virus, Bwamba virus, C virus, California encephalitis virus, Capim virus, Gamboa virus, Guama virus, Koongol virus, Minatitlan virus, Nyando virus, Olifantsvlei virus, Patois virus, Simbu virus, Tete virus, Turlock virus, Hantavirus, Hantaan virus, Nairovirus, Crimean-Congo hemorrhagic fever virus, Dera Ghazi Khan virus, Hughes virus, Nairobi sheep disease virus, Qalyub virus, Sakhalin virus, Thiafora virus, Crimean-congo hemorrhagic fever virus, Phlebovirus, Sandfly fever virus, Bujaru complex, Candiru complex, Chilibre complex, Frijoles complex, Punta Toro complex, Rift Valley fever complex, Salehabad complex, Sandfly fever Sicilian virus, Uukuniemi virus, Uukuniemi virus, Tospovirus, Tomato spotted wilt virus, Calicivirus, Vesicular exanthema of swine virus, Capillovirus, Apple stem grooving virus, Carlavirus, Carnation latent virus, Caulimovirus, Cauliflower mosaic virus, Circovirus, Chicken anemia virus, Closterovirus, Beet yellows virus, Comovirus, Cowpea mosaic virus, Fabavirus, Broad bean wilt virus 1, Nepovirus, Tobacco ringspot virus, Coronavirus, Avian infectious bronchitis virus, Bovine coronavirus, Canine coronavirus, Feline infectious peritonitis virus, Human coronavirus 299E, Human coronavirus OC43, Murine hepatitis virus, Porcine epidemic diarrhea virus, Porcine hemagglutinating encephalomyelitis virus, Porcine transmissible gastroenteritis virus, Rat coronavirus, Turkey coronavirus, Rabbit coronavirus, Torovirus, Berne virus, Breda virus, Corticovirus, Alteromonas phage PM2, Pseudomonas Phage phi6, Deltavirus, Hepatitis delta virus, Dianthovirus Carnation ringspot virus, Red clover necrotic mosaic virus, Sweet clover necrotic mosaic virus, Enamovirus, Pea enation mosaic virus, Filovirus, Marburg virus, Ebola virus Zaire, Flavivirus, Yellow fever virus, Tick-borne encephalitis virus, Rio Bravo Group, Japanese encephalitis, Tyuleniy Group, Ntaya Group, Uganda S Group, Dengue Group, Modoc Group, Pestivirus, Bovine diarrhea virus, Hepatitis C virus, Furovirus, Soil-borne wheat mosaic virus, Beet necrotic yellow vein virus, Fusellovirus, Sulfobolus virus 1, Subgroup I, II, and III geminivirus, Maize streak virus, Beet curly top virus, Bean golden mosaic virus, Orthohepadnavirus, Hepatitis B virus, Avihepadnavirus, Alphaherpesvirinae, Simplexvirus, Human herpesvirus 1, Varicellovirus, Human herpesvirus 3, Cytomegalovirus, Human herpesvirus 5, Muromegalovirus, Mouse cytomegalovirus 1, Roseolovirus, Human herpesvirus 6, Lymphocryptovirus, Human herpesvirus 4, Rhadinovirus, Ateline herpesvirus 2, Hordeivirus, Barley stripe mosaic virus, Hypoviridae, Hypovirus, Cryphonectria hypovirus 1-EP713, Idaeovirus, Raspberry bushy dwarf virus, Inovirus, Coliphage fd, Plectrovirus, Acholeplasma phage L51, Iridovirus, Chilo iridescent virus, Chloriridovirus, Mosquito iridescent virus, Ranavirus, Frog virus 3, Lymphocystivirus, Lymphocystis disease virus flounder isolate, Goldfish virus 1, Levivirus, Enterobacteria phage MS2, Allolevirus, Enterobacteria phage Qbeta, Lipothrixvirus, Thermoproteus virus 1, Luteovirus, Barley yellow dwarf virus, Machlomovirus, Maize chlorotic mottle virus, Marafivirus, Maize rayado fmo virus, Microvirus, Coliphage phiX174, Spiromicrovirus, Spiroplasma phage 4, Bdellomicrovirus, Bdellovibrio phage MAC 1, Chlamydiamicrovirus, Chlamydia phage 1, T4-like phages, coliphage T4, Necrovirus, Tobacco necrosis virus, Nodavirus, Nodamura virus, Influenzavirus A, B and C, Thogoto virus, Polyomavirus, Murine polyomavirus, Papillomavirus, Rabbit (Shope) Papillomavirus, Paramyxovirus, Human parainfluenza virus 1, Morbillivirus, Measles virus, Rubulavirus, Mumps virus, Pneumovirus, Human respiratory syncytial virus, Partitivirus, Gaeumannomyces graminis virus 019/6-A, Chrysovirus, Penicillium chrysogenum virus, Alphacryptovirus, White clover cryptic viruses 1 and 2, Betacryptovirus, Parvovirinae, Parvovirus, Minute