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Welcome to the BV-BRC SARS-CoV-2 Real-time Tracking and Early Warning System for Variants and Lineages of Concern
(VoCs/LoCs)
For more information, please see The BV-BRC Real-time Tracking and Early Warning System for SARS-CoV-2 Variants and Lineages of Concern (VoCs/LoCs) Tutorial.
VoCs/LoCs are sequence variants or lineages that may significantly affect vaccine efficacy, transmissibility,
disease outcomes,
or other factors critical to gaining control of COVID-19 disease.
The VoC list is based on variants compiled by the CDC.
The VoI list is based on work by the NIAID SAVE Early Detection Working Group [public hyperlink].
The SARS-CoV-2 Variants and Lineages of Concern resource
- Identifies and tracks emerging variants and lineages through daily processing of publicly available SARS-CoV-2 sequences
- Performs risk assessment on the variants to identify candidate VoCs/LoCs by leveraging a growing knowledgebase of sequence features, including protein domains, functional regions, and immune epitopes
- Provides detailed information about each VoC/LoC
- Provides their sequence prevalence in various countries and regions over time using interactive dashboards and charts
- Provides integrated view of the VoCs/LoCs and important sequence features using genome browsers, protein structure viewers, and phylogenetic trees
For more information, please see The BV-BRC Real-time Tracking and Early Warning System for SARS-CoV-2 Variants and Lineages of Concern (VoCs/LoCs) Tutorial.
Currently Monitored Variants / Lineages
| WHO Name | PANGO Lineage | NextStrain Lineage | Emergence Location | Emergence Date | AA Substitutions vs Wuhan-Hu-1: Spike | AA Substitutions vs Wuhan-Hu-1: Non-Spike | Representative Strain |
|---|---|---|---|---|---|---|---|
| Omicron | JN.4 | 23I (Omicron) | Denmark/Israel/USA | September 2023 | A27S, A264D, A475V, A570V, D405N, D614G, D796Y, E484K, E554K, F157S, F486P, G142D, G446S, H69del, H245N, H655Y, ins16MPLF, K356T, K417N, L24del, L212I, L216F, L452W, N211del, N440K, N450D, N460K, N481K, N679K, N764K, N969K, P25del, P26del, P621S, P681R, P1143L, Q954H, R21T, R158G, R403K, R408S, S50L, S371F, S373P, S477N, S939F, T19I, T376A, T478K, V70del, V127F, V213G, V445H, V483del, Y144del | E T9I; M A63T, A104V, D3H, Q19E, T30A; N E31del, G204R, P13L, Q229K, R32del, R203K, S33del, S413R; NS3 T223I; NS7a S37F; NSP1 S135R; NSP2 A31D, K500N; NSP3 A1892T, G489S, K1155R, N1708S, T24I, V238L; NSP4 L264F, T492I; NSP5 P132H; NSP6 F108del, G107del, S106del, V24F; NSP9 T35I; NSP12 P323L; NSP13 R392C; NSP14 I42V; NSP15 T112I | SARS-CoV-2/human/USA/MD-MDH-9069/2023 |
| Omicron | HK.3.2 | 23F (Omicron) | Indonesia/France | August 2023 | A27S, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q14K, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I; NS6: L15V; NS7a: T115I; NS7b: I7T; NS8: G8stop; NSP1: E148A, K47R, S135R; NSP2: A510V; NSP3: G489S, G1001S, T24I; NSP4: A380V, L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: D63N, G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/NJ-CDC-QDX85241599/2023 |
| Omicron | GW.5.1.1 | 22F (Omicron) | India | August 2023 | A27S, A475V, D405N, D614G, D796Y, E484A, E554K, F79S, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478I, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, P80S, R32del, R203K, S33del, S413R; NS3: G172C, T223I, W149C; NSP1: K47R, P62L, S135R; NSP2: S122F; NSP3: G489S, P1261Q, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: K90R, P132H; NSP6: F108del, G107del, S106del; NSP9: P80L; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/MN-CDC-VSX-A09331/2023 |
