ABRTUVWXYZAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYBABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZCACBCCCDCECFCGCHCICJCKCLCMCNCOCPCQCR
1
Spike sequence relative to commonly circulating lineagesCommon PANGO designations ("-v" indicates subvariant of listed PANGO)PriorityH69V70Y144K147W152F157I210G257G339R346K417N440K444G446L452N460F486Q493N658Substitutions (relative to Wu-1 - deletions indicated by -)Number of sequences and dateCountries where lineage has been detected and dateExample of a sequence with this form of Spike from GISAID or GENBANKSuggested by whomReasonPrevious ranksNew ranks
2
NTDRBDFurinCambridgeKorberHarmScheuermannGodzikJakeTomerMorganeAnnaWastewaterCambridgeKorberHarmScheuermannGodzikJakeTomerMorganeWastewaterConsensusCambridgeKorberHarmElliotGodzikJakeTomerMorganeWastewaterConsensus
3
Ongoing investigations
4
JN.1JN.1 (B.1.1.529.2.86.1.1 or BA.2.86.1.1---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, V483K, E484-, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L14 exact matches, 44 are labeled JN.1 in GISAID as of 2023-10-16
France,United-Kingdom,Iceland
EPI_ISL_18300149Bette/MarcThis sequence is beginning to expand, and Marc was intrigued by the L455S mutation, which he felt would likely add resistance to the BA.2.86.1 backbone.11111.375
5
6
Current prioritisation (2024-08-09)
7
8
Current prioritisation without splitting
9
JN.1 + S31- + F456L + Q493E + V1104LKP.3.1.11---..S..HTNK.SWKPE.in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, Q493E, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LBK: 2024-06-24: 69 exact matches, 79 contain the patternSpain, USA, IrelandEPI_ISL_19176351BetteIncreasing rapidly: S31del in a KP.3 backbone: KP.3 is currently the most rapidly increasing major lineage, and this lineage of KP.3 is increasing the fastest within KP.31
10
JN.1 + S31- + Q183H + R346T + F456LLB.11---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, Q183H, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LBK: 2024-06-24: 530 exact matches, 640 contain the patternCanada, USA, New ZealandEPI_ISL_19021287BetteIncreasing particularly in the northeastern USA, carries S31del but in a JN.1.9 backbone, not in a KP backbone, and generally its rate of increase is slower than KP.3 and KP.22
11
JN.1 + S31- + H146Q + R346T + F456L + V1104LKP.2.31---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, H146Q, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LBK: 2024-06-24 exact matches 245, contain these mutations 308 Canada, USA, FranceEPI_ISL_1899933087, 90%KP.2 without additional mutations is not increasing as fast as KP.3, but this form of KP.2 with S31del is increasing.333
12
JN.1 + F59L + R346T + F456L + V1104L + K1266RKP.2.22---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L, K1266RBK (via ST): 458 exactSam (from Bette's update)4
13
JN.1 + F59S + R346T + F456L + K1086R + V1104LKP.1.1.52---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59S, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, P1143LBK (via ST): 40 exactSam (from Bette's update)6
14
JN.1 + F59S + R346T + F456L + T572I + K1086R + V1104LKP.1.1.5v2---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59S, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, P1143LBK (via ST): 45 exactSam (from Bette's update)6
15
JN.1 + F456L + Q493E + V1104LKP.33---..S..HTNK.SWKPE.in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483K, E484-, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L898 designated in GISAID as of May 13, 2024 -- bkCanada,USA,AustraliaEPI_ISL_18993074Bette1100, consistently increasing, 80%Increase very swifly, likely immunological implications1117
16
JN.1 + R346T + F456L + V1104LKP.23---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L1,502 KP.2 designations in GISAID as of May 13, 2024 -- bkUSA, Brazil, CanadaEPI_ISL_18912216Bette700, 45%Combination of recurrent mutations2227
