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Welcome to the Regeneron COVID-19 Dashboard

This dashboard contains aggregated information on SARS-CoV-2 (hCoV-19) genomes and associated patient metadata, gathered in partnership with the GISAID initiative.

The goal of the dashboard is to enable scientists to understand the evolution of this emerging coronavirus by monitoring and displaying pertinent information. For example, the dashboard displays the novel mutations in SARS-CoV-2 (hCoV-19) genomes across time and geographical location, which facilitates the identification of a mutation that may increase transmission or virulence.

In addition, there is de-identified patient demographic information such as country of origin, patient status, and age, which provides further insights into the populations most susceptible to the virus.

15,519,961

SARS-CoV-2 (hCoV-19) genomes

September 09, 2023

03:35 AM ET

Last data update

Top Lineages Per Country (Past 12 Weeks)

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Lineage WHO Label Country Percent Lineage Count Total Count
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Russia 55% 34 62
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Luxembourg 50% 186 373
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Portugal 45% 271 597
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Belgium 41% 146 355
EL.1EL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (83%), N440K, V445P (90%), G446S (90%), N460K, S477N, T478K, E484A, F486P, F490S, Q498R (89%), N501Y (89%), Y505H (88%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A (90%), G142D, Y144- (89%), H146Q (89%), Q183E, V213E, G252V (82%), D614G, H655Y, Q675H, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Slovenia 39% 33 85
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Denmark 37% 251 682
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Germany 36% 255 703
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA France 32% 1,118 3,518
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Switzerland 30% 91 299
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Netherlands 28% 99 353
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Sweden 28% 302 1,078
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Ireland 27% 217 792
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Norway 27% 23 84
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Italy 26% 294 1,135
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Iceland 26% 48 186
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron United Kingdom 25% 1,433 5,644
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Austria 25% 62 249
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Greece 22% 14 63
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA United Kingdom 21% 1,172 5,644
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Spain 20% 662 3,284
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Norway 19% 16 84
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Ireland 18% 142 792
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Iceland 17% 32 186
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Finland 17% 60 353
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Switzerland 17% 50 299
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Netherlands 16% 57 353
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Finland 16% 55 353
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Finland 14% 51 353
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Spain 13% 432 3,284
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Austria 12% 30 249
XBB.1.9.2XBB.1.9.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (86%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (88%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Germany 12% 82 703
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France 12% 410 3,518
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Denmark 12% 79 682
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Belgium 12% 41 355
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Luxembourg 12% 43 373
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Greece 11% 7 63
XBB.1.16.6XBB.1.16.6 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Iceland 11% 20 186
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label Country Percent Lineage Count Total Count
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA Dominican Republic 55% 128 231
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Costa Rica 51% 91 177
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Guatemala 31% 73 238
FU.2FU.2 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (90%), S371F (89%), S373P (90%), S375F (89%), T376A (89%), D405N (89%), R408S (87%), K417N (83%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V, T547I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Guatemala 26% 63 238
XBB.1.28XBB.1.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)L335S, G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K (89%), D405N, R408S (84%), K417N (86%), N440K (81%), V445P (81%), G446S (81%), N460K (81%), S477N (85%), E484A (86%), F486P (78%), F490S (86%), Q498R (86%), N501Y (87%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Martinique) 24% 16 66
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Canada 22% 1,369 6,140
FE.1.1FE.1.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I (89%), L24- (87%), P25- (87%), P26- (87%), A27S (87%), V83A (89%), G142D (88%), Y144- (85%), H146Q (86%), Q183E (89%), V213E (89%), G252V (79%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Puerto Rico 19% 102 530
XBB.2.3XBB.2.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (84%), K417N (84%), N440K (88%), V445P (89%), G446S (89%), N460K (89%), S477N, T478K (89%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24- (90%), P25- (90%), P26- (90%), A27S, V83A, G142D, Y144- (85%), H146Q, Q183E, V213E, D253G (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Costa Rica 16% 29 177
