Sars-CoV-2 circulating variants
This page describes circulating SARS-CoV-2 variants - Last updated 1/February/2024. Variant sequences can be parsed from UniProt P0DTC2 at COVID-19 pre-release portal.
Variants are lineages that contain fixed mutations in their genome. Spike protein mutations affect both tropism (receptor binding) and immune evasion and are therefore the focus of surveillance. However, other viral protein mutations can also have effects on pathogenesis, cellular tropism and transmission.
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Variants of Concern (VOC): Click to display variant sites (zoom in PDB window for a better view)
|
| Reference sequence | ||||||
| Lineage | Synonyms | Emergence | Spike protein | Other proteins | Consensus sequences | Phenotypes |
|---|---|---|---|---|---|---|
| 19A | Wuhan-Hu-1, nCoV | China, Dec 2019 | None | (ORF8: L84S in outbreak.info reference) | GenomeSpike proteinAll proteins | Reference for variants |
| Lineage | Synonyms | Emergence | Spike protein | Other proteins | Consensus sequences | Phenotypes |
|---|---|---|---|---|---|---|
| Omicron BA.2.86 (+JN.1) CoVariants.org oubtbreak.info; /world prevalence /mutations | BA.2.86 23I | Africa, August 2023(JN.1: Luxembourg, August 2023) |
T19I
R21T
LPPA24-27S
S50L
H69del
V70del
V127F
G142D
Y144del
F157S
R158G
N211I
212del
V213G
L216F
H245N
A264D
I332V
G339H
K356T
S371F
S373P
S375F
T376A
R403K
D405N
R408S
K417N
N440K
V445H
G446S
N450D
L452W
(JN.1 L455S)
N460K
S477N
T478K
N481K
V483del
E484K
F486P
Q498R
N501Y
Y505H
E554K
A570V
D614G
P621S
H655Y
N679K
P681R
N764K
D796Y
S939F
Q954H
N969K
P1143L
|
N:P13L, 31-33del, R203K, G204R, q229K, S413R
ORF1ab; nsp1:S135R, A211D
ORF1ab; nsp3:T842I, V1056L, G1307S, K1973R, N2526S, A2710T
ORF1ab; nsp4:L3027F, T3090I, T3201I,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6: SGF3675-3677del, R3821K
ORF1ab; nsp9 T4175I
ORF1ab; RdRp:P4715L
ORF1ab; nsp13:R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I
M: D3H, Q19E, T30A, A63T, A104V
ORF6: D61L
ORF8: S84L
|
Genome (JN.1 Genome) Spike protein NCBI (JN.1 Spike protein NCBI) | |
| Omicron EG.5.1PANGO oubtbreak.info; /world prevalence /mutations | EG.5.1XBB.1.9.2.5.1 | China, March 2023 |
(In red: differences with XBB.1.5)
T19I
LPPA24-27S
V83A
Q52H
G142D
Del144
H146Q
Q183E
V213E
G252V
G339H
R346T
L368I
S371F
S373P
S375F
T376A
D405N
R408S
K417N
N440K
V445P
G446S
F456L
N460K
S477N
T478K
E484A
F486P
F490S
Q498R
N501Y
Y505H
D614G
H655Y
N679K
P681H
N764K
D796Y
Q954H
N969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:K47R, S135R,
ORF1ab; nsp2:A690V
ORF1ab; nsp3:T842I, G1307S, G1819S,
ORF1ab; nsp4:L3027F, T3090I,A3143V, T3201I,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6: SGF3675-3677del
ORF1ab; nsp9 T4175I,
ORF1ab; RdRp:P4715L, G5063S
ORF1ab; nsp13:G5360S, R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I, T11A
M: Q19E, A63T
ORF6: D61L
ORF8: G8-stop
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Variant EG.5.1 is an evolution of XBB.1.5. S:F456L reduces humoral response vs people immunized with xbb.1.5 |