17
JN.1 + R346T + F456LJN.1.16.1, KR.13---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L98, 8 March 2024USA, SingaporeEPI_ISL_18958515Sam295, 52%432.005
18
JN.1 + R346T + F456L + T572I KZ.1.1.1, KR.1v3---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, T572I, S477N, T478K, N481K, V483K, E484-, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L2024-04-29: exact matches in 13, contained in 20AustraliaEPI_ISL_19028189Bette26, Mostly Aus, stagnated, 53%Contains all three mutations that are under positive selection with the JN.1 lineages.6425
19
JN.1 + R346T + F456L + T572I + V1104LKP.2.93---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, T572I, S477N, T478K, N481K, V483K, E484-, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L11, 76%648
20
21
22
Current prioritisation split into structural categories
23
RBD: Incremental substitutions from widely circulating lineages
24
JN.1 + F456L + Q493E + V1104LKP.33---..S..HTNK.SWKPE.in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483K, E484-, F486P, Q493E, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L898 designated in GISAID as of May 13, 2024 -- bkCanada,USA,AustraliaEPI_ISL_18993074Bette1100, consistently increasing, 80%Increase very swifly, likely immunological implications1117
25
JN.1 + R346T + F456L + V1104LKP.23---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L1,502 KP.2 designations in GISAID as of May 13, 2024 -- bkUSA, Brazil, CanadaEPI_ISL_18912216Bette700, 45%Combination of recurrent mutations2227
26
JN.1 + R346T + F456LJN.1.16.1, KR.13---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L98, 8 March 2024USA, SingaporeEPI_ISL_18958515Sam295, 52%432.005
27
JN.1 + R346T + F456L + T572I KZ.1.1.1, KR.1v3---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, T572I, S477N, T478K, N481K, V483K, E484-, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L2024-04-29: exact matches in 13, contained in 20AustraliaEPI_ISL_19028189Bette26, Mostly Aus, stagnated, 53%Contains all three mutations that are under positive selection with the JN.1 lineages.6425
28
JN.1 + R346T + F456L + T572I + V1104LKP.2.93---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211I, L212G, V213-, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, T572I, S477N, T478K, N481K, V483K, E484-, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L11, 76%648
29
30
NTD: Incremental substitutions from widely circulating lineages
31
JN.1 + S31del + F456L + Q493E + V1104LKP.3.1.11---..S..HTNK.SWKPE.in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, Q493E, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LBK: 2024-06-24: 69 exact matches, 79 contain the patternSpain, USA, IrelandEPI_ISL_19176351BetteIncreasing rapidly: S31del in a KP.3 backbone: KP.3 is currently the most rapidly increasing major lineage, and this lineage of KP.3 is increasing the fastest within KP.31
32
JN.1 + S31- + Q183H + R346T + F456LLB.11---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, Q183H, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143LBK: 2024-06-24: 530 exact matches, 640 contain the patternCanada, USA, New ZealandEPI_ISL_19021287BetteIncreasing particularly in the northeastern USA, carries S31del but in a JN.1.9 backbone, not in a KP backbone, and generally its rate of increase is slower than KP.3 and KP.22
33
JN.1 + S31- + H146Q + R346T + F456L + V1104LKP.2.31---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S31-, S50L, H69-, V70-, V127F, G142D, Y144-, H146Q, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143LBK: 2024-06-24 exact matches 245, contain these mutations 308 Canada, USA, FranceEPI_ISL_1899933087, 90%KP.2 without additional mutations is not increasing as fast as KP.3, but this form of KP.2 with S31del is increasing.333
34
JN.1 + F59L + R346T + F456L + V1104L + K1266RKP.2.22---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, V1104L, P1143L, K1266RBK (via ST): 458 exactSam (from Bette's update)4
