Mutations that confer genetic stability to additional genes in influenza viruses
The disclosure provides for an isolated recombinant influenza virus having at least one of: a PA gene segment encoding PA with a residue at position 443 that is not arginine, a PB1 gene segment encoding PB1 with a residue at position 737 that is not lysine, a PB2 gene segment encoding PB2 with a residue at position 25 that is not valine or a residue at position 712 that is not glutamic acid, a NS gene segment encoding a NS1 with a residue at position 167 that is not proline, a HA gene segment encoding a HA with a residue at position 380 that is not threonine, or any combination thereof, and methods of making and using the virus.
1. An isolated recombinant influenza A virus having PA, PB1, PB2, NP, NS, M, NA, and HA viral segments, wherein at least one of the viral segments is a PA viral segment encoding PA with a residue at position 443 that is not arginine, a PB1 viral segment encoding PB1 with a residue at position 737 that is not lysine, a PB2 viral segment encoding PB2 with a residue at position 25 that is not valine or a residue at position 712 that is not glutamic acid, a NS viral segment encoding a NS1 with a residue at position 167 that is not proline, or any combination thereof, wherein the recombinant influenza A virus has enhanced replication relative to a corresponding recombinant influenza A virus with a residue at position 443 in PA that is arginine, a residue at position 737 in PB1 that is lysine, a residue at position 25 in PB2 that is valine, a residue at position 712 in PB2 that is glutamic acid, a residue at position 167 in NS1 that is proline, wherein the position 443 in the PA corresponds to position 443 in a PA encoded by SEQ ID NO:1, wherein the position 737 in the PB1 corresponds to position 737 in a PB1 encoded by SEQ ID NO:2, wherein the position 25 or 712 in the PB2 corresponds to position 25 or 712 in a PB2 encoded by SEQ ID NO:3, or wherein the position 167 in the NS1 corresponds to position 167 in a NS1 encoded by SEQ ID NO:6.
2. The recombinant virus of claim 1 wherein the residue at position 443 of PA encoded by the PA viral segment is K or H, the residue at position 737 of PB1 encoded by the PB1 viral segment is H or R, the residue at position 25 of PB2 encoded by the PB2 viral segment is A, L, T, I, or G, the residue at position 712 of PB2 encoded by the PB2 viral segment is D, the residue at position 167 of NS1 encoded by the NS viral segment is S, C, M, A, L, I, G or T, or any combination of the PA viral segment, the PB1 viral segment, the PB2 viral segment or the NS viral segment.
3. The recombinant virus of claim 1 wherein at least one of the viral segments includes a heterologous gene sequence encoding a gene product.
4. The recombinant virus of claim 3 wherein the heterologous sequence is in the NS viral segment, M viral segment, NP viral segment, PA viral segment, PB I viral segment, or the PB2 viral segment.
5. The recombinant virus of claim 3 wherein the heterologous sequence is 5′ or 3′ to the PA coding sequence in the PA viral segment, or 5′ or 3′ to the PB1 coding sequence in the PB1 viral segment.
6. The recombinant virus of claim 3 wherein the heterologous sequence is 5′ or 3′ to the PB2 coding sequence in the PB2 viral segment.
7. The recombinant virus of claim 3 wherein the heterologous sequence is 5′ or 3′ to the NS1 coding sequence in the NS viral segment.
8. The recombinant virus of claim 1 which comprises a further viral segment comprising a heterologous gene sequence encoding a gene product.
9. The recombinant virus of claim 8 wherein the further viral segment is a NS viral segment, a M viral segment, a NP viral segment, a PA viral segment, a PB1 viral segment or a PB2 viral segment.
10. A vaccine having the isolated recombinant virus of claim 1 .
11. The recombinant virus of claim 1 wherein the residue at position 443 of PA is K or H.
12. The recombinant virus of claim 1 wherein the residue at position 737 of PB1 is H or R.
13. The recombinant virus of claim 1 wherein the residue at position 25 of PB2 is A, L, T, I, or G.
14. The recombinant virus of claim 1 wherein the residue at position 712 of PB2 is D.
15. The recombinant virus of claim 1 wherein the residue at position 167 of NS1 is S, C, M, A, L, I, G or T.
16. A method to prepare influenza A virus, comprising:
contacting a cell with:
a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus PA DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus PB1 DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus PB2 DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus HA DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus NP DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus NA DNA linked to a transcription termination sequence, a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus M DNA linked to a transcription termination sequence, and a vector for influenza A virus vRNA production comprising a promoter operably linked to an influenza A virus NS DNA linked to a transcription termination sequence, wherein the PB1, PB2, PA, NP, NS, and M DNAs in the vectors for vRNA production encode at least one of: PA with a residue at position 443 that is not arginine, PB I with a residue at position 737 that is not lysine, PB2 with a residue at position 25 that is not valine or a residue at position 712 that is not glutamic acid, or NS1 with a residue at position 167 that is not proline, wherein the position 443 in the PA corresponds to position 443 in a PA encoded by SEQ ID NO: 1, wherein the position 737 in the PB1 corresponds to position 737 in a PB1 encoded by SEQ ID NO:2, wherein the position 25 or 712 in the PB2 corresponds to position 25 or 712 in a PB2 encoded by SEQ ID NO:3, or wherein the position 167 in the NS1 corresponds to position 167 in a NS1 encoded by SEQ ID NO:6; and optionally
a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus PA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus PB1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus PB2, and a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus NP, and optionally a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus HA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza A virus NA, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M1, a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus M2, or a vector for mRNA production comprising a promoter operably linked to a DNA segment encoding influenza virus NS2;
in an amount effective to yield infectious influenza virus.
17. The method of claim 16 wherein the cell is an avian cell or a mammalian cell.
18. The method of claim 17 wherein the cell is a Vero cell, a human cell or a MDCK cell.
19. The method of claim 16 wherein the wherein the PB1, PB2, PA, NP, NS, and M DNAs in the vectors for vRNA productions have a sequence that corresponds to one that encodes a polypeptide having at least 95% amino acid sequence identity to a corresponding polypeptide encoded by SEQ ID NOs:1-6 or 10-15.
20. Virus obtained by the method of claim 16 .
21. The method of claim 16 wherein the residue at position 443 of PA encoded by the PA viral segment is K or H, the residue at position 737 of PB1 encoded by the PB1 viral segment is H or R, the residue at position 25 of PB2 encoded by the PB2 viral segment is A, L, T, I, or G, the residue at position 712 of PB2 encoded by the PB2 viral segment is D, the residue at position 167 of NS1 encoded by the NS viral segment is S, C, M, A, L, I, G or T, or any combination of the PA viral segment, the PB1 viral segment, the PB2 viral segment or the NS viral segment.