mice virus, Erythrovirus, B19 virus, Dependovirus, Adeno-associated virus 1, Densovirinae, Densovirus, Junonia coenia densovirus, Iteravirus, Bombyx mori virus, Contravirus, Aedes aegypti densovirus, Phycodnavirus, 1- Paramecium bursaria Chlorella NC64A virus group, Paramecium bursaria chlorella virus 1, 2- Paramecium bursaria Chlorella Pbi virus, 3-Hydra viridis Chlorella virus, Enterovirus, Human poliovirus 1, Rhinovirus Human rhinovirus 1A, Hepatovirus, Human hepatitis A virus, Cardiovirus, Encephalomyocarditis virus, Aphthovirus, Foot-and-mouth disease virus, Plasmavirus Acholeplasma phage L2, Podovirus, Coliphage T7, Ichnovirus, Campoletis sonorensis virus, Bracovirus, Cotesia melanoscela virus, Potexvirus, Potato virus X, Potyvirus, Potato virus Y, Rymovirus, Ryegrass mosaic virus, Bymovirus, Barley yellow mosaic virus, Orthopoxvirus, Vaccinia virus, Parapoxvirus, Orf virus, Avipoxvirus, Fowlpox virus, Capripoxvirus, Sheep pox virus, Leporipoxvirus, Myxoma virus, Suipoxvirus, Swinepox virus, Molluscipoxvirus, Molluscum contagiosum virus, Yatapoxvirus, Yaba monkey tumor virus, Entomopoxviruses A, B, and C, Melolontha melolontha entomopoxvirus, Amsacta moorei entomopoxvirus, Chironomus luridus entomopoxvirus, Orthoreovirus, Mammalian orthoreoviruses, reovirus 3, Avian orthoreoviruses, Orbivirus, African horse sickness viruses 1, Bluetongue viruses 1, Changuinola virus, Corriparta virus, Epizootic hemarrhogic disease virus 1, Equine encephalosis virus, Eubenangee virus group, Lebombo virus, Orungo virus, Palyam virus, Umatilla virus, Wallal virus, Warrego virus, Kemerovo virus, Rotavirus, Groups A-F rotaviruses, Simian rotavirus SA11, Coltivirus, Colorado tick fever virus, Aquareovirus, Groups A-E aquareoviruses, Golden shiner virus, Cypovirus, Cypovirus types 1-12, Bombyx mori cypovirus 1, Fijivirus, Fijivirus groups 1-3, Fiji disease virus, Fijivirus groups 2-3, Phytoreovirus, Wound tumor virus, Oryzavirus, Rice ragged stunt, Mammalian type B retroviruses, Mouse mammary tumor virus, Mammalian type C retroviruses, Murine Leukemia Virus, Reptilian type C oncovirus, Viper retrovirus, Reticuloendotheliosis virus, Avian type C retroviruses, Avian leukosis virus, Type D Retroviruses, Mason-Pfizer monkey virus, BLV-HTLV retroviruses, Bovine leukemia virus, Lentivirus, Bovine lentivirus, Bovine immunodeficiency virus, Equine lentivirus, Equine infectious anemia virus, Feline lentivirus, Feline immunodeficiency virus, Canine immunodeficiency virus Ovine/caprine lentivirus, Caprine arthritis encephalitis virus, Visna/maedi virus, Primate lentivirus group, Human immunodeficiency virus 1, Human immunodeficiency virus 2, Human immunodeficiency virus 3, Simian immunodeficiency virus, Spumavirus, Human spuma virus, Vesiculovirus, Vesicular stomatitis Indiana virus, Lyssavirus, Rabies virus, Ephemerovirus, Bovine ephemeral fever virus, Cytorhabdovirus, Lettuce necrotic yellows virus, Nucleorhabdovirus, Potato yellow dwarf virus, Rhizidiovirus, Rhizidiomyces virus, Sequivirus, Parsnip yellow fleck virus, Waikavirus, Rice tungro spherical virus, Lambda-like phages, Coliphage lambda, Sobemovirus, Southern bean mosaic virus, Tectivirus, Enterobacteria phage PRDl, Tenuivirus, Rice stripe virus, Nudaurelia capensis beta-like viruses, Nudaurelia beta virus, Nudaurelia capensis omega-like viruses, Nudaurelia omega virus, Tobamovirus, Tobacco mosaic virus (vulgare strain; ssp. NC82 strain), Tobravirus, Tobacco rattle virus, Alphavirus, Sindbis virus, Rubivirus, Rubella virus, Tombusvirus, Tomato bushy stunt, virus, Carmovirus, Carnation mottle virus, Turnip crinkle virus, Totivirus, Saccharomyces cerevisiae virus, Giardiavirus, Giardia lamblia virus, Leishmaniavirus, Leishmania brasiliensis virus 1-1, Trichovirus, Apple chlorotic leaf spot virus, Tymovirus, Turnip yellow mosaic virus, Umbravirus, and Carrot mottle virus.