XBB.1.5.10XBB.1.5.10 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (89%), N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (90%), Q183E, V213E, G252V (79%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Puerto Rico 16% 85 530
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA United States 15% 4,227 27,471
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Martinique) 15% 10 66
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mexico 14% 41 285
XBB.2.3.5XBB.2.3.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (78%), K417N (80%), N440K (88%), V445P (89%), G446S (89%), N460K (90%), S477N, T478N, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (90%), H146Q, Q183E, V213E, D253G (79%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Costa Rica 14% 25 177
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron United States 14% 3,735 27,471
XBB.1.16.6XBB.1.16.6 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Puerto Rico 13% 68 530
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Dominican Republic 13% 29 231
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mexico 12% 34 285
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Puerto Rico 12% 63 530
XBB.2.3XBB.2.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (84%), K417N (84%), N440K (88%), V445P (89%), G446S (89%), N460K (89%), S477N, T478K (89%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24- (90%), P25- (90%), P26- (90%), A27S, V83A, G142D, Y144- (85%), H146Q, Q183E, V213E, D253G (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Guatemala 11% 26 238
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Canada 11% 666 6,140
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Martinique) 11% 7 66
XBB.1.5.59XBB.1.5.59 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T (89%), L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (85%), N440K, V445P, G446S, L455F (54%), F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (90%), Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Martinique) 11% 7 66
XBB.1.5.28XBB.1.5.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (89%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (90%), H146Q, Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mexico 11% 30 285
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label Country Percent Lineage Count Total Count
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Kazakhstan 54% 39 72
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA China 50% 3,215 6,470
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Laos 39% 29 74
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Malaysia 37% 58 156
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Thailand 32% 141 434
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Hong Kong 31% 33 105
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brunei 30% 29 97
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron India 30% 57 191
XBB.1.9.2XBB.1.9.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (86%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (88%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Israel 23% 237 1,018
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Singapore 23% 309 1,369
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Taiwan 22% 69 311
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Japan 20% 2,061 10,293
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Israel 20% 203 1,018
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Japan 20% 2,045 10,293
XBB.1.16.2XBB.1.16.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (88%), D405N (89%), R408S (86%), K417N (85%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q (90%), E180V, Q183E, V213E, G252V (88%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Laos 19% 14 74
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA South Korea 19% 1,361 7,352
XBB.1.16.1XBB.1.16.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (87%), D405N (89%), R408S (85%), K417N (83%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q, E180V, Q183E, V213E, G252V (88%), T547I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Malaysia 17% 26 156
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Laos 16% 12 74
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Taiwan 16% 49 311
XBB.2.3XBB.2.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (84%), K417N (84%), N440K (88%), V445P (89%), G446S (89%), N460K (89%), S477N, T478K (89%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24- (90%), P25- (90%), P26- (90%), A27S, V83A, G142D, Y144- (85%), H146Q, Q183E, V213E, D253G (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron India 16% 30 191
XBB.1.16.1XBB.1.16.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (87%), D405N (89%), R408S (85%), K417N (83%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q, E180V, Q183E, V213E, G252V (88%), T547I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brunei 14% 14 97
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Korea 14% 1,018 7,352
FY.3FY.3 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (69%), Q183E, Y200C, V213E, G252V, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA China 13% 853 6,470
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Hong Kong 12% 13 105
XBB.2.3.2XBB.2.3.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (87%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (88%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (85%), H146Q (88%), Q183E, G184V, V213E, D253G (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brunei 12% 12 97
XBB.2.3.2XBB.2.3.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (87%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (88%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (85%), H146Q (88%), Q183E, G184V, V213E, D253G (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron India 12% 22 191
