WO1997041245A1

WO1997041245A1 - Generation of viral transfectants using recombinant dna-derived nucleocapsid proteins

Info

Publication number: WO1997041245A1
Application number: PCT/US1997/007277
Authority: WO
Inventors: Michael W. Shaw; Mark L. Hemphill; Xiyan Xu
Original assignee: The Government Of The United States Of America, Represented By The Secretary Of The Department Of Health And Human Services
Priority date: 1996-05-01
Filing date: 1997-04-30
Publication date: 1997-11-06
Also published as: CA2253595A1; EP0906442A1; AU2749297A; JP2000509280A

Abstract

This invention provides a method of producing viral transfectants (viruses containing a heterologous nucleic acid) that eliminates the need for purified RNP complexes or for purified viral RNA polymerases. The method generally involves: (i) combining a ribonucleic acid (nucleic acid transcript) with an isolated nucleoprotein (NP) of the virus to form a synthetic ribonucleoprotein complex (RNP); (ii) transfecting a host cell with the synthetic ribonucleoprotein complex; and (iii) holding (culturing) the host cell under conditions permitting replication of the virus.

Description

GENERATION OF VIRAL TRANSFECTANTS USING RECOMBINANT DNA-DERIVED NUCLEOCAPSID PROTEINS

BACKGROUND OF THE INVENTION

The development of reverse genetics for influenza viruses has allowed the direct manipulation of virion gene products and the creation of entirely new recombinant viruses not seen in nature (see, e.g., Enami et al. (1990) Proc. Natl. Acad. Sci. USA, 87: 3802-3805; Castxucci et al. (1992) J. Virol. , 66: 4647-4653; Li et al. (1992) J. Virol. , 66: 399-404; Liu et al. (1993) Virol. , 194: 403-407; Subbarao et al. (1993) 7. Virol. , 67: 7223-7228; and Zurcher et α/. (1994) 7. Virol. , 68: 75748-5754). Generally, the production of recombinant influenza viruses has required the combination of purified proteins from virion ribonucleoprotein (RNP) cores with a synthetic RNA transcript followed by transfection into cells previously infected with a helper virus (Enami et al. (1991) 7. Virol. 65: 2711-2713).

The purified RNP cores typically include the RNA polymerase proteins (e.g. , PBl , PB2 and PA) in addition to a viral nucleoprotein (NP) (see, e.g. , Ishihama et al. (1988) CRC Crir. Rev. Biochem. 23: 27-76). In part, because of their complex structure, the purification of the RNP complex proteins from virions represents one of the most labor-intensive aspects of the procedure requiring multiple gradient fractionations (Enami et ai , supra.). Previous viral transfection methods were also complex because it was believed that viral RNA polymerase was required in addition to the viral nucleoprotein to effect viral transfection (see, e.g. U.S. Patent 5,166,057). Provision of viral RNA polymerase in addition to nucleoprotein (NP> required an elaborate cloning system or time consuming and laborious isolation and purification procedures (see, e.g. , Kimura et al. (1992) 7. Virol. , 1321-1328).

SUMMARY OF THE INVENTION This invention provides a method of producing viral transfectants that eliminates the need for purified RNP complexes or for purified viral RNA polymerases. The methods of this invention thus dramatically simplify the preparation of viral transfectants.

It was a surprising discovery of this invention that a viral RNP complex comprising only a viral nucleoprotein (NP) and a nucleic acid transcript (e.g. , an RNA) is sufficient to mediate the replication of a virus (e.g. , influenza) when cultured with a simple helper virus.

In one embodiment, this invention therefore provides a method of preparing a viral transfectant ( virus bearing a preselected ribonucleic acid). The method includes the steps of: i) combining the ribonucleic acid (nucleic acid transcript) with an isolated nucleoprotein (NP) of the virus to form a synthetic ribonucleoprotein complex (RNP); ii) transfecting a host cell with the synthetic ribonucleoprotein complex; and iii) holding (culturing) the host cell under conditions permitting replication of the virus. Replication of the virus in the host cell from the RNP complex is accomplished by providing a host cell capable of complementing the subject virus (e.g., a host cell recombinantly engineered to express viral RNA polymerase) or more preferably by providing a host cell infected with a helper virus. The host cell can be infected with the helper virus before, during, or after the transfection with the synthetic ribonucleoprotein complex (RNP). Preferred helper viruses include attenuated live vaccine parent strains (e.g. , A/Leningrad/57 or A/ Ann Arbor/6/60) or laboratory adapted wild-type viruses (e.g. , A/PR/8/34 or A/WSN/33).

The isolated viral nucleoprotein (NP) is preferably isolated away from other viral proteins, in particular it is essentially free of viral RNA polymerase proteins. Preferred isolated viral nucleoprotein s are recombinantly expressed, more preferably recombinantly expressed in a eukaryotic expression system (e.g, in an insect system such as SP19 cells in a baculovirus vector). Preferred viral nucleoproteins include NPs from influenza, parainfluenza, or measles virus, with influenza (e.g. , type A, B, or C) NPs being more preferred, and influenza type A Nps being most preferred.

The host cell can be any cell in which it is possible to culture the viral transfectant. Particularly preferred cells are eukaryotic cells with cells from a hens egg or kidney cells (e.g., MDCK cells) being most preferred. Subject viruses to be transfected include RNA viruses that typically contain a nucleoprotein complex (RNP) or equivalent structure. Particularly preferred viruses include the orthomyxoviridae more preferably influenza, and paramyxoviruses such as parainfluenza and measles, with influenza being most preferred.

In a particularly preferred embodiment, the subject virus is an influenza virus, the nucleoprotein is a recombinantly expressed influenza nucleoprotein substantially free of a viral RNA polymerase and the host cell is an egg or a kidney cell infected with an influenza helper virus.

The isolated NP protein when combined with an RNA substantially protects the RNA from ribonucleases and guides the RNA to the nucleus of the host cell. Thus, in another embodiment, this invention provides a method of introducing a ribonucleic acid (e.g., a RNA transcript) into the nucleus of a host cell. The method involves the steps of: i) combining the ribonucleic acid with an isolated nucleoprotein (NP) of a virus to form a synthetic ribonucleoprotein complex (RNP); and ii) transfecting the host cell with the synthetic ribonucleoprotein complex. The method can further include infecting the host cell with a helper virus. Any ofthe viral nucleoproteins (NPs) discussed above, and any ofthe RNA transcripts, host cells and transfection methods discussed herein are suitable.

In still another embodiment, this invention provides a transfection composition comprising an isolated viral nucleoprotein combined with a ribonucleic acid (e.g., RNA transcript) thereby forming a synthetic ribonucleoprotein complex that is capable of mediating viral replication in a host cell. Any of the NP and RNA transcripts described above and herein are suitable.

The methods of this invention can be used to produce transfectant host cells (i.e. , expressing a heterologous nucleic acid) or transgenic viruses (viral transfectants). Thus in another embodiment this invention provides for host cells transfected with, or viruses produced (derived) from, a synthetic ribonucleoprotein complex (RNP) where the RNP is an isolated viral nucleoprotein (NP) combined with a ribonucleic acid (e.g., an RNA transcript). Any of the viruses, host cells, NPs and RNPs described above and herein are suitable. In one embodiment, the RNA transcript expresses an antigenic determinant of a human pathogen (e.g. , gpl20 or a subsequence thereof) which is displayed by the virus. The virus can be dead (unable to infect or replicate) or a live attenuated virus.

Finally, this invention also provides for kits for the practice of the methods described above. In particular, the kits are suitable for the preparation of host cells containing preselected RNA transcripts or for the preparation of viral transcripts. This kits include a container containing a synthetic ribonucleoprotein complex (RNP) where the RNP is an isolated viral nucleoprotein (NP) combined with a ribonucleic acid (e.g. , an RNA transcript). The kit can additionally include one or more of the following: instructions teaching the methods described above and below herein, buffers, host cells, culture media, helper viruses, and the like.

DefinitiorLS

The term "subject virus", as used herein, is intended to refer to the virus into which is inserted a nucleic acid transcript. The subject virus is thus distinguished from the helper virus which serves to facilitate the replication of the subject virus.

A "helper virus" refers to a virus that provides the functions necessary for the replication of a defective virus. In the present invention, helper viruses provide functions necessary for replication of the subject virus from a synthetic ribonucleoprotein complex (e.g. , NP combined with a nucleic acid transcript). The term helper virus can also just refer to just the combination of components of the helper virus that are necessary to replication of the subject virus.