| Omicron | HV.1 | 23F (Omicron) | Indonesia/France | July 2023 | A27S, D405N, D614G, D796Y, E484A, F157L, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L452R, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E T9I, T11A; M A63T, Q19E; N E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3 T223I; NS7a T115I; NS8 G8stop; NSP1 K47R, S135R; NSP2 A510V; NSP3 G489S, G1001S, S1039L, T24I; NSP4 A380V, L264F, L438F, T327I, T492I; NSP5 P132H; NSP6 F108del, G107del, S106del; NSP9 T35I; NSP12 G671S, P323L; NSP13 R392C, S36P; NSP14 I42V; NSP15 T112I | SARS-CoV-2/human/USA/MD-CDC-LC1057321/2023 |
| Omicron | HK.2 | 23F (Omicron) | Indonesia/France | June 2023 | A27S, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q14H, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y505H | E T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I, Y211H; NS8: G8stop; NSP1: K47R, S135R; NSP2: A510V; NSP3: G489S, G1001S, K1943R, T24I; NSP4: A380V, L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: D63N, G671S, P323L; NSP13: R392C, S36P; NSP14: A96V, I42V; NSP15: T112I | UNKNOWN-OY779846 |
| Omicron | FL.1.5.2 | 23D (Omicron) | Indonesia/Israel/Singapore | June 2023 | A27S, A701V, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, N440K, N460K, N481K, N501Y, N679K, N764K, N969K, P25del, P26del, P681R, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I; NS8: G8stop; NSP1: K47R, S135R; NSP3: G175S, G489S, G1001S, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I; NSP16: K160R | SARS-CoV-2/human/USA/MA-CDC-QDX85193071/2023 |
| Omicron | JF.1 | 23B (Omicron) | India | June 2023 | A27S, D405N, D614G, D796Y, E180V, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478R, V83A, V213E, V445P, Y144del, Y505H | E T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I, Y211H; NS8: G8stop; NSP1: K47R, S135R; NSP3: G489S, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, L260F, S106del; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: D222Y, I42V; NSP15: T112I | SARS-CoV-2/human/USA/FL-CDC-QDX83301046/2023 |
| Omicron | DV.7.1 | 23C (Omicron) | Austria | May 2023 | A27S, D405N, D614G, D796Y, E484A, F157L, F456L, F486S, G142D, G257S, G339H, G446S, H655Y, I210V, K147E, K417N, K444T, L24del, L452R, L455F, L858I, N185D, N440K, N460K, N501Y, N764K, N969K, P25del, P26del, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V213G, W152R, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: A72T, A110V, T223I; NSP1: E37G, S135R; NSP3: E52D, G145D, G489S, P822S, Q380K, S403L, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: A285V, P132H; NSP6: F108del, G107del, S106del; NSP8: N118S; NSP12: A529V, G671S, L49I, P323L; NSP13: R392C; NSP14: I42V, V182I; NSP15: K89R, T112I; NSP16: Q28R | SARS-CoV-2/human/USA/CA-LACPHL-AY01271/2023 |
| Omicron | JD.1.1.1 | 23A (Omicron) | Austria/India/Bangladesh | April 2023 | A27S, A475V, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y248H, Y505H | E T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I; NS8: G8stop; NSP1: K47R, S135R; NSP3: G489S, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP10: T12I; NSP12: A250V, G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/IL-CDC-QDX85193109/2023 |
| Omicron | GW.5 | 22F (Omicron) | India | April 2023 | A27S, D405N, D614G, D796Y, E484A, E554K, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478I, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, P80S, R32del, R203K, S33del, S413R; NS3: T223I, NS7b C41Y; NSP1: G82del, H83del, K47R, M85del, S135R, V84del, V86del; NSP2: I514V, S122F; NSP3: G489S, P1261Q, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: P80L; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/NY-CDC-QDX84542137/2023
SARS-CoV-2/human/USA/MI-CDC-2-7320511/2023 |