| Omicron BQ.1.1PANGOCoVariants.org oubtbreak.info: /world prevalence /mutations BV-BRC | BQ.1.122E | Nigeria, Jul 2022 |
T19I
LPPA24-27S
H69del
V70del
V213G
G142D
G339D
R346T
S371F
S373P
S375F
T376A
D405N
R408S
K417N
N440K
K444T
L452R
N460K
S477N
T478K
E484A
F486V
Q498R
N501Y
Y505H
D614G
H655Y
N679K
P681H
N764K
D796Y
Q954H
N969K
|
ORF1ab; nsp1:S135R
ORF1ab; nsp2:376K
ORF1ab; nsp3:T842I, G1307S
ORF1ab; nsp4:L3027F, T3090I, T3201I
ORF1ab; nsp5:P3395H
ORF1ab; nsp6:SGF3675-3677del, L3829F
ORF1ab; nsp12:Y4665H, P4715L
ORF1ab; nsp13:M5557I, N5592S, R5716C
ORF1ab; nsp14:I5967V
ORF1ab; nsp15:T6564I
ORF3a:T223I
E:T9I
M:D3N, Q19E, A63T
N:P13L, ERS31-33del, E136D, R203K, G204R, S413R
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations 
|
| Omicron XBB.1.5PANGOCoVariants.org oubtbreak.info; /world prevalence /mutations BV-BRC | XBB.1.523A | USA, Nov 2022 |
T19I
LPPA24-27S
V83A
G142D
Del144
H146Q
Q183E
V213E
G252V
G339H
R346T
L368I
S371F
S373P
S375F
T376A
D405N
R408S
K417N
N440K
V445P
G446S
N460K
S477N
T478K
E484A
F486P
F490S
Q498R
N501Y
Y505H
D614G
H655Y
N679K
P681H
N764K
D796Y
Q954H
N969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:K47R, S135R,
ORF1ab; nsp3:T842I, G1307S,
ORF1ab; nsp4:L3027F, T3090I, T3201I
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6: SGF3675-3677del
ORF1ab; RdRp:P4715L, G5063S
ORF1ab; nsp13:G5360S, R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I, T11A
M: Q19E, A63T
ORF6: D61L
ORF8: G8-stop
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Variant XBB is the result of recombination between omicron BJ.1 and BM.1.1, moreover XBB.1.5 do not express ORF8. Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.1>PANGOCoVariants.org oubtbreak.info: /world prevalence /mutations BV-BRC | BA.1 (previously B.1.1.529),21K | South Africa, Dec 2021 |
A67V69-70delT95IGVYY142-145DNL211-212Iins214EPEG339DS371LS373PS375FK417NN440KG446SS477NT478KE484AQ493RG496SQ498RN501YY505HT547KD614GH655YN679KP681HN764KD796YN856KQ954HN969KL981F
|
N:P13L, 31-33del, R203K, G204R
ORF1ab; nsp3: K856R, SL2083I, A2710T
ORF1ab; 3CL: T3255I, P3395H
ORF1ab; nsp6: del 3674-3676, I3758V
ORF1ab; RdRp: P4715L
ORF1ab; nsp14: I5967V
E:T9I
M:D3G, Q19E, A63T
Orf9b:P10S, 27-29del
|
Genome Spike Protein NCBI | Less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.2>PANGOCoVariants.org oubtbreak.info: /world prevalence /mutations BV-BRC | BA.221L | South Africa, Dec 2021 |
T19ILPPA24-27SG142DV213GG339DS371FS373PS375FT376AD405NR408SK417NN440KS477NT478KE484AQ493RQ498RN501YY505HD614GH655YN679KP681HN764KD796YQ954HN969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:S135R,
ORF1ab; nsp3:T842I, G1307S,
ORF1ab; nsp4:L3027F, T3090I, L3201F,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6:del 3675-3677
ORF1ab; RdRp:P4715L
ORF1ab; nsp13:R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I
M: Q19E, A63T
ORF6: D61L
