TABLE 2.

Nonsynonymous SNPs in SARS-CoV-2 spike protein^a

Genomic locus	Gene locus	Amino acid change	Domain	No. of nonsynonymous SNPs
				Wave 1 (n = 1,026)	Wave 2 (n = 4,059)	Total (n = 5,085)
21575	C13T	L5F	S1	11	25	36
21578	G16T	V6F	S1		1	1
21587	C25T	P9S	S1	2		2
21588	C26T	P9L	S1	1	1	2
21594	T32C	V11A	S1		1	1
21597	C35T	S12F	S1		6	6
21604	G42T	Q14H	S1		1	1
21614	C52T	L18F	S2—NTD	1	11	12
21618	C56T	T19I	S2—NTD	1	1	2
21621	C59T	T20I	S2—NTD		1	1
21624	G62T	R21I	S2—NTD		6	6
21624	G62A	R21K	S2—NTD		1	1
21624	G62C	R21T	S2—NTD		3	3
21627	C65T	T22I	S2—NTD	2	4	6
21638	C76T	P26S	S2—NTD		17	17
21641	G79T	A27S	S2—NTD	1	1	2
21641	G79A	A27T	S2—NTD	1		1
21642	C80T	A27V	S2—NTD		1	1
21648	C86T	T29I	S2—NTD	1	4	5
21707	C145T	H49Y	S2—NTD		142	142
21713	A151G	T51A	S2—NTD		1	1
21724	G162T	L54F	S2—NTD		11	11
21754	G192T	W64C	S2—NTD		1	1
21767	C205T	H69Y	S2—NTD	1	7	8
21770	G208A	V70I	S2—NTD		1	1
21770	G208T	V70F	S2—NTD	1		1
21774	C212T	S71F	S2—NTD		1	1
21784	T222A	N74K	S2—NTD	1		1
21785	G223C	G75R	S2—NTD		1	1
21793	G231T	K77N	S2—NTD		1	1
21824	G262A	D88N	S2—NTD		1	1
21834	A272T	Y91F	S2—NTD		1	1
21846	C284T	T95I	S2—NTD	1	10	11
21852	A290G	K97R	S2—NTD		1	1
21855	C293T	S98F	S2—NTD	1	2	3
21861	T299C	I100T	S2—NTD		2	2
21918	T356C	I119T	S2—NTD	1		1
21930	C368T	A123V	S2—NTD		1	1
21941	G379T	V127F	S2—NTD		1	1
21942	T380C	V127A	S2—NTD		4	4
21974	G412T	D138Y	S2—NTD	2		2
21985	G423T	L141F	S2—NTD		1	1
21986	G424A	G142S	S2—NTD		2	2
21993	A431G	Y144C	S2—NTD	1		1
21995	T433C	Y145H	S2—NTD	2		2
21998	C436T	H146Y	S2—NTD	1	2	3
22014	G452A	S151N	S2—NTD		1	1
22014	G452T	S151I	S2—NTD		2	2
22017	G455T	W152L	S2—NTD	1	1	2
22021	G459T	M153I	S2—NTD		1	1
22021	G459A	M153I	S2—NTD		1	1
22022	G460A	E154K	S2—NTD		1	1
22028	G466C	E156Q	S2—NTD	2		2
22037	G475A	V159I	S2—NTD	1		1
22097	C535T	L179F	S2—NTD		1	1
22104	G542T	G181V	S2—NTD		1	1
22107	A545G	K182R	S2—NTD		1	1
22135	A573T	E191D	S2—NTD		1	1
22139	G577T	V193L	S2—NTD		1	1
22150	T588G	N196K	S2—NTD	1		1
22175	T613G	S205A	S2—NTD		1	1
22205	G643T	D215Y	S2—NTD		1	1
22206	A644G	D215G	S2—NTD		2	2
22214	C652G	Q218E	S2—NTD		1	1
22227	C665T	A222V	S2—NTD		1	1
22241	G679A	V227I	S2—NTD		2	2
22242	T680C	V227A	S2—NTD	1		1
22244	G682C	D228H	S2—NTD		2	2
22245	A683G	D228G	S2—NTD	1		1
22246	T684G	D228E	S2—NTD	2		2
22248	T686G	L229W	S2—NTD	1		1
