Vero cell-based influenza virus strains and vaccines

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 362355SequenceListing.txt, a creation date of Sep. 4, 2008, and a size of 55 KB. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.

FIELD OF THE INVENTION

The present invention relates to an influenza virus stain. In particular, the present invention relates to an influenza A virus strain suitable for increased production of an influenza A virus vaccine from a mammalian host cell, and the vaccine produced therefrom.

BACKGROUND OF THE INVENTION

Influenza viruses, particularly types A and B viruses, have been associated with major outbreaks of influenza, and are a serious cause of morbidity and mortality of animals. Infection with type B influenza is usually milder than type A. Influenza A viruses are hosted by birds, but may infect several species of mammals. All known subtypes of influenza A are endemic in birds. Birds have the greatest number and range of influenza strains. The influenza virus strains have been and are undergoing antigenic drift, probably driven by selective antibody pressure in the populations of humans infected, leading to seasonal epidemics in several geographical regions. Recently, it was found that highly pathogenic avian influenza A viruses of the H5N1 subtype were circulating in eastern Asia. Some strains of the human H5N1 viruses were isolated and studied. In 2005, some H5N1 isolates lacking the polybasic cleavage site in the hemagglutinin gene were produced by reverse genetics in anticipation of the possible need to vaccinate humans. See Emerging Infectious Disease (2005) 11(10):1515-1521.

An influenza virus is an RNA virus of the Orthomyxoviridae family and comprises a segment negative RNA genome, which codes for about 10 influenza proteins. The 10 influenza proteins include RNA-directed RNA polymerase proteins (PB2, PB1 and PA), nucleoprotein (NP), neuraminidase (NA), hemagglutinin (HA, which after enzymatic cleavage is made up of the association of subunits HA1 and HA2), the matrix proteins (M1 and M2) and the non-structural proteins (NS1 and NS2) (Krug et al. (1989) in The Influenza Viruses (R. M. Krug, ed.), Plenum Press (New York) pages 89-152).

For the past several decades, fertilized chicken eggs have been used as a host system to replicate influenza viruses for use in vaccine production. African green monkey kidney (Vero) cells and Madin-Darby canine kidney (MDCK) cells have been widely used for manufacturing seasonal influenza vaccines (Audrey et al. (2004) Expert Opin. Biol. Ther. 4(5):709-17 and Ghendon et al. (2005) Vaccine 23(38):4678-84).

A current influenza H5N1 vaccine strain, NIBRG-14, was provided by the National Institute of Biological and Serum Control, the United of Kingdom (UK NIBSC), which is a reassortant virus containing HA and NA gene segments of A/Vietnam/1194/2004 (H5N1) virus and the other six internal gene segments of A/PuertoRico/8/1934 (H1N1) virus. It was found that this vaccine strain could grow efficiently in chicken embryonated eggs and MDCK cells but not in Vero cells (Govorkova et al. (1999) Dev. Biol. Stand. 98:39-51). However, in the case of a pandemic influenza, chicken eggs would be insufficient and suboptimal for influenza vaccine production, and there are concerns over the tumorogenic potential of MDCK cells.

Therefore, there is a need for an influenza virus strain that is able to grow efficiently in Vero cells and suitable for increased production of an influenza vaccine from a mammalian host cell. The present invention satisfies this need.

BRIEF SUMMARY OF THE INVENTION

In one aspect, embodiments of the present invention relate to an isolated influenza A virus strain that is able to grow efficiently in a mammalian host cell and is suitable for increased production of an influenza vaccine from the mammalian host cell. The isolated influenza A virus strain comprises at least one gene that encodes at least one modified influenza protein, as described herein below, wherein expression of the at least one modified influenza protein results in an increased production of the influenza virus from a mammalian host cell.

In another aspect, embodiments of the present invention relate to an influenza vaccine. The vaccine comprises an influenza A virus strain according to an embodiment of the invention and a pharmaceutically acceptable carrier. Embodiments of the present invention also relate to a method of preparing the influenza vaccine.

Isolated nucleic acid molecules that encode a modified influenza protein and the isolated modified influenza proteins are also provided. Other aspects, features and advantages of the invention will be apparent from the following disclosure, including the detailed description of the invention and the appended claims.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The foregoing summary, as well as the following detailed description of preferred

embodiments of the invention, will be better understood when read in conjunction with the appended drawings. For purposes of illustrating the invention, there are shown in the drawings embodiments which are presently preferred. It should be understood, however, that the invention is not limited to the precise embodiments shown.

FIG. 1 shows an image of the plaque morphology of the strain NIBRG-14 (FIG. 1A) and the influenza virus strains Vero-15 (FIG. 1B) and Vero-16 (FIG. 1C) after 6 days (for the strain NIBRG-14) and 3 days (for the strains Vero-15 and Vero-16) post-infection in Vero cells.