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.2.12.1>PANGOCoVariants.org BV-BRC oubtbreak.info: /world prevalence /mutations | BA.2.12.122C | North-America, Dec 2021 |
T19ILPPA24-27SG142DV213GG339DS371FS373PS375FT376AD405NR408SK417NN440KL452QS477NT478KE484AQ493RQ498RN501YY505HD614GH655YN679KP681HS704LN764KD796YQ954HN969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:S135R,
ORF1ab; nsp3:T842I, G1307S,
ORF1ab; nsp4:L3027F, T3090I, L3201F,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6:del 3675-3677
ORF1ab; RdRp:P4715L (=ORF1b: P314L)
ORF1ab; nsp13:R5716C (=ORF1b: R1315C)
ORF1ab; nsp14: I5967V (=ORF1b: I1566V)
ORF1ab; nsp15: T6564I (=ORF1b: T2163I)
ORF3a: T223I
E:T9I
M: Q19E, A63T
ORF6: D61L
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.2.75>PANGOCoVariants.org BV-BRC oubtbreak.info: /world prevalence /mutations | BA.2.7522D | India, spring 2022 |
T19ILPPA24-27SG142DK147EW152RF157LI210VV213GG257SG339HS371FS373PS375FT376AD405NR408SK417NN440KG446NN460KS477NT478KE484AQ498RN501YY505HD614GH655YN679KP681HN764KD796YQ954HN969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:S135R,
ORF1ab; nsp3:T842I, S1221L, G1307S, P1640S
ORF1ab; nsp4:L3027F, T3090I, L3201F,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6:del 3675-3677
ORF1ab; nsp8:N4060S
ORF1ab; RdRp:P4715L, G5063S
ORF1ab; nsp13:R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I, T11A
M: Q19E, A63T
ORF6: D61L
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.4>PANGOCoVariants.org oubtbreak.info: /world prevalence /mutations BV-BRC | BA.422A | South Africa, Jan 2022 |
T19ILPPA24-27SDel 69-70G142DV213GG339DS371FS373PS375FT376AD405NR408SK417NN440KL452RS477NT478KE484AF486VQ498RN501YY505HD614GH655YN679KP681HN764KD796YQ954HN969K
|
N:P13L, 31-33del, P151S, R203K, G204R, S413R
ORF1ab; nsp1:S135R, Del141-143
ORF1ab; nsp3:T842I, G1307S,
ORF1ab; nsp4:L3027F, T3090I,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6:del 3675-3677
ORF1ab; RdRp:P4715L
ORF1ab; nsp13:R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I
M: Q19E, A63T
ORF6: D61L
ORF7b: L11F
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Omicron BA.5>PANGOCoVariants.org BV-BRC oubtbreak.info: world prevalence /mutations | BA.522B | South Africa, Jan 2022 |
T19ILPPA24-27SDel 69-70G142DV213GG339DS371FS373PS375FT376AD405NR408SK417NN440KL452RS477NT478KE484AF486VQ498RN501YY505HD614GH655YN679KP681HN764KD796YQ954HN969K
|
N:P13L, 31-33del, R203K, G204R, S413R
ORF1ab; nsp1:S135R,
ORF1ab; nsp3:T842I, G1307S,
ORF1ab; nsp4:L3027F, T3090I,
ORF1ab; 3CL:T3255I, P3395H
ORF1ab; nsp6:del 3675-3677
ORF1ab; RdRp:P4715L
ORF1ab; nsp13:R5716C
ORF1ab; nsp14: I5967V
ORF1ab; nsp15: T6564I
ORF3a: T223I
E:T9I
M: D3N, Q19E, A63T
Orf9b:P10S, 27-29del
|
Genome Spike protein NCBI | Omicrons are less pathogenic than previous variants because of S and NSP6 mutations
|
| Other Variants | ||||||
| Lineage | Synonyms | Emergence | Spike protein | Other proteins | Consensus sequences | Phenotypes |
|---|---|---|---|---|---|---|
| Alpha>PANGOCoVariants.org outbreak.info | B.1.1.7, 20I/501Y.V1,VOC 202012/01 | UK, Sep 2020 |
