From: Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing
 |  |  |  |  |  | Frequency (in %) |  | |||
---|---|---|---|---|---|---|---|---|---|---|
Segment | Position | Type | Reference | Allele | aa change | Illumina MiSeq | Ion Torrent PGM | Function/location | ||
PB2 | 416 | SNP | A | G | silent | 1.55 | 1.30 | 0.59 | 0.57 | / |
PB1 | 1486 | SNP | A | G | Lys481Arg | 2.52 | 2.80 | 1.79 | 2.37 | K481 crucial for polymerase function in vivo, not in vitro [47] |
PA | 212 | SNP | G | T | Glu56Asp | 5.72 | 4.85 | 2.09 | 2.18 | |
PA | 1139 | SNP | G | T | Gln365His | 2.50 | 2.40 | 1.00 | 1.05 | located in PB1 interacting domain [60] |
HA | 524 | SNP | A | C | Ser158Arg | 13.17 | 12.93 | 9.70 | 9.63 | Compensatory mutation in [61], located in Ca antigenic site [54] |
HA | 524 | SNP | A | T | Ser158Cys | 0.98 | 0.90 | 0.61 | 0.63 | located in variable Ca antigenic site [54] |
HA | 607 | SNP | A | G | silent | 1.54 | 1.43 | 2.23 | 2.47 | / |
HA | 747 | SNP | A | G | Glu232Gly | 39.95 | 40.14 | 36.74 | 36.02 | receptor specificity [50] |
HA | 765 | SNP | A | G | Asp238Gly | 3.17 | 3.07 | 1.50 | 1.44 | enables binding to α2,3- and α2,6-linked sialic acids [52,53] |
HA | 823 | SNP | A | G | Ile257Met | 2.92 | 3.08 | 1.49 | 1.64 | located in head domain close to Sa antigenic site [54] |
HA | 828 | SNP | A | G | Glu259Gly | 5.17 | 4.96 | 2.09 | 1.95 | located on surface head domain close to Sa antigenic site [54] |
HA | 1088 | SNP | T | A | Phe346Ile | 6.99 | 6.76 | 3.75 | 4.18 | located in fusion peptide [62] |
HA | 1090 | SNP | T | G | Phe346Leu | 1.28 | 1.09 | 0.59 | 0.69 | |
HA | 1109 | SNP | A | G | Ile353Val | 59.69 | 60.02 | 62.48 | 61.74 | |
HA # | 1199 | SNP | A | G | Ser383Gly | 1.13 | 1.18 | 0.97 | 1.05 | located in stem domain |
HA | 1330 | SNP | A | G | silent | 1.59 | 1.67 | 1.94 | 1.14 | / |
HA | 1424 | SNP | G | T | Val458Leu | 3.43 | 3.13 | 1.63 | 1.64 | located in stem domain, not surface exposed |
HA | 1430 | SNP | A | G | Asn460Asp | 10.08 | 9.60 | 5.82 | 6.10 | present in the PR8 quasispecies grown on MDCK cells [65] |
HA | 1431 | SNP | A | G | Asn460Ser | 14.79 | 14.62 | 10.15 | 10.29 | located in stem domain |
HA | 1487 | SNP | G | A | Gly479Arg | 1.59 | 1.39 | 0.61 | 0.57 | located in stem domain, not surface exposed |
NP | 635 | SNP | G | A | silent | 4.44 | 3.93 | 2.45 | 1.87 | / |
NP# | 739 | SNP | T | C | Ile225Thr | 1.11 | 1.15 | 0.52 | 0.56 | surface exposed, in NP-NP interaction domain [56] |
NA | 476 | SNP | T | A | Cys146Ser | 6.85 | 6.71 | 4.33 | 3.85 | located in head domain, involved in coupling of subunits [66] |
NA | 994 | SNP | C | T | silent | 1.03 | 1.00 | 0.60 | 0.65 | / |
M | 354 | SNP | C | T | introduced | 99.96 | 99.96 | 99.61 | 99.62 | / |
M | 645 | SNP | A | T | introduced | 99.95 | 99.95 | 99.95 | 99.95 | / |
NS | 409 | SNP | G | T | NS1: Gln121His | 40.37 | 39.54 | 31.96 | 32.61 | situated next to the NS1122–130 CTL epitope [67] |
NS | 549 | SNP | G | A | NS1: Gly168Glu | 1.27 | 1.20 | 0.71 | 0.59 | NS1: located in effector domain [68] |
NS2: N-terminal domain | ||||||||||
NS2: Asp11Asn | ||||||||||
NS# | 564 | SNP | A | G | NS1: Asp173Gly | 1.05 | 1.10 | 0.65 | 0.64 | NS1: located in effector domain [68] |
NS2: Met16Val | NS2: Met16 is involved in nuclear export NP [69] |