Big sublineage of BN.1.3 defined by Orf7b:C41W emerged in Vietnam977sequences as 2023/02/02

[FedeGueli]

I randomly met this sublineage while checking airport surveillance it caught my attention cause its main mutation Orf7b:C41W (T27878G) sounded new to me and collection dates were all quite recent.
Digging a bit more i found that this sublineage of BN.1.3 is circulating with a significant prevalence in South Korea hanging around 2% of samples in the last few weeks while growing to 0,5% of cases in Japan.

So i decided to check growth advantages in SOuth Korea and it has a slight but solid advantage versus parental BN.1.3

It seems ahead of BQ.1 clan while just ahead the leading group with CH.1.1, even if it is still far from XBB.1.5.

I would like to highlight that a sublineage of this one gained a further ORf7b:W41L mutation with G27877T (15 sequences) ( @thomaspeacock could you check if i got it right please). Considering those sequences too the advantage seems slighty bigger

Defining mutations:
BN.1.3 + ORF1a:M3627I (G11146T) > ORF1a:H110Y (C593T) > C7390A > Orf7b:C41W (T27878G )

Usher Tree: i would like to highlight the big saltation branch on the top of the USher tree currently circulating in Japan and internationally and the little cluster with S:E471Q in the bottom part of the tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2143_5e6d10.json?c=country&label=id:node_7869439

Gisaid query: NS7b_C41W,E_T11A,NS3_T229I
finds 455 Sequences :