The term "synthetic ribonucleoprotein complex" or "synthetic RNP" as used herein referes to a ribonucleoprotein complex containing a nucleoprotein (NP) that has been isolated away from its related nucleic acid polymerase proteins prior to incoφoration into the complex. It will be recognized that the RNP complex is generally used to refer to the association of an RNA, a nucleoprotein (NP), and viral RNA polymerase proteins.

However, as used herein the RNP complex can refer simply to the asociation of a nucleic acid transcript and a nucleoprotein (NP) recognizing that the combination of the NP/RNA RNP with viral RNA polymerase proteins (e.g. , supplied by a helper virus) either before, during, or after transfection of a host cell with the RNP, will provide an RNP capable of mediating replication of the subject virus.

The term "complex" when used in the context of RNP complex is not intended to imply a particular structural relationship, but simply indicates the presence of the RNP components, in particular an NP and an RNA, in an association that permits replication of the subject virus. The term "recombinant" when used with reference to a cell indicates that the cell replicates or expresses a nucleic acid, or expresses a peptide or protein encoded by a nucleic acid whose origin is exogenous to the cell. Recombinant cells can express genes that are not found within the native (non-recombinant) form of the cell. Recombinant cells can also express genes found in the native form of the cell wherein the genes are re¬ introduced into the cell by artificial means, for example under the control of a heterologous promoter.

The term "heterologous" when used with reference to a nucleic acid transcript (i.e., a cRNA) indicates that the nucleic acid is in a non-native state. The heterologous nucleic acid can be a modification (e.g., contain a deletion, mutation, insertion) of the native nucleic acid or can include or be replaced by a nucleic acid sequence not found in the resulting state in nature. Thus a virus containing a heterologous nucleic acid contains a nucleic acid from a source other than that virus, or a nucleic acid from the same virus where the nucleic acid is reintroduced into the virus (e.g., after being deliberately modified).

The terms "viral transfectant" or "transgenic virus" refer to a virus containing a heterologous nucleic acid.

The term "subsequence" in the context of a particular nucleic acid or polypeptide sequence refers to a region of the nucleic acid or polypeptide equal to or smaller than the particular nucleic acid or polypeptide.

The term "nucleic acid" or "nucleic acid transcript" refer to a deoxyribonucleotide or ribonucleotide polymer in either single-or double-stranded form, and unless otherwise limited, would encompass known analogs of natural nucleotides that can function in a similar manner as naturally occurring nucleotides. The bases in the nucleic acid may be joined by a linkage other than a phosphodiester bond, so long as it does not interfere the function of the nucleic acid. Thus, for example, the nucleic acid may be a peptide nucleic acid in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. In paticular, the terms "nucleic acid transcript" or "RNA transcript" are used herein to refer to the heterologous RNA to be introduced into a virus.

The phrase "substantially purified" or "isolated" when referring to a protein (e.g. , a viral nucleoprotein (NP)) means a chemical composition which is essentially free of other cellular or viral components with which the protein normally occurs. It is preferably in a homogeneous state although it can be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein which is the predominant species present in a preparation is isolated or substantially purified. Generally, a substantially purified or isolated protein will comprise more than 80% of all macromolecular species present in the preparation. Preferably, the protein is purified to represent greater than 90% of all macromolecular species present. More preferably the protein is purified to greater than 95 % , and most preferably the protein is purified to essential homogeneity, wherein other macromolecular species are essentially not detected by conventional techniques.

The phrase "recombinant protein" or "recombinantly produced protein" refers to a peptide, polypeptide, or protein produced using cells that do not have an endogenous copy of DNA able to express the protein. The cells produce the protein because they have been genetically altered by the introduction of the appropriate nucleic acid sequence.

The term "influenza virus", as used herein, refers to members ofthe family Orthomyxoviridae and includes, but is not limited to the influenza type A, B, and C viruses, and the tick-borne Orthomyxoviruses. Parainfluenza viruses and measles are members ofthe Paramyxoviridae although measles is sometimes referred to as a morbillivirus.

A nucleoprotein (NP) is a protein naturally found in close association with the nucleic acid (e.g., RNA) found in a virus. For example in influenza, the nucleoprotein associates with RNA to form a helical structure, the nucleocapsid. The nucleoproteins are thus analogous to the eukaryotic nistone proteins. Influenza nucleoproteins are type specific antigens and occur in one of three antigenic forms; these different forms provide the basis for the classification of human influenza viruses into types A, B, and C.

A virus "derived from" a synthetic ribonucleoprotein complex of this invention refers to a virus that was replicated from the synthetic ribonucleoprotein complex of this invention, or to a virus that is the progeny of a virus that was that was replicated from the synthetic ribonucleoprotein complex of this invention. Similarly, a host cell transfected with a viral transfectant vector compπsing a synthetic ribonucleoprotein complex refers to the host cell so transfected or to the progeny of such a host cell that still contain either a viral RNP of a virus derived from the synthetic RNP of this invention or the derived virus itself

A "conservative substitution", when describing a protein refers to a change in the amino acid composition ofthe protein that does not substantially alter the protein's activity (e.g., nucleoprotein activity). Thus, "conservatively modified variations" of a particular amino acid sequence refers to amino acid substitutions of those amino acids that are not critical for protein activity or substitution of amino acids with other amino acids having similar properties (e.g., acidic, basic, positively or negatively charged, polar or non-polar, etc.) such that the substitutions of even critical amino acids do not substantially alter activity Conservative substitution tables providing functionally similar amino acids are well known in the art The following six groups each contain amino acids that are conservative substitutions for one another

1) Alanine (A), Serine (S), Threonine (T),

2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V), and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W)

See also, Creighton (1984) Proteins W.H. Freeman and Company. In addition, individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids in an encoded sequence are also "conservatively modified variations"

DETAILED DESCRIPTION This invention provides a new method of producing virus containing a heterologous nucleic acid sequence or subsequence, a viral transfectant Typically production of viral transfectants, particularly influenza viral transfectants involves the combination of purified proteins from virion ribonucleoprotein (RNP) cores with a synthetic RNA transcript followed by transfection into cells previously infected with a helper virus (Enami et al. (1991) J. Virol. 65. 271 1-2713). These purified proteins typically include the constituents ofthe ribonucleoprotein complex (RNP) The ribonucleoprotein complex is a heterogenous association of molecules including an RNA, a nucleoprotein (NP) and viral RNA polymerase proteins (e.g., PA, PBl, PB2). In part, because of the complex structure of the RNP and the intimate association between the protein and RNA components, the purification of the RNP complex proteins from virions represents one of the most labor-intensive aspects of the viral transfection procedure requiring multiple gradient fractionations (Enami et al., supra.). In addition to requiring considerable labor, previous viral transfection methods were also complex because it was believed that viral RNA polymerase was required in addition to the viral nucleoprotein to effect viral transfection. Provision of viral RNA polymerase in addition to nucleoprotein (NP) required an elaborate cloning system or time consuming and laborious isolation and purification procedures (see, e.g., Kimura et al. (1992) 7. Virol., 1321-1328).

It was thus a suφrising discovery of this invention that the viral nucleoprotein (NP) alone is sufficient to form a nucleoprotein complex with a nucleic acid (e.g. , RNA) and that this nucleoprotein complex, together with a helper virus, or equivalent replication machinery, is sufficient to achieve viral replicaiton in a host cell. This invention thus eliminates the labor intensive steps required for the purification of the ribonucleoprotein complex (RNP). Instead, a nucleic acid transcript can simply be combined with a pre-purified (e.g. , recombinantly expressed) nucleoprotein and then transfected into a host cell to achieve where the subject virus replicates incorporating the nucleic acid transcript. The purified nucleoprotein or the nucleoprotein/RNA complex can be provided as stock reagents thereby allowing the routine and rapid creation of viral transfectants.

In addition to a dramatic reduction in the labor required to prepare viral transfectants, elimination of the requirement for purified RNP complex proteins eliminates the possibility of introducing virus genes which might be present in the RNP proteins purified from virions. This makes it easier to maintain the transfectant phenotype (e.g. , an attenuated influenza) since no wild-type genes are present except for those deliberately introduced. J, Vims transfection.

As indicated above, this invention provides a method of preparing a viral transfectant (a virus containing a heterologous nucleic acid). In general, the method of this invention involves combining a nucleic acid transcript with an isolated viral nucleoprotein (NP) to form a synthetic nucleoprotein complex (RNP). The complex is then transfected into a host cell where, in combination with a helper virus, or equivalent replication machinery, it mediates viral replication thereby generating a multiplicity of virions each containing a copy of the nucleic acid transcript.

