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HR.1 (XBB.1.5.77.1 with S:478R) sublineage with S:K304N (250 seqs in 13 countries ), 20% prevalence in Costa Rica #2372

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HynnSpylor opened this issue Nov 14, 2023 · 0 comments

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@HynnSpylor
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*Transferred from sars-cov-2-variants/lineage-proposals#623
Defining mutations:
HR.1>C27005T>G9203A (ORF1a:D2980N)>T15717C>C27881T>A22474C (S:K304N)
GISAID query: T15717C, A22474C,A29147G
Earliest seq: 2023-07-05 (US- EPI_ISL_18022790)
Most recent seq: 2023-07-30 (Italy- EPI_ISL_18064404)
Countries detected: Canada (160), US (52, including Puerto Rico 4), Costa Rica (22), Australia (6), Spain (3), UK (2), Slovenia (2), Denmark (1), Mexico (1), Montenegro (1)

Usher Tree:
QQ截图20231114133632

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2eaf6_2d32a0.json

It emerged in 4 months ago and nowadays becomes a large branch with 200+seqs mainly in North and Central America (Canada, US and Costa Rica). Usher shows some notable sub-branch including S:E780D branch, S:A67S branch.

Genomes:
EPI_ISL_18037184, EPI_ISL_18057049, EPI_ISL_18057638, EPI_ISL_18060341, EPI_ISL_18060349, EPI_ISL_18060390, EPI_ISL_18060426, EPI_ISL_18069941, EPI_ISL_18073945, EPI_ISL_18093873, EPI_ISL_18098935, EPI_ISL_18105091, EPI_ISL_18105138, EPI_ISL_18105141, EPI_ISL_18105198, EPI_ISL_18114125, EPI_ISL_18114551, EPI_ISL_18114614, EPI_ISL_18114622, EPI_ISL_18121479, EPI_ISL_18124316,
EPI_ISL_18150897, EPI_ISL_18151147, EPI_ISL_18151153, EPI_ISL_18151158, EPI_ISL_18153006, EPI_ISL_18157402, EPI_ISL_18163089, EPI_ISL_18164336, EPI_ISL_18168457, EPI_ISL_18169193, EPI_ISL_18210449, EPI_ISL_18224369, EPI_ISL_18224400, EPI_ISL_18225949, EPI_ISL_18226676, EPI_ISL_18238989, EPI_ISL_18239019, EPI_ISL_18239924,EPI_ISL_18247421, EPI_ISL_18258644, EPI_ISL_18258651,
EPI_ISL_18259564, EPI_ISL_18260844, EPI_ISL_18270472, EPI_ISL_18277508, EPI_ISL_18277832, EPI_ISL_18277952, EPI_ISL_18282487, EPI_ISL_18284333, EPI_ISL_18284355, EPI_ISL_18284358, EPI_ISL_18291962, EPI_ISL_18299134, EPI_ISL_18303640, EPI_ISL_18304798, EPI_ISL_18305500, EPI_ISL_18305502, EPI_ISL_18305505-18305508, EPI_ISL_18305578, EPI_ISL_18306093, EPI_ISL_18310451, EPI_ISL_18322962, EPI_ISL_18323533, EPI_ISL_18323554-18323557, EPI_ISL_18323564, EPI_ISL_18323574, EPI_ISL_18323577, EPI_ISL_18323590, EPI_ISL_18323592-18323595, EPI_ISL_18327813, EPI_ISL_18330039, EPI_ISL_18330164, EPI_ISL_18340409, EPI_ISL_18342168, EPI_ISL_18343546, EPI_ISL_18343664, EPI_ISL_18343667, EPI_ISL_18344274, EPI_ISL_18344360-18344361, EPI_ISL_18344623, EPI_ISL_18344627, EPI_ISL_18344636, EPI_ISL_18344640, EPI_ISL_18351445, EPI_ISL_18351451, EPI_ISL_18351532,