22250	C688A	P230T	S2—NTD	1		1
22253	A691G	I231V	S2—NTD	1		1
22254	T692C	I231T	S2—NTD	1		1
22259	A697G	I233V	S2—NTD	1		1
22260	T698C	I233T	S2—NTD	1		1
22262	A700G	N234D	S2—NTD	1		1
22266	T704C	I235T	S2—NTD	1		1
22281	C719T	T240I	S2—NTD		5	5
22286	C724T	L242F	S2—NTD		1	1
22295	C733T	H245Y	S2—NTD		2	2
22304	T742C	Y248H	S2—NTD		3	3
22311	C749T	T250I	S2—NTD	1	4	5
22313	C751T	P251S	S2—NTD		2	2
22320	A758G	D253G	S2—NTD		2	2
22320	A758C	D253A	S2—NTD	1		1
22323	C761T	S254F	S2—NTD		3	3
22329	C767T	S256L	S2—NTD	1		1
22335	G773T	W258L	S2—NTD	1		1
22344	G782T	G261V	S2—NTD	3		3
22346	G784T	A262S	S2—NTD		4	4
22350	C788T	A263V	S2—NTD	1		1
22382	A820G	T274A	S2—NTD		1	1
22398	A836T	Y279F	S2—NTD	1		1
22408	T846G	N282K	S2—NTD		1	1
22425	C863T	A288V	S2—NTD		1	1
22430	G868T	D290Y	S2—NTD	1		1
22484	G922T	V308L	S1		3	3
22487	G925C	E309Q	S1		1	1
22532	G970C	E324Q	S1		1	1
22533	A971T	E324V	S1		1	1
22535	T973C	S325P	S1		1	1
22536	C974T	S325F	S1		1	1
22550	C988T	P330S	S2—RBD		2	2
22574	T1012C	F338L	S2—RBD	1		1
22608	C1046T	S349F	S2—RBD		1	1
22616	G1054T	A352S	S2—RBD		7	7
22661	G1099T	V367F	S2—RBD		1	1
22673	T1111C	S371P	S2—RBD		3	3
22679	T1117C	S373P	S2—RBD		1	1
22712	C1150T	P384S	S2—RBD		1	1
22716	C1154T	T385I	S2—RBD	3		3
22785	G1223C	R408T	S2—RBD		1	1
22793	G1231T	A411S	S2—RBD		1	1
22818	C1256T	A419V	S2—RBD	1		1
22895	G1333T	V445F	S2—RBD		1	1
22899	G1337T	G446V	S2—RBD	2		2
22928	T1366C	F456L	S2—RBD	1		1
23001	G1439T	C480F	S2—RBD		1	1
23012	G1450C	E484Q	S2—RBD	1		1
23046	A1484C	Y495S	S2—RBD		1	1
23111	C1549T	L517F	S2—RBD		1	1
23120	G1558T	A520S	S2—RBD	1	6	7
23121	C1559T	A520V	S2—RBD		1	1
23127	C1565T	A522V	S2—RBD	1	1	2
23145	A1583G	K528R	S2—RBD		2	2
23149	G1587T	K529N	S1		1	1
23170	C1608A	N536K	S1		1	1
23202	C1640A	T547K	S1		2	2
23202	C1640T	T547I	S1		1	1
23223	A1661T	E554V	S1		2	2
23224	G1662T	E554D	S1	4	31	35
23270	G1708T	A570S	S1		3	3
23277	C1715T	T572I	S1	5	5	10
23282	G1720T	D574Y	S1		1	1
23292	G1730T	R577L	S1	1		1
23311	G1749T	E583D	S1		6	6
23312	A1750G	I584V	S1		1	1
23315	C1753T	L585F	S1	1	7	8
23349	G1787A	S596N	S1		1	1
23373	C1811T	T604I	S1		2	2
23380	C1818A	N606K	S1		2	2
23403	A1841G	D614G	S1	841	4,054	4,895
23426	G1864T	V622F	S1		2	2
23426	G1864C	V622L	S1		2	2
23435	C1873T	H625Y	S1		1	1
23439	C1877T	A626V	S1		1	1
23444	C1882G	Q628E	S1		7	7
