Table 1.
Variants of SARS-CoV-2 based on three nomenclature methods, location and date of detection, and the location of mutations in the genome of the virus.
| GISAID clades |
PANGO lineages | Nextstrain clades | Notable and elevated risk variants | WHO label | First detection |
Mutations | ||
|---|---|---|---|---|---|---|---|---|
| Location | Date | |||||||
| S | A.1–A.6 | 19B | “reference sequence” hCoV-19/Wuhan/WIV04/2019 (WIV04) | Shenzhen China | Jan 2020 | C8782T,T28144C includes NS8-L84S | ||
| L |
B.3-B.7, B.9, B.10, B.13–B.16 | 19A | Wuhan China |
Dec 2019 | C241,C3037,A23403,C8782,G11083,G26144,T28144 | |||
| O | France | Jan 2020 | ||||||
| V | B.2 | South Korea | Feb 2020 | G11083T,G26144T NSP6-L37F + NS3-G251V | ||||
| G |
B.2 |
B.1.5–B.1.72 |
20A |
20A/S:S477N (EU2) |
Australia, western Europe | Jun-Oct 2020 Outbreak [63], [64], [67] |
S:S477N, N:M234I, N:A376T, ORF1b:A176S, ORF1b:V767L, ORF1b:K1141R, ORF1b:E1184D | |
|
G/484 K.V3 20A/S.484 K (B.1.525) |
Eta (VOI) |
North America, Europe, Asia, Africa, and Australia | late 2020 | S:A67V, S:E484K, D614G,S:Q677H, S:F888L, N:A12G deletion of S: 69, 70, 144 deletion of ORF1a (3675–3677) |
||||
| 20A/S:439 K | emerged twice independently in Europe | Apr 2020 [63], [65], [76] |
S:S439K ORF1a:I2501T deletion of S: 69 |
|||||
| 20A/S:98F | Belgium | Jul 2020 | S:S98F, N:P199L, ORF3a:Q38R, ORF3a:G172R ORF3a:V202L |
|||||
| A.23.1 | Uganda | Oct 2020 [77] |
S:F157L, S:V367F, S:Q613H, S:P681R | |||||
|
B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 |
21A/S:154 K |
B.1.617.1 G/452R.V3 |
Kappa (VOI) |
India | October 2020 | S) L452R, E484Q, D614G, P681R, E154K, Q1071H) | ||
| 21A/S:478 K |
B.1.617.2 G/452R.V3 |
Delta (VOC) |
India | October 2020 | S(L452R, D614G, P681R, T19R, R158G, T478K, D950N), | |||
| GH |
B.1.3–B.1.66 |
20C 21F Derived from 20A, |
CAL.20C 20C/S.452R (B.1.427/B.1.429) |
Epsilon (VOI) |
United States [78], Southern California | October 2020 [64] |
S:S13I, S:W152C, S:L452R, ORF1a:I4205V, ORF1b:D1183Y | |
| 20C/S.484 K, (B.1.526) |
Iota (VOI) |
USA, particularly in New York state |
Late 2020 | S:L5F, S:T95I, S:D253G, S:E484K, S:A701V, ORF1b:Q1011H, ORF3a:P42L N:P199L, N:M234I, ORF8:T11I deletion of ORF1a (3675–3677) |
||||
|
20G (“20C-US”) Derived from 20C |
S:677H.Robin1 |
USA dominant in Wisconsin |
Jan '21 [69] |
S:Q677H, N:P67S, N:P199L, N:D377Y, ORF1a:T265I, ORF1a:L3352F, ORF1b:N1653D, ORF1b:R2613C | ||||
| 20G/S:677P.Pelican | USA. dominant in Louisiana | early 2021 [69] |
S:Q677P, N:P67S, N:P199L, ORF1a:T265I ORF1a:L3352F, ORF1b:N1653D ORF1b:R2613C |
|||||
| 21H | B.1.621 |
Mu (VOI) |
Colombia | Jan 2021 | T95I, Y144S, Y145N, R346K, E484K N501Y, D614G, P681H, D950N |
|||
|
|
20H Derived from 20C |
(B.1.351) 20H:501Y.V2 |
Beta (VOC) | South Africa |
Dec 2020 [79] |
S:N501Y, K417N, E484K, S:L18F and S:D80A deletion of ORF1a (3675–3677) deletion at Spike positions 242-245 mutation in Nucleocapsid:N:T205I |
||
| GR |
B.1.1 |
20B | B.1.1.207 | Nigeria | Mar 2020 | P681H | ||
| 20B/S:1122L (B.1.1302) |
Sweden, Norway and Denmark | Jul 2020 | S:V1122L | |||||
| 20B/S:626S (B1.1.277) |
Norway, Denmark, UK | Jul 2020 | S:A626S | |||||
| 20 J |
20 J/S:501Y.V3 (B.1.1.28.1) (P.1) |
Gamma (VOC) |
Brazil, Japan [72] |
January 2021 | S:N501Y, S:E484K, S:D614G S:K417T S: L18F, S: K417N, S: H655Y. deletion of ORF1a (3675–3677) N:P80R N:R203K, N:G204R |
|||
|
20D Derived from 20B |
20B/S.484 K (P.2) |
Zeta (VOI) |
Brazil | January 2021 | S:E484K, N:A119S, N:M234I, ORF1a:L3458V , ORF1a:L3930F | |||
|
20B/S:265C |
P.3 |
Theta (VOI) |
Philippines |
Jan-2021 | S (E484K, N501Y, D614G, P681H, E1092K, H1101Y, V1176F) ORF1ab (L3201P, D3681E, L3930F, P4715L), ORF8 (K2Q), N (R203K,G204R) |
|||
| 20D |
GR/452Q.V1 C.37 |
Lambda (VOI) |
Peru | Jun 2021 | G75V, T76I, R246N, DEL247/253, L452Q, F490S, D614G, T859N | |||
|
20F Derived from 20B |
Australia | Jun-Oct 2020 outbreak | S:S477N |
|||||
|
20I Derived from 20B |
GRY (B.1.1.7) 20I/S:501Y.V1 |
Alpha (VOC) |
United Kingdom [80] |
18 Dec 2020 | S:N501Y, S:A570D 69–70del, P681H (adjacent to the furin cleavage site). deletion of ORF8 (3675–3677) and ORF1a(Nsp6) Q27 |
|||
| GV | B.1.177 | 20E (EU1) Derived from 20A, | 20I/501Y.V1 | Spain [81] |
early summer of 2020 | S:A222V ORF10:V30L N:A220V |
||