EPI_ISL_18364631, EPI_ISL_18364717-18364718, EPI_ISL_18364806, EPI_ISL_18364955, EPI_ISL_18368426, EPI_ISL_18370341,
EPI_ISL_18371955, EPI_ISL_18371983, EPI_ISL_18372061, EPI_ISL_18372085, EPI_ISL_18372114, EPI_ISL_18372203, EPI_ISL_18372254, EPI_ISL_18372314, EPI_ISL_18372363, EPI_ISL_18372527, EPI_ISL_18373772, EPI_ISL_18377098, EPI_ISL_18377678, EPI_ISL_18383654, EPI_ISL_18386524-18386528, EPI_ISL_18386533-18386535, EPI_ISL_18386543, EPI_ISL_18386556, EPI_ISL_18386967, EPI_ISL_18388244, EPI_ISL_18389504-18389505, EPI_ISL_18389824, EPI_ISL_18391288, EPI_ISL_18393296, EPI_ISL_18395058, EPI_ISL_18395207, EPI_ISL_18395428, EPI_ISL_18395531, EPI_ISL_18396264, EPI_ISL_18396269, EPI_ISL_18396403, EPI_ISL_18396615-18396616, EPI_ISL_18400748, EPI_ISL_18401586, EPI_ISL_18404787, EPI_ISL_18415407, EPI_ISL_18426688, EPI_ISL_18426696, EPI_ISL_18426803,
EPI_ISL_18426888, EPI_ISL_18426987, EPI_ISL_18426995-18426996, EPI_ISL_18426999, EPI_ISL_18427001-18427003, EPI_ISL_18427005,
EPI_ISL_18427009, EPI_ISL_18427103, EPI_ISL_18427152, EPI_ISL_18427164, EPI_ISL_18427202-18427204, EPI_ISL_18427241,
EPI_ISL_18427414, EPI_ISL_18427555-18427556, EPI_ISL_18427565, EPI_ISL_18427620, EPI_ISL_18429427-18429428,
EPI_ISL_18429430-18429431, EPI_ISL_18429434-18429436, EPI_ISL_18429440-18429442, EPI_ISL_18429444-18429448,
EPI_ISL_18429452-18429455, EPI_ISL_18430507, EPI_ISL_18434495-18434496, EPI_ISL_18435137, EPI_ISL_18435143, EPI_ISL_18435162,
EPI_ISL_18435188, EPI_ISL_18435192, EPI_ISL_18435201, EPI_ISL_18435212, EPI_ISL_18435214, EPI_ISL_18435216-18435217,
EPI_ISL_18435219, EPI_ISL_18435221, EPI_ISL_18435297, EPI_ISL_18437110, EPI_ISL_18437192, EPI_ISL_18437327,
EPI_ISL_18439731, EPI_ISL_18447968, EPI_ISL_18448032, EPI_ISL_18448556, EPI_ISL_18448558-18448559, EPI_ISL_18448561,
EPI_ISL_18450027, EPI_ISL_18451121, EPI_ISL_18451141-18451143, EPI_ISL_18453238, EPI_ISL_18455939, EPI_ISL_18457086,
EPI_ISL_18457089, EPI_ISL_18464065, EPI_ISL_18464751, EPI_ISL_18467536, EPI_ISL_18468049, EPI_ISL_18470421, EPI_ISL_18471230, EPI_ISL_18471329, EPI_ISL_18471577, EPI_ISL_18471640, EPI_ISL_18471735, EPI_ISL_18472132, EPI_ISL_18473803, EPI_ISL_18473805, EPI_ISL_18492868, EPI_ISL_18492955, EPI_ISL_18493085, EPI_ISL_18493492, EPI_ISL_18493516, EPI_ISL_18493521, EPI_ISL_18493526,
EPI_ISL_18493547, EPI_ISL_18493551, EPI_ISL_18493557,

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