T-cell COVID-19 Atlas (T-CoV)

Browse how SARS-CoV-2 mutations affect CD8 and CD4 T-cell epitopes

May 2022 update: the Omicron BA.3 and BA.4 variants are now avaiable on T-CoV.
Frebruary 2022 update: haplotype-level analysis is now avaiable on T-CoV. Browse 
November 2021 update: the Omicron BA.1 and BA.2 variants are now avaiable on T-CoV.

Individual allele-level analysis

Variant First detected GISAID accession CD8 epitopes (HLA‑I) CD4 epitopes (HLA‑II)
Omicron (BA.4) Denmark hCoV-19/Denmark/DCGC-469344/2022
EPI_ISL_11873073
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Omicron (BA.3) Denmark hCoV-19/Denmark/DCGC-362114/2022
EPI_ISL_9854919
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Omicron (BA.2) USA hCoV-19/USA/CA-CDPH-3000303104/2022
EPI_ISL_9884589
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Omicron (BA.1) South Africa hCoV-19/South Africa/CERI-KRISP-K032226/2021
EPI_ISL_6699752
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Delta G/478K.V1 (B.1.617.2+AY.1+AY.2) India hCoV-19/India/ILSGS00941/2020
EPI_ISL_1663516
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Alpha 202012/01 GRY (B.1.1.7) UK hCoV-19/England/MILK-9E2FE0/2020
EPI_ISL_581117
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Beta GH/501Y.V2 (B.1.351) South Africa hCoV-19/South Africa/KRISP-K004312/2020
EPI_ISL_660190
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Gamma GR/501Y.V3 (P.1) Brazil/Japan hCoV-19/Japan/IC-0561/2021
EPI_ISL_792680
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Lambda GR/452Q.V1 (C.37) Peru hCoV-19/Peru/LIM-INS-869/2020
EPI_ISL_1534645
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Mu GH (B.1.621+B.1.621.1) Colombia hCoV-19/Spain/MD-51402239/2021
EPI_ISL_3099892
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Epsilon GH/452R.V1 (B.1.429+B.1.427) USA/California hCoV-19/USA/CA-CZB-12872/2020
EPI_ISL_648527
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Zeta GR/484K.V2 (P.2) Brazil hCoV-19/England/PORT-2EAFC1/2020
EPI_ISL_842052
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Eta G/484K.V3 (B.1.525) UK/Nigeria hCoV-19/England/CAMC-C769B3/2020
EPI_ISL_760883
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Theta GR/1092K.V1 (P.3) Philippines hCoV-19/Norway/3458/2021
EPI_ISL_1073934
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Iota GH/253G.V1 (B.1.526) USA/New York hCoV-19/USA/NY-MSHSPSP-PV21166/2020
EPI_ISL_801973
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Kappa G/452R.V3 (B.1.617.1) India hCoV-19/India/ILSGS00308/2020
EPI_ISL_1372093
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If your variant of interest is not present in the table above, please contact us at snersisyan@hse.ru.

Please cite one of these papers if you are using T-CoV in your work:

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