| Omicron | JN.1 | 23I (Omicron) | Luxembourg/Iceland | January 2023 | A27S, A264D, A570V, D405N, D614G, D796Y, E484K, E554K, F157S, F486P, G142D, G339H, G446S, H69del, H245N, H655Y, I332V, ins16MPLF, K356T, K417N, L24del, L212I, L216F, L452W, L455S, N211del, N440K, N450D, N460K, N481K, N501Y, N679K, N764K, N969K, P25del, P26del, P621S, P681R, P1143L, Q498R, Q954H, R21T, R158G, R403K, R408S, S50L, S371F, S373P, S375F, S477N, S939F, T19I, T376A, T478K, V70del, V127F, V213G, V445H, V483del, Y144del, Y505H | E T9I; M A63T, A104V, D3H, Q19E, T30A; N E31del, G204R, P13L, Q229K, R32del, R203K, S33del, S413R; NS3 T223I; NS7b F19L; NSP1 S135R; NSP2 A31D; NSP3 A1892T, G489S, K1155R, N1708S, T24I, V238L; NSP4 L264F, T327I, T492I; NSP5 P132H; NSP6 F108del, G107del, R252K, S106del, V24F; NSP9 T35I; NSP12 P323L; NSP13 R392C; NSP14 I42V; NSP15 T112I | SARS-CoV-2/human/BEL/rega-20174/2021 |
| Omicron | HK.3 | 23H (Omicron) | Austria/India/Bangladesh | January 2023 | A27S, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G120V, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T34A, T223I; NS8: G8stop; NSP1: K47R, S135R; NSP2: A510V; NSP3: G489S, G1001S, T24I; NSP4: A380V, L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: D63N, G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/NY-CDC-QDX84734656/2023 |
| Omicron | EG.5.1 | 23F (Omicron) | Indonesia/France | January 2023 | A27S, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I; NS8: G8stop; NSP1: K47R, S135R; NSP2: A510V, S99F; NSP3: G489S, G1001S, T24I; NSP4: A380V, L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | hCoV-19/Switzerland/ZH-UZH-IMV-3ba6ae5d/2023 |
| Omicron | FL.1.5.1 | 23D (Omicron) | Indonesia/Israel/Singapore | October 2022 | A27S, A701V, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478R, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I; NS8: G8stop; NSP1: K47R, S135R; NSP3: G175S, G489S, G1001S, T24I; NSP4: L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: S147I, T112I; NSP16: K160R | SARS-CoV-2/human/USA/NY-CDC-QDX84971198/2023 |
| Omicron | JD.1.1 | 23A (Omicron) | Indonesia/France | October 2022 | A27S, A475V, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E T9I, T11A; M A63T, Q19E; N G204R, P13L, R203K, S413R; NS3 T223I; NS8 G8stop; NSP1 K47R, S135R; NSP3 G489S, T24I; NSP4 L264F, L438F, T327I, T492I; NSP5 P132H; NSP6 F108del, G107del, S106del; NSP12 A250V, G671S, P323L; NSP13 R392C, S36P; NSP14 I42V; NSP15 T112I | SARS-CoV-2/human/USA/FL-BPHL-1807/2020 |
| Omicron | XBB.1 | 22F (Omicron) | USA/Singapore | September 2022 | T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486S, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:K47R, S135R; nsp3:T24I, G489S; nsp4:L264F, T327I, L438F, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-; nsp12:P323L, G671S; nsp13:S36P, R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I, T11A; M:Q19E, A63T; ORF8:G8stop; N:P13L, E31-, R32-, S33-, R203K, G204R, S413R | SARS-CoV-2/human/USA/AZ-CDC-STM-PX93VHGWN/2022 |
| Omicron | XBB | 22F (Omicron) | USA/Singapore | August 2022 | T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486S, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:K47R, G82D, S135R; nsp3:T24I, G489S; nsp4:L264F, T327I, L438F, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-; nsp12:P323L, G671S; nsp13:S36P, R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I,T11A; M:Q19E, A63T; N:P13L, E31-, R32-, S33-, R203K, G204R, S413R | SARS-CoV-2/human/USA/MI-CDC-STM-C932986AR/2022 |
| Omicron | BQ.1.1 | 22E (Omicron) | Nigeria | July 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444TL452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp2:Q376K; nsp3:T24I, G489S; nsp4:L264F, T327I, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-, L260F; nsp12:Y273H, P323L; nsp13:M233I, N268S, R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:D3N, Q19E, A63T; N:P13L, E31-, R32-, S33-, E136D, R203K, G204R, S413R | SARS-CoV-2/human/USA/IL-CDC-QDX40817824/2022 |
