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Added lineage A.29 with 112 new sequence designations
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Chris Ruis committed May 21, 2021
1 parent 91742c9 commit 2324171
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1 change: 1 addition & 0 deletions lineage_notes.txt
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Expand Up @@ -30,6 +30,7 @@ A.25 Ugandan lineage
A.26 UK lineage
A.27 Mayotte/ European cluster with 18 changes in the long branch leading to this cluster, including 7 NS changes in the spike (L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V), on a 614D background. pango-designation issue #11.
A.28 This lineage has 9 changes on its basal branch, including the 69-70del, N501T (not Y) and H655Y. (This variant is picked up by the qPCR S drop). pango-designation issue #12
A.29 Lineage circulating in multiple countries from pango-designation issue #78
B Second major haplotype (and first to be discovered)
B.1 A large European lineage the origin of which roughly corresponds to the Northern Italian outbreak early in 2020.
B.1.1 European lineage with 3 clear SNPs `28881GA`,`28882GA`,`28883GC`
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113 changes: 113 additions & 0 deletions lineages.csv
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Expand Up @@ -456411,3 +456411,116 @@ Brazil/SC-FIOCRUZ-11054/2021,P.1
Brazil/ES-FIOCRUZ-16386/2021,P.1
Brazil/AM-FIOCRUZ-21890078NR/2021,P.1
Brazil/AM-FIOCRUZ-21895614MA/2021,P.1
Brazil/PR-FIOCRUZ-5241/2021,P.1
Wales/ALDP-12A1A2C/2021,A.29
Ireland/D-NVRL-21IRL43704/2021,A.29
Ireland/D-NVRL-21IRL43705/2021,A.29
Norway/4474/2021,A.29
England/CAMC-1395C7F/2021,A.29
England/CAMC-13A55F9/2021,A.29
Germany/NW-RKI-I-037718/2021,A.29
Australia/NSW-R0166/2021,A.29
Scotland/CAMC-13D357A/2021,A.29
Scotland/QEUH-13CEF47/2021,A.29
Scotland/QEUH-13D6331/2021,A.29
England/CAMC-13DC83C/2021,A.29
England/CAMC-13DCAFA/2021,A.29
England/CAMC-13D3941/2021,A.29
England/QEUH-134BA32/2021,A.29
England/CAMC-137A7CA/2021,A.29
Australia/NSW-R0171/2021,A.29
Scotland/QEUH-13FA522/2021,A.29
Germany/NW-HHU-3046/2021,A.29
Germany/NI-RKI-I-044403/2021,A.29
Germany/BY-RKI-I-049749/2021,A.29
Belgium/UGent-3338/2021,A.29
England/CAMC-13EE59A/2021,A.29
Scotland/QEUH-140516B/2021,A.29
Scotland/QEUH-14067D1/2021,A.29
Scotland/QEUH-13F3ADF/2021,A.29
Australia/NSW1518/2021,A.29
Scotland/QEUH-1425B85/2021,A.29
Scotland/QEUH-1409CFD/2021,A.29
Scotland/QEUH-1413610/2021,A.29
Scotland/CAMC-13EF0C5/2021,A.29
Belgium/UGent-3548/2021,A.29
England/QEUH-14208B0/2021,A.29
Scotland/QEUH-143E9F8/2021,A.29
Scotland/QEUH-1437115/2021,A.29
Scotland/QEUH-1441691/2021,A.29
England/CAMC-141DD02/2021,A.29
Scotland/QEUH-142E69A/2021,A.29
Scotland/QEUH-14311C0/2021,A.29
India/WB-1931500873716/2021,A.29
India/WB-1931500896207/2021,A.29
India/WB-1931500924386/2021,A.29
Germany/NW-RKI-I-051656/2021,A.29
England/QEUH-1469E40/2021,A.29
England/QEUH-1449013/2021,A.29
England/ALDP-14596D2/2021,A.29
England/ALDP-1458BF2/2021,A.29
England/ALDP-144AF15/2021,A.29
England/ALDP-144AC3C/2021,A.29
England/ALDP-144AE54/2021,A.29
England/ALDP-1441D32/2021,A.29
England/ALDP-146D5A1/2021,A.29
England/ALDP-145E752/2021,A.29
England/ALDP-1470DEF/2021,A.29
England/CAMC-144B3CD/2021,A.29
England/CAMC-143DA32/2021,A.29
England/ALDP-1496EC2/2021,A.29
England/MILK-148C937/2021,A.29
England/MILK-148CEB0/2021,A.29
England/MILK-148AE3A/2021,A.29
England/QEUH-144DA02/2021,A.29
England/ALDP-1495F2A/2021,A.29
England/ALDP-147A8A8/2021,A.29
England/CAMC-144B7A3/2021,A.29
Scotland/QEUH-1497D4C/2021,A.29
Scotland/QEUH-14865FD/2021,A.29
Scotland/QEUH-147EC11/2021,A.29
Scotland/QEUH-146E8D4/2021,A.29
Scotland/QEUH-146C2D8/2021,A.29
Scotland/QEUH-145674B/2021,A.29
Scotland/QEUH-14563CF/2021,A.29
Scotland/QEUH-1456462/2021,A.29
Scotland/QEUH-145E260/2021,A.29
Scotland/QEUH-145E048/2021,A.29
Scotland/QEUH-145141C/2021,A.29
England/ALDP-14B2C02/2021,A.29
England/MILK-14CC704/2021,A.29
Scotland/QEUH-14BA1FC/2021,A.29
England/CAMC-14D5F79/2021,A.29
England/QEUH-14D9485/2021,A.29
Scotland/QEUH-14BD7CA/2021,A.29
England/QEUH-148F196/2021,A.29
England/QEUH-14C1DA3/2021,A.29
England/QEUH-14C1EEC/2021,A.29
England/QEUH-14C1FF8/2021,A.29
England/MILK-14DD014/2021,A.29
England/MILK-14BEC9D/2021,A.29
England/QEUH-14D06B5/2021,A.29
England/QEUH-14E75BE/2021,A.29
England/QEUH-14E87A8/2021,A.29
England/QEUH-14E876C/2021,A.29
England/QEUH-14E75FA/2021,A.29
England/CAMC-15038A3/2021,A.29
England/CAMC-15036B8/2021,A.29
England/CAMC-15028FF/2021,A.29
England/ALDP-151204F/2021,A.29
Gambia/22181/2021,A.29
Gambia/22160/2020,A.29
Gambia/22178/2020,A.29
Gambia/22176/2020,A.29
Gambia/22175/2020,A.29
Gambia/22139/2021,A.29
Gambia/22138/2020,A.29
France/PAC-B114-71/2021,A.29
Sweden/9230928955/2021,A.29
USA/WI-UW-4206/2021,A.29
Jordan/AM-Biolab022/2021,A.29
England/ALDP-152F7B3/2021,A.29
England/CAMC-133C8C1/2021,A.29
India/TG-CCMB-BJ479/2021,A.29
Germany/NW-HHU-3574/2021,A.29
USA/DC-DFS-PHL-0487/2021,A.29

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