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Taiwan 11% 35 311
GE.1GE.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (89%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q, Q183E, N185-, F186I, V213E, D253G (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA India 11% 21 191
XBB.2.3.2XBB.2.3.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (87%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (88%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (85%), H146Q (88%), Q183E, G184V, V213E, D253G (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Singapore 11% 148 1,369
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label Country Percent Lineage Count Total Count
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New Zealand 16% 150 938
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Australia 13% 374 2,778
XBC.1.6XBC.1.6 Mutations
ProteinMutations
Spike (RBD)R346S, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, L452R, S477N, T478K, E484A, F486P, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, P25S, G142D, Y144-, E156G, F157-, R158-, P209L, L212S, D215H, A222V, A243- (87%), L244- (87%), S256L (88%), D614G, H655Y, N679K, P681H, N703I, N764K, D796Y, Q954H, N969K
NA Australia 13% 355 2,778
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label Country Percent Lineage Count Total Count
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Colombia 71% 142 201
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Peru 44% 72 165
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Ecuador 43% 43 99
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Argentina 32% 36 113
XBB.1.5.59XBB.1.5.59 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T (89%), L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (85%), N440K, V445P, G446S, L455F (54%), F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (90%), Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brazil 21% 97 453
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brazil 21% 94 453
XBB.1.5.55XBB.1.5.55 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K (90%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (88%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Peru 20% 33 165
FE.1.2FE.1.2 Mutations
ProteinMutations
Spike (RBD)G339H, R346T (67%), L368I (86%), S371F (86%), S373P (88%), S375F (87%), T376A (87%), D405N, R408S (86%), K417N (78%), N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A (89%), F486P, F490S, Q498R (85%), N501Y (86%), Y505H (85%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (82%), H146Q (87%), Q183E, V213E, G252V, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Brazil 15% 67 453
XBB.1XBB.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (84%), S371F (84%), S373P (84%), S375F (84%), T376A (83%), D405N (85%), R408S (79%), K417N (76%), N440K (82%), V445P (80%), G446S (81%), N460K (82%), S477N (80%), T478K (80%), E484A (78%), F486S (76%), F490S (81%), Q498R (84%), N501Y (86%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (85%), H146Q (87%), Q183E, V213E, G252V (77%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Ecuador 13% 13 99
EG.5EG.5 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (89%), T376A (90%), D405N, R408S (90%), K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (80%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Colombia 11% 23 201
XBB.1.5.20XBB.1.5.20 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N (89%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (90%), H146Q, Q183E, V213E, G252V (70%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Ecuador 11% 11 99
XBB.1.5.10XBB.1.5.10 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (89%), N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (90%), Q183E, V213E, G252V (79%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Peru 11% 18 165
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label Country Percent Lineage Count Total Count
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Réunion Island) 43% 46 106
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mauritius 26% 18 68
XBB.2.3.2XBB.2.3.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (87%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (88%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (85%), H146Q (88%), Q183E, G184V, V213E, D253G (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mauritius 22% 15 68
XBB.1.5.53XBB.1.5.53 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K, D405N, K417N (79%), N440K (80%), V445P (81%), G446S (81%), N460K (80%), S477N (86%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, F140I, G142D, Y144-, H146Q, Q183E, V213E, G252V, L582F, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Africa 18% 27 146
XBB.2.3.11XBB.2.3.11 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N (90%), R408S (86%), K417N (86%), N440K (90%), V445P, G446S, N460K (89%), S477N, T478R (90%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E (86%), D253G (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Réunion Island) 18% 19 106
XBB.1.16.2XBB.1.16.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (88%), D405N (89%), R408S (86%), K417N (85%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q (90%), E180V, Q183E, V213E, G252V (88%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mauritius 16% 11 68
XBB.1.28XBB.1.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)L335S, G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K (89%), D405N, R408S (84%), K417N (86%), N440K (81%), V445P (81%), G446S (81%), N460K (81%), S477N (85%), E484A (86%), F486P (78%), F490S (86%), Q498R (86%), N501Y (87%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Africa 16% 23 146
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Africa 14% 20 146
BA.2.86BA.2.86 (Omicron) Mutations
ProteinMutations
