cov-lineages/pango-designation issues and pull requests

#2805 - LF.7+C6310T+S:A475V(31 seqs, 45% Qatar)

Issue - State: open - Opened by xz-keg about 1 month ago - 2 comments

#2804 - KP.3.1.1+S:D111N(53 seqs,>10 places)

Issue - State: open - Opened by xz-keg about 1 month ago - 5 comments

#2803 - XEC+Orf1a:A599T+S:T572I(19 seqs, 10 places)

Issue - State: open - Opened by xz-keg about 1 month ago - 2 comments

#2802 - XEC +Orf1a:A599T+ S:I68F(10 seqs, 7 places)

Issue - State: open - Opened by xz-keg about 1 month ago - 1 comment

#2801 - KP.3.1.1+S:F186S(53 seqs, 9 places)

Issue - State: open - Opened by xz-keg about 2 months ago - 1 comment

#2800 - KP.4.1 got Deflirt and it is still circulating in three continents in September (67, 14 places including Iraq) with a recent minibranch adding S:T22N (2, Australia, QLD)

Issue - State: open - Opened by FedeGueli about 2 months ago

#2799 - KP.2.3+S:Q173R(68 seqs, >10 places, 8 with S:T22N, 2 with further S:146P)

Issue - State: open - Opened by xz-keg about 2 months ago - 2 comments

#2798 - KP.3.1.1 plus S:A435S (31 seqs, > 10 Places, 4 continents)

Issue - State: open - Opened by FedeGueli about 2 months ago - 2 comments

#2797 - LB.1.7 + S:185-189del (40 Us, Canada)

Issue - State: closed - Opened by FedeGueli about 2 months ago - 1 comment

#2796 - KP.3.1.1 subbranch with M:I80L, Orf9b:R47P (43 sequences, 8 countries)

Issue - State: open - Opened by Over-There-Is about 2 months ago - 8 comments

#2795 - LY.1 + ORF1a:S1189R (188 mostly Texas USA)

Issue - State: open - Opened by Fearuncle about 2 months ago - 1 comment

#2794 - MC.1 subbranch with S:A942S (75 seqs, 12 countries)

Issue - State: open - Opened by Over-There-Is about 2 months ago - 5 comments

#2793 - MC.13 with S:Q613E (24 seqs, 5 countries)

Issue - State: open - Opened by NkRMnZr about 2 months ago - 6 comments

#2792 - LB.1 (JN.1.9.2.1) with ORF1a:M2606I (nsp3_M1788I ) S:T240I and S:T478R (80 seqs, 3+1 countries)

Issue - State: open - Opened by NkRMnZr about 2 months ago - 2 comments

#2791 - Recombinant of KP.1.1 + Orf1b:L2213F + S:N185del+S:F186I (#2649) that acquired in a stepwise manner S:S31F S:K478T (rev) before recombination. Then with recombination it lost S:K1086R and acquired S:T22N (15, 6 places including India,Hawaii,Singapore)

Issue - State: open - Opened by FedeGueli about 2 months ago - 24 comments

#2790 - KP.X (KP.1.1.3/KP.3.1.1 recomb?): S:∆S31, R346T, Q493E, ORF6:L61I, N:R413L (23 seqs, 3 countries, dying branch)

Issue - State: closed - Opened by ryhisner about 2 months ago - 3 comments

#2789 - Suggestion to broaden XDV.1.2 to include everything under S:R346T branch.

Issue - State: open - Opened by xz-keg about 2 months ago - 7 comments

#2788 - XDV.1.5+8-nuc,6-aa including S:F59S(27 seqs, >10 places, 17 with S:T22N)

Issue - State: open - Opened by xz-keg 2 months ago - 18 comments

#2787 - KP.2.3+S:S31del+Orf1a:1973S+S:R190S,K478T(rev)(21 seqs, 10 places with continuous GBW from India)

Issue - State: open - Opened by xz-keg 2 months ago - 7 comments

#2786 - JN.1*/LF.1.1.1 recombinant(91 seqs,>10 places, 40% in St Petersburg in September )

Issue - State: closed - Opened by aviczhl2 2 months ago - 1 comment

#2785 - KS.1.1+Orf1a:N470T+S:R190S (37 seqs, >10 places, >50% Uzbekistan)

Issue - State: open - Opened by xz-keg 2 months ago - 6 comments

#2784 - New KP.3.2 + S:S31del emerged recently (52, >10 places, first sampled in India)

Issue - State: open - Opened by FedeGueli 2 months ago - 4 comments

#2783 - KP.2.3/KP.3.3 recombinant (24 seqs, 4 places in USA, 17 with S:R346T)

Issue - State: open - Opened by xz-keg 2 months ago - 3 comments

#2782 - KP.3.1.1+S:A575S(64 seqs, >10 places, 10 with S:R346T)