FIG. 2 shows the growth curve in terms of HA titer (50 μl) (FIG. 2A) or infectious virus titer (PFU/ml) (FIG. 2B) of the strain NIBRG-14 in Vero cells as a function of days post-infection (DPI);

FIG. 3 shows the growth curve in teems of HA titer (50 μl) (FIG. 3A) or infectious virus titer (TCID50/ml) (FIG. 3B) of the strain Vero-15 in Vero cells as a function of days post-infection (DPI);

FIG. 4 shows the growth curve in terms of HA titer (50 μl) (FIG. 4A) or infectious virus titer (TCID50/ml) (FIG. 4B) of the strain Vero-16 in Vero cells as a function of days post-infection (DPI);

FIG. 5 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus PB 1 protein (FIG. 5B) and their corresponding nucleotide (NT) sequences (FIG. 5A) among the strains Vero-15, Vero-16 and NIBRG-14;

FIG. 6 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus PB2 protein (FIG. 6B) and their corresponding nucleotide (NT) sequences (FIG. 6A) among the strains Vero-15, Vero-16 and NIBRG-14;

FIG. 7 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus NP protein (FIG. 7B) and their corresponding nucleotide (NT) sequences (FIG. 7A) among the strains Vero-15, Vero-16 and NIBRG-14;

FIG. 8 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus M protein (FIG. 8B) and their corresponding nucleotide (NT) sequences (FIG. 8A) among the strains Vero-15, Vero-16 and NIBRG-14;

FIG. 9 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus PA protein (FIG. 9B) and their corresponding nucleotide (NT) sequences (FIG. 9A) among the strains Vero-15, Vero-16 and NIBRG-14; and

FIG. 10 illustrates the sequence alignment analysis of the amino acid (AA) sequences of the influenza virus NS protein (FIG. 10B) and their corresponding nucleotide (NT) sequences (FIG. 10A) among the strains Vero-15, Vero-16 and NIBRG-14.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to high-growth influenza virus strains, which are suitable

for replicating in mammalian host cells. In accordance with embodiments of the present invention, a H5N1 vaccine virus strain, such as the strain NIBRG-14, was subjected to serial passages in mammalian primary cells, such as Vero cells, and the high-growth strains were selected, isolated, and characterized.

Unless defined otherwise, all technical and scientific terms used herein have the same

meaning as commonly understood to one of ordinary skill in the art to which this invention pertains. In this application, certain terms are used frequently, which shall have the meanings as set forth in the specification. It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.

As used herein, a “reassortant” virus refers to a virus which contains gene segments

originated from two or more different virus strains. The reassortant virus will share properties of its parental lineages. For example, a reassortant virus can have gene segments encoding antigenic proteins from a virus strain of interest (e.g., HA and NA genes) and have gene segments encoding other viral proteins, such as the polymerase complex (e.g., PB2, PB1 and PA genes) and other viral proteins (e.g., non-glycoprotein genes, including M genes, NS genes, and NP genes) from viruses adapted for growth in culture (or attenuated viruses). The reassortant virus thus carries the desired antigenic characteristics in a background or master strain that permits efficient production in a host cell. Such a reassortant virus is a desirable “virus seed” for production of virions for vaccine production. In one embodiment of the present invention, the reassortant virus includes strain NIBRG-14 and any modified strain of NIBRG-14, such as the Vero-15 or Vero-16 strains, described herein below.

As used herein, the term “modified strain” means a strain of a first virus strain obtained by serial passages and/or selection of the first virus and its progenies in a mammalian host cell. In one embodiment of the present invention, the modified strain has increased virus production from the mammalian host cell compared to that of the first virus strain.

As used herein, the term “influenza protein” refers to any polypeptide or protein encoded

by an influenza gene.

As used herein, a “gene” is a segment of nucleic acid molecule involved in producing a

peptide, polypeptide, or protein, and the mRNA encoding such protein species, including the coding region, non-coding regions preceding (“5′UTR”) and following (“3′UTR”) the coding region. A “gene” may also include intervening non-coding sequences (“introns”) between individual coding segments (“exons”). A gene may further include a regulatory sequence, which controls the expression of the gene. A “regulatory sequence” can include promoters, enhancers and other expression control elements such as polyadenylation signals, ribosome binding site (for bacterial expression), and/or, an operator. A “promoter” means a regulatory sequence that is involved in the binding of RNA polymerase to initiate transcription of a gene. Promoters are often upstream (“5′ to”) the transcription initiation site of the gene. An “enhancer” means a regulatory sequence that can regulate the expression of a gene in a distance- and orientation-dependent fashion. A “coding region” refers to the portion of a gene that encodes amino acids and the start and stop signals for the translation of the corresponding polypeptide via triplet-base codons.

As used herein, an “influenza gene” can be any gene originally isolated and/or identified from an influenza virus. The influenza gene can be a gene originally isolated and/or identified from any influenza virus. In particular embodiments of the present invention, the influenza gene is originally isolated and/or identified from an influenza A virus.

