XBB.1.5 sublineage with S:Q613H, S:H1058Y and NSP5_M17V (160 seq in 14 countries)

[Over-There-Is]

XBB.1.5> T17124C> T10204C> C4993T, A10103G(Orf1a:M3280V = NSP5_M17V), C12025T> T23488C, C24734T(S:H1058Y)> G29543T> G23401T(S:Q613H)

Transfer from sars-cov-2-variants/lineage-proposals#105

GISAID Query: A10103G, G23401T
Earliest Sequence: 02-07 Texas, US EPI_ISL_17018910
Latest Sequence: 10-01 Ontario, Canada EPI_ISL_18372133
Regions Detected:
US 69 (Texas 19, Florida 10, Ohio 9, California 9, New Mexico 6, Pennsylvania 4, Minnesota 2, Arizona 1, Delaware 1, Georgia 1, Illinois 1, Maine 1, Maryland 1, Mississippi 1, New York 2, S. Carolina 1), Canada 37 (Ontario 23, Quebec 9, BC 3, Manitoba 1, Saskatchewan 1), Jamaica 2, Mexico 1(Zacatecas);
China 41 (Guangdong 17[5 imported], Shanghai 7 [1 from HK, 1 from Macao, 2 from Japan, 2 from S. Korea], Sichuan 6, Hubei 2, Xinjiang 2, Fujian 1, Gansu 1, Tibet 1, Hong Kong 4), Singapore 2(1 from China), Japan 1;
Italy 2(Emilia-Romagna 1, Lombardy 1), Austria 1(Kärnten), Norway 1(Viken), Spain 1(Madrid), UK 1(Scotland);
NZ 1(Auckland)

Genome Tree

Sequences:

