Influenza virus replication by inhibiting microRNA lec7C binding to influenza viral cRNA and mRNA
A vector, composition and method to improve influenza virus replication by inhibiting miRNA lec-7C binding to influenza virus mRNA and/or cRNA.
1. A recombinant vector comprising an influenza M viral segment having a nucleotide other than U/T at position 1011, a nucleotide other than G at position 1012, a nucleotide other than A at position 1013, a nucleotide other than U/T at position 1014, a nucleotide other than G at position 1015, a nucleotide other than G at position 1016, a nucleotide other than A at position 1017, or any combination thereof, wherein the numbering refers to cRNA + corresponding to a sequence having SEQ ID NO:16.
2. The vector of claim 1 wherein the viral segment has a nucleotide other than G at position 1012, a nucleotide other than A at position 1013, and a nucleotide other than U at position 1014.
3. The vector of claim 1 wherein the viral segment has at least two of a nucleotide other than G at position 1012, a nucleotide other than A at position 1013, or a nucleotide other than U at position 1014.
4. A method to prepare influenza virus, comprising: contacting a cell with at least one of:
a vector comprising a promoter operably linked to an influenza virus PA cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus PB1 cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus PB2 cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus HA cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus NP cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus NA cDNA linked to a transcription termination sequence, a vector comprising a promoter operably linked to an influenza virus M cDNA linked to a transcription termination sequence, and a vector comprising a promoter operably linked to an influenza virus NS cDNA linked to a transcription termination sequence, wherein the mutant M cDNA has a nucleotide other than U/T at position loll, a nucleotide other than G at position 1012, a nucleotide other than A at position 1013, a nucleotide other than U/T at position 1014, a nucleotide other than G at position 1015, a nucleotide other than 0 at position 1016, a nucleotide other than A at position 1017, or any combination thereof, wherein the numbering refers to cRNA + corresponding to a sequence having SEQ ID NO:16 and optionally wherein the cDNA for HA and/or NA has sequences for a heterologous HA or NA; and optionally,
a vector comprising a promoter operably linked to a DNA segment encoding influenza virus PA, a vector comprising a promoter operably linked to a DNA segment encoding influenza virus PB1, a vector comprising a promoter operably linked to a DNA segment encoding influenza virus PB2, and a vector comprising a promoter operably linked to a DNA segment encoding influenza virus NP, and optionally a vector comprising a promoter operably linked to a DNA segment encoding influenza virus HA, a vector comprising a promoter operably linked to a DNA segment encoding influenza virus NA, a vector comprising a promoter operably linked to a DNA segment encoding influenza virus M1, a vector comprising a promoter operably linked to a DNA segment encoding influenza virus M2, or a vector comprising a promoter operably linked to a DNA segment encoding influenza virus NS2.
5. The method of claim 4 further comprising isolating the virus.
6. Virus obtained by the method of claim 5 .
7. An isolated recombinant influenza virus comprising a viral segment for PB1, PB2, PA, and NP, a viral segment for M having a nucleotide other than U/T at position 1011, a nucleotide other than G at position 1012, a nucleotide other than A at position 1013, a nucleotide other than U/T at position 1014, a nucleotide other than G at position 1015, a nucleotide other than G at position 1016, a nucleotide other than A at position 1017, or any combination thereof, wherein the numbering refers to cRNA + corresponding to a sequence having SEQ ID NO:16, a viral segment for NS, a viral segment, for a heterologous NA, and a viral segment for a heterologous HA.
8. The isolated recombinant influenza virus of claim 7 wherein the viral segment for PB1, PB2, PA, NS, M, and NP encode viral proteins having at least 90% amino acid sequence identity to proteins encoded by SEQ ID Nos. 1-6.
9. The isolated recombinant influenza virus of claim 7 wherein the viral segment for HA is for H1, H3, H5 or H7.
10. The isolated recombinant influenza virus of claim 7 wherein the viral segment for PB2 encodes a PB2 with a serine at position 360 and has at least 90% amino acid sequence identity to a polypeptide encoded by II) NO:3 but which viral segment does not encode a PB2 with SEQ ID NO:3.
11. The isolated recombinant virus of claim 7 which has one or more but less than 25 substitutions in PB2 relative to PB2 encoded by SEQ ID NO:3.
