XBB.1.16.13 with S:K304N circulating in South Korea and Japan ( 155 seqs)

[FedeGueli]

We tracked this one for a while : https://github.com/sars-cov-2-variants/lineage-proposals/issues/298 EDITED Just noticed that the parental lineage with Orf1a:G519S and Orf1a:G1101D has been designated XBB.1.16.13. Sorry for being late in the update. It is def worth a rapid review and eventually a designation.

With @ryhisner we tracked for a while S:K304Q sublineages of XBB.1.5 but none of them took off as first we thought. Then we kept spotting variation at 304 but also at 307 (mainly with @hynnspylor) with some more success. Here i want to propose a sublineage of XBB.1.16 that seems fast and is spreading in South Korea and Japan.

Gisaid query: C17949T, C25006T,A22474C

Defining mutations: XBB.1.16.13 (Orf1a:G519S +Orf1a:G1101D =NSP3_G283D) >>> C17949T, C25006T > S:K304N (A22474C)

Samples: First : hCoV-19/USA/WA-GBW-H20-312-9890/2023 | Original | EPI_ISL_17700412 | 2023-05-10 (Travel related with South Korea) Last: hCoV-19/Singapore/R42MR63/2023 | Original | EPI_ISL_17837587 | 2023-06-15 (local case in an elderly people)

IDS:

EPI_ISL_17685653, EPI_ISL_17700412, EPI_ISL_17730673, EPI_ISL_17741288, EPI_ISL_17741320, EPI_ISL_17741374, EPI_ISL_17741397, EPI_ISL_17778963, EPI_ISL_17779097, EPI_ISL_17779216, EPI_ISL_17779312, EPI_ISL_17779342, EPI_ISL_17779344, EPI_ISL_17779443, EPI_ISL_17780164, EPI_ISL_17788737, EPI_ISL_17788935, EPI_ISL_17789145, EPI_ISL_17789270, EPI_ISL_17790707, EPI_ISL_17796659, EPI_ISL_17806884-17806885, EPI_ISL_17807115, EPI_ISL_17807449, EPI_ISL_17807461, EPI_ISL_17807528, EPI_ISL_17807826, EPI_ISL_17807864, EPI_ISL_17815255, EPI_ISL_17815741, EPI_ISL_17816404, EPI_ISL_17816522, EPI_ISL_17816580, EPI_ISL_17816589, EPI_ISL_17816622, EPI_ISL_17831217, EPI_ISL_17834715, EPI_ISL_17834831, EPI_ISL_17834875, EPI_ISL_17834930, EPI_ISL_17835021, EPI_ISL_17835183, EPI_ISL_17835223, EPI_ISL_17835327, EPI_ISL_17835360, EPI_ISL_17835374, EPI_ISL_17835376, EPI_ISL_17835397, EPI_ISL_17835468, EPI_ISL_17835489, EPI_ISL_17835766, EPI_ISL_17837587, EPI_ISL_17853927, EPI_ISL_17853953, EPI_ISL_17856343, EPI_ISL_17856704, EPI_ISL_17882477, EPI_ISL_17882660, EPI_ISL_17882684, EPI_ISL_17883111, EPI_ISL_17883938, EPI_ISL_17883947-17883948, EPI_ISL_17884021, EPI_ISL_17884125, EPI_ISL_17884164-17884165, EPI_ISL_17927763, EPI_ISL_17927778, EPI_ISL_17927823, EPI_ISL_17927853, EPI_ISL_17927880, EPI_ISL_17927920, EPI_ISL_17927928, EPI_ISL_17927980, EPI_ISL_17928040, EPI_ISL_17928057, EPI_ISL_17928061, EPI_ISL_17928150, EPI_ISL_17930348, EPI_ISL_17930435, EPI_ISL_17930494, EPI_ISL_17930513, EPI_ISL_17930655, EPI_ISL_17930658, EPI_ISL_17930685, EPI_ISL_17930720, EPI_ISL_17930775, EPI_ISL_17932506, EPI_ISL_17932551, EPI_ISL_17932592, EPI_ISL_17949234, EPI_ISL_17950544, EPI_ISL_17950604, EPI_ISL_17950710, EPI_ISL_17952421, EPI_ISL_17952561, EPI_ISL_17952579, EPI_ISL_17955536

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_18248_3444d0.json?c=country&label=id:node_6604002

Growth advantage: Apparently it has a good chance to be faster than other xbb.1.16 circulating in South Korea: https://cov-spectrum.org/explore/South%20Korea/AllSamples/from%3D2023-05-01%26to%3D2023-06-30/variants?nextcladePangoLineage=XBB.1.16*&aaMutations1=S%3AK304N&nextcladePangoLineage1=xbb.1.16*&analysisMode=CompareToBaseline&

Ping @corneliusroemer @InfrPopGen

[HynnSpylor]

139 seqs now with rapid increasing I suppose it deserves to be designated quickly @corneliusroemer

[FedeGueli]

C17949T, C25006T,A22474C

Mainly SOuth Korea or increasing also in Japan?

[FedeGueli]

13 new samples one from Us, one from Aus the rest from Japan. Ping @corneliusroemer it is growing fast.

[alurqu]

Is this now designated HF.1?

[FedeGueli]

https://github.com/cov-lineages/pango-designation/commit/c36d5d613c740826d2ec46a4a99fb3e9ad542db2