Table 1 Missense mutations acquired by SARS-CoV-2 during serial passaging.

From: An inactivated SARS-CoV-2 vaccine based on a Vero cell culture-adapted high-titer virus confers cross-protection in small animals

Nucleotide level

Mutation frequency

Amino acid level

Pos1

Ref2

Alt3

Patient swab4

P4

P23

P37

P59

P70

P88

AA change5

Protein

2392

T

A

–

–

3

7

11

24

20

F529L

nsp2

4340

A

G

–

–

4

8

34

65

65

I541V

nsp3

5979

C

T

–

0.3

95

85

87

96

91

S1087F

nsp3

7185

T

C

–

–

3

14

7

1

4

I1489T

nsp3

7869

C

T

–

–

–

–

–

–

7

S1717L

nsp3

8240

C

T

–

–

1

28

95

99

99

H1841Y

nsp3

10,116

C

T

–

–

–

–

1

11

56

T21I

nsp5

12,008

C

T

–

–

–

–

–

2

6

L56F

nsp7

12,789

C

T

–

–

1

–

34

86

97

T35I

nsp9

18,675

A

C

–

–

–

–

8

3

3

R212S

nsp14

19,398

G

T

–

–

–

–

–

–

15

E453D

nsp14

19,610

C

T

–

–

–

–

2

13

56

T524I

nsp14

19,682

A

C

–

–

–

5

53

89

97

E21A

nsp15

21,759

A

G

–

47

100

99

100

100

100

H66R

S

21,846

C

T

–

–

1

24

99

100

100

T95I

S

21,861

T

C

–

–

–

–

34

85

99

I100T

S

22,017

G

T

–

–

–

2

45

87

98

W152L

S

22,206

A

G

–

12

–

–

–

–

–

D215G

S

22,296

A

G

–

17

–

–

–

–

–

H245R

S

22,326

C

T

–

–

2

37

–

–

–

S255F

S

22,487

A

G

18

86

99

99

100

100

99

K309E

S

23,014

A

T

–

–

–

–

21

26

27

E484D

S

23,606

C

T

–

–

7

99

99

100

99

R682W

S

23,999

A

C

–

–

77

100

100

100

100

S813L6

S

24,000

G

T

–

–

100

99

100

100

100

S

24,374

C

T

–

–

74

81

89

99

100

L938F

S

24,507

C

T

–

–

–

–

15

27

34

S982L

S

24,771

C

A

–

–

–

–

31

64

56

A1070E

S

25,047

C

T

–

–

–

25

35

32

49

P1162L

S

25,335

A

T

–

–

–

–

3

7

11

E1258V

S

25,418

C

T

–

–

–

2

8

0.5

–

T9I

ORF3a

26,257

G

C

–

–

–

10

60

69

64

V5L

E

26,257

G

T

–

–

99

90

40

30

35

V5F

E

26,320

T

C

–

–

–

4

18

3

1

F26L

E

28,093

C

T

–

–

–

–

–

1

7

S67F

ORF8

29,451

C

T

–

–

–

–

1

2

9

T393I

N

  1. Missense mutations with a frequency of ≥ 5% in at least one of the sequences are shown. 1Position according to Genbank MZ049597, consensus sequence of the isolate SARS-CoV-2/human/DNK/DK-AHH1/2020 from a patient swab. 2Reference nucleotide according to the Genbank MZ049597 consensus sequence. 3Nucleotide in sequenced sample. 4Sequence of the SARS-CoV-2/human/DNK/DK-AHH1/2020 isolate, indicating a quasispecies at nucleotide position 22,487. 5Amino acid residue listed prior to the position number is according to the Genbank MZ049597 consensus sequence; amino acid residue listed after the position number specifies the changed amino acid encoded by the respective nucleotide change. 6In P23: 77% S813L (encoded by A23999C + G23400T) and 22% S813I (encoded by G23400T); in P37-P88: 100% S813L (encoded by A23999C + G23400T). Pos, position. Ref, reference nucleotide. Alt, alternative nucleotide. P, passage. AA, amino acid. –, not detected. nsp, non-structural protein. S, spike protein. ORF, open reading frame. E, envelope protein. N, nucleocapsid protein.
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