As used herein, the term “modified influenza protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza protein. The modification includes, for example, an insertion, substitution, or deletion of one or more amino acid residues of an unmodified or reference influenza protein. Therefore, the modified influenza protein can have at least one modified amino acid residue and/or codon occupying an identified location of an unmodified or reference protein.

For the purpose of simplicity and clarity, a modification in a modified influenza protein

is identified by its corresponding position in an influenza protein from a particular reference influenza virus strain, i.e., influenza NIBRG-14. However, such identification is not meant to limit the modified influenza protein to a modified influenza NIBRG-14 protein only. The modified influenza protein can be a modified influenza protein from any influenza virus that contains the modification at a position corresponding to that in the influenza NIBRG-14 protein. One of skill in the art can identify such corresponding positions in other influenza viruses utilizing standard techniques.

As used herein, the term “an amino acid substitution” refers to the presence of the amino acid at an identified location in the amino acid sequence of a modified protein. The amino acid substitution occurs relative to any other amino acid that could have occupied that location of an unmodified or reference protein. The modified protein comprising the amino acid substitution can also include other modifications.

As used herein, a “modified influenza PB1 protein comprising a leucine residue at the position corresponding to position 195 of SEQ ID NO:1” refers to a modified influenza PB1 protein that has a leucine residue at the position corresponding to position 195 of SEQ ID NO:1. The modified influenza PB1 protein is not limited to a modified PB1 protein from influenza NIBRG-14 that has the substitution of lysine to leucine at position 195 of SEQ ID NO:1. The leucine residue occurs relative to any other amino acid residues that could have occupied that location of an unmodified or reference PB1 protein. The modified influenza PB1 protein can be a modified PB1 protein from influenza A viruses other than NIBRG-14 so long as the modified PB1 protein has a leucine residue at the position corresponding to position 195 of SEQ ID NO:1. The modified influenza PB1 protein can also include modifications in addition to the specified leucine residue. As used herein, “position 195 of SEQ ID NO:1” refers to the 195^thamino acid residue of SEQ ID NO:1 counting from the N-terminal end of SEQ ID NO:1. In view of the present disclosure, the position in PB1 proteins from other influenza viruses A corresponding to position 195 of SEQ ID NO:1 can be readily identified by the skilled artisan using methods known in the art, such as sequence alignment analysis. Similar interpretations apply to other modified influenza proteins, such as PB2, NP, M, PA and NS, that are herein described in a similar manner.

As used herein, the term “modified influenza PB1 protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza PB1 protein. An influenza PB1 protein, encoded by an influenza PB1 gene, is a subunit of an influenza RNA-dependent RNA polymerase. The influenza PB1 gene is located on segment 2 of the segmented negative strand influenza A genome. Examples of influenza PB1 genes include, but are not limited to, the PB1 gene of influenza A virus, e.g., having the nucleotide sequence of SEQ ID NO:2 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—0049111.1 isolated from influenza A/Hong Kong/1073/99(H9N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007372.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007375.1 isolated from influenza A/Korea/426/68(H2N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—002021.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having the nucleotide sequence set forth in GenBank Accession No. NC_—007358.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “modified influenza PB2 protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza PB2 protein. An influenza PB2 protein, encoded by an influenza PB2 gene, is also a subunit of an influenza RNA-dependent RNA polymerase. The influenza PB2 gene is located on segment 1 of the segmented negative strand influenza A genome. Examples of influenza PB2 genes include, but are not limited to, the PB2 gene of influenza A virus, e.g., having the nucleotide sequence set forth in SEQ ID NO:4 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—004910.1 isolated from influenza A/Hong Kong/1073/99(H9N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007373.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007378.1 isolated from influenza A/Korea/426/68(H2N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—002023.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having the nucleotide sequence set forth in GenBank Accession No. NC_—007357.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “modified influenza NP protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza NP protein. An influenza NP protein, encoded by an influenza NP gene, is an influenza nucleoprotein. The influenza NP gene is located on segment 5 of the segmented negative strand influenza A genome. Examples of influenza NP genes include, but are not limited to, the NP gene of influenza A virus, e.g., having the nucleotide sequence set forth in SEQ ID NO:6 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—004905.2 isolated from influenza A/Hong Kong/1073/99(H9N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007369.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank GeneID: 3655111 isolated from influenza A/Korea/426/68(H2N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—002019.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having the nucleotide sequence set forth in GenBank Accession No. NC_—007360.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “modified influenza M protein” refers to a protein that includes

