Sars-CoV-2 circulating variants

This page describes circulating SARS-CoV-2 variants - Last updated 04/21/2021.
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 may also have implications for 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 mutation sites (zoom in PDB window for a better view)
    D614G
    B.1.1.7
    B.1.351
    P1
    B.1.427, B.1.429
    variant


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

image

Reference sequence
LineagesynonymsEmergenceSpike substitutionsOther substitutionsConsensus fastaPhenotypes
19AWuhan-Hu-1, nCoV China, Dec. 2019NoneNoneGenome
Spike protein
All proteins
Reference for variants

Variant of concern (VOC):variants for which there is evidence of an increase in transmissibility, more severe disease and or escape of neutralization by antibodies
LineagesynonymsEmergenceSpike substitutionsOther substitutionsConsensus fastaPhenotypes
B.1.1.7
>PANGO
>BV-BRC
20I/501Y.V1,
VOC 202012/01
UK, September 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:S235Fgenome
Spike protein
All proteins
Increased transmissibility: 36-75%. Potential increase in risk of hospitalization (40-64%) and risk of death (30-70%). No adverse effects on vaccine efficacy
B.1.351
>PANGO
>BV-BRC
20H/501Y.V2South Africa, Aug 2020 (L18F), D80A, D215G , (Del 242-244), K417N, E484K, N501Y, D614G, A701V E:P71L, N:T205I, orf1a:K1655Ngenome
Spike protein
All proteins
Increased transmissibility: approximately 50%. Potential increase in risk of death during hospitalization (20%). Impacts immune escape after infection and after vaccination.
P.1
>PANGO
>BV-BRC
B.1.1.28.1, 20J/501Y.V3Brazil, July 2020 L18F, T20N, P26S, D138Y, R190S, K417N/T, E484K, N501Y, D614G, H655Y, T1027I, V1176Forf1ab:S1188L, orf1ab:K1795Q, del:11288:9,
orf3a:G174C, orf8:E92K
N:P80R
genome
Spike protein
All proteins
Increased transmissibility: 40-120%. No impact reported on disease severity. Impacts immune escape after infection and after vaccination.
B.1.427
>PANGO
California(CA)USA Sept. 2020S13I, W152C, L452R, D614Gorf1a:T265I, S3158T, orf1b:P314L, P976L, D1183Y,
orf3a:Q57H,
N:T205I
Increased transmission (20%) and decreased neutralization by convalescent plasma and vaccines
B.1.429
>PANGO
>BV-BRC
CAL.20CCalifornia July 2020S13I, W152C, L452R, D614Gorf1a:T265I, I4205V, orf1b:P314L, D1183Y,
orf3a:Q57H,
N:T205I
genome
Spike protein
All proteins
Increased transmission (20%) and decreased neutralization by convalescent plasma and vaccines
,
Variant of Interest (VOI):A variant with specific genetic markers that have been associated with changes that may impact public health.
LineagesynonymsEmergenceSpike substitutionsOther substitutionsConsensus fastaPhenotypes
P.2
>PANGO
B.1.1.28.2Brasil, Oct. 2020E484K, D614G, (T859I), (V1176F)No impact on public health reported (April 2021).
B.1.1.318
>PANGO
Switzerland, Janv 2021T95I, DelY144, E484K, D614G, P681H, D796H
B.1.375
>PANGO
>BV-BRC
USA, Sept 2020Del H69-V70
D614G
orf1ab:T1828A,
orf1b:E1264D,
orf3a: T151I,
M:I48V
genome
S Protein
All proteins
S gene target failure (SGTF)
B.1.525
>PANGO
Worldwide Dec.2020 Q52R, E484K, D614G, Q677H, F888L orf1ab:L4715F, E:L21F, E:I82T, del:11288:9, del:21765:6, del:28278:3No impact on public health reported (April 2021)
B.1.526
>PANGO
USA Sept 2020L5F, T95I, D253G, (S477N), (E484K), D614G, A701V
B.1.177
>PANGO
20A.EU1Europe, Jul. 2020A222V, D614G
B1.?20A.EU2Europe; Jun. 2020S477N, D614GMay increase resistance to mAb
A.23.1
>PANGO
Uganda Oct.2020 (R102I), F157L, V367F, Q613H, (P681R)nsp3: E95K, nsp6: M86I, L98F, ORF 8: L84S, E92K and ORF9 N: S202N, Q418HN.D.
B.1.616
>PANGO
France, britanny Jan.2021 H66D, Del144/145, D215G, V483A, H655Y, G669S, Q949R, N1187D NDAltered detection in upper respiratory tract, responsible of false negative diagnosis
B.1.617
>PANGO
India, Oct.2020 L452R,(E484Q),P681R ORF1b:P314L
N:D377Y, R203M
ORF3a: S26L
ORF7a: V82A
B.1.214.2
>PANGO
Europe, nov.2020 ins214TDR, Q414K, N450K, D614G, T716I N:T205I
ORF1a:A4016V,T1881I,I1398V
ORF1b:P314L
ORF9b:S50L