| Omicron | BQ.1 | 22E (Omicron) | Nigeria | July 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444TL452R, N460, KS477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp2:Q376K; nsp3:T24I, G489S; nsp4:L264F, T327I, T492I; nsp5: P132H; nsp6:S106-, G107-, F108-, L260F; nsp12:Y273H, P323L; nsp13: M233I, R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:D3N, Q19E, A63T; N:P13L, E31-, R32-, S33-, E136D, R203K, G204R, S413R | SARS-CoV-2/human/USA/MI-CDC-QDX40579621/202 |
| Omicron | BA.2.75* | 22D (Omicron) | India | June 2022 | T19I, L24-, P25-, P26-, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, G339H, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, R493Q, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1: S135R; nsp3: T24I, S403L, G489S, P822S; nsp4: L264F, T327I, L438F, T492I; nsp5: P132H; nsp6: S106-, G107-, F108-; nsp8: N118S; nsp12: P323L, G671S; nsp13: R392C; nsp14: I42V; nsp15: T112I; ORF3a:T223I; E:T9I, T11A; M:Q19E, A63T; ORF6:D61L; N:P13L, E31-, R32-, S33-, R203K, G204R, S413R | SARS-CoV-2/human/USA/IL-CDC-STM-G6D8GUH6S/2022 |
| Omicron | BF.7 | 22B (Omicron) | Multiple | June 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp3:T24I, G489S; nsp4:L264F, L327I, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-; nsp12:P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:D3N, Q19E, A63T; N:P13L,E31-, R32-, S33-, P151S, R203K, G204R, S413R | SARS-CoV-2/human/USA/UT-IDEL20220621042 |
| Omicron | BA.4.6 | 22A (Omicron) | USA | April 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N658S, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R, 141, 142-, 143-; nsp2:Q376K; nsp3:T24I, G489S; nsp4:L264F, T327I, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-; nsp12:P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:Q19E, A63T; ORF6:D61L; ORF7b:L11F; ORF8:S84L; N:P13L, E31-, R32-, S33-, P151S, R203K, G204R, S413R | SARS-CoV-2/human/SouthAfrica/NHLS-UCT-LA-Z997/2022 |
| Omicron | JG.3 | 23F (Omicron) | Indonesia/France | January 2022 | A27S, D405N, D614G, D796Y, E484A, F456L, F486P, F490S, G142D, G252V, G339H, G446S, H146Q, H655Y, K417N, L24del, L368I, L455F, N440K, N460K, N501Y, N679K, N764K, N969K, P25del, P26del, P681H, Q52H, Q183E, Q498R, Q954H, R346T, R408S, S371F, S373P, S375F, S477N, S704L, T19I, T376A, T478K, V83A, V213E, V445P, Y144del, Y505H | E: T9I, T11A; M: A63T, Q19E; N: E31del, G204R, P13L, R32del, R203K, S33del, S413R; NS3: T223I, NS7a K53I; NS8: G8stop; NSP1: K47R, S135R; NSP2: A510V, R362C; NSP3: G489S, G1001S, T24I, T1456I; NSP4: A380V, L264F, L438F, T327I, T492I; NSP5: P132H; NSP6: F108del, G107del, S106del; NSP9: T35I; NSP12: G671S, P323L; NSP13: R392C, S36P; NSP14: I42V; NSP15: T112I | SARS-CoV-2/human/USA/UT-UPHL-231109691269/2023 |
| Omicron | BA.5* | 22B (Omicron) | Southern Africa | January 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp2:Q376K; nsp3:T24I, G489S; nsp4:L264F, T327I, T492I; nsp5:P132H; nsp6:S106-, G107-, F108-; nsp12:P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:D3N, Q19E, A63T; N:P13L, E31-, R32-, S33-, R203K, G204R, S413R | SARS-CoV-2/human/USA/MI-CDC-ASC210848963/2022 |
| Omicron | BA.4* | 22A (Omicron) | Southern Africa | January 2022 | T19I, L24-, P25-, P26-, A27S, H69-, V70-, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp3:T24I, G489S; nsp4:L264F, T327I, T492I; nsp5: P132H; nsp6:S106-, G107-, F108-; nsp12:P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:Q19E, A63T; ORF6:D61L; ORF7b: L11F; N:P13L, E31-, R32-, S33-, P151S, R203K, G204R, S413R | SARS-CoV-2/human/USA/PA-CDC-LC0583069/2022 |