35
JN.1 + F59S + R346T + F456L + K1086R + V1104LKP.1.1.52---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59S, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, P1143LBK (via ST): 40 exactSam (from Bette's update)6
36
JN.1 + F59S + R346T + F456L + T572I + K1086R + V1104LKP.1.1.5v2---..S..HTNK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, F59S, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, R346T, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, F456L, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, T572I, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, K1086R, V1104L, P1143LBK (via ST): 45 exactSam (from Bette's update)6
37
38
Other: Incremental substitutions from widely circulating lineages
39
No prioritized lineages this month
40
41
Many substitutions relative to widely circulating lineages / recombinants
42
No prioritized lineages this month
43
44
45
Well Studied
46
B.1.617.2 (Delta) partial backbone (and also some AY.3).....-........R....T19R, G142D, E156-, F157-, R158G, L452R, T478K, D614G, P681R, D950N (E156-, F157-, R158G is equivalent to E156G, F157-, R158-)8/14/2021 over the full database: 560 carry this pattern, 227 exactly match. BetteLoss of N-glycan at N17. L452R gives Class 2/3 escape. 478 sits on the loop which contains 484 but independent antigenic role unclear.This the the 2nd most commonly sampled backbone form of Delta globally, the more common form also has the T95II see 12k+ genomes with this exact pattern, part of a puzzling group of Delta genomes without any NTD mutations
47
P.1 (Gamma)..........T........L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176FL18F, T20N, D138Y, and R190S are cat 1a substitutions in NTD. T20N AND R190S result in 2 novel glycosylation sites. K417T, N501Y and E484K are cat 1a substitutions in RBD.Shows a growth in sequence prevalence of ~3.6-fold to 6.0% in APR2021 in the US; high prevalence in Brazil, Columbia, Argentina, Canada, and Chile in APR2021; global sequence prevalence has increased ~1.7 fold in APR2021#2 still growing, now spliting into subvarriants (P.1.1), especially P.1.7 is growing recently
48
B.1.351 (Beta)..........N........L18F, D80A, D215G, L241-, L242-, A243-, K417N, E484K, N501Y, D614G, A701V (L241-, L242-, A243- is equivalent to L242-, A243-, L244-)L18F is a cat 1a substitution in NTD. 241-243 deletion in NTD supersite loop is cat 1a. K417N, N501Y and E484K are cat 1a substitutions in RBD.9/30/2021: The reduced potency of neut antibodies to this form makes it of conintued interes, even though it is disappearing.Global prevalence remains low at 1.3%
in APR2021; showing high sequence prevalence in Philippines (100%), South Africa (85%), Bangladesh (77%), Malaysia (40%), Singapore (26%); sequence prevalence remains low at 0.6% in the US overall
in APR2021; certain pockets in the US are worth monitoring, including 7% sequence prevalence in South Carolina
neutral, growing and reinfecting in SA, but not so much in other parts of the worldsee outputs in Broad_lineage_ranking tab
49
B.1.617.1 (Kappa)..............R....T95I, G142D, E154K, L452R, E484Q, D614G, P681R, Q1071HL452R, E484Q double mutant in RBD cat 1. Across Barnes Class 2 and 3.Most common "double mutant" variant in recent GISAID India sample, add in D614G for consistency.seems to be diminishing in sequence prevalence due to growth of B.1.617.2#4 rapid growth in last week
50
B.1.1.7 + E484K---................H69-, V70-, Y144-, E484K, N501Y, A570D, D614G, P681H, T716I, S982A, D1118HIn many other variants / Escape Class 2 strongly / Many fixations / Frequency rank drop (B.1.1.7 vs. overall) / SAVE all RBD substitutions priority 1 (Cambridge 1a.1)This took a while to increase relative to other B.1.1.7s, but was beginning to gain ground within B.1.1.7 in some places just as Delta was replaced both forms.