It was a suφrising discovery of this invention that a helper virus, or equivalent replication machinery, is capable of supplying all of the protein components required for viral replication and that the only necessary protein component of the subject virus is the viral nucleoprotein (NP). It was previously believed that other virion proteins, in particular those that form the RNA-directed RNA polymerase (e.g. , PA, PBl, PB2) were required for successful viral replication (see, e.g. , U.S. Patent 5, 166,057). Elimination of the requirement for RNP polymerase proteins from the transfected virus provides for a greatly simplified means of producing transfected viruses. In general, the method includes the following steps: i) combining a nucleic acid transcript (e.g., RNA) with an isolated nucleoprotein (NP) ofthe virus to form a synthetic ribonucleoprotein complex (RNP); ii) transfecting a host cell with the synthetic ribonucleoprotein complex; and iii) holding said host cell under conditions permitting the replication ofthe virus. Preferred subject (transfectant) viruses are, of course, viruses in which replication is mediated, at least in part, by a nucleoprotein (NP). Such viruses are well known to those of skill in the art and include, for example members of the Myxoviridae including Orthomyxoviridae such as influenza viruses, and Paramyxoviridae such as parainfluenza viruses, measles viruses, and the like. Other suitable viruses include the Rhabdoviruses (e.g., rabies). In a particularly preferred embodiment, the subject virus is an influenza virus (e.g. , an influenza type A, B, or C). As indicated above, the synthetic nucleoprotein complex is used to transfect a host cell where, in conjunction with a helper virus, it mediates viral replication. The viral cultures are maintained under standard conditions and those host cells containing viral transfectants are selected and isolated according to standard methods in the art. The various steps of the method are described in detail below.

TT. Preparation of Synthetic Nucleoprotein Complex.

As indicated above the methods of this invention involve preparation of a synthetic nucleoprotein complex. As used herein, a synthetic nucleoprotein complex refers to the combination of, and association between a nucleic acid and a viral NP protein. In a preferred embodiment, the synthetic nucleoprotein complex involves the association of a ribonucleic acid (e.g. , an RNA transcript) with an NP protein selected from influenza, parainfluenza, measles, or rabies, with influenza NP being most preferred. Particularly preferred synthetic ribonucleoprotein complexes are not associated with and do not include nucleic acid polymerases of the subject virus. Preparation of the nucleoprotein, the nucleic acid transcript and the synthetic nucleoprotein complex is described below.

A) Preparation of viral nucleoprotein.

Viral nucleoproteins (NPs) are well known to those of skill in the art. For example, in influenza viruses, the nucleoprotein is a protein closely associated with the viral RNA. The RNA and NP associate together to form a helical structure, the nucleocapsid. The nucleoprotein (NP) has a molecular weight of approximately 60 kDa and there are approximately 1000 molecules in each virus particle. The influenza NP is a type-specific antigen and occurs in one of three antigenic forms. These different forms provide the basis for the classification of human influenza viruses into types A, B, and C. Proteins analogous to the influenza NP are known in other viruses. Thus, for example, parainfluenza, rhabdoviruses, morbilliviruses, and the like contain proteins analogous to the influenza NP (see, e.g. , Fields Virology, 2nd ed. (1990) Raven Press, N.Y.). The viral nucleoproteins of this invention include nucleoproteins in their native conformation and sequence. However, the nucleoproteins of this invention also include NPs modified in a variety of ways that do not adversely effect their activity and in fact, may improve various properties including, but not limited to transfection stability or efficiency, viral replication rate, infectivity, and the like. Preferred modifications will include conservative substitutions as defined above. Some modifications may be made to facilitate the cloning, expression, or purification of the nucleoprotein. Such modifications are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons. One preferred modification is the addition of a carboxyl terminal polyhistidine (e.g., His₆) to facilitate protein purification (e.g. , using an Ni-NTA column). Other modifications can also be made. Thus, for example, amino acid substitutions may be made to improve association with the nucleic acid transcript, to improve viral packaging, or to increase viral replication rate or viability, etc. Alternatively, non-essential regions of the NP molecule may be shortened or eliminated entirely. Thus, where there are regions of the molecule that are not themselves involved in the activity of the molecule, they may be eliminated or replaced with shorter segments that merely serve to maintain the correct spatial relationships between the active components of the molecule.

Viral nucleoproteins are well characterized and the full amino acid and corresponding nucleic acid sequences are known (see, e.g. , Cox et al. (1983) Bull. World. Health. Org., 61: 143-152 and Rota (1989) Nucl. Acids Res. , 17: 3595). Methods of preparing isolated nucleoprotein (NP) are also well known to those of skill in the art and include isolation from a viral culture, de novo chemical synthesis, and recombinant expression.

Means of purifying viral nucleoprotein are known to those of skill in the art (see, e.g. , U.S. Patent 5,316,910 and WO 92/16619)). In a preferred embodiment, the nucleoprotein is purified away from other viral proteins, especially other viral proteins involved with or comprising the viral RNA-directed RNA polymerase (e.g. , PB2, PBl, PA, etc.).

Alternatively, using the amino acid sequence information known to those of skill in the art, the viral nucleoprotein (NP) can be chemically synthesized de novo in a wide variety of well-known ways. Polypeptides of relatively short size are typically synthesized in solution or on a solid support in accordance with conventional techniques (see, e.g., Merrifield (1963) 7. Am. Chem. Soc. 85:2149-2154; Barany and Merrifield, Solid-Phase Peptide Synthesis; pp. 3-284 in The Peptides: Analysis, Synthesis, Biology. Vol. 2: Special Methods in Peptide Synthesis, Part A; and Stewart et al , (1984) Solid Phase Peptide Synthesis, 2nd ed. , Pierce Chem. Co., Rockford, 111. Various automatic synthesizers and sequencers are commercially available and can be used in accordance with known protocols. See, e.g., Stewart and Young (1984) Solid Phase Peptide Synthesis, 2d. ed., Pierce Chemical Co. Peptides of longer size can be prepared by the chemical synthesis of shorter segments which are then coupled together in a condensation reaction between the carboxyl and amino termini of sequential segments thereby resulting in a single continuous polypeptide.

In a preferred embodiment, the viral nucleoproteins are produced by recombinant expression of a nucleic acid encoding the polypeptide followed by purification using standard techniques. Such recombinant methods typically involve providing a nucleic acid sequence encoding the viral NP, inserting the sequence into a vector, transfecting a host cell with the vector, culturing the host cell under conditions where the nucleoprotien is expressed and isolating and purifying the expressed nucleoprotein.

As indicated above, amino acid and hence nucleic acid sequences of viral nucleoproteins, especially influenza, parainfluenza, and measles nucleoproteins, are known. Nucleic acid sequences encoding these peptides can be made using standard recombinant or synthetic techniques. Using chemical techniques, DNA encoding the viral nucleoproteins of this invention may be prepared by any suitable method, including, for example, methods such as the phosphotriester method of Narang et al. (1979) Meth. Enzymol. 68: 90-99; the phosphodiester method of Brown et ai , (1979) Meth. Enzymol. 68: 109-151; the diethylphosphoramidite method of Beaucage et al. (1981) Tetra. Lett. , 22: 1859-1862; and the solid support method of U.S. Patent No. 4,458,066.

Given the nucleic acids encoding the viral nucleoprotein (NP), one of skill can construct a variety of clones containing the same, or functionally equivalent nucleic acids, such as nucleic acids which encode the same, or functionally equivalent nucleoproteins. Cloning methodologies to accomplish these ends, and sequencing methods to verify the sequence of nucleic acids are well known in the art. Examples of appropriate cloning and sequencing techniques, and instructions sufficient to direct persons of skill through many cloning exercises are found in Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology volume 152 Academic Press, Inc., San Diego, CA (Berger); Sambrook et al. (1989) Molecular Cloning - A Laboratory Manual (2nd ed.) Vol. 1-3; and Current Protocols in Molecular Biology , F.M. Ausubel et al. , eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1994 Supplement) (Ausubel). Product information from manufacturers of biological reagents and experimental equipment also provide information useful in known biological methods. Such manufacturers include the Sigma Chemical Company (Saint Louis, Missouri, USA), R&D systems (Minneapolis, Minnesota, USA), Pharmacia LKB Biotechnology (Piscataway, New Jersey, USA), Clontech Laboratories, Inc. (Palo Alto, California, USA), Chem Genes Coφ., Aldrich Chemical Company

(Milwaukee, Wisconsin, USA), Glen Research, Inc., Gibco BRL Life Technologies, Inc. (Gaithersberg, Maryland, USA), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), Invitrogen (San Diego, California USA), and Applied Biosystems (Foster City, California, USA), as well as many other commercial sources known to one of skill.