Spike (RBD)I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, K417N, N440K (87%), V445H (65%), G446S (65%), N450D (57%), N460K (57%), S477N (61%), T478K (57%), F486P, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y (70%), S939F, Q954H, N969K, P1143L
Omicron South Africa 11% 16 146
XBB.1.9.2XBB.1.9.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (86%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (88%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mauritius 10% 7 68
*Criteria: Above 10%, minimum of 50 samples per country.
Lineage WHO Label State Percent Lineage Count Total Count
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Massachusetts 26% 38 147
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Georgia 22% 50 227
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Washington 22% 160 738
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Nevada 22% 70 324
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Alaska 20% 21 105
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Tennessee 20% 23 115
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Wisconsin 20% 41 208
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Delaware 20% 21 107
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Iowa 19% 57 298
XBB.1.16.6XBB.1.16.6 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mississippi 19% 48 259
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Missouri 19% 5 27
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Virginia 18% 131 711
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Colorado 18% 181 991
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Minnesota 18% 35 197
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New Mexico 18% 27 153
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA California 18% 1,434 8,152
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Arkansas 17% 11 63
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Ohio 17% 76 436
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Maryland 17% 26 150
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Arizona 17% 154 900
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron North Carolina 17% 90 529
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New Jersey 17% 161 967
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Indiana 16% 14 86
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Pennsylvania 16% 30 185
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Illinois 16% 64 406
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New York 16% 459 2,917
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Carolina 15% 16 104
XBB.1.28XBB.1.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)L335S, G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K (89%), D405N, R408S (84%), K417N (86%), N440K (81%), V445P (81%), G446S (81%), N460K (81%), S477N (85%), E484A (86%), F486P (78%), F490S (86%), Q498R (86%), N501Y (87%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Louisiana 15% 44 292
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Hawaii 15% 143 951
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Nebraska 15% 15 100
XBB.2.3.3XBB.2.3.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (88%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, K182N, Q183E, V213E, D253G (87%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Nebraska 15% 15 100
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Michigan 15% 55 371
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA District of Columbia 14% 12 83
XBB.1.16.1XBB.1.16.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (87%), D405N (89%), R408S (85%), K417N (83%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q, E180V, Q183E, V213E, G252V (88%), T547I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Utah 14% 57 408
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Texas 13% 455 3,449
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Alabama 13% 7 54
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Alabama 13% 7 54
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Connecticut 13% 41 326
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA West Virginia 12% 3 24
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron West Virginia 12% 3 24
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Kentucky 12% 4 33
XBB.2.3.3XBB.2.3.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (88%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, K182N, Q183E, V213E, D253G (87%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Oregon 12% 27 224
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA Rhode Island 11% 16 140
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Florida 11% 162 1,424
*Criteria: Minimum of 20 samples per state.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Austria 2023-08-07 17% -> 43% (+26%) 29 / 173 16 / 37
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Switzerland 2023-08-21 13% -> 34% (+21%) 18 / 136 18 / 53
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Sweden 2023-08-07 17% -> 38% (+21%) 41 / 235 120 / 315
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Norway 2023-08-07 17% -> 37% (+20%) 5 / 30 10 / 27
XBB.1.9.2XBB.1.9.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (86%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (88%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Finland 2023-08-21 2% -> 22% (+20%) 2 / 91 11 / 49
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Germany 2023-07-10 15% -> 34% (+19%) 20 / 137 52 / 153
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Iceland 2023-07-24 12% -> 31% (+19%) 5 / 41 11 / 35
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Denmark 2023-07-24 21% -> 38% (+17%) 17 / 81 54 / 143
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Luxembourg 2023-07-24 4% -> 19% (+15%) 2 / 52 21 / 110
XBB.1.16.6XBB.1.16.6 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Ireland 2023-08-21 3% -> 17% (+14%) 8 / 247 13 / 75