51
B.1.1.7 (Alpha)---................H69-, V70-, Y144-, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H69, 70, 144 deletion in NTD is cat 1a. N501Y is cat 1a in RBD.Remains the dominant lineage throughout the world with a sequence prevalence of 75% in APR2021; continues to increase in sequence prevalence in the US to ~63% in the records for April 2021 and is present in all 50 states, eight major B.1.1.7 sub-lineages are currently circulating in the US
, the parent B.1.1.7 sub-lineage is now 34% in US in April
, second most prevalent sub-lineage at 7.6% carries the additional K1191N substitution
; an additional sub-lineage carrying the S494P substitution that may impact therapeutic antibody and convalescent polyclonal sera binding increased in sequence prevalence 2.5-fold in APR2021
#3 the largest and still growing, but loosing to B.1.617.2 in most placesranks based on relative transmissibility model
52
B.1.427/429 (Epsilon)....C.........R....S13I, W152C, L452R, D614GW152C is cat 1a in NTD, and L452R is cat 1a in RBD. W152C is a particularly large phenotypic change according to the BLOSUM90 matrix; indicates particularly strong selection?B.1.429 sequence prevalence dropped in APR2021 from 10% to 4%; remains the predominant lineage in Hawaii at 38%slowly dissapearing, downgrade
53
R.1....L..............W152L, E484K, D614G, G769VW152L is cat 1b in NTD. E484K is cat 1a in RBD. W152L is a cat particularly large change according to the BLOSUM90 matrix; indicates particularly strong selection?Expansion in Japan, also found in the US, NY... caused outbreak in a nursing home in GerogiaProminent in Japan in APR2021 (21%); sequence prevalence remains low elewhere in the world.
neutral, seems to be slowing down
54
B.1.526 with E484K (was B.1.526)...................L5F, T95I, D253G, E484K, D614G, A701VD253G is cat 1a in NTD, and E484K is cat 1a in RBD.Slightly increased in sequence prevalence in APR2021 to 8.6%; especially high prevalence of B.1.526 in the northeast - New York, New Jersey, North Carolina, Delaware, and Connecticutneutral, slowing down
55
P.2 (Zeta)...................E484K, D614G, V1176FE484K is cat 1a in RBD. However, let critical to do E484K alone in this relatively simple background if we are doing it in several other backgrounds already.9/28/2021: not sampled in the last 60 days. neutral, never took of the same way as P.1 did
56
B.1.526 with L452R (was B.1.526.1)..-..S........R....D80G, Y144-, F157S, L452R, D614G, T859N, D950HY144-, and F157S are cat 1a and 1b in NTD respectively. L452R is cat 1a in RBD.This form is very distinct from other B.1.526 Pango lineage members throughout the full genome. It is complete different in Spike. Pango lineage designations have been changing, From B.1.526 to subdivisions, and back again.Slightly increased in sequence prevalence in APR2021 to 3.2%, same as B.1.526
57
A.23.1.....L.............F157L, V367F, Q613H, P681RF157L is cat 1a in NTD. V367F is cat 2 and is at RBD/RBD interface giving potential issues with Bloom data as it is a "Class 2" position on opposing RBD).A.23.1: originally found in Uganda, spreading in Central Africa, found in 21 nations, including the US, UK and Canada.slowly dissapearing, downgrade
58
C.37 (Lambda)..............Q....G75V, T76I, R246-, S247-, Y248-, L249-, T250-, P251-, G252-, D253N, L452Q, F490S, D614G, T859N (R246-, S247-, Y248-, L249-, T250-, P251-, G252-, D253N is equivalent to R246N, S247-, Y248-, L249-, T250-, P251-, G252-, D253-)Loss of large portion of supersite loop (20% of supersite). R246N coupled with the deletion results in N246 glycosylation.9/28/2021 Declinging in Chile and Peru where it had been very common, but still present. Older comments: Rapid expansion in Chile in a surge time in a highly vaccinated group, also found in the US (Florida), and found in Israel, another highly vaccinated population in JuneSeen in vaccinated individualsRise in sequence prevalence in Chile to 25% in APR2021 (co-dominating with P.1); also at relatively high sequence prevalence in Argentina, Ecuador, and Colombia; 9-fold growth in sequence prevalence in California to 0.7% in APR2021#5 variant with added critical spike mutations + nsp6 deletion cluster