In some embodiments, the methods described herein may be used to mitigate the spread of a coronavirus infection. A “coronavirus infection” as used herein refers to an infection caused by or otherwise associated with growth of a coronavirus in a subject, in the family Coronaviridae (subfamily Coronavirinae).

Coronaviruses are species of virus belonging to the subfamily Coronavirinae in the family Coronaviridae , in the order Nidovirales . Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome and with a nucleocapsid of helical symmetry. The genomic size of coronaviruses ranges from approximately 26 to 32 kilobases, the largest for an RNA virus. The name “coronavirus” is derived from the Latin corona, meaning crown or halo, and refers to the characteristic appearance of virions under electron microscopy with a fringe of large, bulbous surface projections creating an image reminiscent of a royal crown or of the solar corona. This morphology is created by the viral spike (S) peplomers, which are proteins that populate the surface of the virus and determine host tropism. Proteins that contribute to the overall structure of all coronaviruses are the spike (S), envelope (E), membrane (M) and nucleocapsid (N) proteins. In the specific case of the SAR coronavirus and SAR coronavirus 2, a defined receptor-binding domain on S mediates the attachment of the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2). Some coronaviruses (specifically the members of Betacoronavirus subgroup A) also have a shorter spike-like protein called hemagglutinin esterase (HE).

In some embodiments, the viral infection as mitigated by the methods of the present disclosure comprises a coronavirus infection. In some embodiments, the coronavirus infection is an infection of the upper and/or lower respiratory tract. The “upper respiratory tract” includes the mouth, nose, sinus, middle ear, throat, larynx, and trachea. The “lower respiratory tract” includes the bronchial tubes (bronchi) and the lungs (bronchi, bronchioles and alveoli), as well as the interstitial tissue of the lungs.

