Sars-CoV-2 circulating variants

This page describes circulating SARS-CoV-2 variants - Last updated 12/January/2023.

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.



PDBe Molstar viewer documentation (external)

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)

  • Omicron (XBB.1.5)
  • Omicron (BA.4/5)
  • Omicron (BA.2.12.1)
  • Omicron (BA.2)
  • Omicron (BA.1)
  • B.1.427, B.1.429 (Epsilon)
  • P1 (Gamma)
  • B.1.617.2 (Delta)
  • B.1.351 (Beta)
  • B.1.1.7 (Alpha)
  • D614G



Reference sequence
LineageSynonymsEmergenceSpike proteinOther proteinsConsensus 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 proteinOther proteinsConsensus sequencesPhenotypes
Omicron BQ.1.1
PANGO
CoVariants.org
oubtbreak.info:
/world prevalence
/mutations
BV-BRC
BQ.1.1
22E
Nigeria, Jul 2022 Genome
Spike protein NCBI
Omicron XBB.1.5
PANGO
CoVariants.org
oubtbreak.info;
/world prevalence
/mutations
BV-BRC
XBB.1.5
22F
USA, Nov 2022 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
Omicron BA.1
>PANGO
CoVariants.org
oubtbreak.info:
/world prevalence
/mutations
BV-BRC
BA.1 (previously B.1.1.529),
21K
South Africa, Dec 2021 Genome
Spike Protein NCBI
Omicron BA.2
>PANGO
CoVariants.org
oubtbreak.info:
/world prevalence
/mutations
BV-BRC
BA.2
21L
South Africa, Dec 2021 Genome
Spike protein NCBI
Omicron BA.2.12.1
>PANGO
CoVariants.org
BV-BRC
oubtbreak.info:
/world prevalence
/mutations
BA.2.12.1
22C
North-America, Dec 2021 Genome
Spike protein NCBI
Omicron BA.2.75
>PANGO
CoVariants.org
BV-BRC
oubtbreak.info:
/world prevalence
/mutations
BA.2.75
22D
India, spring 2022 Genome
Spike protein NCBI
Omicron BA.4
>PANGO
CoVariants.org
oubtbreak.info:
/world prevalence
/mutations
BV-BRC
BA.4
22A
South Africa, Jan 2022 Genome
Spike protein NCBI
Omicron BA.5
>PANGO
CoVariants.org
BV-BRC
oubtbreak.info:
world prevalence
/mutations
BA.5
22B
South Africa, Jan 2022 Genome
Spike protein NCBI



Other Variants
LineageSynonymsEmergenceSpike proteinOther proteinsConsensus sequencesPhenotypes
Alpha
>PANGO
CoVariants.org
outbreak.info
B.1.1.7, 20I/501Y.V1,
VOC 202012/01
UK, Sep 2020 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
CoVariants.org
outbreak.info
B.1.351, 20H/501Y.V2 South Africa, Aug 2020 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
CoVariants.org
outbreak.info
P.1, B.1.1.28.1, 20J/501Y.V3 Brazil, Jul 2020 Genome
Spike protein NCBI
Increased transmissibility: 38% . No impact reported on disease severity. Impacts immune escape after infection and after vaccination.
Delta
>PANGO
CoVariants.org
outbreak.info
B.1.617.2, 21J India,Dec 2020 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 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 Genome
Spike protein NCBI
No impact on public health reported (April 2021).
Eta
>PANGO
B.1.525, 20A/S:484K Worldwide, Dec 2020 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 Increased transmissibility. Potential reduction in neutralization by some monoclonal antibody treatments.
Iota
>PANGO
B.1.526, 21F USA, Nov 2020 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 Genome
Spike protein NCBI
Increased transmissibility. Potential reduction in neutralization by some monoclonal antibody treatments.
Lambda
>PANGO
CoVariants.org
C.37, B.1.1.1.C37 Peru, Dec 2020 Genome
Spike protein NCBI
Increased transmissibility
B.1.1.318
>PANGO
Switzerland, Jan 2021
B.1.375
>PANGO
>BV-BRC
USA, Sep 2020 S gene target failure (SGTF)
B.1.177
>PANGO
20A.EU1 Europe, Jul 2020
B1.? 20A.EU2 Europe, Jun 2020 S477N
D614G
May increase resistance to mAb
A.23.1
>PANGO
Uganda, Oct 2020
B.1.616
>PANGO
France (Britanny), Jan 2021 ND Altered detection in upper respiratory tract, responsible of false negative diagnosis
B.1.214.2
>PANGO
Europe, Nov 2020