59
B.1.621 (Mu)..S......K.........T95I, in43T, Y144S, Y145N, R346K, E484K, N501Y, D614G, P681H, D950N528 exact matches through July 31,2021Aruba US ItalyEPI_ISL_2828019BetteNovel modification to the supersite Beta-turn in the NTD. R346K gives Class 3 escape. Also has E484K (Class 2 escape) and N501Y (ACE2 affinity effects, antigenic role unclear?).9/30/2021: The of neut potency to this form is diminished so it continues to be of importance for monitoring. It is still persisting in some populations. 8/72021: The form of B.1.621 that someone had originally entered was problematic, and does not exist in GISAID. This version is correct and actually the best representaion of the expanding form. All B.1.621 carry D614G, and a majority Spikes with clear sequences in this region carry an insertion at 144. It is important form as it has 3 RBD mutations, changes in the NTDss and an 681H, and was increasing at least prior to Delta. also expanding in California, Hawaii and Washington, new sublineage B.1.621.2 with addition of Spike_S939F in a minor (4%) variant
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B.1.617.2 + E484Q .....-........R....T19R, G142D, E156-, F157-, R158G, L452R, T478K, E484Q, D614G, P681R, D950NE484Q Class 2 heavy hitter / E484Q K478T is B.1.617.1-like9/30/2021: THE MORE COMMON FORM with E484Q includes K77T, number 48. Rare, sampled first in India; we think it is a plausible Delta recombinantion with Kappa: B.1.617.2 acquiring B.1.617.1's 484Q; 23 with out T478K.
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B.1.617.2 + V70F + A222V + K417N (AY.2).F...-....N...R....T19R, V70F, G142D, E156G, F157-, R158-, A222V, K417N, L452R, T478K, D614G, P681R, D950NJun-Jul 2021, 636 include this pattern, 194 exact matchesUS:CA US:NVEPI_ISL_3018105Bette417N adds a class 1 substitution --> top right? / 417N in B.1.3519/30/2021: V70F in the NTD, K417N in the RBD. The Bloom lab web page: 417 mutations are associated with reduced binding of convalescent and Moderna vaccine sera and class 2,3 antibodies (https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/).
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B.1.617.2 + T95I + W258L + K417N (AY.1).....-....N...R....T19R, T95I, G142D, E156G, F157-, R158-, W258L, K417N, L452R, T478K, D614G, P681R, D950N417N adds a class 1 substitution --> top right? / 417N in B.1.3519/30/2021: NTDss and RBD, 417 mutations also found in: Beta (N), Gamma (T). K417N is enriched in Delta Pango AY.1 and AY.2 designations, and Delta variants carrying K417N seem to be what was meant when referring to "Delta +" in the press. The site at 258 is associated with in vitro escape (see: McCallum et al., Cell 184:9 2332-2347.e16 (2021) and Cerutti et al, Cell Host and Microbe 29:5 819-833.e7 (2021). The Bloom lab web page summarizing mutations that confer reduced Ab binding in the RBD region identify site 417 mutations associated with reduced binding of convalescent and Moderna vaccine sera and class 2,3 antibodies (https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/). subvariant of B.1.617.2 with extra W258L K417N mutations
63
B.1.525 (Eta)---................Q52R, A67V, H69-, V70-, Y144-, E484K, D614G, Q677H, F888LH69-, V70-, Y144- deletion in NTD is cat 1a. E484K is cat 1a in RBD.9% sequence prevalence in Canada in APR2021neutral, still expanding in Nigeria, but mostly flat elsewhere
64
B.1.1.519...................T478K, D614G, P681H, T732AT478K is cat 2 in RBD. Likely Barnes class 2 possibly not seeing Bloom as in interface. We have no high-priority positions here, only one class 2 substitution.Increasing sequence prevalence in US prior to APR2021; dropping in prevalence in APR2021; however, it continues to show a high sequence prevalence of >50% in Alaska and the upper Midwest - 17% in Idaho, 10% in Montana, and 11% in Utah.neutral, B.1.1.222 has no P681H nor T478K and some non-spike mutations distinct from B.1.1.519 (NS8_I10V, orf3bG174C)
65
