Sars-CoV-2 circulating variants

This page describes circulating SARS-CoV-2 variants - Last updated 08/Jul/2021.
It includes all variants designated as "Variant of Concern" (VOC) or "Variant of Interest" (VOI) from WHO.
Variant sequences can be parsed from UniProt P0DTC2 at COVID-19 pre-release portal.

Variants are lines 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.



SARS-CoV-2 Spike protein: Click to highlight 3D structure regions of interest

  • S1 chain
    • N-Terminal domain (NTD)- Antibody binding
    • Receptor binding domain(RBD)- Receptor and antibody binding
    • Main domains targeted by neutralizing antibodies
  • S2 chain
    • Heptad repeat1 (HR1)- fusion helix
  • RGD motif

Variants of Concern (VOC): Click to display variant sites (zoom in PDB window for a better view)

  • D614G
  • B.1.1.7 (Alpha)
  • B.1.351 (Beta)
  • P1 (Gamma)
  • B.1.617.2 (Delta)
  • B.1.427, B.1.429 (Epsilon)



Table below in PDF: Table-Variants-SARS-CoV-2.pdf

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Reference sequence
LineageSynonymsEmergenceSpike variantsOther variantsConsensus sequencesPhenotypes
19A Wuhan-Hu-1, nCoV China, Dec 2019 None None Genome
Spike protein
All proteins
Reference for variants

Variant of concern (VOC): A variant for which there is evidence of an increase in transmissibility, more severe disease and or escape of neutralization by antibodies
LineageSynonymsEmergenceSpike variantsOther variantsConsensus sequencesPhenotypes
Alpha
>PANGO
>BV-BRC
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
ORF1ab: T1001I
ORF1ab: A1708D
ORF1ab: I2230T, del:11288:9, del:21765:6, del:21991:3
ORF8: R52I
ORF8: Q27*
ORF8: Y73C
N: D3L
N: S235F
Genome
Spike protein UniProt
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
>PANGO
>BV-BRC
B.1.351, 20H/501Y.V2 South Africa, Aug 2020 (L18F)
D80A
D215G
(Del 241-243)
K417N
E484K
N501Y
D614G
A701V
E: P71L
N: T205I
ORF1a: K1655N
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
>PANGO
>BV-BRC
P.1, B.1.1.28.1, 20J/501Y.V3 Brazil, Jul 2020 L18F
T20N
P26S
D138Y
R190S
K417N/T
E484K
N501Y
D614G
H655Y
T1027I
V1176F
ORF1ab: S1188L, K1795Q, del:11288:9
ORF3a: S253P
ORF8: E92K
N: P80R
Genome
Spike protein UniProt
Spike protein NCBI
Increased transmissibility: 38% . No impact reported on disease severity. Impacts immune escape after infection and after vaccination.
Delta
>PANGO
>BV-BRC
B.1.617.2, 20A/452R India,Dec 2020 T19R
(G142D)
156del
157del
R158G
L452R
T478K
D614G
P681R
D950N
nsp3:P1469S
nsp12:P323L, G671S
nsp13:P77L
ORF3a:S26L
M:I82T
ORF7a:V82A, T120I
N:D63G, R203M, D377Y
Genome
Spike protein NCBI
Increased transmissibility: 97%


Variant of Interest (VOI): A variant with specific genetic markers that have been associated with changes that may impact public health.
LineageSynonymsEmergenceSpike variantsOther variantsConsensus sequencesPhenotypes
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
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 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 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
Increased transmissibility. Potential reduction in neutralization by some monoclonal antibody treatments.
Lambda
>PANGO
C.37, B.1.1.1.C37 Peru, Dec 2020 G75V
T76I
Del 246-252
L452Q
F490S
D614G
T859N
Increased transmissibility


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Other Variants
LineageSynonymsEmergenceSpike variantsOther variantsConsensus sequencesPhenotypes
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