The nucleic acid sequences encoding the nucleoproteins may be expressed in a variety of host cells, including E. coli and other bacterial hosts. However, in a preferred embodiment, the nucleoproteins used in this invention are expressed in various eukaryotic cells such as yeast, the COS, CHO and HeLa cells lines and myeloma cell lines, and insect cell lines.

The recombinant NP gene will be operably linked to appropriate expression control sequences for each host. For E. coli this includes a promoter such as the T7, tip, or lambda promoters, a ribosome binding site and preferably a transcription termination signal. For eukaryotic cells, the control sequences will include a promoter and preferably an enhancer derived from immunoglobulin genes, SV40, cytomegalovirus, etc., and a polyadenylation sequence, and may include splice donor and acceptor sequences. Plasmids encoding the viral nucleoproteins of this invention can be transferred into the chosen host cell by well-known methods such as calcium chloride transformation for E. coli and calcium phosphate treatment or electroporation for eukaryotic cells. Cells transformed by the plasmids can be selected by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes. Once expressed, the recombinant nucleoproteins can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like (see, generally, R. Scopes, Protein Purification, Springer- Verlag, N.Y. (1982), Deutscher, Methods in Enzymology Vol. 182: Guide to Protein Purification. , Academic Press, Inc. N.Y. (1990)). Substantially pure compositions of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity are most preferred. Once purified, partially or to homogeneity as desired, the nucleoproteins can then be used to form synthetic nucleoprotein complexes according to the methods of this invention. One of skill in the art would recognize that after chemical synthesis, biological expression, or purification, the nucleoproteins may possess a conformation substantially different than their native conformation. In this case, it may be necessary to denature and reduce the polypeptide and then to cause the polypeptide to re-fold into the preferred conformation. Methods of reducing and denaturing proteins and inducing re- folding are well known to those of skill in the art. (See, Debinski et al. J. Biol. Chem. ,

268: 14065-14070 (1993); Kreitman and Pastan, Bioconjug. Chem. , 4: 581-585 (1993); and Buchner, et al, Anal Biochem., 205: 263-270 (1992)). Debinski et al , for example, describe the denaturation and reduction of inclusion body proteins in guanidine-DTE. The protein is then refolded in a redox buffer containing oxidized glutathione and L-arginine. One of skill would recognize that modifications can be made to the recombinant nucleoproteins without diminishing their biological activity. Some modifications may be made to facilitate the cloning, expression, or purification of the nucleoprotein. Such modifications are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons.

In a particularly preferred embodiment, the NPs used in this invention are expressed in Spodoptera frugiperda (S19) insect cells using a baculovirus vector as described in U.S. Patent 5,316,910 and WO 92/16619. m Preparation of nucleic acid transcript.

Virtually any nucleic acid can serve as a nucleic acid transcript for use in the present invention. Typically, nucleic acid transcripts will be chosen that express a non- naturally occurring (e.g., heterologous) gene product, that express an endogenous gene product at elevated levels, that alter the infectivity or pathogenicity ofthe virus, or that act as or encode detectable markers. The nucleic acid transcript can be expressed in appropriate host cell systems, or can provide recombinant viruses that express, package, and/or present the heterologous gene product. The gene products can be advantageously used in a variety of contexts, for example, in vaccine formulations. Where heterologous genes are to be encoded by the transcript, the gene may be selected for its effect on the virus, for its effect on the host cell, or simply for the fact that the virus/host cell provide an opportune, convenient, or particularly optimal system for expression ofthe gene product.

Genomic RNA ofthe Myxoviridae is of negative sense (complementary to that of mRNA) and thus, if the nucleic acid transcript is to express a gene product, it too should be of negative sense. The RNA transcript can be prepared by any of a number of means well known to those of skill in the art. In a preferred embodiment, the RNA templates are prepared by transcription of appropriate DNA sequences using a DNA-directed RNA polymerase such as bacteriophage T7, T3 or the Sp6 polymerase. Using influenza, for example, the DNA is constructed to encode the message-sense of the heterologous gene sequence flanked upstream ofthe ATG by the complement of the viral polymerase binding site/promoter of influenza, i.e., the complement of the 3'-terminus of a genome segment of influenza. For rescue in virus particles, it may be preferred to flank the heterologous coding sequence with the complement of both the 3'-terminus and the 5 '-terminus of a genome segment of influenza. After transcription with a DNA-directed RNA polymerase, the resulting RNA template will encode the negative polarity ofthe heterologous gene sequence and will contain the vRNA terminal sequences that enable the viral RNA-directed RNA polymerase to recognize the transcript. Detailed protocols for the production of RNA transcripts (templates) are provided in U.S. Patent 5, 166,057.

The nucleic acid transcript, however, need not encode an expressed protein. For example, the nucleic acid transcript can itself act as an antisense molecule targeting host cell DNA or mRNA. In addition, the nucleic acid transcript can alter the function (e.g., infectivity, pathogenicity, etc.) of the virus itself by introducing deletions, insertions, point mutations, and frameshift mutations. These various functions are discussed below in Section VI.

In principal, the RNA transcript can replace all or part of any component of the viral genome Thus for example, in the case ofthe influenza virus, one can, in principle replace any one of the eight gene segments, or part of any one ofthe eight segments with the foreign sequence. However, a necessary part of this equation is the ability to propagate the defective virus (defective because a normal viral gene product is missing or altered).

A number of possible approaches exist to circumvent this problem. Briefly, these approaches include, but are not limited to culture with helper viruses expressing the defective gene, culture in cell lines engineered to complement the defective gene, selection of natural host range systems that allow propagation of defective virus, and co-cultivation with wild-type virus (see U.S Patent 5,166,057) and are discussed in more detail in Section IV below

In the case of influenza, for example, the nucleic acid transcript can replace all or part of PB2, PB 1, PA, NP, HA, NA, NS, or M gene segments The gene segments coding for the PB2, PBl, PA and NP proteins contain a single open reading frame with 24-45 untranslated nucleotides at their 5'-end, and 22-57 untranslated nucleotides at their 3'-end. Insertion of a foreign gene sequence into any of these segments could be accomplished by either a complete replacement ofthe viral coding region with the foreign gene or by a partial replacement

The HA and NA proteins, coded for by separate gene segments, are the major surface glycoproteins ofthe virus. Consequently, these proteins are the major targets for the humoral immune response after infection. They have been the most widely-studied of all the influenza viral proteins as the three-dimensional structures of both these proteins have been solved

The three-dimensional structure ofthe H3 hemagglutinin along with sequence information on large numbers of variants has allowed for the elucidation of the antigenic sites on the HA molecule (Webster et al, 1983, pp 127-160 In Genetics Of Influenza Virus, P. Palese and D W Kingsbury, eds., Springer-Verlag, Vienna). These sites fall into four discrete non-overlapping regions on the surface ofthe HA. These regions are highly variable and have also been shown to be able to accept insertions and deletions Therefore, substitution of these sites within HA (e.g., site A, amino acids 122-147 of the A/HK/68 HA) with a portion of a foreign protein may provide for a vigorous humoral response against this foreign protein In a different approach, the foreign peptide sequence may be inserted within the antigenic site without deleting any viral sequences. Expression products of such constructs may be useful in vaccines against the foreign antigen, and may circumvent the problem of propagation ofthe recombinant virus in the vaccinated host An intact HA molecule with a substitution only in antigenic sites may allow for HA function and thus allow for the construction of a viable virus. Therefore, this virus can be grown without the need for additional helper functions. Of course, the virus should be attenuated in other ways to avoid any danger of accidental escape Other hybrid constructions can be made to express proteins on the cell surface or enable them to be released from the cell. As a surface glycoprotein, the HA has an amino-terminal cleavable signal sequence necessary for transport to the cell surface, and a carboxy-terminal sequence necessary for membrane anchoring In order to express an intact foreign protein on the cell surface it may be necessary to use these HA signals to create a hybrid protein Alternatively, if only the transport signals are present and the membrane anchoring domain is absent, the protein may be excreted out ofthe cell