In another embodiment, the coronavirus infection is an infection of the gastrointestinal tract. The “gastrointestinal tract” may include any area of the canal from the mouth to the anus, including the mouth, esophagus, stomach, and intestines.

In yet other embodiments, the coronavirus infection is a renal infection.

It is understood and herein contemplated that the coronavirus infections disclosed herein can cause a pathological state associated with the coronavirus infection referred to herein as a “coronavirus disease”. In some embodiments the coronavirus disease is selected from a common cold, pneumonia, pneumonitis, bronchitis, severe acute respiratory syndrome (SARS), coronavirus disease 2019 (COVID-2019), Middle East respiratory syndrome (MERS), sinusitis, porcine diarrhea, porcine epidemic diarrhea, avian infections, bronchitis, otitis, pharyngitis. In particular embodiments, the coronavirus infection is selected from SARS, COVID-19, and MERS. In a particular embodiments, the coronavirus infection is COVID-19.

The coronavirus causing the infection may be selected from an alphacoronavirus, a betacoronavirus, a gammacoronavirus, or a deltacoronavirus.

Representative examples of alphacoronaviruses include, but are not limited to, a colacovirus (e.g., Bat coronavirus CDPHE15), a decacovirus (e.g., Bat coronavirus HKU10, Rhinolophus ferrumequinum alphacoronavirus Hub-2013), a duvinacovirus (e.g., Human coronavirus 229E), a luchacovirus (e.g., Lucheng Rn rat coronavirus), a minacovirus (e.g., Ferret coronavirus, Mink coronavirus 1), a minunacovirus (e.g., Miniopterus bat coronavirus 1, Miniopterus bat coronavirus HKU8), a myotacovirus (e.g., Myotis rickettii alphacoronavirus Sax-2011), a nyctaco virus (e.g., Nyctalus velutinus alphacoronavirus SC-2013), a pedaco virus (e.g., Porcine epidemic diarrhea virus (PEDV), Scotophilus bat coronavirus 512), a rhinacovirus (e.g., Rhinolophus bat coronavirus HKU2), a setracovirus (e.g., Human coronavirus NL63, NL63-related bat coronavirus strain BtKYNL63-9b), and ategacovirus (e.g. Alphacoronavirus 1).

Representative examples of betacoronaviruses include, but are not limited to an embecovirus 1 (e.g., Betacoronavirus 1, Human coronavirus OC43, China Rattus coronavirus HKU24, Human coronavirus HKU1, Murine coronavirus), a hibecovirus (e.g., Bat Hp-betacoronavirus Zhejiang2013), a merbecovirus (e.g., Hedgehog coronavirus 1, Middle East respiratory syndrome- related coronavirus (MERS-CoV), Pipistrellus bat coronavirus HKU5, Tylonycteris bat coronavirus HKU4), a nobecovirus (e.g., Rousettus bat coronavirus GCCDC1, Rousettus bat coronavirus HKU9), a sarbeco virus (e.g., severe acute respiratory syndrome coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Representative examples of gammacoronaviruses include, but are not limited to, a cegacovirus (e.g., Beluga whale coronavirus SQ1) and an Igacovirus (e.g., Avian coronavirus (IBV)).

Representative examples of deltacoronaviruses include, but are not limited to, an andecovirus (e.g., Wigeon coronavirus HKU20), a buldecovirus (e.g., Bulbul coronavirus HKU11, Porcine coronavirus HKU15 (PorCoV HKU15), Munia coronavirus HKU13, White-eye coronavirus HKU16), a herdecovirus (e.g., Night heron coronavirus HKU19), and a moordecovirus (e.g., Common moorhen coronavirus HKU21).

In some embodiments, the coronavirus is a human coronavirus. Representative examples of human coronaviruses include, but are not limited to, human coronavirus 229E (HCoV-229E), human coronavirus OC43 (HCoV-OC43), human coronavirus HKU1 (HCoV-HKUl), Human coronavirus NL63 (HCoV-NL63), severe acute respiratory syndrome coronavirus (SARS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Middle East respiratory syndrome-related coronavirus (MERS-CoV).

