Table 3 Total proportion of each nucleotide mutation found in viral sequences across the sample set. Overall, 43 different nucleotide mutations were reported across the participant samples over the time course. Using default parameters in snipit [43]. * denotes nucleotide mutations found in < 1% and † in < 5% of SARS-CoV-2 genome sequences submitted to GISAID before March 2024

C241T

5′ UTR

1.00

C14408T

NSP12

P323L

1.00

C527T*

NSP1

L88L

0.04

T14669C*

NSP12

V410A

0.04

C635T*

NSP1

R124C

0.04

C18877T*

NSP14

L280L

1.00

C683T*

NSP1

L140L

0.04

C19593T*

NSP14

N518N

0.04

C882T*

NSP2

A26V

0.80

G19999T*

NSP15

V127F

0.04

C900T*

NSP2

S32L

0.04

G20853T*

NSP16

M65I

0.80

G2782T*

NSP3

V21V

0.04

G21850T*

S

E96D

0.16

C3037T

NSP3

F106F

1.00

G21989T*

S

V143F

0.48

C4158T*

NSP3

A480V

0.16

A22255T*

S

I231I

0.76

C6990T*

NSP3

S1424F

0.64

C22444T*

S

D294D

0.16

C7926T†

NSP3

A1736V

0.04

C22995A

S

T478K

0.04

G9092A*

NSP4

V180I

0.04

A23403G

S

D614G

1.00

C9120T*

NSP4

T189I

0.16

C23635T*

S

S691S

0.04

G9526T*

NSP4

M324I

0.32

C23638T*

S

I692I

0.80

C9679T*

NSP4

F375F

0.04

C25521T*

ORF3a

F43F

0.44

G10300T*

NSP5

M82I

0.80

G25563T†

ORF3a

Q57H

1.00

C11224T*

NSP6

V84V

0.16

C25710T*

ORF3a

L106L

0.80

C11941T*

NSP7

V33V

0.20

C26735T*

M

Y71Y

1.00

C12043T*

NSP7

D67D

0.16

C28253T†

ORF8

F120F

0.04

C12242T*

NSP8

R51C

0.20

C28854T*

N

S194L

1.00

G13624T*

NSP12

D62Y

0.04

C29358T*

N

T362I

0.80

G14055T*

NSP12

L205L

0.80