In the case ofthe NA protein, the three-dimensional structure is known but the antigenic sites are spread out over the surface ofthe molecule and are overlapping This indicates that if a sequence is inserted within the NA molecule and it is expressed on the outside surface of the NA it is likely to be immunogenic Additionally, as a surface glycoprotein, the NA exhibits two striking differences from the HA protein Firstly, the NA does not contain a cleavable signal sequence; in fact, the amino-terminal signal sequence acts as a membrane anchoring domain The consequence of this, and the second difference between the NA and HA. is that the NA is orientated with the amino-terminus in the membrane while the HA is orientated with the carboxy-terminus in the membrane. Therefore it may be advantageous in some cases to construct a hybrid NA protein, since the fusion protein will be orientated opposite of a HA-fusion hybrid

The unique property of the NS and M segments as compared to the other six gene segments of influenza virus is that these segments code for at least two protein products In each case, one protein is coded for by an mRNA which is co-linear with genomic RNA while the other protein is coded for by a spliced message However, since the splice donor site occurs within the coding region for the co-linear transcript, the NSI and NS2 proteins have an identical 10 amino acid amino terminus while Ml and M2 have an identical 14 amino acid amino terminus

As a result of this unique structure, recombinant viruses may be constructed so as to replace one gene product within the segment while leaving the second product intact. For instance, replacement ofthe bulk ofthe NS2 or M2 coding region with a foreign gene product (keeping the splice acceptor site) could result in the expression of an intact NSI or Ml protein and a fusion protein instead of NS2 or M2. Alternatively, a foreign gene may be inserted within the NS gene segment without affecting either NS 1 or NS2 expression. Although most NS genes contain a substantial overlap of NSI and NS2 reading frames, certain natural NS genes do not. For example, in the NS gene segment from

A/Ty/Or/71 the NSI protein terrninates at nucleotide position 409 ofthe NS gene segment while the splice acceptor site for the NS2 is at nucleotide position 528 (Norton et al., (1987), Virology 156: 204-213). Therefore, a foreign gene could be placed between the termination codon ofthe NSI coding region and the splice acceptor site ofthe NS2 coding region without affecting either protein It may be necessary to include a splice acceptor site at the 5' end ofthe foreign gene sequence to ensure protein production (this would encode a hybrid protein containing the amino-terminus of NSI). In this way, the recombinant virus should not be defective and should be able to be propagated without need of helper functions.

The insertions into and/or replacements of all or part of various viral genes described above, can be performed according to standard methods well known to those of skill in the art. In a preferred embodiment, the RNA transcripts of this invention can be prepared through the use of PCR-directed mutagenesis Detailed methods for the construction of RNA transcripts suitable for the production of viral transfectants can be found in U.S. Patent 5,166,057.

CΛ Combination of transcript with nucleoprotein to form synthetic nucleprotein complex.

The RNA transcript can be combined with the nucleoprotein (NP) before, during, or after transfection However, because the nucleoprotein affords the RNA transcript some protection from ribonucleases during transfection, in a preferred embodiment, the NP is combined with the RNA transcript before transfection The RNA transcript and the nucleoprotein can be combined before transfection by simple admixture. Similarly, the transcript and nucleoprotein can be combined during transfection by placing both components in the transfection mixture. The components can be combined after transfection by simply transfecting one component followed by the other component and allowing the components to combine when inside the host cell. In a particularly preferred embodiment, however, the formation ofthe synthetic nucleoprotein complex occurs with preparation ofthe nucleic acid transcript. Thus, for example, the nucleoprotein can be added to the reaction mixture (e.g., amplification, reverse transcription, etc.) in which the nucleic acid transcript is produced thereby facilitating the rapid association ofthe NP with the transcript. As NP helps prevent RNA degradation, this approach improves the stability.

For example, in one approach, the nucleic acid transcript is produced by reverse transcription from a cDNA clone encoding the desired RNA transcript in the presence of a nucleoprotein. Typically the cDNA is placed behind a promoter (e.g., a T7 RNA polymerase promoter) situated to allow transcription to begin on the correct nucleotide. Reverse transcription is performed according to standard methods known to those of skill (see, e.g., Sambrook et al., supra., Ausubel et al , supra.; Van Gelder, et al., (1990) Proc. Natl. Acad Sci. USA, 87: 1663-1667; and Eberwine et al. Proc. Natl. Acad. Sci. USA, 89: 3010-3014). This approach is illustrated in Example 1.

m. Transfection of Host Cell.

The synthetic nucleprotein complex is transfected into a host cell where it is allowed to replicate. Virtually any host cell can be transfected in this manner. However, in a preferred embodiment, the host cell is one that is compatible with infection and culture ofthe particular subject virus. Thus, for example where the transfected virus is an influenza virus, preferred host cells include those cells commonly used to culture influenza. Such cells include, but are not limited to cells of the amniotic membrane of embryonated eggs, tissue cultures of kidney tissue from rhesus monkeys, baboons, chicks, or a variety of other species. Particularly preferred cells include, for example, primary chick kidney (PCK) cells, Madin- Darby canine kidney (MDCK) cells, Madin-Darby bovine kidney (MDBK) cells and the like. As indicated above, in one embodiment, the methods of this invention are not used simply to prepare viral transfectants, but rather to provide host cells containing a heterologous nucleic acid. In this context, the synthetic nucleoprotein complex can be used simply to direct the heterologous nucleic acid to the nucleus ofthe host cell. The host cell in this case, can be any cell it is desired to transfect with the heterologous nucleic acid transcript. The synthetic ribonucleoprotein complex can be transfected into the host cell according to any of a number of transfection methods well known those of skill in the art. Suitable transfection methods include, but are not limited to calcium chloride transformation e.g., for E. coli, and calcium phosphate treatment, electroporation, or ballistic transfection (e.g. , high velocity gold microspheres) for eukaryotic cells. In a particularly preferred embodiment, the host cells are transfected by electroporation or by the DEAE-dextran

DMSO protocol (see, e.g. , Al-Molish et al. (1973) J. Gen. Virol, 18: 189-193; and Lopata et al. (1984) Nucl. Acids Res. 12: 5707-5717), with electroporation being most preferred.

TV. Viral Culture. After transfection of cells by the synthetic ribonucleoprotein complex, the cells are preferably cultured under conditions that permit replication ofthe subject virus. One of skill in the art will appreciate that a ribonucleoprotein complex (RNP) comprising just an RNA and an NP is generally insufficient to replicate the subject virus alone and additional "replication machinery" is typically required In addition, where the nucleic acid transcript includes a heterologous nucleic acid, the

is often "defective" because a normal viral gene product is often missing or altered.

As indicated above, a number of possible approaches exist to circumvent this problem Mutants (transfectants) ofthe virus (e.g., influenza) can be grown in cell lines constructed to constitutively express the ' defective" gene (see, e.g., Krystal et al, (1986) Proc. Natl. Acad. Sci. USA 83: 2709-2813 who grew mutants of influenza virus defective in the PB2 and NP proteins in cell lines which were constructed to constitutively express the polymerase and NP proteins). These cell lines which are made to express the viral protein may be used to complement the defect in the recombinant virus and thereby propagate it (see, e.g., Kimura et al (1992) J. Gen. Virol, 73 1321-1328) Alternatively, certain natural host range systems may be available to propagate recombinant virus. An example of this approach concerns the natural influenza isolate CR43-3 This virus will grow normally when passaged in primary chick kidney cells (PCK) but will not grow in Madin-Darby canine kidney ceils (MDCK), a natural host for influenza (Maassab & DeBorde (1983) Virology, 130 342-350) This virus codes for a defective NS 1 protein caused by a deletion of 12 amino acids The PCK cells contain some activity which either complements the defective NS 1 protein or can completely substitute for the defective protein.

As indicated above, it was a surprising discovery and advantage of this invention that synthetic ribonucleoprotein complexes (RNPs) completely lacking RNA polymerase of the subject virus are fully capable of replicating when complemented by a helper virus This invention thereby eliminates the requirement for purified RNP proteins or recombinantly engineered host cells for viral propagation

Thus, in a preferred embodiment, the viral transfectant is propagated through involve co-cultivation with wild-type or helper virus This can be done by simply taking recombinant virus and co-infecting cells with the synthetic RNP and a wild-type (e.g., a vaccine strain) or a helper virus The wild-type or helper virus should complement for the defective virus gene product and allow growth of both the helper or wild-type and recombinant virus

Where co-cultivation is with wild-type virus, this is analogous to the propagation of defective-interfering particles of influenza virus (Nayak et al , (1983) In Genetics of Influenza Viruses, P. Palese and D W Kingsbury, eds., Springer-Verlag, Vienna, pp 255-279) In the case of defective-interfering viruses, conditions can be modified such that the majority of the propagated virus is the defective particle rather than the wild-type virus Therefore this approach may be useful in generating high titer stocks of recombinant virus However, these stocks would necessarily contain some wild-type virus

In a particularly preferred embodiment, the synthetic RNPs are cultured in the presence of a helper virus. Suitable helper viruses are well known to those of skill and include, but are not limited to wild-type (e.g., A/PR S/34 or A/WSN/33) or live attenuated vaccine strains (e.g., A/Leningrad/57 or A Ann Arbcr/6/60)

The host cell can be infected with the helper virus prior to, along with, or after transfection of the synthetic ribonucleoprotein comp.ex into the cell according to standard methods well known to those of skill in the art (see, e g.. Enami M and Palese, P (1991) J. Virol, 65' 271 1) Similarly, transgenic viruses produced according to the method of this invention can also be cultured in the presence of appropriate complementing wild-type or helper virus.