one or more modifications to the amino acid sequence of an unmodified or reference influenza M protein. An influenza M protein is the larger protein of the two influenza matrix proteins encoded by an influenza M gene. The influenza M gene is located on segment 7 of the segmented negative strand influenza A genome. Examples of influenza M genes include, but are not limited to, the M gene of influenza A virus, e.g., having the nucleotide sequence set forth in SEQ ID NO:8 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—004907.1 isolated from influenza A/Hong Kong/1073/99(H9N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007367.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007377.1 isolated from influenza A/Korea/426/68(H2N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—002016.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having the nucleotide sequence set forth in GenBank Accession No. NC_—007363.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “modified influenza PA protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza PA protein. An influenza PA protein, encoded by an influenza PA gene, is an influenza polymerase PA. The influenza PA gene is located on segment 3 of the segmented negative strand influenza A genome. Examples of influenza PA genes include, but are not limited to, the PA gene of influenza A virus, e.g., having the nucleotide sequence set forth in SEQ ID NO:10 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—004912.1 isolated from influenza A/Hong Kong/1073/99(H9N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007371.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—007376.1 isolated from influenza A/Korea/426/68(H2N2), having the nucleotide sequence set forth in GenBank Accession No. NC_—002022.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having GenBank Accession No. NC_—007359.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “modified influenza NS protein” refers to a protein that includes one or more modifications to the amino acid sequence of an unmodified or reference influenza NS protein. An influenza NS protein, encoded by an influenza NS gene, is an influenza non-structural protein. The influenza NS gene is located on segment 8 of the segmented negative strand influenza A genome. Examples of influenza NS genes include, but are not limited to, the NS gene of influenza A virus, e.g., having the nucleotide sequence set forth in SEQ ID NO:12 isolated from NIBRG-14 virus; having the nucleotide sequence set forth in GenBank Accession No. NC_—004906.1 isolated from influenza A/Hong Kong/1073/99(H9N2), having the nucleotide sequence set forth in GenBank Accession No. NC_—007370.1 isolated from influenza A/New York/392/2004(H3N2); having the nucleotide sequence set forth in GenBank Gene ID 3655110 isolated from influenza A/Korea/426/68(H2N2); having the nucleotide sequence set forth in GenBank Accession No. NC_—002020.1 isolated from influenza A/Puerto Rico/8/34(H1N1); or having the nucleotide sequence set forth in GenBank Accession No. NC_—007364.1 isolated from influenza A/Goose/Guangdong/1/96(H5N1).

As used herein, the term “nucleotide sequence” refers to the arrangement of either

deoxyribonucleotide or ribonucleotide residues in a polymer in either single- or double-stranded form. Nucleic acid sequences can be composed of natural nucleotides of the following bases: thymidine, adenine, cytosine, guanine, and uracil; abbreviated T, A, C, G, and U, respectively, and/or synthetic analogs of the natural nucleotides.

As used herein, an “isolated” nucleic acid molecule is one that is substantially separated from at least one of the other nucleic acid molecules present in the natural source of the nucleic acid, or is substantially free of at least one of the chemical precursors or other chemicals when the nucleic acid molecule is chemically synthesized. An “isolated” nucleic acid molecule can also be, for example, a nucleic acid molecule that is substantially free of at least one of the nucleotide sequences that naturally flank the nucleic acid molecule at its 5′ and 3′ ends in the genomic DNA of the organism from which the nucleic acid is derived. A nucleic acid molecule is “substantially separated from” or “substantially free of” other nucleic acid molecule(s) or other chemical(s) in preparations of the nucleic acid molecule when there is less than about 30%, 20%, 10%, or 5% or less, and preferably less than 1%, (by dry weight) of the other nucleic acid molecule(s) or the other chemical(s) (also referred to herein as a “contaminating nucleic acid molecule” or a “contaminating chemical”).

Isolated nucleic acid molecules include, without limitation, separate nucleic acid molecules (e.g., cDNA or genomic DNA fragments produced by PCR or restriction endonuclease treatment) independent of other sequences, as well as nucleic acid molecules that are incorporated into a vector, an autonomously replicating plasmid, a virus (e.g., a retrovirus, adenovirus, or herpes virus), or into the genomic DNA of a prokaryote or eukaryote. In addition, an isolated nucleic acid molecule can include a nucleic acid molecule that is part of a hybrid or fusion nucleic acid molecule. An isolated nucleic acid molecule can be a nucleic acid sequence that is: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) synthesized by, for example, chemical synthesis; (iii) recombinantly produced by cloning; or (iv) purified, as by cleavage and electrophoretic or chromatographic separation.

As used herein, the terms “polypeptide” and “protein” are used herein interchangeably to refer to amino acid chains in which the amino acid residues are linked by peptide bonds or modified peptide bonds. The amino acid chains can be of any length of greater than two amino acids. Unless otherwise specified, the terms “polypeptide” and “protein” also encompass various modified forms thereof. Such modified forms may be naturally occurring modified forms or chemically modified forms. Examples of modified forms include, but are not limited to, glycosylated forms, phosphorylated forms, myristoylated forms, palmitoylated forms, ribosylated forms, acetylated forms, ubiquitinated forms, etc. Modifications also include intra-molecular crosslinking, and covalent attachment to various moieties such as lipids, flavin, biotin, polyethylene glycol or derivatives thereof, etc. In addition, modifications may also include cyclization, branching and cross-linking. Further, amino acids other than the conventional twenty amino acids encoded by the codons of genes may also be included in a polypeptide.