12. The isolated recombinant virus of claim 11 wherein the one or more substitutions include conservative substitutions.
13. The isolated recombinant influenza virus of claim 7 further comprising one or more of the following: 142N, 225C, 356R, or 550L in PA relative to numbering of positions in a PA encoded by SEQ ID NO:1; 112G, 247H, 507V, or 644A in PB1 relative to numbering in positions in a PB1 encoded by SEQ ID NO:2; 202L, 323L or 504V in PB2 relative to numbering of positions in a PB2 encoded by SEQ ID NO:3; 74K, 112L, 116L, 417D, or 442A in NP relative to numbering of positions in a NP encoded by SEQ ID NO:4; 97A and/or 100H in M1 relative to numbering of positions in a M1 encoded by SEQ ID NO:5; and/or 55E and/or 140Q in NS1 relative to numbering of positions in a NS1 encoded by SEQ ID NO:6, or combinations thereof, and optionally at least one of 142N in PA1, 55K in NS1 or 97A and/or 100H in M1; or further comprising one or more of the following: 40I, 40L, 112G, 180W, 247H, 507V, or 644A in PB1; 202L and/or 323L in PB2; 74K, 112L, 116L, 377N, 417D, or 422L in NP; 30P, 55K, 118K, 161T or 140Q in NS1; 142N, 225C, 356R, 401K, or 550L in PA; or one or more of 247H in PB1; 202L and/or 323L in PB2; 74K in NP; 55E in NS1; or 142N in PA.
14. The isolated recombinant virus of claim 7 which has a U at position 4 in the viral segment for any one of PB1, PB2 or PA.
15. The isolated recombinant influenza virus of claim 7 wherein at least one of the PA, PB1, PB2, NP, NS, and M viral segments has a C to U promoter mutation.
16. The isolated recombinant influenza virus of claim 8 wherein the PA, PB1, PB2, NP, NS, and M viral segments comprise sequences for at least one of the following: a PB1 having the amino acid sequence encoded by SEQ ID NO:2 or PB1 with at least 95% amino acid sequence identity to the PB1 encoded by SEQ ID NO:2; a PB2 having the amino acid sequence encoded by SEQ ID NO:3 or PB2 with at least 95% amino acid sequence identity to the PB2 encoded by SEQ NO:3; a PA having the amino acid sequence encoded by SEQ ID NO:1 or PA with at least 95% amino acid sequence identity to the PA encoded by SEQ ID NO:1; a NP having the amino acid sequence encoded by SEQ ID NO:4 or NP with at least 95% amino acid sequence identity to the NP encoded by SEQ ID NO:4; a M having the amino acid sequence encoded by SEQ ID NO:5 or M with at least 95% amino acid sequence identity to the M encoded by SEQ ID NO:5; or a NS having the amino acid sequence encoded by SEQ ID NO:6 or NS with at least 95% amino acid sequence identity to the NS encoded by SEQ ID NO:6 or wherein the PA, PB1, PB2, NP, NS, and M viral segments comprise sequences for at least one of the following: a PB1 having the amino acid sequence encoded by SEQ ID NO:10 or PB1 with at least 95% amino acid sequence identity to the PB1 encoded by SEQ ID NO:10; a PB2 having the amino acid sequence encoded by SEQ ID NO:11 or PB2 with at least 95% amino acid sequence identity to the PB2 encoded by SEQ ID NO:11; a PA having the amino acid sequence encoded by SEQ ID NO:12 or PA with at least 95% amino acid sequence identity to the PA encoded by SEQ ID NO:12; a NP having the amino acid sequence encoded by SEQ ID NO:13 or NP with at least 95% amino acid sequence identity to the NP encoded by SEQ ID NO:13; a M having the amino acid sequence encoded by SEQ ID NO:14 or M with at least 95% amino acid sequence identity to the M encoded by SEQ ID NO:14; or a NS having the amino acid sequence encoded by SEQ ID NO:15 or NS with at least 95% amino acid sequence identity to the NS encoded by SEQ ID NO:15.
17. A cell infected in vitro with the virus of claim 7 .
18. The cell of claim 17 which is a cell in an embryonated egg.
19. The cell of claim 17 which is a Vero cell.