BA.1 (previously B.1.1.529) (Omicron)---.....D.NK.S...R.A67V, H69-, V70-, T95I, G142D, V143-, Y144-, Y145-, N211-, L212I, in214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981FAs of Jan 30, there are,
48516 exact matches to this sequenc and 107260 contina the full set of mutations.		GlobalEPI_ISL_6795847Florian via BetteMany changes. NTD: Modification of supersite beta hairpin with 3aa deletion and proximal substitution 142D (142D in Delta as well). Loss of 69-70 region as in Alpha with proximal 67V substitution (potential for re-orientation of glycan at N61). Deletion at RDR3 outsite the supersite (211) with proximal substitution 212I and insertion at 214. RBD: 417N Class 1 substitution shared by several other VOCs like Beta and Gamma. Excellent Class 2 escape from 484A (better than 484K according to Bloom data) and 493R. Many Class 3 substitutions unseen in VOCs until now including 446S, 498R, 496S, and 440K. The class 3 substitution 346K is found in some B.1.1.529 sequences as well. The common 501Y is present along with 505H. The structural proximity of 505H to 501Y suggests they may act synergistically. The RBD also has substitutions at both 477 and 478 (the loop containing 484). The function as of yet is unclear but again proximity suggests synergistic action. Cluster of substitutions at 371, 373, 375 have unclear role in escape or ACE2 affinity but are closely clustered structurally and 371L requires a double-substitution to achieve. These 3 substitutions may have a role in lipid-binding and RBD dynamics. Furin: 681H and 679K introduce 2 additional units of positive charge at the furin cleavage site which may improve recognition and cleavage by the protease as the recognition peptide is positively charged. While more structurally more distant, 655Y plays a known role in improving furin cleavage. S2: 954H, 969K, and 981F are all mutations in heptad-repeat region 1 (HR1).Well studied. This was the consensus and most common form of the Omicron Spike as it began to spread, but BA.1 with A701V is now more common. Many of the Spike sequences have stretches of N's... it is difficult to track exact forms. Thus I look for mutations in Omicron in the GISAID.few non-spike mutations are also interesting (N_R203K, NSP6_105-107del, NSP4_T492)
66
BA.2........D.NK.....R.T19I, L24-, P25-, P26-, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969KBA.2: 741 sequences 1/5/2022
Denmark, Sweden,India
EPI_ISL_7190366BetteFewer sequences than BA.1, but bigger threat than Delta, which is a known quantityCurrent blobally dominant form. Very distinctive relative to BA.1, very rapidly increasingly sampled, now found in several dozen countries, and as soon as it is detected it begins to rapidly increase. Particularly in Denmark, India, Sweden, Singapore. Still new in the US, but on the rise.
67
BA.1.1 (BA.1 + R346K)---.....DKNK.S...R.A67V, H69-, V70-, T95I, G142D, V143-, Y144-, Y145-, N211-, L212I, in214EPE, G339D, R346K, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981FAs of Jan 30, there are 31232 exact matches to this sequence, and 34062 include this pattern of mutation. USA UKEPI_ISL_6956014BetteSome evidence of increase in frequency across numerous countries. Ho paper shows 346K escapes some additional antibodies. Well studied. Omicron with R346K is very common, and gradually globally
68
BA.4 / BA.5 (BA.2+H69-+V70-+L452R+F486V+Q493_)--......D.NK..R.V..T19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, F486V, E484A, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
33 exactly match, contained in 73, among complete Spike. Not most BA.4 and BA.5 are not complete, there are roughly 400 of these to Pango lineages total 2022-04-20
EPI_ISL_11207535BetteThese two lineages are expanding relative to BA.2 in South Africa, and are sampled internationally, and both BA.4 and BA.5 share at least this form of Spike, but the majority of seuqences that have been given these Pango lineage designation are incomplete and the mutations patterns are spotty, with irratic patterns of reversion, so I would prefer given these lineage few more days before highlighting other variants.