Issue - State: open - Opened by xz-keg 2 months ago - 3 comments

#2781 - MC.10+S:A435S,Orf9b:R47H (92 seqs, >10 places)

Issue - State: open - Opened by xz-keg 2 months ago - 10 comments

#2780 - KP.2.3 subbranch with Orf3d-2:K6* (205 sequences, 11 or 12 countries, mainly in US-TX)

Issue - State: open - Opened by Over-There-Is 2 months ago - 12 comments

#2779 - KP.2.3+S:S31del+S:K478T(rev)+Orf8:S67F,S:R190S (14 seqs, 10 countries)

Issue - State: open - Opened by xz-keg 2 months ago - 3 comments

#2778 - KP.3.1.1+S:N1187H( 68 seqs, >10 places, 5 with S:S46L)

Issue - State: open - Opened by xz-keg 2 months ago - 4 comments

#2776 - KP.1.1.1 became DeFLiRT starting with N:S183P (44 samples US, Canada,France and China)

Issue - State: closed - Opened by FedeGueli 2 months ago - 3 comments

#2775 - KP.3.1 subbranch with S:N185D and Orf1a:V3917I (117, 7 countries, Mainly in US)

Issue - State: open - Opened by Over-There-Is 2 months ago - 6 comments

#2774 - XEK: KP.2.3/XEC Recombinant(45 seqs, 12 countries)

Issue - State: closed - Opened by Fearuncle 2 months ago - 27 comments

#2773 - KP.2.8 with S:255-257 deletions (34 seqs, 12 countries)

Issue - State: closed - Opened by NkRMnZr 2 months ago - 1 comment

#2772 - KP.3.3.1+S:H146N (77 seqs, 11 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 4 comments

#2771 - KP.3.3+Orf1b:A1603S+Orf10 frameshift, S:F59S(84 seqs, 8 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 8 comments

#2770 - KP.2 Plus S:I934V and S:N30K emerged in China (60 , >10 countries)

Issue - State: open - Opened by FedeGueli 3 months ago - 8 comments

#2769 - LB.1 + S:K478T (rev) + S:E96V emerged in Nepal (11)

Issue - State: closed - Opened by FedeGueli 3 months ago - 2 comments

#2768 - Second branch of XEC with Orf1a:I1367L (167, >20 places)

Issue - State: closed - Opened by FedeGueli 3 months ago - 11 comments

#2767 - KP.2.3 (pre C28714T branch) with ORF1a:Q884E / nsp3_Q66E (225 seqs, 8+4 countries); Further with S:Q677H (multiple sub-branches) and S:F1103L

Issue - State: open - Opened by NkRMnZr 3 months ago - 3 comments

#2766 - LB.1.7+S:R190S with C22096T branch (23 seqs)

Issue - State: open - Opened by DailyCovidCases 3 months ago - 5 comments

#2765 - KP.2.3+S:A1174V (232 seqs, >10 places) 27% in Brazil ,Sep

Issue - State: open - Opened by xz-keg 3 months ago - 7 comments

#2764 - KP.3.2+S:S31P widespread in China(39 seqs, >10 places)

Issue - State: open - Opened by xz-keg 3 months ago - 13 comments

#2763 - Usher placement shift of MC.1

Issue - State: closed - Opened by aviczhl2 3 months ago - 1 comment

#2762 - Proposal to include MU.1 without C26735T.

Issue - State: open - Opened by xz-keg 3 months ago - 3 comments

#2759 - KP.4.2+Orf1a:Q575R+S:S256L+S:S31del(31 seqs,>10 places, 24 with S:R190S)

Issue - State: open - Opened by xz-keg 3 months ago - 6 comments

#2758 - JN.1.67.1 subbranch with S:F59S, R346T on G1126A branch (51, 8 regions, mainly found in CN-LN)

Issue - State: open - Opened by Over-There-Is 3 months ago - 7 comments

#2757 - JN.1.4.5+S:F456L with C28948T branch (29 seqs)

Issue - State: closed - Opened by DailyCovidCases 3 months ago - 4 comments

#2755 - KP.1.1.3 sublineage got S:R190S (135 from >20 countries including Philippines, Kenya, India,) with a S:K478T sublineage (5 India, California)

Issue - State: open - Opened by FedeGueli 3 months ago - 16 comments

#2751 - KS.1.1/JN.1* recombinant (334 seqs, >10 places, 16% South Korea 8% Hong Kong)

Issue - State: open - Opened by xz-keg 3 months ago - 29 comments

#2750 - KP.1.1.5+Orf1a:A2785V,A4357V+S:S680Y(84 seqs, 11 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 5 comments