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Italy 2023-08-07 20% -> 32% (+13%) 42 / 212 77 / 237
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Netherlands 2023-07-10 8% -> 20% (+12%) 5 / 64 18 / 89
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA France 2023-07-24 19% -> 31% (+12%) 89 / 478 161 / 527
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Portugal 2023-08-07 42% -> 54% (+11%) 56 / 132 166 / 309
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA United Kingdom 2023-08-21 24% -> 35% (+10%) 522 / 2,147 203 / 584
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Spain 2023-08-21 28% -> 37% (+9%) 217 / 786 100 / 272
XBB.2.3.11XBB.2.3.11 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N (90%), R408S (86%), K417N (86%), N440K (90%), V445P, G446S, N460K (89%), S477N, T478R (90%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E (86%), D253G (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Belgium 2023-08-21 4% -> 13% (+9%) 6 / 142 12 / 90
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
XBB.1.28XBB.1.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)L335S, G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K (89%), D405N, R408S (84%), K417N (86%), N440K (81%), V445P (81%), G446S (81%), N460K (81%), S477N (85%), E484A (86%), F486P (78%), F490S (86%), Q498R (86%), N501Y (87%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Martinique) 2023-08-07 12% -> 43% (+31%) 3 / 25 9 / 21
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Puerto Rico 2023-08-07 3% -> 24% (+21%) 5 / 194 5 / 21
XBB.2.3XBB.2.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (84%), K417N (84%), N440K (88%), V445P (89%), G446S (89%), N460K (89%), S477N, T478K (89%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24- (90%), P25- (90%), P26- (90%), A27S, V83A, G142D, Y144- (85%), H146Q, Q183E, V213E, D253G (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Costa Rica 2023-07-24 11% -> 28% (+17%) 7 / 63 11 / 39
FU.2FU.2 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (90%), S371F (89%), S373P (90%), S375F (89%), T376A (89%), D405N (89%), R408S (87%), K417N (83%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V, T547I, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Guatemala 2023-08-07 25% -> 40% (+15%) 20 / 81 8 / 20
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA Dominican Republic 2023-07-24 55% -> 68% (+13%) 50 / 91 32 / 47
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Canada 2023-07-10 7% -> 18% (+10%) 83 / 1,161 198 / 1,129
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Mexico 2023-07-10 5% -> 15% (+10%) 2 / 37 16 / 105
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Hong Kong 2023-07-24 24% -> 50% (+26%) 13 / 55 10 / 20
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Taiwan 2023-07-10 3% -> 22% (+19%) 2 / 71 17 / 77
XBB.2.3XBB.2.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N, R408S (84%), K417N (84%), N440K (88%), V445P (89%), G446S (89%), N460K (89%), S477N, T478K (89%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24- (90%), P25- (90%), P26- (90%), A27S, V83A, G142D, Y144- (85%), H146Q, Q183E, V213E, D253G (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron India 2023-08-07 10% -> 23% (+13%) 6 / 59 12 / 52
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Israel 2023-07-10 8% -> 20% (+12%) 14 / 178 34 / 169
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Japan 2023-08-21 29% -> 42% (+12%) 576 / 1,962 66 / 159
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA China 2023-08-07 57% -> 69% (+12%) 810 / 1,429 790 / 1,153
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Singapore 2023-08-21 33% -> 43% (+9%) 40 / 121 100 / 235
XBB.1.16.2XBB.1.16.2 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (89%), S371F (88%), S373P (89%), S375F (87%), T376A (88%), D405N (89%), R408S (86%), K417N (85%), N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (88%), H146Q (90%), E180V, Q183E, V213E, G252V (88%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Thailand 2023-08-07 10% -> 18% (+8%) 9 / 92 10 / 55
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA South Korea 2023-07-10 11% -> 18% (+7%) 231 / 2,162 421 / 2,321
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Malaysia 2023-07-10 37% -> 42% (+5%) 28 / 76 24 / 57
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New Zealand 2023-08-21 31% -> 54% (+23%) 64 / 207 44 / 82
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Australia 2023-08-07 8% -> 21% (+13%) 48 / 577 87 / 412
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
XBB.1.5.59XBB.1.5.59 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T (89%), L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (85%), N440K, V445P, G446S, L455F (54%), F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q (90%), Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Brazil 2023-08-07 12% -> 31% (+19%) 10 / 83 20 / 65
EG.5EG.5 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (89%), T376A (90%), D405N, R408S (90%), K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (80%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Colombia 2023-07-10 7% -> 21% (+14%) 9 / 131 14 / 68
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label Country 2-Week Period Change Previous Support Current Support
XBB.2.3.11XBB.2.3.11 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N (90%), R408S (86%), K417N (86%), N440K (90%), V445P, G446S, N460K (89%), S477N, T478R (90%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E (86%), D253G (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron France (Réunion Island) 2023-08-07 10% -> 49% (+39%) 2 / 21 17 / 35
XBB.1.28XBB.1.28 (Omicron) Mutations
ProteinMutations
