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Table 9 Mutant PR8 quasispecies sequenced in duplicate on both Illumina MiSeq and Ion Torrent PGM

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

located in endonuclease domain [58,59]

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

located in fusion peptide [62,63]

HA

1109

SNP

A

G

Ile353Val

59.69

60.02

62.48

61.74

described as fusion peptide pseudorevertant [62,64]

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]

  1. #not present in Genbank or Influenza Research Database.
  2. Bold = variants also present in PR8 quasispecies.
  3. HA segment = numbering of HA amino acid residues is based on the PR8 HA open reading frame with the starting methionine as position = 1.