69
BA.5 + R346TBF.7, BA.5.2.6, BF.11--......DTNK..R.V..T19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K1225USA, EuropeEPI_ISL_15157485Adam53277.667
70
BA.2 + L452Q + S704LBA.2.12.1........D.NK..Q..R.T19I, L24-, P25-, P26-, A27S, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452Q, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, S704L, N764K, D796Y, Q954H, N969K
5599 exact match, among complete Spike sequences. 2022-05-03 updates
USA,Canada,United-Kingdom
EPI_ISL_10783322BetteThis one may be important. The New York sequencing groups started noting this form in their samples, and when I looked in GISAID found it was expanding at a rapid clip compared to baseline BA.2 in many states across the US, with New York in the lead.
71
BA.2.75 (BA.2 +[K147E,W152R,F157L,I210V,G257S,G339H,G446S,N460K] - [G339D,Q493R])BA.2.75...ERLVSH.NK.S.K...T19I, L24-, P25-, P26-, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, G339H, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K15 exact matches on 2022/07/06, India, UK, US, New Zealnd, Canada, JapanEPI_ISL_13583301Bette Expanding in India, many partial or revertant mutations in Indian sequences, this is the internationally expanding form.
72
BA.4 + R346T + N658SBA.4.6--......DTNK..R.V.ST19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, L452R, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N658S, N679K, P681H, N764K, D796Y, Q954H, N969KRichardRelatively high prevalence in July
73
BA.2.75 + R346T + F486S + D1199NBA.2.75.2...ERLVSHTNK.S.KS..T19I, L24-, P25-, P26-, A27S, G142D, K147E, W152R, F157L, I210V, V213G, G257S, G339H, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, G446S, N460K, S477N, T478K, E484A, F486S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K, D1199N62 (29-Aug-2022)India:15, USA: 10, South Korea: 8, Singapore:7, New Zealand:5, Australia:4, Japan:3, Germany:3, UK:3, Spain:2, Canada:1, Sweden:1EPI_ISL_14600448AnnaMay have a growth advantage.low7522.333
74
BA.5 + R346T + K444T + N460KBQ.1.1, BQ.1.1.13, BQ.1.1.18--......DTNKT.RKV..T19I, L24-, P25-, P26-, A27S, H69-, V70-, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K
224 of this lineages, 2022-09-30
US, many European countries, Nigeria, Israel, Japan, Australia...
EPI_ISL_14752457BetteRapid increase in Sept, carries both R346T and BA.2.75's N460K
I think K444 mutations are simultaneously expanding in a number sublineages. According to Cao et al. K444 mutations are a potent escape form in both BA.2.75 and BA.5 lienage backbones. I think further exploration of viruses carrying these mutations is merited. (Cao et al: https://www.biorxiv.org/content/10.1101/2022.09.15.507787v1.full) K444T/M/N/R are all sampled, with the K444T form dominating the rapidly increasing BQ variants, arising in a BA.5 lineage framework, and simultaneous arising in a BA.2.75 framework -- see sames (CH.1.1 entry below).