#2748 - KP.2.2 + S:T22N (192, sampled in >25 places , likely emerged in Nepal) with several sublineages of interest: S:K97E/478T (9) / S:K478E (3) / NY cluster with S:244-247 (15)/ 475V sublineage (9) with further S:ins678THKLL-S:K679E (4)

Issue - State: open - Opened by FedeGueli 3 months ago - 17 comments

#2747 - KP.1.1+S:S71Y,S31del or JN.1.11.1/LP.2 recombinant(60 seqs, 14 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 12 comments

#2746 - LB.1+S:R190S (51 seqs, 15 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 9 comments

#2745 - JN.1+S:F456L+Orf1a:Y1734H,S:S60P starting and still circulating in Vietnam(61 seqs, 11 countries with two S:T572I branches 9 and 6 seqs )

Issue - State: open - Opened by xz-keg 3 months ago - 10 comments

#2744 - KP.3.3 + S:I844V has spread globally from Australia ( 236 Samples, 14 countries)

Issue - State: closed - Opened by FedeGueli 3 months ago - 4 comments

#2743 - KP.3.1 subbranch with S:N>K679R(188 seqs, 20 regions, mainly in Spain) and further S:L176F(38, 8 regions)

Issue - State: open - Opened by Over-There-Is 3 months ago - 8 comments

#2740 - KP.2.5+Orf1a:N704K, S:S31del (75 seqs, 13 countries, 19 with S:A688V, 5 with S:T22N)

Issue - State: open - Opened by xz-keg 3 months ago - 9 comments

#2739 - JN.1.4+S:S31del, S:R346T, Orf7a:Q94H (54 seqs, 3 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 3 comments

#2738 - JN.1.4+S:S31del,Orf8:E106Q+S:R346T(77 seqs, 6 countries)

Issue - State: closed - Opened by xz-keg 3 months ago - 9 comments

#2736 - KP.2+Orf1a:P1803L, S:K558N, S:F32del(62 seqs, 14 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 3 comments

#2732 - KP.2.3 + S:S31del branch with N:H145Y + S:K679R + ORF1a:T2016K (239 in 12 countries) + Branch with S:G184S (14) and a Branch with ORF1a:S944L + S:E1202G (26)

Issue - State: closed - Opened by Fearuncle 3 months ago - 11 comments

#2731 - KP.2/KP.3.2.3 recombinant. most have additional S:S31F (46 seqs, 12 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 5 comments

#2730 - KP.2.6+S:L441F(97 seqs, 11 countries)

Issue - State: open - Opened by xz-keg 3 months ago - 3 comments

#2729 - KP.3.1.1+S:R346T (169 seqs, >10 places, 12 with Orf9b:I5T)

Issue - State: open - Opened by xz-keg 4 months ago - 20 comments

#2728 - KP.3.3+Orf9b:V37G(118 seqs, 9 countries)

Issue - State: open - Opened by xz-keg 4 months ago - 2 comments

#2727 - Suggestion to alter KP.3.1.3 designation to only the G25644T branch

Issue - State: open - Opened by xz-keg 4 months ago - 5 comments

#2722 - KP.2.3(no 31del)+S:T572I(289 seqs, >10 places )

Issue - State: open - Opened by xz-keg 4 months ago - 10 comments

#2718 - KP.2.2+S:T572I (52 seqs) and its sublineage with S:K182R,S:A846V (36 seqs)

Issue - State: open - Opened by DailyCovidCases 4 months ago - 18 comments

#2717 - XEC/24F: Potential KS.1.1/KP.3.3 recombinant (35 sequences, 9 countries)

Issue - State: closed - Opened by Over-There-Is 4 months ago - 25 comments

#2715 - KP.2+S:F32del (111 seqs, 11 countries, 27% Ecuador, 13 with S:I101T)

Issue - State: open - Opened by xz-keg 4 months ago - 11 comments

#2713 - LB.1.7+S:R190S(88 seqs, 7 countries)

Issue - State: open - Opened by xz-keg 4 months ago - 11 comments

#2709 - KP.3.1 subbranch with S:L84I(61 seqs, 9 countries)

Issue - State: closed - Opened by Over-There-Is 4 months ago - 7 comments

#2705 - JN.1+S:T22N,F456L,Q493E(Designated JN.1.16.5)+S:S31P( 89 seqs, 8 countries, 11 with S:T1273I)

Issue - State: open - Opened by xz-keg 4 months ago - 23 comments

#2698 - KP.2+S:H146Y misread on GISAID (176 seqs, >10 places)

Issue - State: open - Opened by xz-keg 4 months ago - 7 comments

#2697 - LF.3.1 sub-branch with S:D745A ( 110 seqs, 13 countries, 4 of them in South America)

