Extended Data Table 2 |. Amino acid changes identified in cultured SARS-CoV-2 isolates.
Cultured virus isolates were resequenced and the consensus genomes were compared to the reference genome (Accession MN908947) using Nextclade (https://clades.nextstrain.org/). Letters indicate amino acids, numbers indicate amino acid positions, asterisks indicate stop codon mutations, and dashes indicate deletions. Abbreviations: E, envelope; M, membrane; N, nucleocapsid; ORF, open reading frame; S, spike.
| Lineage GenBank Accession | A MZ468053 |
B.1.526a MZ467323 |
B.1.526b MZ467333 |
B.1.1.7a MZ202178 |
B.1.517 MZ468008 |
B.1.526c MZ201303 |
B.1.617.2 MZ468047 |
R.1 MZ467697 |
B.1.427 MZ467318 |
B.1.526d MZ467322 |
B.1.429 MZ467319 |
B.1.525 MZ467313 |
B.1.617.1 MZ468046 |
P.1 MZ202306 |
B.1 MZ467989 |
B.1.1.7b MZ467988 |
B.1.351a MZ468007 |
B.1.351b MZ202314 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| E | V62F | L21F | P71L | P71L | ||||||||||||||
| M | I82T | F28L T175M |
I82T | I82S | ||||||||||||||
| N | P13L S202R A414V |
P199L M234I |
D3L R203K G204R S235F |
S206F | P199L M234I |
D63G R203M D377Y |
S187L R203K G204R Q418H |
T205I T362I |
T205I M234I |
T205I M234I |
M1- S2M D3Y A12G T205I |
R203M D377Y |
P80R R203K G204R |
D3Y T205I |
D3L R203K G204R S235F |
T205I | T205I | |
| ORF1a | T265I T1840I G1946S L3201P S3675- G3676- F3677- |
T265I A1352V L3201P P3504S S3675- G3676- F3677- |
T1001I P1213L A1708D I2230T M2259I S3675- G3676- F3677- |
T265I A541S G989V H1580Y |
T265I T2977I L3201P S3675- G3676- F3677- |
P309L A405V P1640L A3209V V3718A |
T265I S3158T |
T265I T2087I K3162E L3201P A3209V P3359S S3675- G3676- F3677- V3847I L4126F |
T265I I4205V |
T2007I L2609I S3675- G3676- F3677- |
T1567I T3646A |
S1188L K1795Q G2941S S3675- G3676- F3677- |
G150S T265I V649F T708I A1049V T1854I K2497N R3542C M4375T |
E913D T1001I A1306T A1708D P2046L I2230T M2259I S3675- G3676- F3677- L3736F L3829F |
T265I T333M Y1598C K1655N E1843D T2174I K3353R S3675- G3676- F3677- T4065I |
T265I K1655N K3353R S3675- G3676- F3677- |
||
| ORF1b | P314L Q1011H | P314L Q1011H | P218L P314L A1432V |
P314L D1506N P2633S |
P314L Q1011H R1078C |
P314L G662S P1000L P1570L |
P314L G814C G1362R P1936H |
P314L P976L D1183Y |
P314L | P314L D1183Y G2436C |
P314F | P314L G1129C A1291S M1352I K2310R S2312A |
P314L A1219S E1264D |
T132I P314L |
P218L P314L T1511I |
P314L T1050I Y2608H |
P314L | |
| ORF3a | P42L Q57H |
P42L Q57H |
Q57H D210E |
P42L Q57H |
S26L | Q57H | P42L Q57H |
Q57H | S92L | S26L | Q57H S253P |
Q57H P104S S171L |
Q57H S171L | Q57H W131L S171L |
||||
| ORF6 | M1- F2M |
|||||||||||||||||
| ORF7a | L116F | V82A L116F T120I |
P34S | A105S | N43Y V82A | V93F | ||||||||||||
| ORF8 | L84S | T11I | T11I | Q27* R52I K68* Y73C |
E59* | T11I | D119- F120- |
T11I P36S A51S |
V100L | E92K | E106D | Q27* R52I K68* Y73C |
I121L | R115L | ||||
| ORF9b | P10S | T83I | T60A | H9D | Q77E | |||||||||||||
| S | L5F T95I D253G S477N D614G Q957R |
L5F T95I D253G S477N D614G A701V |
H69- V70- Y144- N501Y A570D D614G P681H T716I S982A D1118H |
N501T Q613H D614G G639V |
L5F T95I D253G E484K D614G A701V |
T19R E156 F157- R158G L452R T478K D614G P681R D950N L1141W |
W152L E484K K558N D614G G769V |
S13I W152C L452R D614G |
D80G Y144- F157S L452R D614G T791I T859N D950H |
S13I W152C L452R D614G |
H69- V70- Y144- Q52R A67V E484K D614G Q677H F888L |
T95I G142D E154K L452R E484Q D614G P681R Q1071H |
L18F T20N P26S D138Y R190S K417T E484K N501Y D614G H655Y T1027I V1176F |
E484K N501T D614G |
H69- V70- Y144- E484K N501Y A570D D614G P681H T716I S982A D1118H |
D80A D215G L241- L242- A243- K417N E484K N501Y D614G A701V |
L18F D80A D215G L241- L242- A243- K417N E484K N501Y D614G Q677H R682W A701V |
Abbreviations: E = envelope, M = membrane, N = nucleocapsid, ORF = open reading frame, S = spike.