EPI_ISL_17018910, EPI_ISL_17128466, EPI_ISL_17134670,
EPI_ISL_17147355, EPI_ISL_17180122, EPI_ISL_17240790,
EPI_ISL_17240820, EPI_ISL_17251151, EPI_ISL_17307062,
EPI_ISL_17328203, EPI_ISL_17333504, EPI_ISL_17384370,
EPI_ISL_17428843, EPI_ISL_17430630, EPI_ISL_17442452,
EPI_ISL_17466859, EPI_ISL_17478010, EPI_ISL_17486149,
EPI_ISL_17490820, EPI_ISL_17490828, EPI_ISL_17490840-17490841,
EPI_ISL_17490843, EPI_ISL_17495826-17495827, EPI_ISL_17495830,
EPI_ISL_17513804, EPI_ISL_17526677, EPI_ISL_17537178,
EPI_ISL_17537425, EPI_ISL_17537546, EPI_ISL_17543608,
EPI_ISL_17543762, EPI_ISL_17543766, EPI_ISL_17546803,
EPI_ISL_17582017, EPI_ISL_17582875, EPI_ISL_17589757,
EPI_ISL_17590587, EPI_ISL_17635248, EPI_ISL_17641720,
EPI_ISL_17645061, EPI_ISL_17645836, EPI_ISL_17648261,
EPI_ISL_17651042, EPI_ISL_17651443, EPI_ISL_17651516,
EPI_ISL_17651539, EPI_ISL_17653325, EPI_ISL_17680721,
EPI_ISL_17680723-17680724, EPI_ISL_17684163-17684164, EPI_ISL_17687653,
EPI_ISL_17690049, EPI_ISL_17693975, EPI_ISL_17693983,
EPI_ISL_17697653, EPI_ISL_17697716, EPI_ISL_17697854,
EPI_ISL_17698017, EPI_ISL_17698088, EPI_ISL_17711169,
EPI_ISL_17711499, EPI_ISL_17714292, EPI_ISL_17717370,
EPI_ISL_17718430, EPI_ISL_17722753, EPI_ISL_17722767,
EPI_ISL_17724530, EPI_ISL_17725128-17725129, EPI_ISL_17727015,
EPI_ISL_17727142, EPI_ISL_17744319, EPI_ISL_17744321-17744322,
EPI_ISL_17744333, EPI_ISL_17763572, EPI_ISL_17764393,
EPI_ISL_17765395, EPI_ISL_17775378, EPI_ISL_17775477,
EPI_ISL_17778265, EPI_ISL_17782073, EPI_ISL_17782082,
EPI_ISL_17789672, EPI_ISL_17790551, EPI_ISL_17795103,
EPI_ISL_17795530, EPI_ISL_17797681, EPI_ISL_17801945,
EPI_ISL_17809778, EPI_ISL_17810540, EPI_ISL_17811083,
EPI_ISL_17811134, EPI_ISL_17850757, EPI_ISL_17852382,
EPI_ISL_17852481, EPI_ISL_17853376, EPI_ISL_17854944,
EPI_ISL_17859915, EPI_ISL_17861080, EPI_ISL_17861548,
EPI_ISL_17862584, EPI_ISL_17871147, EPI_ISL_17871169,
EPI_ISL_17879902, EPI_ISL_17959985, EPI_ISL_17962607,
EPI_ISL_17965691, EPI_ISL_17965757, EPI_ISL_17965770,
EPI_ISL_17972215, EPI_ISL_17979460, EPI_ISL_17987472,
EPI_ISL_17989048, EPI_ISL_17990205, EPI_ISL_17990326,
EPI_ISL_18007540, EPI_ISL_18030510, EPI_ISL_18033771,
EPI_ISL_18034288, EPI_ISL_18034785, EPI_ISL_18034825,
EPI_ISL_18034873, EPI_ISL_18034945, EPI_ISL_18035997,
EPI_ISL_18036116, EPI_ISL_18036383, EPI_ISL_18036766,
EPI_ISL_18036857, EPI_ISL_18037246, EPI_ISL_18069682,
EPI_ISL_18073942, EPI_ISL_18079559, EPI_ISL_18133926,
EPI_ISL_18146101, EPI_ISL_18277671, EPI_ISL_18278007,
EPI_ISL_18278021, EPI_ISL_18279864, EPI_ISL_18279889,
EPI_ISL_18298722, EPI_ISL_18304737, EPI_ISL_18317390,
EPI_ISL_18343607, EPI_ISL_18357799, EPI_ISL_18372133,
EPI_ISL_18380996, EPI_ISL_18589034, EPI_ISL_18672275,
EPI_ISL_19020834, EPI_ISL_19093455, OQ867774.1

An Australian sequence with S:Q613H dropout (not including in counting): EPI_ISL_17683550

[Over-There-Is]

I am sure that the G9805A, T18765A branch is still circulating in Guangdong until June. Wait for uploading.

[FedeGueli]

This should be designated to me is coming from an area with low sequencing, it could be also in some countries with good coverage as China or Japan, to say, but with regions less sequenced.

[Over-There-Is]

I am sure that the G9805A, T18765A branch is still circulating in Guangdong until June. Wait for uploading.

A sequence with G9805A, T18765A from Macao is detected by Shanghai, and Macao is a city next to Guangdong.

[Over-There-Is]

Slovakia 04-19

[FedeGueli]

Ping @corneliusroemer @InfrPopGen this should be designated S:Q613H is still one of the mutations giving some (slight)advantage.

[Over-There-Is]

Slovakia 04-19

Convergence

[Over-There-Is]

Italy EPI_ISL_17990205 07-04

[Over-There-Is]

Guangdong +12, 5 imported

[Over-There-Is]

One more Chinese province detected

[Over-There-Is]

Hubei/HCDC-YC2612/2023|EPI_ISL_18146101|2023-08-09 F456L

[FedeGueli]

Query for the 456L sublineage : A5584G, T22930A, G25526T

tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ae22_f36430.json?c=userOrOld&label=id:node_10784159

[FedeGueli]

The 456L branch seems dead could be removed from the proposal i think

[FedeGueli]

146 ses for the wider branch very slow, i suggest to close it directly.