23453	C1891T	P631S	S1	1		1
23457	C1895T	T632I	S1		1	1
23481	C1919T	S640F	S1	1	42	43
23486	G1924T	V642F	S1		1	1
23502	C1940T	A647V	S1		1	1
23536	C1974A	N658K	S1		4	4
23564	G2002T	A668S	S1		1	1
23586	A2024G	Q675R	S1		14	14
23587	G2025C	Q675H	S1		1	1
23587	G2025T	Q675H	S1		4	4
23589	C2027T	T676I	S1	1	2	3
23593	G2031T	Q677H	S1	1	1	2
23595	C2033T	T678I	S1	1		1
23624	G2062T	A688S	S2		4	4
23625	C2063T	A688V	S2		16	16
23655	C2093T	S698L	S2		1	1
23664	C2102T	A701V	S2		21	21
23670	A2108G	N703S	S2		1	1
23679	C2117T	A706V	S2		1	1
23684	T2122C	S708P	S2		1	1
23709	C2147T	T716I	S2		1	1
23718	C2156T	T719I	S2		1	1
23745	C2183T	P728L	S2	1		1
23755	G2193T	M731I	S2	3	1	4
23798	T2236C	S746P	S2		1	1
23802	C2240T	T747I	S2		1	1
23804	G2242A	E748K	S2		1	1
23832	G2270T	G757V	S2		1	1
23856	G2294T	R765L	S2		1	1
23868	G2306T	G769V	S2		3	3
23873	G2311T	A771S	S2		8	8
23877	T2315C	V772A	S2		1	1
23895	C2333T	T778I	S2		1	1
23900	G2338C	E780Q	S2		1	1
23936	C2374T	P792S	S2		1	1
23948	G2386T	D796Y	S2		2	2
23955	G2393T	G798V	S2	1		1
23987	C2425T	P809S	S2		2	2
23988	C2426T	P809L	S2		1	1
23997	C2435T	P812L	S2		1	1
24003	A2441G	K814R	S2		1	1
24014	A2452G	I818V	S2—FP		5	5
24026	C2464T	L822F	S2—FP		97	97
24041	A2479T	T827S	S2—FP		4	4
24077	G2515T	D839Y	S2	2		2
24089	G2527A	D843N	S2	1	1	2
24095	G2533T	A845S	S2		5	5
24099	C2537T	A846V	S2		1	1
24129	A2567G	N856S	S2		7	7
24138	C2576T	T859I	S2		5	5
24141	T2579C	V860A	S2		1	1
24170	A2608G	I870V	S2		3	3
24188	G2626T	A876S	S2		1	1
24197	G2635T	A879S	S2		31	31
24198	C2636T	A879V	S2		1	1
24212	T2650G	S884A	S2		11	11
24237	C2675T	A892V	S2		1	1
24240	C2678T	A893V	S2	1		1
24268	G2706T	M902I	S2		1	1
24287	A2725G	I909V	S2—HR1		2	2
24314	G2752C	E918Q	S2—HR1	1		1
24328	G2766C	L922F	S2—HR1		2	2
24348	G2786T	S929I	S2—HR1		1	1
24356	G2794T	G932C	S2—HR1		1	1
24357	G2795T	G932V	S2—HR1		1	1
24368	G2806A	D936N	S2—HR1		3	3
24368	G2806C	D936H	S2—HR1		1	1
24368	G2806T	D936Y	S2—HR1	3	4	7
24374	C2812T	L938F	S2—HR1		3	3
24378	C2816T	S939F	S2—HR1		4	4
24380	T2818G	S940A	S2—HR1		5	5
24389	A2827G	S943G	S2—HR1		6	6
24463	C2901A	S967R	S2—HR1	2		2
24507	C2945T	S982L	S2—HR1		1	1
24579	C3017T	T1006I	S2—CH		1	1
24588	C3026G	T1009S	S2—CH		1	1
24621	C3059T	A1020V	S2—CH	1		1
24638	G3076T	A1026S	S2—CH		2	2
24642	C3080T	T1027I	S2—CH	5		5
24649	G3087T	M1029I	S2—CH		1	1