 OngoingOngoing21881625.375
75
XBB (BJ.1/BM.1.1.1 (=BA.2.75.3.1.1.1) recombinant with breakpoint in S1 between 446 and 460)XBB..-.....HTNK.S.KS..T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486S, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K83 (Oct 3, 2022)India, Singapore, Bangladesh, USA, Canada, Germany, Japan, UK, Australia Italy, Israel, Denmark (Oct 3, 2022)OP449358.1 / EPI_ISL_15000639AnnaRapid increase in Sept, carries R346T,V445P,G446S,N460K plus other escape muts. in NTDOngoingOngoing5101377510.75
76
XBB + E180V + G252V +T478R + F486P (XBB.1.16)XBB.1.16, XBB.1-v..-.....HTNK.S.KP..T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, E180V, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478R, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K EPI_ISL_17363327Richard/Zach1020211015
77
XBB + G252V + S486P (XBB.1.5, XBB.1.9)XBB.1.5, XBB.1.9.1..-.....HTNK.S.KP..T19I, L24-, P25-, P26-, A27S, V83A, G142D, Y144-, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K EPI_ISL_16343798Richard/ZachContinuing interest as its the vaccine antigen.102017515
78
BA.2.86BA.2.86, BA.2.86.1 ---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, R408S, D405N, K417N, N440K, V445H, G446S, N450D, L452W, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L
136, but many with high levels of ambiguity
16:UK(48),South Africa(17),Denmark(15)EPI_ISL_18114953BetteThis is the consensus form of the BA.2.86 lineageThis sequence exactly matches the consensus form of the colleaction of BA.2.86 Spikes, and differs from our BA.2.86v by one amino acid, being ancetral at48153113
79
80
81
82
83
84
85
86
87
RETIRED LINEAGES
88
89
Retired (2024-05-03)
90
JN.1 + S680FJN.1.37---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, S680F, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L401 in all lineagesUS, Thailand, UKEPI_ISL_18851710Adamfound in several JN.1 branches, S680Y also growing, seen before in AY.466719%75054
91
BA.2.87.1---.L...D.TKN.MK...C15-, V16-, N17-, L18-, T19-, T20-, R21-, T22-, Q23-, L24-, P25-, P26-, A27S, H69-, V70-, G75D, S98F, V126A, C136-, N137-, D138-, P139-, F140-, L141-, G142-, V143-, Y144-, Y145-, H146-, W152L, R190S, V213G, D215G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417T, N440K, K444N, V445G, L452M, N460K, S477N, N481K, E484A, Q498R, N501Y, Y505H, D614G, P621S, V642G, H655Y, N679R, P681H, S691P, N764K, T791I, D796H, D936G, Q954H, N969KSampled only 8 times, last fallSouth AfricaEPI_ISL_18849986|Bette
Only sampled 8 times in S. Africa, but with highly mutated Spike and 2 large deletions in the NTD.
4444.333-954
92
93
94
95
Retired (2024-04-05)
96
JN.1 + M1229IJN.1.2---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L, M1229I
Commonly but early and not increasing
Canada, USA, Netherlands
EPI_ISL_18486527Bette2236, declineM1229I, most common JN.1 variant form after the consensus, but not increasing relative to other JN.1's so likely just a founder effect.66214.62543
97
JN.1 + Q183HJN.1.9---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, Q183H, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, D405N, R408S, K417N, N440K, V445H, G446S, N450D, L452W, L455S, N460K, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L828 in all lineagesUS, UKEPI_ISL_18849815Adam1825, flat / declinecousin of a better known Q183E688.2543
98
BA.2.86 + A475VJN.4, JN.10---..S..H.NK.SWKP..in16MPLF, T19I, R21T, L24-, P25-, P26-, A27S, S50L, H69-, V70-, V127F, G142D, Y144-, F157S, R158G, N211-, L212I, V213G, L216F, H245N, A264D, I332V, G339H, K356T, S371F, S373P, S375F, T376A, R403K, R408S, D405N, K417N, N440K, V445H, G446S, N450D, L452W, N460K, A475V, S477N, T478K, N481K, V483-, E484K, F486P, Q498R, N501Y, Y505H, E554K, A570V, D614G, P621S, H655Y, N679K, P681R, N764K, D796Y, S939F, Q954H, N969K, P1143L
Belgium,Spain,Netherlands
EPI_ISL_18331408Bette987, decline
Rare and not designated in GISAID, bu A475 is interesting and on BA.2.86 too(35 with A475V are in BA.2.86, 17 in BA.2.86.1)
710827.87543
99
100