An “isolated protein” or “isolated polypeptide” is one that is substantially separated from at least one of the other proteins present in the natural source of the protein, or is substantially free of at least one of the chemical precursors or other chemicals when the protein is chemically synthesized. A protein is “substantially separated from” or “substantially free of” other protein(s) or other chemical(s) in preparations of the protein when there is less than about 30%, 20%, 10%, or 5% or less, and preferably less than 1%, (by dry weight) of the other protein(s) or the other chemical(s) (also referred to herein as a “contaminating protein” or a “contaminating chemical”).

Isolated proteins can have several different physical forms. The isolated protein can exist as a full-length nascent or unprocessed polypeptide, or as a partially processed polypeptide or as a combination of processed polypeptides. The full-length nascent polypeptide can be postranslationally modified by specific proteolytic cleavage events that result in the formation of

fragments of the full-length nascent polypeptide. A fragment, or physical association of fragments can have the biological activity associated with the full-length polypeptide; however, the degree of biological activity associated with individual fragments can vary.

An isolated polypeptide or isolated protein can be a non-naturally occurring polypeptide. For example, an isolated polypeptide can be a “hybrid polypeptide.” An isolated polypeptide can also be a polypeptide derived from a naturally occurring polypeptide by additions or deletions or substitutions of amino acids. An isolated polypeptide can also be a “purified polypeptide” which is used herein to mean a specified polypeptide in a substantially homogeneous preparation substantially free of other cellular components, other polypeptides, viral materials, or culture medium, or when the polypeptide is chemically synthesized, chemical precursors or by-products associated with the chemical synthesis. A “purified polypeptide” can be obtained from natural or recombinant host cells by standard purification techniques, or by chemical synthesis, as will be apparent to skilled artisans.

An “isolated influenza virus strain” or “isolated influenza virus” is one virus that is substantially separated from at least one of the other viruses present in the natural environment of the virus, or is substantially free of a parental virus strain when the virus is derived, modified, or otherwise originated from the parental virus strain. A virus is “substantially separated from” or “substantially free of” other virus(es) when there is less than about 30%, 20%, 10%, or 5% or less, and preferably less than 1%, (by dry weight) of the other virus(es) (also referred to herein as a “contaminating virus”).

In one aspect, the present invention thus relates to an isolated influenza virus strain that produces high titer virus in mammalian cells. Embodiments of the present invention relate to an isolated influenza virus strain that comprises at least one gene that encodes at least one modified influenza protein, and the expression of the at least one modified protein results in an increased production of the influenza virus from a mammalian host cell. In accordance with examples of the invention, the host cells may be selected from the group consisting of mammalian cells suitable for preparing vaccine for use in humans. As a specific example of the invention, the mammalian cells may be Vero cells approved and certified according to the World Health Organization (WHO) requirements for vaccine production. The at least one modified influenza protein includes, but is not limited to, a protein selected from group consisting of:

(a) a modified influenza PB1 protein comprising a leucine residue at the position corresponding to position 195 of SEQ ID NO:1;

(b) a modified influenza PB2 protein comprising a tyrosine residue at the position corresponding to position 359 of SEQ ID NO:3;

(c) a modified influenza NP protein comprising an aspartic acid residue and two phenylalanine residues at the positions corresponding to positions 255, 410 and 446 of SEQ ID NO:5, respectively;

(d) a modified influenza M protein comprising a phenylalanine residue at the position corresponding to position 236 of SEQ ID NO:7;

(e) a modified influenza PA protein comprising a histidine residue or a glycine residue at the position corresponding to position 465 or 494 of SEQ ID NO:9, respectively;

(f) a modified influenza NS protein comprising

- (i) two proline residues at the positions corresponding to positions 90 and 110 of SEQ ID NO:11; or
- (ii) a stop codon at the position corresponding to position 122 of SEQ ID NO:11.

One particular example of an embodiment of the invention relates to an influenza virus strain Vero-15. The isolated and modified influenza virus strain Vero-15 comprises a PB1 gene encoding a protein comprising an amino acid sequence of SEQ ID NO:1 with a leucine substitution at position 195 of SEQ ID NO:1, a PB2 gene encoding a protein comprising an amino acid sequence of SEQ ID NO:3 with a tyrosine substitution at position 359 of SEQ ID NO:3, a PA gene encoding a protein having an amino acid sequence of SEQ ID NO:9 with a glycine substitution at position 494 of SEQ ID NO:9, and an NS gene encoding a protein having an amino acid sequence of SEQ ID NO:11 with two proline substitutions at positions 90 and 110 of SEQ ID NO:11, respectively. The influenza virus strain Vero-15 further comprises an HA gene encoding a protein comprising the amino acid sequence of SEQ ID NO:13, an NA gene encoding a protein comprising the amino acid sequence of SEQ ID NO:15, an NP gene encoding a protein comprising the amino acid sequence of SEQ ID NO:5, and an M gene encoding a protein comprising the amino acid sequence of SEQ ID NO:7.

