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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)

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

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