24710	A3148T	M1050L	S2		1	1
24710	A3148G	M1050V	S2	1	1	2
24712	G3150T	M1050I	S2		2	2
24718	C3156A	F1052L	S2	1	166	167
24770	G3208T	A1070S	S2		2	2
24794	G3232T	A1078S	S2—CD	3	2	5
24812	G3250T	D1084Y	S2—CD	1	29	30
24834	G3272T	R1091L	S2—CD	1		1
24867	G3305T	W1102L	S2—CD		1	1
24872	G3310T	V1104L	S2—CD		1	1
24893	G3331C	E1111Q	S2—CD		2	2
24897	C3335T	P1112L	S2—CD	2	2	4
24912	C3350T	T1117I	S2—CD		1	1
24923	T3361C	F1121L	S2—CD		2	2
24933	G3371T	G1124V	S2—CD	1	2	3
24959	G3397T	V1133F	S2—CD		1	1
24977	G3415T	D1139Y	S2—CD		1	1
24986	C3424A	Q1142K	S2	1		1
24998	G3436T	D1146Y	S2		4	4
24998	G3436C	D1146H	S2		13	13
25019	G3457T	D1153Y	S2		11	11
25032	A3470T	K1157M	S2	1		1
25046	C3484T	P1162S	S2		5	5
25047	C3485T	P1162L	S2		3	3
25050	A3488T	D1163V	S2		2	2
25088	G3526T	V1176F	S2		18	18
25101	A3539G	Q1180R	S2		1	1
25104	A3542G	K1181R	S2		4	4
25116	G3554A	R1185H	S2		2	2
25121	A3559T	N1187Y	S2		1	1
25135	G3573T	K1191N	S2		1	1
25137	A3575C	N1192T	S2	1		1
25158	A3596C	D1199A	S2		1	1
25160	C3598T	L1200F	S2		1	1
25163	C3601A	Q1201K	S2		1	1
25169	C3607T	L1203F	S2	1		1
25183	G3621T	E1207D	S2		1	1
25186	G3624T	Q1208H	S2	1		1
25217	G3655T	G1219C	S2	1	3	4
25234	G3672T	L1224F	S2		1	1
25241	A3679G	I1227V	S2	1		1
25244	G3682T	V1228L	S2		2	2
25249	G3687T	M1229I	S2		1	1
25249	G3687C	M1229I	S2		2	2
25250	G3688A	V1230M	S2		1	1
25266	G3704T	C1235F	S2		4	4
25273	G3711T	M1237I	S2		2	2
25284	G3722T	C1241F	S2		1	1
25287	G3725T	S1242I	S2		4	4
25297	G3735T	K1245N	S2		1	1
25301	T3739G	C1247G	S2		1	1
25302	G3740T	C1247F	S2		4	4
25305	G3743T	C1248F	S2		2	2
25317	C3755T	S1252F	S2		1	1
25340	G3778T	D1260Y	S2		2	2
25350	C3788T	P1263L	S2	1	2	3
25352	G3790T	V1264L	S2		1	1
25365	T3803C	V1268A	S2		1	1

^aThe domain region of RBD is based on structural information published previously by Cai et al. (93). Forty-nine of these amino acid replacements (V11A, T51A, W64C, I119T, E156Q, S205A, D228G, L229W, P230T, N234D, I235T, T274A, A288V, E324Q, E324V, S325P, S349F, S371P, S373P, T385I, A419V, C480F, Y495S, L517F, K528R, Q628E, T632I, S708P, T719I, P728L, S746P, E748K, G757V, V772A, K814R, D843N, S884A, M902I, I909V, E918Q, S982L, M1029I, Q1142K, K1157M, Q1180R, D1199A, C1241F, C1247G, and V1268A) were not represented in a publicly available database (33) as of 19 August 2020.