In terms of nucleotides, the influenza virus strain Vero-15 comprises a PB1 gene comprising a nucleotide sequence of SEQ ID NO:2 with three thymine substitutions at positions 583, 584 and 1257 and an adenine substitution at position 1737 of SEQ ID NO:2; a PB2 gene comprising a nucleotide sequence of SEQ ID NO:4 with an adenine substitution at position 1077 of SEQ ID NO:4; a PA gene comprising a nucleotide sequence of SEQ ID NO:10 with a guanine substitution at position 1482 of SEQ ID NO:10; and an NS gene comprising a nucleotide sequence of SEQ ID NO:12 with three cytosine substitutions at positions 271, 331 and 335 of SEQ ID NO:12, respectively. The influenza virus strain Vero-15 further comprises a HA gene comprising the nucleotide sequence of SEQ ID NO:14, and an NA gene comprising the nucleotide sequence of SEQ ID NO:16. The influenza virus strain Vero-15 also further comprises an NP gene comprising a nucleotide sequence of SEQ ID NO:6 and an M gene comprising a nucleotide sequence of SEQ ID NO:8.

By comparing the nucleotide sequence of the strain Vero-15 with that of the strain NIBRG-14, there are 1 to 4 nucleotide differences in the 4 segments PB2, PB1, PA and NS, even though the nucleotide sequences in the HA, NA, NP and M segments are not different from those of the strain NIBRG-14. The detailed comparisons are shown in Table 1 and FIGS. 5 through 10.

In another example of and embodiment of the invention, a modified influenza virus strain Vero-16 is provided. The influenza virus strain Vero-16 comprises a PB1 gene encoding a protein comprising an amino acid sequence of SEQ ID NO:1 with a leucine substitution at position 195 of SEQ ID NO:1; a PB2 gene encoding a protein comprising an amino acid sequence of SEQ ID NO:3 with a tyrosine substitution at position 359 of SEQ ID NO:3; an NP gene encoding a protein comprising an amino acid sequence of SEQ ID NO:5 with an aspartic acid substitution and two phenylalanine substitutions at positions 255, 410 and 446 of SEQ ID NO:5, respectively; an M gene encoding a protein comprising an amino acid sequence of SEQ ID NO:7 with a phenylalanine substitution at position 236 of SEQ ID NO:7; a PA gene encoding a protein comprising an amino acid sequence of SEQ ID NO:9 with a histidine substitution at position 465 of SEQ ID NO:9; and an NS gene encoding a protein comprising an amino acid sequence of SEQ ID NO:11 with a stop codon substitution at position 122 of SEQ ID NO:11. The influenza virus strain further comprises a HA gene encoding a protein comprising the amino acid sequence of SEQ ID NO:13 and an NA gene encoding a protein comprising the amino acid sequence of SEQ ID NO:15.

In terms of nucleotides, the influenza virus strain Vero-16 comprises a PB1 gene comprising a nucleotide sequence of SEQ ID NO:2 with three thymine substitutions at positions 583, 584, and 1257 and an adenine substitution at position 1737 of SEQ ID NO:2, respectively; a PB2 gene comprising a nucleotide sequence of SEQ ID NO:4 with an adenine substitution at position 1077 of SEQ ID NO:4; an NP gene comprising a nucleotide sequence of SEQ ID NO:6 with four thymine substitutions at positions 921, 1229, 1337 and 1413 of SEQ ID NO:6, respectively; an M gene comprising a nucleotide sequence of SEQ ID NO:8 with two thymine substitutions at positions 694 and 706 of SEQ ID NO:8, respectively; a PA gene comprising a nucleotide sequence of SEQ ID NO:10 with three cytosine substitutions at positions 895, 1054, and 1394 of SEQ ID NO:10, respectively; and an NS gene comprising a nucleotide sequence of SEQ ID NO:12 with a nucleotide deletion at position 365 of SEQ ID NO:12. The influenza virus strain Vero-16 further comprises an HA gene comprising the nucleotide sequence of SEQ ID NO:14 and an NA gene comprising the nucleotide sequence of SEQ ID NO:16.

By comparing the nucleotide sequence of the strain Vero-16 with that of the strain NIBRG-14, there are 1 to 5 nucleotide differences in the 6 segments PB2, PB1, PA, NS, NP and M, even though the nucleotide sequences in the HA and NA segments are not different from those of the strain NIBRG-14. The detailed comparisons are shown in Table 1 and FIGS. 5 through 10.