Issue - State: closed - Opened by FedeGueli 4 months ago - 11 comments

#2694 - KP.3.1.1 + ORF1a:T2274I (545 seq.) >20% of cases in Iceland after June 15

Issue - State: open - Opened by Fearuncle 4 months ago - 4 comments

#2687 - KP.2.2+Orf9b:N62S(614 seqs, >10 places)

Issue - State: open - Opened by xz-keg 5 months ago - 13 comments

#2681 - KR.1 (FLiRT) got S:F59S (109, >10 countries including Philippines and Japan) with a branch with S:A435S,S:S680P (12, South Korea,US)

Issue - State: open - Opened by FedeGueli 5 months ago - 7 comments

#2661 - New JN.1.16.1 plus S:S31del after Orf1b:Q215K (C14110A) (124 samples, 7 countries including Mexico)

Issue - State: closed - Opened by FedeGueli 5 months ago - 12 comments

#2650 - JN.1+S:Q677L+S:F456L with C14676T branch (67 seqs)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 11 comments

#2649 - KP.1.1+Orf1b:L2213F+S:N185del, F186I(331 seqs, >10 places, 17 with S:S31F, 7 with further S:K478T rev, 6 with further S:F32S, further recombinant proposed in #2791)

Issue - State: open - Opened by xz-keg 6 months ago - 26 comments

#2644 - Suggestion to broaden JN.1.39.1

Issue - State: open - Opened by xz-keg 6 months ago - 3 comments

#2631 - Lineage note distinctive mutation for JN.1.56 is incorrect.

Issue - State: closed - Opened by alurqu 6 months ago - 3 comments

#2621 - JN.1 + S:F456L with Orf3a:A54S (32 seqs) of which 27 seqs has S:G213E (T22200A)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 7 comments

#2613 - JN.1+S:F456L with Orf10:P10S (107 seqs)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 17 comments

#2607 - JN.1.4.5 + S:F456L with C28201T branch (96 seqs)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 6 comments

#2602 - JN.1.4 with Orf1a:D4117N, S:T22N and S:R346T (54 seqs)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 4 comments

#2601 - JN.1.4.5 + S:R346T that further gained S:T732I (77 seqs)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 4 comments

#2600 - JN.1+S:R346T on C2395T branch (35 seqs, 4 countries)

Issue - State: closed - Opened by DailyCovidCases 6 months ago - 2 comments

#2589 - Another JN.1 + FLiRT lineage emerged in the Iberian Peninsula (Now LF.6) with a S:Q493E branch (2, Spain)

Issue - State: closed - Opened by FedeGueli 6 months ago - 36 comments

#2542 - JN.1.11 (S:V1104L) got S:R346T being caught multiple times in GBW samples (119) and further gaining S:F59L (17)

Issue - State: closed - Opened by FedeGueli 8 months ago - 8 comments

#2534 - JN.2+Orf1a:C3059S+S:L455S(80 seqs, 6 countries)

Issue - State: closed - Opened by xz-keg 8 months ago - 2 comments

#2525 - JN.1.8.1+S:H146Q(285 seqs, 8 countries)

Issue - State: closed - Opened by aviczhl2 8 months ago - 9 comments

#2470 - XBB.2.3.3 Sublineage w/new S2' FCS—S:N450D, S:K478R, S:P812R, S:V1264L + 4x ORF1ab (6 countries, 48 seq, Jan 21)

Issue - State: open - Opened by ryhisner 10 months ago - 2 comments

#2453 - HK.3.2 sublineage with S:L216F, S:E554K(42 sequences, 12 countries)

Issue - State: open - Opened by Over-There-Is 11 months ago - 4 comments

#2431 - HK.3.2 sublineage with S:E471Q(40 sequences, 13 countries)

Issue - State: open - Opened by Over-There-Is 11 months ago - 3 comments

#2421 - HK.3.2 sublineage with S:A352S(40 sequences, 8 countries, mainly in Scandinavia)

Issue - State: open - Opened by Over-There-Is 11 months ago - 1 comment

#2369 - HK.3.2 sublineage with S:R214H(117 sequences, 16 countries), most with S:I1221T(87)

Issue - State: open - Opened by Over-There-Is about 1 year ago - 12 comments

#1988 - Variant spotters community announcement: new issue tracker for small, unclear, ambiguous, slow lineages

Issue - State: open - Opened by FedeGueli over 1 year ago - 32 comments

#1219 - CB.1 (BA.2.75.9.1) diversity issue

Issue - State: open - Opened by corneliusroemer about 2 years ago - 3 comments

#100 - Would you add sequences' accession ID information to the lineages.metadata.csv?

Issue - State: closed - Opened by gotao2 over 3 years ago - 2 comments
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GitHub / cov-lineages/pango-designation issues and pull requests