Table 8 Wild type PR8 quasispecies sequenced in duplicate on both Illumina MiSeq and Ion Torrent PGM

PB1

1482

Deletion

A

-

frameshift

1.87

2.19

3.18

2.88

PB1

1486

SNP

A

G

Lys481Arg

2.32

2.62

1.91

1.91

K481 crucial for polymerase function in vivo, not in vitro [47]

PA

539

SNP

A

G

silent

1.37

1.42

0.56

0.54

/

HA

607

SNP

A

G

silent

1.60

1.56

2.02

1.85

/

HA^#

659

SNP

G

A

Glu203Lys

1.13

1.23

0.65

0.60

enhanced receptor binding activity [48]

HA

660

SNP

A

G

Glu203Gly

3.11

3.02

1.76

1.55

slightly increased α2-6 and decreased α2-3 binding [49]

HA

747

SNP

A

G

Glu232Gly

11.56

11.43

7.29

7.19

receptor specificity [50]

HA

764

SNP

G

A

Asp238Asn

0.83

0.80

0.65

0.60

enables binding to α2.3- and α2.6-linked sialic acids [51]

HA

765

SNP

A

G

Asp238Gly

39.73

39.43

35.33

35.00

enables binding to α2.3- and α2.6-linked sialic acids [52,53]

HA

768

SNP

A

G

Gln239Arg

2.81

3.12

1.43

1.23

preferential binding to α-2,3-linked glycans [52]

HA

823

SNP

A

G

Ile257Met

1.76

1.54

0.72

0.74

located in head domain close to Sa antigenic site [54]

HA ^#

1199

SNP

A

G

Ser383Gly

1.41

1.15

1.14

1.29

located in stem domain

HA

1330

SNP

A

G

silent

1.59

1.50

1.02

1.20

/

HA

1424

SNP

G

A

Val458Met

95.25

95.67

97.85

97.77

located in stem domain

HA

1440

SNP

A

G

Glu463Gly

1.91

1.75

0.58

0.56

located in stem domain

HA

1451

SNP

A

G

Ser467Gly

0.70

0.81

0.62

0.63

located in stem domain

NP

212

SNP

C

T

silent

1.80

1.76

0.83

0.64

/

NP

1249

SNP

A

G

Asn395Ser

10.71

11.01

5.97

6.76

located in NP-NP and NP-PB2 interaction domain [55,56]

NP

1324

SNP

T

G

Phe420Cys

3.43

3.41

1.31

1.15

located in the hypervariable NP_418-426 CTL epitope [57]