| Omicron | BA.2.12.1 | 22C (Omicron) | Canada/USA | December 2021 | T19I, L24-, P25-, P26-, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp3:T24I, nsp3:G489S; nsp4:L264F, T327I, L438F, T492I; nsp5:P132H; nsp6:-106-108; nsp12 P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:Q19E, A63T; ORF6:D61L; ORF8:S84L; N:P13L, -31/33, R203K, G204R, S413R | SARS-CoV-2/human/USA/NY-CDC-LC0553978/2022 |
| Omicron | BA.2 + BA.2* | 21L (Omicron) | Southern Africa | November 2021 | T19I, L24-, P25-, P26-, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1:S135R; nsp3:T24I, nsp3:G489S; nsp4:L264F, T327I, L438F, T492I; nsp5:P132H; nsp6:-106-108; nsp12 P323L; nsp13:R392C; nsp14:I42V; nsp15:T112I; ORF3a:T223I; E:T9I; M:Q19E, A63T; ORF6:D61L; ORF8:S84L; N:P13L, -31/33, R203K, G204R, S413R | SARS-CoV-2/human/USA/FL-CDC-STM-77CPCCUR3/2022 |
| Omicron | BA.3 | 21K (Omicron) | Southern Africa | November 2021 | A67V, H69-, V70-, T95I, G142D, V143-, Y144-, Y145-, N211-, L212I, G339D, S371F, S373P, S375F, D405N, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K | nsp1: S135R; nsp3: T24I, G489S, nsp4: L264F, T327I, L438F, T492I: nsp5: P132H; nsp6: S106-, G107-, F108-; nsp12: P323L; nsp13: R392C; nsp14: I42V; nsp15: T112I; ORF3a: T223I; E: T9I; M: Q19E, A63T; N: P13L, E31-, R32-, S33-, R203K, G204R, S413R | UNKNOWN-OV494217 |
| Omicron | BA.1 + BA.1.* | 21K (Omicron) | Southern Africa | November 2021 | A67V, H69-, V70-, T95I, G142D, V143-, Y144-, Y145-, N211-, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F | nsp3: K38R, S1265-, L1266I, A1892T; nsp4: T492I; nsp5: P132H; nsp6: L105-, S106-, G107-, I189V; nsp12: P323L; nsp14: I42V; E: T9I; M: D3G, Q19E, A63T; N: P13L, E31-, R32-, S33-, R203K, G204R | SARS-CoV-2/human/BEL/rega-20174/2021 |
* denotes mutations found in at least >25% variants, but not in all sequences
** denotes mutations found in more than one VoC indicating possible positive selection, shared ancestry and/or convergent evolution
Help Documents
Acknowledgements
We gratefully acknowledge the authors, originating and submitting laboratories that have shared their SARS-CoV-2 genomic data via GenBank and SRA and COG-UK, which is used to build this system.
Recent PubMed Articles
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* denotes mutations found in at least >25% variants, but not in all sequences
** denotes mutations found in more than one VoC indicating possible positive selection, shared ancestry and/or convergent evolution
Protein Structure
| PDB ID | Title | Oragnism Name | UniProtKB Accession | Gene | Product | Method | Resolution | PMID | Institution | Authors | Release Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 6M0J | Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 | Homo sapiens;Severe acute respiratory syndrome coronavirus 2 | P0DTC2; Q9BYF1 | ACE2, S | surface glycoprotein | X-ray diffraction | 32225176 | Ge, J.;Wang, Q.;Shi, X.;Fan, S.;Lan, J.;Shan, S.;Yu, J.;Zhou, H.;Zhang, L.;Wang, X.;Zhang, Q. | 3/18/20 | ||
| 6W41 | Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 | Homo sapiens;Severe acute respiratory syndrome coronavirus 2 | P0DTC2 | S | surface glycoprotein | X-ray diffraction | 32245784 | So, R.T.Y.;Wilson, I.A.;Lee, C.D.;Yuan, M.;Zhu, X.;Wu, N.C.;Lv, H.;Mok, C.K.P. | 3/25/20 | ||
| 6VXX | Structure of the SARS-CoV-2 spike glycoprotein (closed state) | Severe acute respiratory syndrome coronavirus 2 | P0DTC2 | S | surface glycoprotein | Electron microscopy | 2.8 | 32155444 | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | Wall, A.;Park, Y.J.;McGuire, A.T.;Veesler, D.;Tortorici, M.A.;Walls, A.C. | 3/11/20 |
| 6VYB | SARS-CoV-2 spike ectodomain structure (open state) | Severe acute respiratory syndrome coronavirus 2 | P0DTC2 | S | surface glycoprotein | Electron microscopy | 3.2 | 32155444 | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | Tortorici, M.A.;Walls, A.C.;Veesler, D.;Wall, A.;McGuire, A.T.;Park, Y.J. | 3/11/20 |
