Open Over-There-Is opened 1 month ago
Tree now: usher @corneliusroemer Is this branch worth a designation?
Tree now: usher
thanks for sharing interestingly it has as main branch orf1a:A599V awhile XEC main branch has Orf1a:A599T
cc @ryhisner do we know what that residue could mean?
This has quite faded away weirdly
Now 96 seqs with G12014A, G15372T, A22115G
One only recent sample maybe time to close this
117
it gets much slower now.
Transferred from sars-cov-2-variants/lineage-proposals#1853 KP.3.1> G12014A(ORf1a:V3917I)> A22115G(S:N185D)
Query: G12014A, G15372T, A22115G Queries for sequences with dropout: C2061T, G12014A, G15372T, -A22115G(8) C2061T, -G12014A, G15372T, A22115G(4) G12014A, G15372T, C23410T, -A22115G(1) G12014A, G15372T, T25485C, -A22115G(1)
Earliest sequence: 04-08 Illinois, USA EPI_ISL_19070161 Earliest sequence(without S:N185D): 03-27 Santa Clara, California, USA EPI_ISL_19145504 Latest sequence: 08-25 San Antonio, Texas, USA EPI_ISL_19408671 Regions Detected: US 97(Texas 23, California 15[1 not on GISAID], South Carolina 14, Louisiana 10, Illinois 8, New York 4, Hawaii 3, Colorado 2, Michigan 4, Ohio 2, Connecticut 1, Arizona 1 not on GISAID, DC 1, Delaware 1, Georgia 1, Maryland 1, Mississippi 1, North Carolina 1, Pennsylvania 1, Tennessee 1, Virginia 1, Wisconsin 1), Canada 3(BC 2, Saskatchewan 1); Denmark 2, Spain 2(Catalunya), Belgium 1(Flanders), France 1(Bourgogne-Franche-Comté), Netherlands 1(Zuid Holland).
EPI_ISL_19214043, EPI_ISL_19214047 and EPI_ISL_19293512 share C2061T and A17697G with other sequences, and have no coverage on S:185. But it's still not sure that if EPI_ISL_19143101 and EPI_ISL_19145504 have S:N185D or not.
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_65bef_451870.json?c=country>=nuc.1314C&label=id:node_7106449
Sequences:
EPI_ISL_19070161, EPI_ISL_19116334, EPI_ISL_19143101, EPI_ISL_19145504, EPI_ISL_19155522, EPI_ISL_19168892, EPI_ISL_19188485, EPI_ISL_19197416, EPI_ISL_19205513, EPI_ISL_19214016, EPI_ISL_19214043, EPI_ISL_19214047, EPI_ISL_19216229, EPI_ISL_19223749, EPI_ISL_19224132, EPI_ISL_19224161, EPI_ISL_19232929, EPI_ISL_19245476, EPI_ISL_19245500, EPI_ISL_19251035, EPI_ISL_19257071, EPI_ISL_19258111, EPI_ISL_19261840, EPI_ISL_19262350, EPI_ISL_19265594, EPI_ISL_19273183, EPI_ISL_19281413, EPI_ISL_19285254, EPI_ISL_19285928, EPI_ISL_19286121, EPI_ISL_19286377, EPI_ISL_19286438-19286439, EPI_ISL_19286452, EPI_ISL_19286529, EPI_ISL_19286567, EPI_ISL_19286727, EPI_ISL_19286800, EPI_ISL_19287409, EPI_ISL_19290154, EPI_ISL_19293512, EPI_ISL_19293534, EPI_ISL_19293618, EPI_ISL_19295220, EPI_ISL_19298224, EPI_ISL_19302502, EPI_ISL_19302607, EPI_ISL_19303440, EPI_ISL_19304230, EPI_ISL_19308466, EPI_ISL_19308526, EPI_ISL_19310695, EPI_ISL_19314232, EPI_ISL_19317468, EPI_ISL_19317741, EPI_ISL_19317747, EPI_ISL_19317777, EPI_ISL_19317786, EPI_ISL_19318204, EPI_ISL_19325464, EPI_ISL_19331991, EPI_ISL_19331993-19331994, EPI_ISL_19332858, EPI_ISL_19334897, EPI_ISL_19337202, EPI_ISL_19343175, EPI_ISL_19343279, EPI_ISL_19345038, EPI_ISL_19345041, EPI_ISL_19345043-19345044, EPI_ISL_19345048, EPI_ISL_19345051, EPI_ISL_19345054-19345055, EPI_ISL_19345057, EPI_ISL_19345059, EPI_ISL_19345561, EPI_ISL_19349188, EPI_ISL_19349546, EPI_ISL_19349959, EPI_ISL_19352806, EPI_ISL_19354372, EPI_ISL_19362207, EPI_ISL_19364571, EPI_ISL_19365679, EPI_ISL_19365732, EPI_ISL_19366037, EPI_ISL_19368076, EPI_ISL_19368215, EPI_ISL_19368810-19368811, EPI_ISL_19375858, EPI_ISL_19378659, EPI_ISL_19379514, EPI_ISL_19387537, EPI_ISL_19392124-19392125, EPI_ISL_19394024, EPI_ISL_19405212, EPI_ISL_19405348, EPI_ISL_19406099, EPI_ISL_19408671, EPI_ISL_19410051, PQ148034.1, PQ212393.1