Spike (RBD)L335S, G339H, R346T, L368I, S371F, S373P, S375F, T376A, R403K (89%), D405N, R408S (84%), K417N (86%), N440K (81%), V445P (81%), G446S (81%), N460K (81%), S477N (85%), E484A (86%), F486P (78%), F490S (86%), Q498R (86%), N501Y (87%), Y505H (86%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (89%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron South Africa 2023-08-07 4% -> 34% (+30%) 1 / 23 17 / 50
*Criteria: >= +5% or >= 2x fold change between 2 week periods with >= 20 samples.
Lineage WHO Label State 2-Week Period Change Previous Support Current Support
XBB.2.3.3XBB.2.3.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (88%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, K182N, Q183E, V213E, D253G (87%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Nebraska 2023-08-21 5% -> 65% (+60%) 2 / 41 13 / 20
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Wisconsin 2023-08-07 16% -> 48% (+32%) 9 / 58 20 / 42
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Oregon 2023-08-21 7% -> 33% (+26%) 5 / 68 7 / 21
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Tennessee 2023-08-07 7% -> 31% (+23%) 2 / 27 11 / 36
XBB.2.3.11XBB.2.3.11 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F (90%), T376A (90%), D405N (90%), R408S (86%), K417N (86%), N440K (90%), V445P, G446S, N460K (89%), S477N, T478R (90%), E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S (90%)
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E (86%), D253G (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron New Jersey 2023-08-21 0% -> 23% (+22%) 1 / 315 10 / 44
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Georgia 2023-07-24 9% -> 31% (+22%) 4 / 45 17 / 55
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Arizona 2023-08-21 22% -> 41% (+20%) 47 / 218 23 / 56
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Mississippi 2023-08-21 14% -> 33% (+19%) 8 / 59 14 / 43
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Rhode Island 2023-07-24 3% -> 20% (+16%) 1 / 31 11 / 56
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Nevada 2023-07-10 2% -> 18% (+16%) 1 / 42 16 / 89
XBB.1.16.6XBB.1.16.6 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V (84%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Maryland 2023-08-21 7% -> 23% (+15%) 3 / 41 5 / 22
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Massachusetts 2023-07-24 16% -> 29% (+14%) 5 / 32 15 / 51
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA California 2023-08-21 24% -> 37% (+13%) 531 / 2,255 58 / 157
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Hawaii 2023-07-24 9% -> 21% (+13%) 20 / 233 62 / 291
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Iowa 2023-07-24 5% -> 18% (+13%) 2 / 40 9 / 51
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Washington 2023-08-21 17% -> 29% (+13%) 28 / 167 24 / 82
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Colorado 2023-07-10 5% -> 18% (+12%) 7 / 128 28 / 158
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Utah 2023-07-24 6% -> 17% (+11%) 7 / 121 22 / 131
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Ohio 2023-07-10 6% -> 16% (+11%) 3 / 54 19 / 116
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA Pennsylvania 2023-07-24 3% -> 14% (+11%) 1 / 29 10 / 71
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Virginia 2023-08-07 15% -> 25% (+10%) 27 / 177 55 / 222
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Louisiana 2023-08-07 10% -> 19% (+9%) 10 / 101 14 / 73
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Minnesota 2023-08-07 12% -> 21% (+9%) 6 / 49 13 / 62
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA New Mexico 2023-07-10 7% -> 15% (+8%) 2 / 29 6 / 39
XBB.1.5XBB.1.5 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (78%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Illinois 2023-07-24 9% -> 17% (+8%) 8 / 85 22 / 126
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Connecticut 2023-07-24 7% -> 14% (+7%) 4 / 61 20 / 143
XBB.2.3.3XBB.2.3.3 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (88%), K417N (87%), N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, P521S
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, K182N, Q183E, V213E, D253G (87%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Michigan 2023-08-07 5% -> 12% (+7%) 6 / 125 7 / 58
XBB.1.16XBB.1.16 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I (87%), S371F (87%), S373P (87%), S375F (86%), T376A (86%), D405N (88%), R408S (83%), K417N (82%), N440K (89%), V445P (90%), G446S, N460K, S477N, T478R, E484A, F486P (90%), F490S, Q498R, N501Y, Y505H (89%)
Spike (non-RBD)T19I, L24- (88%), P25- (88%), P26- (88%), A27S (89%), V83A, G142D, Y144- (82%), H146Q (90%), E180V, Q183E, V213E, G252V (86%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron Alaska 2023-07-10 19% -> 26% (+7%) 9 / 48 7 / 27
FL.1FL.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N (88%), N440K, V445P, G446S, F456L (69%), N460K, S477N, T478R (66%), E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, A701V, N764K, D796Y, Q954H, N969K
NA New York 2023-08-07 11% -> 18% (+7%) 98 / 856 175 / 964
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Florida 2023-08-07 8% -> 15% (+7%) 37 / 437 50 / 331
EG.5.1EG.5.1 Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, F456L, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, Q52H, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V (85%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
NA Texas 2023-08-07 9% -> 15% (+6%) 100 / 1,063 172 / 1,113
XBB.1.9.1XBB.1.9.1 (Omicron) Mutations
ProteinMutations
Spike (RBD)G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S (90%), K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H
Spike (non-RBD)T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144- (89%), H146Q (90%), Q183E, V213E, G252V (81%), D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
Omicron North Carolina 2023-07-10 1% -> 7% (+5%) 1 / 69 5 / 75
*Criteria: >= +5% or >= 2x fold change between 2-week periods with >= 20 samples.