In some embodiments, the pathogen comprises an influenzavirus. Influenzaviruses are RNA viruses that make up four of the seven genera of the family Orlhomyxo viridae : Influenzavirus A, Influenzavirus B, Influenzavirus C, and Influenzavirus D. Each of the above genera comprises a single species. Representative examples of Influenza A serotypes include, but are not limited to, H1N1 (which caused the Spanish Flu and Swine Flu), H2N2 (which caused the Asian Flu), H3N2 (which caused the Hong Kong Flu), H5N1 (which caused Bird Flu), H7N7, H1N2, H9N2, H7N2, H7N3, H10N7, H7N9, and H6N1.

In some embodiments, the pathogen comprises human immunodeficiency virus (HIV). HIV is a member of the genus Lentivirus comprising two species; HIV-1 and HIV-2.

In some embodiments, the pathogen comprises an ebolavirus.

A number of embodiments of the disclosure have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:

1. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: administering a rapid test to the population which a result for infection with the pathogen in less than a day; identifying a first subpopulation within the population which tests positive for infection with the pathogen according to the rapid test; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

2. The method of claim 1, wherein the rapid test comprises a rapid antigen test.

3. The method of claim 1, wherein the rapid test comprises testing of one or more wastewater streams for the population.

4. The method of claim 1, wherein the rapid test comprises odorant testing.

5. The method of claim 1, wherein the rapid test comprises a chemical sensor that detects one or more compounds or biomolecules associated with infection with the pathogen.

6. The method of claim 1, wherein the rapid test comprises an antibody test.

7. The method of any one of claims 1-6, wherein the pathogen comprises a virus, a bacterium, a mycobacterium, a fungus, or an amoeba.

8. The method of any one of claims 1-7, wherein the population comprises an animal population.

9. The method of any one of claims 1-8, wherein the population comprises a human population.

10. The method of any one of claims 1-9, wherein the protocol comprises quarantining the first subpopulation.

11. The method of any one of claims 1-10, wherein the protocol comprises administering a therapeutic agent.

12. The method of any one of claims 1-11, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a polynucleotide from the pathogen.

13. The method of any one of claims 1-12, wherein the pathogen comprises a virus.

14. The method of claim 13, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a viral polynucleotide.

15. The method of claim 14, wherein the polynucleotide comprises viral RNA or viral DNA.

16. The method of any one of claims 13-15, wherein the virus is selected from a coronavirus, such as SARS-CoV-2, or an influenza virus..

17. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: administering a rapid antigen test (RAT) to the population; identifying a first subpopulation within the population which tests positive for the presence of a pathogenic antigen according to the RAT; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

18. The method of claim 17, wherein the pathogen comprises a virus, a bacterium, a mycobacterium, a fungus, or an amoeba.

19. The method of any one of claims 17 or 18, wherein the population comprises an animal population.

20. The method of any one of claims 17 or 18, wherein the population comprises a human population.

21. The method of any one of claims 17-20, wherein the protocol comprises quarantining the first subpopulation.

22. The method of any one of claims 17-21, wherein the protocol comprises administering a therapeutic agent.

23. The method of any one of claims 17-22, wherein the RAT comprises an assay.

24. The method of claim 23, wherein the assay comprises an enzyme-linked immunosorbent assay (ELISA).

25. The method of claim 23, wherein the assay comprises a dipstick immunoassay.

26. The method of claim 23, wherein the assay comprises a fluorescence immunoassay.

27. The method of claim 23, wherein the assay comprises a lateral flow test.

28. The method of any one of claims 17-27, wherein the RAT tests for the presence of an antigen comprising a pathogen protein.

29. The method of any one of claims 17-28, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a polynucleotide from the pathogen.