Accordingly, the present invention also provides an improved method of producing an influenza vaccine (e.g., an H5N1 vaccine). The improvement comprises using a modified seed virus for producing the vaccine. The modified seed virus comprises at least one modification selected from the group consisting of a modified PB1 gene encoding a protein having a leucine residue at the position corresponding to position 195 of SEQ ID NO:1; a modified PB2 gene encoding a protein having a tyrosine residue at the position corresponding to position 359 of SEQ ID NO:3; a modified NP gene encoding a protein having an aspartic acid residue and two phenylalanine residues at positions corresponding to positions 255, 410, and 446 of SEQ ID NO:5, respectively; a modified M gene encoding a protein having a phenylalanine residue at the position corresponding to position 236 of SEQ ID NO:7; a modified PA gene encoding a protein having a histidine residue or a glycine residue at the position corresponding to position 465 or 494 of SEQ ID NO:9, respectively; and a modified NS gene encoding a protein having two proline residues at the positions corresponding to positions 90 and 110 or a stop codon at the position corresponding to position 122 of SEQ ID NO:11, respectively.

In terms of nucleotides, the modified seed influenza virus strain used for producing an influenza vaccine (e.g., an H5N1 vaccine) comprises at least one modification selected from the group consisting of a modified PB1 gene having three thymine residues at positions 583, 584, and 1257 and an adenine residue at position 1737 of SEQ ID NO:2, respectively; a modified PB2 gene having an adenine residue at position 1077 of SEQ ID NO:4; a modified NP gene having a guanine residue at position 763 and four thymine residues at positions 921, 1229, 1337 and 1413 of SEQ ID NO:6, respectively; a modified M gene having two thymine residues at positions 694 and 706 of SEQ ID NO:8, respectively; a modified PA gene having a guanine residue at position 1482 or three cytosine residues at positions 895, 1054, and 1394 of SEQ ID NO:10, respectively; and a modified NS gene having three cytosine residues at positions 271, 331 and 335 or a nucleotide deletion at position 365 of SEQ ID NO:12, respectively.

Another aspect of the present invention relates to an influenza vaccine comprising at least one of the modified influenza virus strains according to embodiments of the invention, or any combination thereof. In accordance with the invention, the influenza virus strains can be attenuated or inactivated, formulated and administered, according to known methods, as a vaccine to induce an immune response in a mammal in view of the present disclosure. Any standard methods which are well known in the art may be used for determining the antigenicity. The vaccine compositions may include a pharmaceutically acceptable carrier. The phrase “pharmaceutically acceptable carrier” refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human. The term “carrier” refers to a diluent, adjuvant, saline solution, and an aqueous dextrose and glycerol solution are employed as a carrier, particularly for an injectable solution. The term “adjuvant” refers to a compound or mixture that enhances the immune response to an antigen.

The vaccine of the present invention may be administered topically, parenterally, transmucosally, e.g., orally, nasally, or rectally, or transdermally. Administration that is parenteral, e.g., via intravenous injection, also includes, but is not limited to, intra-arteriolar, intramuscular, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial.

Aspects of the present invention also relate to isolated nucleic acid molecules encoding modified influenza proteins and methods related to their production, isolation, and use. Such an isolated nucleic acid molecule can be used, for example, for the construction of influenza viruses that grow more efficiently in a host cell. It is discovered in the present invention that an influenza virus grows more efficiently in a host cell when the virus contains one or more of the modified influenza proteins described herein. Therefore, to obtain a fast growing influenza virus, nucleic acid molecules encoding the modified influenza proteins can be combined with virus genes of interest via reassortment or other types of genetic manipulation. Such genetic methods would be known to a person skilled in the art in view of the present invention. The isolated nucleic acid molecule can also be used for the recombinant production of a modified influenza protein encoded by the nucleic acid molecule.

The present invention further relates to isolated modified influenza proteins and methods related to their production, isolation and use. Such isolated proteins can be used, for example, for the production of antibodies to the modified proteins.

The invention will now be described in further detail with reference to the following specific, non-limiting examples:

EXPERIMENTAL EXAMPLES
Example 1
Modification of NIBRG-14 in Vero Cells

The influenza vaccine strain NIBRG-14 was provided by the National Institute from Biological Standards and Control (NIBSC), the United Kingdom (UK), and propagated in embryonated chickens' eggs. The WHO vaccine-approved Vero cells were obtained from the Taiwan Center for Disease Control, and were grown in M199 medium (Gibco BRL, USA) containing 5% fetal bovine serum (FBS) within passages 135 to 150. After 3 serial passages of the Vero cells in T75 flasks supplemented with 2 μg/ml of L-(tosylamido-2-phenyl)ethyl chloromethyl ketone (TPCK) trypsin (Sigma, St. Louis, Mo.), the cell culture supernatant was first inoculated into 96-well plates, followed by 2 rounds of plaque purification in 6-well plates. For each of the clones, virus accumulation was estimated by visual determination of the cytopathic effect and HA titration. The HA titrations were conducted in 96-well microplates using turkey red blood cells (RBC) following the standard technique. The virus infectious titers were measured using the 50% tissue culture infectious doses (TCID50) assay based on cytopathic effect or plaque assay based on plaque forming unit (PFU) in Vero cells supplemented with 4 μg/ml of TPCK-trypsin (WHO manual on animal influenza diagnosis and surveillance, WHO (2002)).