In still yet another approach, infection of host cells with synthetic RNPs encoding all eight influenza virus proteins results in the production of infectious transgenic (transfectant) virus particles. This system would eliminate the need for a selection system, as all recombinant virus produced would be ofthe desired genotype.

The synthetic ribonucleoprotein complexes or the viral transfectants can be cultured in standard culture systems including, for example, embryonated eggs and tissue culture.

A^ Culture in embryonated eggs.

The virus (e.g., influenza) can be cultured by amniotic or allantoic inoculation of 10-12 day embryonated eggs. The virus is absorbed from the fluid ofthe amniotic cavity onto the cells ofthe amniotic membrane in which the y multiply, releasing newly formed virus back into the amniotic fluids. After two to three days' incubation, virus can be present in high titre in the amniotic fluid and can be detected by adding aliquots of harvested amniotic fluid to chick, turkey, guinea-pig or human erythrocytes and observing haemagglutination Detailed protocols for viral culture in embryonated eggs are well known to those of skill in the art and can be found in standard references (see, e.g., Fields Virology, supra.)

B> Tissue culture.

The subject viruses can also be cultured in eukaryotic tissue cultures according to standard methods. For example, influenza can be culture is tissue cultures of kidney from dogs, rhesus monkeys, baboons, chicks, or a variety of other species Particularly preferred cells include, for example H292 cells, primary chick kidney (PCK) cells, Madin-Darby canine kidney (MDCK) cells, Madin-Darby bovine kidney (MDBK) cells, and the like

After absoφtion (transfection) and incubation of virus-infected cells, newly produced virus can be detected in a number of ways In one approach, free virus released into the maintenance medium ofthe tissue culture can be detected (e.g., by haemagglutination with erythrocytes) Alternatively, since virus is slowly released from the cell surface of infected cells, erythrocytes will adhere directly to these infected cells (haemadsoφtion) and can be detected under the microscope. Methods of viral maintenance and propagation in tissue culture are known to those of skill in the art (see, e.g.. Concepts and Proceedures for Laboratory-Based Influenza Surveillance, Dept. Health and Hum Ser , Centers for Disease Control (1982))

V. Selection of Transfectants.

Viral transfectants (transgenic viruses) can be identified and selected according to standard methods known to those of skill in the art. Typically this involves identifying culture cells (or culture supernate) positive for the viral transfectant, and selectively propagating the host cell containing the virus and/or the virus itself from the cell or supernatant Identification of the host cell or supernatant is by means well known to those of skill in the art and typically involves direct or indirect detection ofthe presence or absence of the heterologous RNA (transcript) or its product.

Direct detection involves detection ofthe heterologous RNA (or DNA transcribed therefrom) itself. This can be accomplished by a number of means including, but not limited to detection using a nucleic acid affinity column specific to (containing probes complementary to) the heterologous RNA (or DNA transcribed therefrom) or to subsequences thereof, amplification (e.g., via PCR) of particular target sequences or subsequences in the RNA (or DNA transcribed therefrom), restriction analysis, and so forth In one preferred embodiment, illustrated by Example 1, the heterologous RNA is detected by PCR restriction analysis according to the method of Klimov e?/ α/. (1995) J. Virol. Meth., 52 41-49.

In other embodiments, the viral transfectants, or host celis harboring the viral transfectants, can be identified by detection of the presence or absence of a protein product of activity ofthe protein product expressed by the heterologous nucleic acid Thus, the heterologous nucleic acid can include a sequence that confers antibiotic resistance thereby allowing selection of transfectants by antibiotic resistance ofthe host cells Alternatively, the heterologous nucleic acid can encode a detectable marker as described below.

VI. Uses of viral transfection. The synthetic ribonucleoprotein complexes and the viral transfectants made according to the methods of this invention can be used to express heterologous gene products in host cells or to rescue the heterologous gene in virus particles by cotransfection of host cells with recombinant RNPs and virus. Alternatively, heterologous gene can be rescued in host cells transformed to allow for complementation and rescue of the heterologous gene in virus particles

The expression products and/or chimeric virions obtained may also be advantageously be utilized in vaccine formulations Viral transfectants expressing detectable labels provide effective reporter systems for screening antiviral compounds and investigating viral ecology. Finally, because the NP protein confers protection against ribonuclease activity the RNA/NP ribonuclease complex and viruses derived therefrom provide an effective system for the delivery of antisense RNA. These various uses are discussed more fiilly below.

A) Expression of heterologous gene products using synthetic RNP complexes. The recombinant templates prepared as described above can be used in a variety of ways to express the heterologous gene products in appropriate host cells or to create chimeric viruses that express the heterologous gene products In one embodiment, the recombinant template can be combined with viral polymerase complex purified as described in

Section 6, infra, to produce rRNPs which are infectious. Alternatively, the recombinant template may be mixed with viral polymerase complex prepared using recombinant DNA methods (see, e.g., Kingsbury et al, (1987), Virology 156 396-403) Such rRNPs, when used to transfect appropriate host cells, may direct the expression ofthe heterologous gene product at high levels Host cell systems which provide for high levels of expression include continuous cell lines that supply viral functions such as cell lines supeπnfected with influenza, cell lines engineered to complement influenza viral functions, etc.

B> Use of detectable heterologous sequences. In another embodiment, the heterologous RNA transcript can act as a detectable label or can express a protein that is a detectable label The detectable label allows quantification, or detection of the presence or absence, of the virus in a particular sample. A viral transfectant bearing a detectable label provides an effective indicator for screening for anti-viral drugs in vitro or in vivo. For example, the organism or cell line is infected with the viral transfectant bearing the detectable marker and then treated with one or more test compounds. Quantification of the detectable marker after treatment and comparison of test with control samples provides a measure of the efficacy of the compound tested Where the detectable label is one that can be easily captured (e.g., a particular nucleic acid sequence that can be captured by a nucleic acid affinity column or a polypeptide sequence (e.g., polyhistidine such as His₆ that can be captured using an Ni-NTA column) the viral transfectant can be used to isolate anti-viral antibodies In this embodiment, an organism is challenged with the viral transfectant under conditions that allow the organism to mount an immune response Subsequent capture ofthe viral transfectant (through capture ofthe detectable label) will also capture any antibody binding to the virus

The detectable label can also be used to monitor (e.g., detect and/or quantify) one or more strains of virus (e.g., influenza) in vitro or in vivo. This permits rapid assessment ofthe infectivity and/or the pathogenicity of a particular virus, alone or in combination with other viruses. This permits the assessment ofthe effects of mutations producing various viral strains on the host and on other viral strains Other uses of viral transfectants bearing detectable labels will be known to those of skill in the art

Detectable labels suitable for use in the present invention include any nucleic acid sequence that is detectable (e.g. , via hybridization to a particular probe or capture sequence, or through RFLP or other fingeφrinϋng technique, etc.) or any polypeptide sequence that is detectable including, but not limited to enzymes (e.g. , horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and other polypeptide sequences that can be specifically detected and/or captured (e.g. , polyHis that can be captured using an Ni-NTA column). Means of detecting such labels are well known to those of skill in the art.

C) Use of viral transfectants for vaccine formulations.