Data Timeline

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Dashboard Timeline

November 02, 2022
06:00PM

New emerging mutations graph and improved performance

Added plot to track emerging mutations. Significantly sped up common plots with an application-level cache
August 02, 2022
07:00PM

Cache loading updated

Modified cache loading logic to avoid incomplete loading of cache
July 26, 2022
08:00PM

QC pipeline updated

Began filtering out genomes <= 25kb in length and >30% undetermined bases, and began re-calling undetermined lineages
January 07, 2022
04:30PM

Top/emerging variant graphs updated

Added overlays and country-specific information to variant graphs
November 27, 2021
01:30PM

WHO Labels Updated

Added Omicron WHO variant
November 18, 2021
04:30PM

Dashboard UI/graphs updated

Added WHO labels to lineages
April 16, 2021
08:50PM

Dashboard UI/graphs updated

Added emerging lineages tracking and top lineages tracking per US state to home page
April 16, 2021
08:00PM

Dashboard backend pipeline overhauled

Overhauled backend pipeline to automatically download and QC data from GISAID daily
April 05, 2021
03:30PM

Dashboard UI/graphs updated

Added top and emerging lineage maps and graphs. Overhauled home page
March 23, 2021
06:00PM

Dashboard performance overhauled

Added caching and refactored all graphs for performance before public release
November 13, 2020
04:00PM

Dashboard UI/graphs updated

Broad-scale update across the entire dashboard to prepare for its launch onto the world wide web!
June 15, 2020
12:00AM

Dashboard graphs upgraded

Migrated dashboard graphs from Plotly to ECharts
June 04, 2020
08:06PM

Dashboard data source changed

Upgraded dashboard to use a database vs flat files. 3x reduction in load time
June 02, 2020
12:18PM

Dashboard UI upgraded

Overhauled dashboard user interface to use bs4dash
May 26, 2020
12:00AM

Variant tracking expanded

Began tracking variants in genes ORF1a and ORF1b
May 11, 2020
12:00AM

Variant tracking expanded

Began tracking variants in genes E, M, N, ORF3a, ORF7a, ORF8, and ORF10
April 27, 2020
12:00AM

Phylogenetic analysis added

Added tab containing viral genome evolutionary relationships
April 03, 2020
12:00AM

Automated QC pipeline created

Cleans up metadata fields such as age, collection date, gender, etc
April 02, 2020
10:36AM

First version of dashboard created

Created first version with shinydashboard. Data is ingested from flat files
March 31, 2020
12:00AM

Patient metadata tracking started

Began downloading patient metadata for all genomes
January 10, 2020
12:00AM

First data downloaded

Began downloading genomes from GISAID and subsequent variant calling
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