30. The method of any one of claims 17-29, wherein the pathogen comprises a virus.

31. The method of claim 30, wherein the RAT tests for presence of a viral protein.

32. The method of any one of claims 30 or 31, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a viral polynucleotide.

33. The method of claim 32, wherein the polynucleotide comprises viral RNA or viral DNA.

34. A method for mitigating the spread of infection with SARS-CoV-2 in a population, the method comprising: administering a rapid antigen test (RAT) to the population; identifying a first subpopulation within the population which tests positive for the presence of a SARS-CoV-2 protein according to the RAT; administering a protocol to mitigate spread of infection with SARS-CoV-2 to the first subpopulation; administering a diagnostic test for SARS-CoV-2 infection to the first portion of the first population; identifying a second subpopulation within the first subpopulation that tests positive for SARS-CoV-2 infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for SARS-CoV-2 infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of SARS-CoV-2.

35. The method of claim 34, wherein the population comprises a human population.

36. The method of any one of claims 34 or 35, wherein the RAT comprises a dipstick immunoassay.

37. The method of any one of claims 34 or 35, wherein the RAT comprises a lateral flow test.

38. The method of any one of claims 34-27, wherein the RAT tests for the presence of an antigen comprises the SARS-CoV-2 viral spike (S) glycoprotein.

39. The method of any one of claims 34-28, wherein the protocol to mitigate spread of the infection includes quarantining the first subpopulation.

40. The method of any one of claims 34-29, wherein the protocol to mitigate spread of the infection includes administration of an anti-viral therapeutic.

41. The method of any one of claims 1-40, wherein the diagnostic test comprises a reverse transcriptase polymerase chain reaction (RT-PCR) for SARS-CoV-2 genomic RNA.

42. The method of any one of claims 1-41, further comprising repeating the method at regular intervals within the population.

43. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: testing one or more wastewater streams for the population for the presence of genetic material associated with the pathogen; identifying a first subpopulation within the population associated with one or more wastewater streams which tested positive for genetic material associated with the pathogen; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

44. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: administering an odorant test to the population to determine the presence of anosmia; identifying a first subpopulation within the population having anosmia as determined by the odorant test; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

45. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: administering a breathalyzer test to the population to detect the presence of volatile organic compounds associated with infection with the pathogen; identifying a first subpopulation having the presence of volatile organic compounds associated with infection with the pathogen; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

46. A method for mitigating the spread of infection with a pathogen within a population, the method comprising: administering an antibody test to the population to detect antibodies against the pathogen; identifying a first subpopulation having the presence of antibodies against the pathogen; administering a protocol to mitigate spread of infection with the pathogen to the first subpopulation; administering a diagnostic test for the pathogenic infection to the first subpopulation; identifying a second subpopulation within the first subpopulation that tests positive for the pathogenic infection by the diagnostic test and a third subpopulation within the first subpopulation which tests negative for the pathogenic infection by the diagnostic test; and optionally ceasing administration to the third subpopulation of the protocol to mitigate spread of infection with the pathogen.

47. The method of any one of claims 43-46, wherein the pathogen comprises a virus, a bacterium, a mycobacterium, a fungus, or an amoeba.

48. The method of any one of claims 43-47, wherein the population comprises an animal population.

49. The method of any one of claims 43-48, wherein the population comprises a human population.

50. The method of any one of claims 43-49, wherein the protocol comprises quarantining the first subpopulation.

51. The method of any one of claims 43-50, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a polynucleotide from the pathogen.

52. The method of any one of claims 43-51, wherein the pathogen comprises a virus.

53. The method of claim 42, wherein the diagnostic test comprises a polymerase chain reaction (PCR) test for the presence of a viral polynucleotide.

54. The method of claim 53, wherein the polynucleotide comprises viral RNA or viral DNA.

55. The method of any one of claims 52-54, wherein the virus is selected from a coronavirus, such as SARS-CoV-2, or an influenza virus.