The expression products and/or chimeπc virions obtained can be used in vaccine formulations The use of recombinant influenza for this purpose is especially attractive since influenza demonstrates tremendous strain variability allowing for the construction of a vast repertoire of vaccine formulations The ability to select from thousands of influenza variants for constructing chimeric viruses obviates the problem of host resistance encountered when using other viruses such as vaccinia In addition, since influenza stimulates a vigorous secretory and cytotoxic T cell response, the presentation of foreign epitopes in the influenza virus background may also provide for the induction of secretory immunity and cell-mediated immunity Virtually any heterologous gene sequence may be constructed into the chimeric (transfectant) viruses ofthe invention for use in vaccines Preferably, epitopes that induce a protective immune response to any of a variety of pathogens, or antigens that bind neutralizing antibodies may be expressed by or as part ofthe viral transfectants For example, heterologous gene sequences that can be constructed into the chimeric viruses ofthe invention for use in vaccines include but are not limited to epitopes of human immunodeficiency virus (HIV) such as gpl20; hepatitis B virus surface antigen (HBsAg); the glycoproteins of heφes virus (e.g., gD, gE); VPI of poliovirus; antigenic determinants of non-viral pathogens such as bacteria and parasites, to name but a few. In another embodiment, all or portions of immunoglobulin genes may be expressed. For example, variable regions of anti-idiotypic immunoglobulins that mimic such epitopes may be constructed into the chimeric viruses ofthe invention

Either a live recombinant viral vaccine or an inactiviated recombinant viral vaccine can be formulated. A live vaccine may be preferred because multiplication in the host leads to a prolonged stimulus of similar kind and magnitude to that occurring in natural infections, and therefore, confers substantial, long-lasting immunity. Production of such live recombinant virus vaccine formulations may be accomplished using conventional methods involving propagation ofthe virus in cell culture or in the allantois of the chick embryo followed by purification In this regard, the use of genetically engineered influenza virus (vectors) for vaccine puφoses may require the presence of attenuation characteristics in these strains Current live virus vaccine candidates for use in humans are either cold adapted, temperature sensitive, or passaged so that they derive several (six) genes from avian viruses, which results in attenuation. The introduction of appropriate mutations (e.g., deletions) into the RNA transcripts used for transfection may provide the novel viruses with attenuation characteristics. For example, specific missense mutations which are associated with temperature sensitivity or cold adaption can be made into deletion mutations. These mutations should be more stable than the point mutations associated with cold or temperature sensitive mutants and reversion frequencies should be extremely low. Alternatively, viral transfectants with "suicide" characteristics may be constructed Such viruses would go through only one or a few rounds of replication in the host For example, in influenza, cleavage of HA is necessary to allow for re-initiation of replication. Therefore, changes in the HA cleavage site can produce a virus that replicates in an appropriate cell system but not in the human host. When used as a vaccine, the recombinant virus goes through a single replication cycle and induces a sufficient level of immune response but fails to progress further in the human host and cause disease. Recombinant influenza viruses lacking one or more ofthe essential influenza virus genes would not be able to undergo successive rounds of replication. Such defective viruses can be produced, for example, by co-transfecting reconstituted RNPs lacking specific gene(s) into cell lines which permanently express these gene(s). Viruses lacking essential gene(s) will be replicated in these cell lines but when administered to the human host will not be able to complete a round of replication. Such preparations may transcribe and translate - in this abortive cycle - a sufficient number of genes to induce an immune response. Alternatively, larger quantities ofthe strains could be administered, so that these preparations serve as inactivated (killed) virus, vaccines.

In inactivated vaccines, it is preferred that the heterologous gene product be expressed as a viral component, so that the gene product is associated with the virion. The advantage of such preparations is that they contain native proteins and do not undergo inactivation by treatment with formalin or other agents used in the manufacturing of killed virus vaccines.

In another embodiment of this aspect of the invention, inactivated vaccine formulations may be prepared using conventional techniques to "kill" the viral transfectants.

Inactivated vaccines are "dead" in the sense that their infectivity has been destroyed. Ideally, the infectivity ofthe virus is destroyed without affecting its immunogenicity. In order to prepare inactivated vaccines, the viral transfectant may be grown in cell culture or in the allantois of the chick embryo, purified by zonal ultracentrifugation, inactivated by formaldehyde or beta-propiolactone, and pooled. The resulting vaccine is preferably inoculated intramuscularly.

Inactivated viruses may be formulated with a suitable adjuvant in order to enhance the immunological response. Such adjuvants may include but are not limited to mineral gels, e.g., aluminum hydroxide; surface active substances such as lysolecithin, pluronic polyols, polyanions; peptides; oil emulsions; and potentially useful human adjuvants such as BCG and Coryne bacterium parvum. Many methods may be used to introduce the vaccine formulations described above, into the subject organism (e.g., pig, rabbit, goat, mouse, rat, primate including human, etc.). These include but are not limited to oral, intradermal, intramuscular, intraperitoneal, intravenous, subcutaneous, and intranasal routes. It may be preferable to introduce the chimeric virus vaccine formulation via the natural route of infection ofthe pathogen for which the vaccine is designed. Where a live chimeric virus vaccine preparation is used, it may be preferable to introduce the formulation via the natural route of infection for influenza virus. The ability of influenza virus to induce a vigorous secretory and cellular immune response can be used advantageously. For example, infection ofthe respiratory tract by chimeric influenza viruses may induce a strong secretory immune response, for example in the urogenital system, with concomitant protection against a particular disease causing agent.

DI Modulation of intracellular activity.

The viral transfectants prepared according to the methods of this invention can be used to modulate the intracellular activity ofthe host cell. This modulation can be accomplished directly through the activity ofthe RNA transcript in the viral transfectant or indirectly through a polypeptide encoded by the RNA transcript in the viral transfectant. For example, the RNA transcript can be provided that is complementary (antisense) to regions of the genomic DNA ofthe host cell or to an mRNA expressed by a particular gene. Hybridization of the RNA transcript to the host DNA can inhibit transcription of the target region while hybridization to an mRNA can block the translation of that mRNA and hence the expression of the protein encoded by the mRNA. Similarly binding of the antisense RNA to transcription regulators (e.g., promoters, initiation sites, repressors, etc.) can up-regulate or downregulate transcription of particular targeted genes. The use of antisense molecules to modulate (e.g., upregulate or downregulate) protein expression is well known to those of skill in the art (see, e.g., Castanotto et al (1994) Adv. Pharmacol, 25: 289-317, WO 90/13641, and references cited therein).

Thus, in one embodiment this invention provides for methods and compositions for the delivery of antisense molecules into the nucleus of a cell. As indicated above, the viral nucleoprotein affords the RNA transcript protection from ribonucleases and directs the RNA transcript into the nucleus of the host cell. The ribonucleoprotein complexes comprising an antisense RNA complexed with an NP provide an effective vehicle for delivery ofthe antisense molecule. Similarly, viral transfectants containing the antisense RNA also provide a highly effective delivery system for the antisense molecule.

As indicated above, the RNA transcripts can be selected that modulate intracellular activity through an expressed protein. The expressed protein can be a functional component of an intracellular signaling pathway (e.g., an estrogen receptor (ER), jun, fos Elk, ATF2, a tyrosine kinase, a GTP binding protein such as Ras, Rac, and the like, signaling molecules such as JAKs, PLCs, and PI3K) or, conversely can be a protein that inhibits a component of a signaling cascade Such proteins are well known to those of skill in the art (see, e.g., Darnell and Baltimore, (1986) Molecular Cell Biology, Scientific American Books).

E\ Use of viral transfectants for gene therapy.

The viral transfectants of this invention also provide suitable vectors for gene therapy. The virus, containing an RNA transcript that encodes a protein of therapeutic value. In addition, the RNA transcript can include (or encode) segments that mediate integration of the heterologous gene of interest into the genome ofthe host cell (organism). Segments that mediate integration with the host genome are known to those of skill in the art and include, but are not limited to adeno associated viruses (AAVs), inverted terminal repeats (ITRs), and retroviral LTRs. The selection and design of nucleic acid transcripts suitable for gene therapy is well known to those of skill in the art (see, e.g., Freifelder Molecular Biology, 2nd ed., 1987, Jones and Bartlert, Pub., Boston).