Del 69-70
Del 144
N501Y
A570D
D614G
P681H
T716I
S982A
D1118H
|
N: D3L, N: S235F
ORF1ab; nsp3:T1001I, A1708D, I2230T
ORF1ab; nsp6: del 3675-3677
ORF1ab; RdRp: P4715L
ORF8: R52I
ORF8: Q27*
ORF8: Y73C
|
Genome Spike protein UniProt f Spike protein NCBI | Increased transmissibility: 29% . Potential increase in risk of hospitalization (40-64%) and risk of death (30-70%). No adverse effects on vaccine efficacy |
| Beta>PANGOCoVariants.org outbreak.info | B.1.351, 20H/501Y.V2 | South Africa, Aug 2020 |
(L18F)
D80A
D215G
(Del 241-243)
K417N
E484K
N501Y
D614G
A701V
|
N: T205I
ORF1a; nsp1:T265I
ORF1ab; nsp3: K1655N
ORF1ab; 3CL: K3353R
ORF1ab; nsp6: del 3675-3677
ORF1ab; RdRp:P4715L
E: P71L
|
Genome Spike protein NCBI | Increased transmissibility: 25% . Potential increase in risk of death during hospitalization (20%). Impacts immune escape after infection and after vaccination. |
| Gamma>PANGOCoVariants.org outbreak.info | P.1, B.1.1.28.1, 20J/501Y.V3 | Brazil, Jul 2020 |
L18F
T20N
P26S
D138Y
R190S
K417T
E484K
N501Y
D614G
H655Y
T1027I
V1176F
|
ORF1ab;nsp3: S1188L, K1795Q
ORF1ab; nsp6; del 3675-3677
ORF1ab; RdRp: P4715L
ORF1ab; nsp13:E5665D
ORF3a: S253P
ORF8: E92K
N: P80R
|
Genome Spike protein NCBI | Increased transmissibility: 38% . No impact reported on disease severity. Impacts immune escape after infection and after vaccination.
|
| Delta>PANGOCoVariants.org outbreak.info | B.1.617.2, 21J | India,Dec 2020 |
T19R (G142D) 156del 157del R158G L452R T478K D614G P681R D950N
|
ORF1ab; nsp3: A1306S, P2046L, P2287S
ORF1ab; 3CL:K3255R
ORF1ab; nsp12:P5715L, G5063S
ORF1ab; nsp13:P5401L
ORF1ab; nsp14:A6019V
ORF3a:S26L
M:I82T
ORF7a:V82A, T120I
N:D63G, R203M, D377Y
| Genome Spike protein NCBI | Increased transmissibility: 97%
|
| Epsilon>PANGO B.1.427 >PANGO B.1.429 | B.1.427, California(CA)B.1.429, CAL.20C | USA, Sep 2020 |
S13I
W152C
L452R
D614G
|
ORF1a: T265I, (S3158T), (I4205V)
ORF1b: P314L, (P976L), D1183Y
ORF3a: Q57H
N: T205I
|
Genome Spike protein NCBI | Increased transmissibility: 20%. Decreased neutralization by convalescent plasma and vaccines |
| Zeta >PANGO | P.2, B.1.1.28.2 | Brazil, Oct 2020 |
E484K
(F656L)
D614G
(T859I)
V1176F
|
Genome Spike protein NCBI | No impact on public health reported (April 2021). | |
| Eta>PANGO | B.1.525, 20A/S:484K | Worldwide, Dec 2020 |
(Q52R)
A67V
Del 69-70
Del 144
E484K
D614G
Q677H
F888L
|
ORF1ab: L4715F, E:L21F, E:I82T, del:11288:9, del:21765:6, del:28278:3
|
Genome Spike protein NCBI | Potential reduction in neutralization by some monoclonal antibody treatments |
| Theta >PANGO | P.3,B.1.1.28.3, 21E | Philippines, Jan 2021 |
E484K
N501Y
D614G
P681H
E1092K
H1101Y
V1176F
|
ORF1ab: L3201P, D3681E, L3930F, P4715L
ORF8: K2Q
N: R203K, G204R
|
Increased transmissibility. Potential reduction in neutralization by some monoclonal antibody treatments. | |
| Iota>PANGO | B.1.526, 21F | USA, Nov 2020 |
(L5F)
T95I
D253G
(S477N)
(E484K)
D614G
(A701V)
|
ORF1ab: del3675-3677
|
Genome Spike protein NCBI | Potential reduction in neutralization by some monoclonal antibody treatments. |
