Table 3. Mutations identified at functionally relevant sites.
| Sample | Gene | Nt site | Ref base | Variant base | Coding region change | Freq. | Description | Type |
|---|---|---|---|---|---|---|---|---|
| A/Cambodia/X0128304/2013 | PB2 | 1069 | A | T | N348Y | 6.15% | Putative m7GTP cap binding site[64]. | replication |
| A/Cambodia/V0401301/2011 | PB2 | 1202 | A | C | N392H | 3.61% | Putative m7GTP cap binding site[64]. | replication |
| A/Cambodia/W0112303/2012 | PB2 | 1891 | G | A | E627K | 6.63% | A Lys at 627 enhances mammalian replication[51,53]. | replication |
| A/Cambodia/X0125302/2013 | PB2 | 2022 | G | A | V667I | 2.99% | An Ile at 667 was associated with human-infecting H5N1 virus strains[65]. | replication |
| A/Cambodia/W0112303/2012 | PB2 | 2113 | A | G | N701D | 16.49% | An Asn at 701 enhances mammalian replication[55,56]. | replication |
| A/Cambodia/X0125302/2013 | PB2 | 2163 | A | G | S714G | 9.59% | An Arg at 714 enhances mammalian replication[55]. | replication |
| A/Cambodia/X1030304/2013 | PB1 | 631 | A | G | R211G | 2.34% | Nuclear localization motif. | interaction with host machinery |
| A/Cambodia/X0125302/2013 | PB1 | 1078 | A | G | K353R | 2.94% | An Arg at 353 is associated with higher replication and pathogenicity of an H1N1 pandemic strain[66]. | replication |
| A/Cambodia/X0125302/2013 | PB1 | 1716 | A | T | T566S | 5.20% | An Ala at 566 is associated with higher replication and pathogenicity of an H1N1 pandemic virus[66]. | replication |
| A/Cambodia/X0219301/2013 | PA | 265 | A | G | T85A | 2.84% | An Ile at 85 enhances polymerase activity of pandemic H1N1 in mammalian cells[67]. | replication |
| A/Cambodia/X0128304/2013 | PA | 1868 | A | G | K615R | 2.47% | An Asn at PA 615 has been associated with adaptation of avian influenza polymerases to humans[55]. | replication |
| A/Cambodia/X0207301/2013 | PA | 1903 | A | G | S631G | 1.79% | A Ser at 631 enhances virulence of H5N1 viruses in mice[68]. | virulence |
| A/Cambodia/X0128304/2013 | HA | 299 | A | G | E91G | 6.33% | A Lys at 91 enhances α-2,6 binding[43]. (H5 mature: 75) | receptor binding |
| A/Cambodia/V0417301/2011 | HA | 425 | A | G | E142G | 3.20% | Putative glycosylation site[69]. (H5 mature: 126) | virulence |
| A/Cambodia/V0401301/2011 | HA | 449 | C | T | A150V | 20.24% | A Val at 150 confers enhanced α-2,6 sialic acid binding in H5N1 viruses[58,59]. (H5 mature: 134) | receptor binding |
| A/Cambodia/X0125302/2013 | HA | 449 | C | T | A150V | 15.09% | A Val at 150 confers enhanced α-2,6 sialic acid binding in H5N1 viruses[58,59]. (H5 mature: 134) | receptor binding |
| A/Cambodia/X0128304/2013 | HA | 542 | A | C | K172T | 11.50% | Part of putative glycosylation motif that improves α-2,6 binding[70–72]. (H5 mature: 156) | receptor binding |
| A/Cambodia/V0401301/2011 | HA | 517 | T | C | Y173H | 5.04% | Residue involved in sialic acid recognition[45]. (H5 mature: 157) | receptor binding |
| A/Cambodia/V0401301/2011 | HA | 593 | A | G | N198S | 3.32% | A Lys at 198 confers α-2,6 sialic acid binding [43,73](H5 mature: 182) | receptor binding |
| A/Cambodia/X0128304/2013 | HA | 703 | A | G | T226A | 28.91% | An Ile at 226 enhanced α-2,6 sialic acid binding[63]. (H5 mature: 210) | receptor binding |
| A/Cambodia/V0401301/2011 | HA | 713 | A | T | Q238L | 2.80% | A Leu at 238 confers a switch from α-2,3 to α-2,6 sialic acid binding and is a determinant of mammalian transmission[11,12,73–76]. (H5 mature: 222) | receptor binding |
| A/Cambodia/V0417301/2011 | HA | 713 | A | T | Q238L | 8.45% | A Leu at 238 confers a switch from α-2,3 to α-2,6 sialic acid binding and is a determinant of mammalian transmission[11,12,73–76]. (H5 mature: 222) | receptor binding |
| A/Cambodia/X0125302/2013 | HA | 713 | A | G | Q238R | 40.30% | A Leu at 238 confers a switch from α-2,3 to α-2,6 sialic acid binding and is a determinant of mammalian transmission[11,12,73–76]. (H5 mature: 222) | receptor binding |
| A/duck/Cambodia/Y0224304/2014 | NP | 674 | C | T | T215I | 3.69% | Nuclear targeting motif[77]. | interaction with host machinery |
| A/Cambodia/X1030304/2013 | M2 | 861 | G | A | C50Y | 2.03% | A Cys at position 50 is a palmitoylation site that enhances virulence[78,79]. | virulence |
| A/Cambodia/X0128304/2013 | NS1 | 502 | C | T | P159L | 2.8% | Part of the NS1 nuclear export signal mask[80]. | interaction with host machinery |
| A/duck/Cambodia/Y0224301/2014 | NS1 | 646 | T | C | L207P | 2.22% | NS1 flexible tail, which interacts with host machinery[81]. | interaction with host machinery |
| A/duck/Cambodia/Y0224301/2014 | NS1 | 654 | C | T | P210S | 2.55% | NS1 flexible tail, which interacts with host machinery[81]. | interaction with host machinery |
| A/Cambodia/X0207301/2013 | NEP | 609 | A | G | E47G | 4.59% | This site was implicated in enhanced virulence of H5N1 viruses in ferrets[82]. | virulence |
All nonsynonymous mutations that were identified in sites with putative links to host-specific phenotypes are shown. We identify a handful of amino acid mutations that have been explicitly linked to mammalian adaptation of avian influenza viruses. For HA mutations, all mutations use native H5 numbering, including the signal peptide. For ease of comparison, the corresponding amino acid number in mature, H5 peptide numbering is also provided in parentheses in the description column. Full annotations for all mutations in our data are shown in S1 Table.