VII. Kits for the practice of this invention.

This invention additionally provides for kits for the practice ofthe methods disclosed herein. In a preferred embodiment, the kit contains a container containing an isolated viral nucleoprotein (NP), as described above, for the practice ofthe methods of this invention. The kits additionally include labels or instructions describing the methods of making viral transfectants and/or the methods of introducing a ribonucleic acid into a host cell described above. The NP can be provided alone or complexed with a ribonucleic acid (e.g., RNA transcript). The kit can additionally include one or more of the following elements buffers, host cells, culture media, helper viruses, subject viruses, and the like. EXAMPLES

The following examples are offered to illustrate, but not to limit the present invention

Example l Transfection assays were conducted using nucleprotein (NP) purified from insect cells infected with a recombinant baculovirus expressing type A influenza NP The results demonstrate that virion polymerase proteins are unnecessary n the artificial RNP complexes transfected into cells

Nucleoprotein (NP was purified from SF9 (Spodoptera) cells infected with a recombinant baculovirus expressing the influenza A/ Ann Arbor/6/60 nucleocapsid protein

(see, e.g., Rotal et al (1990) 7. Gen. Virol, 71. 1545-1554, Rota et al, U.S Patent No. 5,316,910 and WO 92/16619) The cells were lysed by refreezing and suspended in 0 01 M Tris-HCl, pH 7 4, containing 0 001 M EDTA and 1 M NaCl After overnight dialysis against phosphate buffered saline (PBS. pH 7 3), the supernate ofthe lysate was fractionated on a column of monoclonal anti-NP IgG (Walls et al. (1986) J. Clin. Microbiol, 23 240-245) coupled to Bio-Rad A- 14 Affigel matrix using the manufacturer's methods and equilibrated in PBS bound protein was eluted in 1 M MgCl₂ and concentrated by dialysis against 50 mM Tris-HCl, pH 7 6, 100 mM NaCl, 10 M MgCl₂, 2 mM DTT, 50% Glycerol Purity was verified by SDS PAGE Aliquots were stored at -70^CC until used in transfection assays For transfection assays, the 25 A- 1 virus, a 7/1 ts reassortment having seven genes from A/PR/8/34 virus and the NS gene from the live-attenuated, cold-adapted A/Leningrad/47/57 virus w as used as a helper A cDNA clone of the A/PR/8/34 virus NS gene placed behind a T7 RNA polymerase promoter situated to allow transcription to begin on the correct nucleotide and havng a BseAI site downstream to allow run off transcripts after treatment with mung bean nuclease was used as the source of RNA for transfection

Transcription reactions were conducted in the presence of 5 μg of purified baculo-expressed nucleoprotein (NP) The resulting synthetic RNP complexes were transfected into MDCK cells that had been infected one nour previously with the 25 A- 1 reassortant helper virus by the electroporation method of Li el al (1995) Virus Res., 37 153-161 After incubation at 34 °C for 18 hours, culture supemates were used to infect confluent MDCK cells for two days at 37°C before plaquing the culture supernates at 39°C for three days A total of 15 plaques were picked, nine of which grew in 10 day embryonated hens' eggs. The origin ofthe NS gene in each clone was determined by PCR restriction analysis (Klimov et al. (1995) J. I ^'irol. Meth., 52: 41-49). Of the nine clones analyzed, four had the A/PR/8/34 NS gene thus demonstrating that functional polymerases are not necessary in the synthetic RNPs transfected into cells. Transfection experiments using DEAE-dextran DMSO protocol (Al-Molish et al. (1973) J. Gen. Virol, 18: 189-193; and Lopata et al

(1984) Nucl Acids Res. 12: 5707-5717), yielded a total of eleven clones, only one of which had the A/PR/8/34 NS gene, thus demonstrating the superior efficiency of electroporation for the generation of influenza virus transfectants.

Without being bound to a particular theory, it is believed the role of NP is two-fold; protection of the RNA transcript from degradation and transport to the cell nucleus where the helper virus supplies the necessary transcription and replication machinery. In addition to eliminating the laborious purification procedure for RNP proteins, the use of recombinant DNA-derived NP eliminates the possibility of introducing virus genes which might be present in the RNP proteins purified from virions. In the case of live-attenuated vaccines, this will make it easier to maintain the attenuated phenotype since no wild-type genes are present, except for those deliberately introduced.

It is understood that the examples and embodiments described herein are for illustrative puφoses only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incoφorated by reference for all purposes.

Claims

WHAT TS CLAIMED IS:

1. A method of preparing a virus bearing a preselected ribonucleic acid, said method comprising the steps of: i) combining said ribonucleic acid with an isolated nucleoprotein (NP) of said virus to form a synthetic ribonucleoprotein complex (RNP); ii) transfecting a host cell with said synthetic ribonucleoprotein complex; and iii) holding said host cell under conditions permitting the replication of said virus.

2. The method of claim 1 , wherein said host cell is infected with a helper virus.

3. The method of claim 2, wherein said helper virus is a laboratory- adapted wild-type virus or a live-attenuated vaccine strain.

4. The method of claim 3, wherein said helper virus is selected from the group consisting of A/PR/8/34, AAVSN 33, A/Leningrad/57, and A/ Ann Arbor /6/60.

5. The method of claim 1 , wherein said isolated nucleoprotein (NP) is substantially free of viral RNA polymerase proteins, before said combining step.

6. The method of claim 5, wherein said isolated nucleoprotein protein is recombinantly expressed

7. The method of claim 6, wherein said isolated nucleoprotein protein is recombinantly expressed in a eukaryotic expression system.

8. The method of claim 1, wherein said virus is selected from the group consisting of an influenza type A virus, an influenza type B virus, and an influenza type C virus.

9. The method of claim 1, wherein said nucleoprotein is a nucleoprotein (NP) of a virus selected from the group consisting an influenza type A virus, an influenza type B virus, and an influenza type C virus.

10. The method of claim 1, wherein said host cell is selected from the group consisting of a kidney cell, a cell from a hen's egg, and a primate primary lung cell.

1 1. The method of claim 1, wherein said virus is an influenza virus; said nucleoprotein is a recombinantly expressed influenza nucleoprotein substantially free of a viral RNA polymerase; and said host cell is infected with an influenza helper virus.

12. A method of introducing a ribonucleic acid into the nucleus of a host cell said method comprising the steps: i) combining said ribonucleic acid with an isolated nucleoprotein (NP) of a virus to form a synthetic ribonucleoprotein complex (RNP); and ii) transfecting said host cell with said synthetic ribonucleoprotein complex.

13. The method of claim 12, further comprising infecting said host cell with a helper virus.

14. The method of claim 13, wherein said helper virus is a laboratory-adapted wild-type virus or a live-attenuated vaccine strain.

15 The method of claim 14, wherein said helper virus is selected from the group consisting of A/PR/8/34, AΛVSN/33, A/Lerungrad/57, and A/ Ann Arbor /6/60.

16 The method of claim 12, wherein said isolated nucleoprotein (NP) is substantially free of viral RNA polymerase proteins, before said combining.

17. The method of claim 16, wherein said isolated nucleoprotein protein is recombinantly expressed.

18. The method of claim 12, wherein said nucleoprotein is a nucleoprotein (NP) of a virus selected from the group consisting of an influenza type A virus, an influenza type B virus, and an influenza type C virus

19 The method of claim 12, wherein said host cell is selected from the group consisting of a kidney cell, a cell from a hen's egg. and a primate primary lung cell

20 A transfection composition comprising an isolated viral nucleoprotein combined with a ribonucleic acid thereby forming a synthetic ribonucleoprotein complex (RNP) that mediates replication of a virus in a host cell.

21 The composition of claim 20, wherein said isolated nucleocapsid protein is substantially free of a viral RNA polymerase

22 The composition of claim 21, wherein said isolated nucleoprotein is recombinantly expressed

23 The composition of claim 20, wherein said nucleocapsid protein is a nucleocapsid protein of a virus selected from the group consisting of an influenza type A virus, an influenza type B virus, and an influenza type C virus

24 A virus expressed from a synthetic ribonucleoprotein complex (RNP), said synthetic nucleoprotein complex comprising an isolated nucleoprotein (NP) combined with a ribonucleic acid (RNA)

25 The virus of claim 24, wherein said isolated nucleocapsid protein (NP) is substantially free of a viral RNA polymerase

26 The virus of claim 24, wherein said isolated nucleocapsid protein is recombinantly expressed

27 The virus of claim 24, wherein said virus is selected from the group consisting of an influenza virus, an influenza type A virus, an influenza type B virus, and an influenza type C virus.

28 The virus of claim 24, wherein said nucleoprotein is a nucleoprotein of a virus selected from the group consisting of parainfluenza virus, a measles virusm, rabies, respiratory syncytial virus

29 The virus of claim 24, wherein said virus is a live-attenuated virus

30 A eukaryotic cell comprising a synthetic ribonucleoprotein complex or a virus derived from said ribonucleoprotein complex where said ribonucleoprotein complex comprises an isolated nucleoprotein (NP) combined with a ribonucleic acid

31. The eukaryotic cell of claim 30, wherein said ribonucleoprotein complex is an influenza ribonucleoprotein complex

32 A kit for the transfection of a virus or a cell, said kit comprising a container containing an isolated viral nucleoprotein (NP) and a label or instructions describing the method of claims 1 or 1 1 33. The kit of claim 32, wherein said NP is provided combined with a ribonucleoprotein thereby forming a synthetic ribonucleoprotein complex.