SARS-CoV-2 Resources
| Resource | Description | Data Types |
|---|---|---|
| BEI SARS-CoV-2 Resources | Information about SARS-CoV-2 strains and reagents. | biomaterial |
| Bloom Lab: ACE-2 Binding affinities | Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding (Reference) | Experiemntal data on point mutations affecting receptor binding |
| Broad Terra cloud commons for pathogen surveillance | The Broad Terra cloud workspace with COVID-19 genomics data and orkflows for genome assembly, quality control, metagenomic classification, and aggregate statistics. | genomics |
| CDC SARS-CoV-2 Sequencing Resources | rowd-sourced collection of information, documentation, protocols and other resources for public health laboratories intending to sequence SARS-CoV-2 samples. | protocols |
| China National Center for Bioinformation's 2019 Novel Coronavirus Resource (2019nCoVR) | A comprehensive resource on COVID-19, combining up-to-date information on all published sequences, mutation analyses, literatures and others. | genomics, variant tracking, literature |
| Coronavirus 3D | Web-based viewer for 3D visualization and analysis of the SARS-CoV-2 protein structures with respect to the CoV-2 mutational patterns | protein structures |
| CoV-GLUE | Amino acid variation database of amino acid replacements, insertions and deletions | variant tracking |
| CoVariants | SARS-CoV-2 variant tracking dashboard largely based on NEXTSTRAIN | Multiple: phylogenomics, variant tracking |
| COVID-19 CoV Genetics Browser | Track transmission, evolution, emergence, immune interactions, diagnostics, therapeutics & vaccines | variant tracking |
| COVID-19 Genome Sequence Dataset on Registry of Open Data on AWS | A centralized sequence repository for all strains of novel corona virus (SARS-CoV-2) submitted to NCBI. Included are both the original sequences submitted by the principal investigator as well as SRA-processed sequences that require the SRA Toolkit for analysis. | genomics |
| CoVizu | Near real-time visualization of hCoV-19 genomic variation | |
| GISAID | International database of hCoV-19 genome sequences and related clinical and epidemiological data | genomics |
| GISAID variant tracking page | GISAID's variant tracking dashboard | Strains, map, graph, metadata, |
| Immune Epitope Database (IEDB) | Experimental data on SARS-CoV-2 antibodies and T cell epitopes | immunology |
| LANL COVID-19 Viral Genome Analysis | Analyses and tools for exploring accruing mutations in SARS-CoV-2, geographically and over time, with an emphasis on the Spike protein. | variant tracking |
| NCBI SARS-CoV-2 Resources | SARS-CoV-2 related data and resources at NCBI, such as nucleotide and protein sequences from GenBank and RefSeq, genomic and metagenomic read sets in SRA, BLAST, PubMed, Clinical Trials. | genomics, literature |
| NextClade | Tool to perform clade assignment, mutation calling, and sequence quality checks/td> | phylogenomics |
| Nextstrain COVID-19 genetic epidemiology | Open-source SARS-CoV-2 genome data and analytic and visualization tools | phylogenomics, variant tracking |
| Pango Lineages | A dynamic nomenclature for SARS-CoV-2 lineages. Pangolin, a tool for global lineage assignment. | phylogenomics, variant tracking |
| Reactome | Open-source curated and peer-reviewed pathway database, including human coronavirus infection pathways. Tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. | genomics, visualization |
| UCSC SARS-CoV-2 Genome Browser | The UCSC SARS-CoV-2 genome browser and COVID-19 lung gene expression datasets. | genome browser |
| UniProtKB SARS-CoV-2 | SARS-CoV-2 proteins and annotations | protein annotation |