| Kappa >PANGO | B.1.617.1, 20A/S:154K | India, Oct 2021 |
(T95I)
G142D
E154K
L452R
E484Q
D614G
P681R
Q1071H
| Genome Spike protein NCBI | Increased transmissibility. Potential reduction in neutralization by some monoclonal antibody treatments. | |
| Lambda >PANGOCoVariants.org | C.37, B.1.1.1.C37 | Peru, Dec 2020 |
G75V
T76I
Del 246-252
L452Q
F490S
D614G
T859N
|
Genome Spike protein NCBI | Increased transmissibility | |
| B.1.1.318>PANGO | Switzerland, Jan 2021 |
T95I
Del Y144
E484K
D614G
P681H
D796H
|
||||
| B.1.375>PANGO>BV-BRC | USA, Sep 2020 |
Del H69-V70
D614G
|
ORF1ab: T1828A
ORF1b: E1264D
ORF3a: T151I, M:I48V
|
S gene target failure (SGTF) | ||
| B.1.177>PANGO | 20A.EU1 | Europe, Jul 2020 |
A222V
D614G
|
|||
| B1.? | 20A.EU2 | Europe, Jun 2020 | S477N D614G | May increase resistance to mAb | ||
| A.23.1>PANGO | Uganda, Oct 2020 |
(R102I)
F157L
V367F
Q613H
(P681R)
|
nsp3: E95K
nsp6: M86I, L98F
ORF8: L84S, E92K
N: S202N, Q418H
|
|||
| B.1.616>PANGO | France (Britanny), Jan 2021 |
H66D
Del 144/145
D215G
V483A
H655Y
G669S
Q949R
N1187D
|
ND | Altered detection in upper respiratory tract, responsible of false negative diagnosis | ||
| B.1.214.2>PANGO | Europe, Nov 2020 |
ins214TDR
Q414K
N450K
D614G
T716I
|
N: T205I
ORF1a: A4016V, T1881I, I1398V
ORF1b: P314L
ORF9b: S50L
|
|||
Sources:
Vipr variants of concern
PANGO lineages Societe Francaise de Microbiologie, Variants The Variant Gambit: COVID's Next Move
Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation
Deng. et al.
medRxiv, Mar 21
A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic
Bugembe et al.
medRxiv, Feb 21
Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021
Finlay Campbell et al.
Euro Surveill. 2021 Jun;26(24)
Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Moyo S, Amoako D, Althaus C, Anyaneji U, Kekana D, Viana R, Giandhari J, Maponga T, Maruapula D, Choga W, Mayaphi S, Mbhele N, Gaseitsiwe S, Msomi N, Naidoo Y, Pillay S, Sanko T, San J, Scott L, Singh L, Magini N, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht F, Venter M, Davids M, Chiloane G, Mendes A, McIntyre C, O'Toole A, Ruis C, Peacock T, Roemer C, Williamson C, Pybus O, Bhiman J, Glass A, Martin D, Rambaut A, Gaseitsiwe S, von Gottberg A, Baxter C, Lessells R, de Oliveira T.
Journal: medRxiv,MEDRXIV-2022-274406v1-deOliveira: (2022)
Coronavirus variant XBB.1.5 rises in the United States - is it a global threat?
Ewen Callaway
Journal: Nature. 2023 Jan;613(7943):222-223
Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation
Da-Yuan Chen, Chue Vin Chin, Devin Kenney, Alexander H. Tavares, Nazimuddin Khan, Hasahn L. Conway, GuanQun Liu, Manish C. Choudhary, Hans P. Gertje, Aoife K. O????????????????????Connell, Scott Adams, Darrell N. Kotton, Alexandra Herrmann, Armin Ensser, John H. Connor, Markus Bosmann, Jonathan Z. Li, Michaela U. Gack, Susan C. Baker, Robert N. Kirchdoerfer, Yachana Kataria, Nicholas A. Crossland, Florian Douam & Mohsan Saeed
Nature. 2023 Jan 11