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Repository for suggesting new lineages that should be added to the current scheme
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XBB.1.16.1 Sublineage with ORF9b:Q70R (A28492G) (164 seq, 19 countries, Jul 4) #2085

Open ryhisner opened 1 year ago

ryhisner commented 1 year ago

(Transferred from pre-proposal page. Original proposal June 13.)

Description

Sub-lineage of: XBB.1.16.1 Earliest sequence: 2023-3-13, India, Delhi — EPI_ISL_17447212 Most recent sequence: 2023-5-31, Australia, New South Wales — EPI_ISL_17784416 Countries circulating: Canada (18), USA (17), India (15), Mauritius (13), Hong Kong (9), Australia (6), Singapore (6), South Korea (4), China (2), Reunion (2), Sweden (2), Iceland (1), Japan (1), Taiwan (1), Thailand (1) Number of Sequences: 97 GISAID AA Query: None GISAID Nucleotide Query: A28447G, A28492G CovSpectrum Query: Nextcladepangolineage:XBB.1.16.1* & A28492G Substitutions on top of XBB.1.16.1: ORF9b: Q70R Nucleotide: A28492G

Phylogenetic Order of Mutations: A28492G (ORF9b:Q70R)

USHER Tree Note that all the long branches in the middle of this tree are garbage, full of false reversions and such. I wish there was a way to mask any sequence you wanted to in Usher. It would make the trees look a whole lot more realistic. For now, we're stuck with these funhouse-mirror trees. https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.16.1_ORF9b_Q70R.json?c=gt-nuc_28492&label=id:node_6574479

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Evidence ORF9b mutations have become remarkably influential in the past several months. This is a relatively new one, and judging by its rapid geographic spread, it seems possible it could be a successful one. It's difficult to tell though, as XBB.1.16.1 itself is also spreading rapidly around the world.

One sequence collected in the US on May 21 has travel history in Mexico and one collected April 23 has travel history in Thailand. One sequence from Singapore has travel history in Indonesia, another Taiwan, and another India. The sequence from Taiwan had travel history in Japan.

Genomes

Genomes EPI_ISL_17391403, EPI_ISL_17431902, EPI_ISL_17447212, EPI_ISL_17447221, EPI_ISL_17447252, EPI_ISL_17447309, EPI_ISL_17447313, EPI_ISL_17447358, EPI_ISL_17466899, EPI_ISL_17526273, EPI_ISL_17539472, EPI_ISL_17548454, EPI_ISL_17588932, EPI_ISL_17588940, EPI_ISL_17595358, EPI_ISL_17595431, EPI_ISL_17595523, EPI_ISL_17605511, EPI_ISL_17605541, EPI_ISL_17605569, EPI_ISL_17605760, EPI_ISL_17611315, EPI_ISL_17614852, EPI_ISL_17620632, EPI_ISL_17630316, EPI_ISL_17630479, EPI_ISL_17631408, EPI_ISL_17633693, EPI_ISL_17644853, EPI_ISL_17657866, EPI_ISL_17660144, EPI_ISL_17660177, EPI_ISL_17660391, EPI_ISL_17662069, EPI_ISL_17669621, EPI_ISL_17686745, EPI_ISL_17689807, EPI_ISL_17689818, EPI_ISL_17689819, EPI_ISL_17690692, EPI_ISL_17695014, EPI_ISL_17697634, EPI_ISL_17697706, EPI_ISL_17699191, EPI_ISL_17699210, EPI_ISL_17699219, EPI_ISL_17699233, EPI_ISL_17701143, EPI_ISL_17701237, EPI_ISL_17701239, EPI_ISL_17701448, EPI_ISL_17706278, EPI_ISL_17709545, EPI_ISL_17715125, EPI_ISL_17716096, EPI_ISL_17718879, EPI_ISL_17720574, EPI_ISL_17722632, EPI_ISL_17724357, EPI_ISL_17724373, EPI_ISL_17726325, EPI_ISL_17729036, EPI_ISL_17729051, EPI_ISL_17730731, EPI_ISL_17734745, EPI_ISL_17761065, EPI_ISL_17761081, EPI_ISL_17762879, EPI_ISL_17762884, EPI_ISL_17762893, EPI_ISL_17762913, EPI_ISL_17764391, EPI_ISL_17766449, EPI_ISL_17767939, EPI_ISL_17767966, EPI_ISL_17768274, EPI_ISL_17778454, EPI_ISL_17779541, EPI_ISL_17779787, EPI_ISL_17784144, EPI_ISL_17784146, EPI_ISL_17784416, EPI_ISL_17784440, EPI_ISL_17786433, EPI_ISL_17787202, EPI_ISL_17788455, EPI_ISL_17788462, EPI_ISL_17788957, EPI_ISL_17789096, EPI_ISL_17790870, EPI_ISL_17791957, EPI_ISL_17791966, EPI_ISL_17791969, EPI_ISL_17791972, EPI_ISL_17791987, EPI_ISL_17792004, EPI_ISL_17792015
FedeGueli commented 1 year ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/177

FedeGueli commented 1 year ago

185 as today i want to ping Cornelius this has also 17 sequences from Japan ( i dont know why are not listed in the @ryhisner proposal probably just a copy past from the original pre proposal)

ryhisner commented 1 year ago

There's also an interesting cluster in this lineage from Sweden that has an out-of-frame, 15-nucleotide deletion in the middle of N. Eight sequences, all uploaded on July 7 and collected from June 6-8. One also has S:G261V.

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Each of these eight sequences also has the classic, three-nuc-mutation, ORF1b novel TRS as well.

image image
DailyCovidCases commented 2 months ago

Please close this issue