In the measurement of virus growth curves in Vero cells, the Influenza H5N1 vaccine virus clones were grown in T75 flasks supplemented with 4 μg/ml of TPCK-trypsin and the supernatant was harvested at day 1 to 5 post-infection for measuring HA titer and infectious virus titer. Two Vero-adapted influenza H5N1 vaccine virus strains with a high growth were selected and named as Vero-15 and Vero-16, respectively. In the measurement of the virus growth curves in Vero cells of the strain NIBRG-14, the multiplicities of infection (MOI) were 10⁻¹, 10⁻², and 10⁻³TCID50/cells. For the Vero-adapted strains Vero-15 and Vero-16, the MOI's were 10⁻³and 10⁻⁴.

As shown in FIGS. 1 and 2, the NIBRG-14 strain formed small and ambiguous plaques after 6 days post-infection in Vero cells, and the peak virus titer thereof was about 10⁶PFU/ml. After serial passages and plaque purifications in Vero cells, the two high-growth virus clones (Vero-15 and Vero-16) were selected from big plaques. Referring to FIGS. 1, 3 and 4, these two Vero-modified virus strains Vero-15 and Vero-16 formed clear and big plaques after 3 days post-infection in Vero cells, and the peak virus titers were about 10⁸TCID50/ml. These two Vero-modified virus strains were further used to produce virus stock in T75 or T150 flasks. The virus stocks of these two Vero-modified virus strains had similar virus titers (1.4×10⁸PFU/ml and 1.86×10⁸TCID50/ml for the Vero-15 and 1×10⁸PFU/ml and 2.9×10⁸TCID50/ml for the Vero-16).

Determination of Virus Nucleotide Sequences and Comparison

For each of the virus strains, the virus RNA was extracted by using a commercial kit (Geneaid, Taoyuan, Taiwan). The extracted virus RNA was amplified using the one-step RT-PCR (Promega, Madison, Wis.) for HA and NA or two-step RT-PCR (Invitrogen, Rockville, Md.) for the other six gene segments. The sequences of the oligonucleotide primers used in this study were readily available based on the gene sequences of NIBRG-14. The amplified DNA was sequenced using the ABI 3730 XL DNA Analyzer (Applied Biosystems Inc., Foster City, Calif.).

A comparison of the Vero-adapted strains Vero-15 and Vero-16 with the strain NIBRG 14 was given in Table 1. Regarding the strain Vero-15, as compared with the strain NIBRG-14, there were 1 to 4 nucleotide differences in the 4 segments PB2, PB1, NS and PA, as shown in Table 1, even though the nucleotide sequences in the HA, NA, NP and M segments were not different from those of the strain NIBRG-14. Regarding the strain Vero-16, there were 1 to 5 nucleotide differences in the 6 segments PB2, PB1, PA, NS, NP and M, as shown in Table 1, even though the nucleotide sequences in HA and NA segments were not different from those of the strain NIBRG-14.

TABLE 1

HA
NA
PB2
PB1
NP
M
PA
NS

Vero-16-NT
0
0
1
4
5
2
3
−1*

Vero-16-AA
0
0
1
1
3
1
1
*

Vero-15-NT
0
0
1
4
0
0
1
3

Vero-15-AA
0
0
1
1
0
0
1
2

*Vero-16 has a nucleotide deletion which introduces a stop codon at position 122 of SEQ ID NO: 11.

NT = Nucleotide

AA = Amino acid

The sequence analyses of the amino acids (AA) and nucleotides (NT) of the segments of the three Influenza virus strains are shown in FIGS. 5 through 10.

Antigenicity Tests

To measure the antigenicity relatedness between NIBRG-14 and the Vero-modified viruses, polyclonal sheep anti-NIBRG-14 standard antisera (NIBSC) was used to measure antibody titers against NIBRG-14 and the Vero-modified virus strains using the standard hemagglutinination inhibition (HI) assay known in the art. See, for example, the WHO manual on animal influenza diagnosis and surveillance, WHO (2002)).

The antigenicity in terms of the HI titer against the strains NIBRG-14, Vero-15 and Vero-16 was determined. The results are shown in Table 2, which indicated that these three viruses had similar antigenicity. Both strains Vero-15 and Vero-16 were suitable for vaccine production.

TABLE 2

Influenza Virus Strain
HI titer

Vero-15
400

Vero-16
400

NIBRG-14 (egg)
800

It will be appreciated by those skilled in the art that changes could be made to the embodiments described above without departing from the broad inventive concept thereof. It is understood, therefore, that this invention is not limited to the particular embodiments disclosed, but it is intended to cover modifications within the spirit and scope of the present invention as defined by the appended claims.

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.

Vero cell-based influenza virus strains and vaccines

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