Expand for EPI_ISLs

EPI_ISL_15280956, EPI_ISL_15341181, EPI_ISL_15609500, EPI_ISL_15609618, EPI_ISL_15609627, EPI_ISL_15641407, EPI_ISL_15653379, EPI_ISL_15671987, EPI_ISL_15672526, EPI_ISL_15694051, EPI_ISL_15695703, EPI_ISL_15695743, EPI_ISL_15712256, EPI_ISL_15732187, EPI_ISL_15732258, EPI_ISL_15732878, EPI_ISL_15733027, EPI_ISL_15736596, EPI_ISL_15755897, EPI_ISL_15756084, EPI_ISL_15756220, EPI_ISL_15757122, EPI_ISL_15757130, EPI_ISL_15757137, EPI_ISL_15783588, EPI_ISL_15783784, EPI_ISL_15784352, EPI_ISL_15794137, EPI_ISL_15794722, EPI_ISL_15804436, EPI_ISL_15811198-15811199, EPI_ISL_15811297, EPI_ISL_15811301, EPI_ISL_15820479, EPI_ISL_15831920, EPI_ISL_15838570, EPI_ISL_15838573, EPI_ISL_15842274, EPI_ISL_15848957, EPI_ISL_15849081, EPI_ISL_15850241, EPI_ISL_15850249, EPI_ISL_15875604, EPI_ISL_15887437, EPI_ISL_15887456, EPI_ISL_15896856, EPI_ISL_15896972, EPI_ISL_15897014, EPI_ISL_15905785, EPI_ISL_15905920, EPI_ISL_15906229, EPI_ISL_15906345, EPI_ISL_15906718, EPI_ISL_15907094, EPI_ISL_15907356, EPI_ISL_15907753, EPI_ISL_15907982, EPI_ISL_15910734, EPI_ISL_15916557, EPI_ISL_15917361, EPI_ISL_15923945, EPI_ISL_15938456, EPI_ISL_15943762, EPI_ISL_15944351, EPI_ISL_15944372, EPI_ISL_15944966, EPI_ISL_15946986, EPI_ISL_15950714, EPI_ISL_15957977, EPI_ISL_15961223, EPI_ISL_15978568, EPI_ISL_15979026, EPI_ISL_15979247, EPI_ISL_15979270, EPI_ISL_15979469, EPI_ISL_15979472, EPI_ISL_15979493, EPI_ISL_15979638, EPI_ISL_15979692, EPI_ISL_15979967, EPI_ISL_15980180, EPI_ISL_15981420, EPI_ISL_15981556-15981557, EPI_ISL_15981660, EPI_ISL_15987669, EPI_ISL_15987677, EPI_ISL_15997256, EPI_ISL_15997337, EPI_ISL_15999784, EPI_ISL_15999963, EPI_ISL_16004094, EPI_ISL_16004167, EPI_ISL_16004234, EPI_ISL_16004466, EPI_ISL_16010751, EPI_ISL_16011832, EPI_ISL_16026624, EPI_ISL_16026626, EPI_ISL_16035681-16035682, EPI_ISL_16036315, EPI_ISL_16036943, EPI_ISL_16040533, EPI_ISL_16048728, EPI_ISL_16051039, EPI_ISL_16051737, EPI_ISL_16051833, EPI_ISL_16058743, EPI_ISL_16058908, EPI_ISL_16059055, EPI_ISL_16060198, EPI_ISL_16060276, EPI_ISL_16060522, EPI_ISL_16060639, EPI_ISL_16060762, EPI_ISL_16067524, EPI_ISL_16069571, EPI_ISL_16073621, EPI_ISL_16073623, EPI_ISL_16077651, EPI_ISL_16077750, EPI_ISL_16077768, EPI_ISL_16077785, EPI_ISL_16077845, EPI_ISL_16078921, EPI_ISL_16086653, EPI_ISL_16091723, EPI_ISL_16091955, EPI_ISL_16092606, EPI_ISL_16093839, EPI_ISL_16096196, EPI_ISL_16099089, EPI_ISL_16105767, EPI_ISL_16107792, EPI_ISL_16109839, EPI_ISL_16109932, EPI_ISL_16110011, EPI_ISL_16111044, EPI_ISL_16112219, EPI_ISL_16112822, EPI_ISL_16114521, EPI_ISL_16115590, EPI_ISL_16115713, EPI_ISL_16120239, EPI_ISL_16120430, EPI_ISL_16120697, EPI_ISL_16125129, EPI_ISL_16125177, EPI_ISL_16125267, EPI_ISL_16128398, EPI_ISL_16128861, EPI_ISL_16129606, EPI_ISL_16129612, EPI_ISL_16130481, EPI_ISL_16131284, EPI_ISL_16132657, EPI_ISL_16133910, EPI_ISL_16133933, EPI_ISL_16135111, EPI_ISL_16135153, EPI_ISL_16135252, EPI_ISL_16135307, EPI_ISL_16135374, EPI_ISL_16135413, EPI_ISL_16135502, EPI_ISL_16135634, EPI_ISL_16135699, EPI_ISL_16135915, EPI_ISL_16135938, EPI_ISL_16135969-16135970, EPI_ISL_16136052, EPI_ISL_16136136, EPI_ISL_16136186, EPI_ISL_16136340, EPI_ISL_16136364, EPI_ISL_16136380, EPI_ISL_16136385, EPI_ISL_16136415, EPI_ISL_16136907, EPI_ISL_16137116, EPI_ISL_16137122, EPI_ISL_16137170, EPI_ISL_16137232-16137239, EPI_ISL_16137285, EPI_ISL_16137341, EPI_ISL_16137385, EPI_ISL_16137401, EPI_ISL_16137403, EPI_ISL_16138779, EPI_ISL_16141406, EPI_ISL_16143511, EPI_ISL_16144052, EPI_ISL_16144120, EPI_ISL_16151787, EPI_ISL_16153376, EPI_ISL_16153523, EPI_ISL_16158537-16158538, EPI_ISL_16161745, EPI_ISL_16161853, EPI_ISL_16165348, EPI_ISL_16165767, EPI_ISL_16167531, EPI_ISL_16169389, EPI_ISL_16173920, EPI_ISL_16173943, EPI_ISL_16174192-16174193, EPI_ISL_16174392, EPI_ISL_16174737, EPI_ISL_16175239, EPI_ISL_16180229, EPI_ISL_16186420, EPI_ISL_16186725, EPI_ISL_16186792, EPI_ISL_16186972, EPI_ISL_16187002, EPI_ISL_16187010, EPI_ISL_16187096, EPI_ISL_16189318, EPI_ISL_16190550, EPI_ISL_16191270, EPI_ISL_16191736, EPI_ISL_16192615, EPI_ISL_16192777, EPI_ISL_16192782, EPI_ISL_16192831, EPI_ISL_16192840, EPI_ISL_16192986, EPI_ISL_16193424, EPI_ISL_16194038, EPI_ISL_16196484, EPI_ISL_16201160, EPI_ISL_16202003, EPI_ISL_16206214, EPI_ISL_16209640, EPI_ISL_16210070, EPI_ISL_16210745, EPI_ISL_16216251, EPI_ISL_16217368, EPI_ISL_16217414, EPI_ISL_16217594, EPI_ISL_16220991, EPI_ISL_16222658, EPI_ISL_16225868, EPI_ISL_16225875, EPI_ISL_16225883, EPI_ISL_16229254, EPI_ISL_16234714, EPI_ISL_16238369, EPI_ISL_16245772, EPI_ISL_16245903, EPI_ISL_16245913, EPI_ISL_16246649, EPI_ISL_16246833, EPI_ISL_16250577, EPI_ISL_16254458, EPI_ISL_16255347, EPI_ISL_16255553, EPI_ISL_16256015, EPI_ISL_16256804, EPI_ISL_16257458, EPI_ISL_16259454, EPI_ISL_16264666, EPI_ISL_16264821, EPI_ISL_16265428, EPI_ISL_16265768, EPI_ISL_16270893, EPI_ISL_16270953, EPI_ISL_16271226, EPI_ISL_16271442, EPI_ISL_16271506, EPI_ISL_16272796, EPI_ISL_16273338, EPI_ISL_16273357, EPI_ISL_16273613, EPI_ISL_16273908, EPI_ISL_16273922, EPI_ISL_16274070, EPI_ISL_16278531, EPI_ISL_16279286, EPI_ISL_16279297, EPI_ISL_16279305, EPI_ISL_16279329, EPI_ISL_16279348, EPI_ISL_16279384, EPI_ISL_16279840, EPI_ISL_16279926, EPI_ISL_16280690, EPI_ISL_16284170, EPI_ISL_16284183, EPI_ISL_16284429, EPI_ISL_16291136, EPI_ISL_16291409, EPI_ISL_16291532, EPI_ISL_16291628, EPI_ISL_16291731, EPI_ISL_16292222, EPI_ISL_16292303, EPI_ISL_16292367, EPI_ISL_16292466, EPI_ISL_16292548, EPI_ISL_16292607, EPI_ISL_16292632, EPI_ISL_16292639, EPI_ISL_16292858, EPI_ISL_16294641, EPI_ISL_16298933, EPI_ISL_16299067, EPI_ISL_16299085, EPI_ISL_16299236, EPI_ISL_16299254, EPI_ISL_16301094, EPI_ISL_16301844, EPI_ISL_16301941, EPI_ISL_16303190, EPI_ISL_16305383, EPI_ISL_16305415, EPI_ISL_16307771, EPI_ISL_16308392, EPI_ISL_16311860, EPI_ISL_16313345, EPI_ISL_16314029, EPI_ISL_16315608, EPI_ISL_16319235, EPI_ISL_16319254, EPI_ISL_16320079, EPI_ISL_16322030, EPI_ISL_16322041-16322042, EPI_ISL_16322296, EPI_ISL_16322310-16322311, EPI_ISL_16323732-16323733, EPI_ISL_16323735, EPI_ISL_16323739, EPI_ISL_16323921, EPI_ISL_16324973, EPI_ISL_16329712, EPI_ISL_16329836, EPI_ISL_16330482, EPI_ISL_16330500, EPI_ISL_16333508, EPI_ISL_16333879, EPI_ISL_16333989, EPI_ISL_16336344, EPI_ISL_16336371, EPI_ISL_16336453, EPI_ISL_16336470, EPI_ISL_16336518-16336519, EPI_ISL_16336523, EPI_ISL_16336621, EPI_ISL_16336644, EPI_ISL_16336689, EPI_ISL_16336772, EPI_ISL_16336812, EPI_ISL_16337870, EPI_ISL_16337981, EPI_ISL_16338035-16338036, EPI_ISL_16338045, EPI_ISL_16338095, EPI_ISL_16338198, EPI_ISL_16338219, EPI_ISL_16338250, EPI_ISL_16339128, EPI_ISL_16339162, EPI_ISL_16339200, EPI_ISL_16339279, EPI_ISL_16339343, EPI_ISL_16339365-16339366, EPI_ISL_16339457, EPI_ISL_16339481, EPI_ISL_16339589, EPI_ISL_16339618, EPI_ISL_16339630, EPI_ISL_16339704, EPI_ISL_16339744, EPI_ISL_16339924, EPI_ISL_16339950, EPI_ISL_16339961, EPI_ISL_16340001, EPI_ISL_16340064, EPI_ISL_16340222, EPI_ISL_16340262, EPI_ISL_16340269, EPI_ISL_16340297, EPI_ISL_16340377, EPI_ISL_16340418, EPI_ISL_16340496, EPI_ISL_16340605, EPI_ISL_16340611, EPI_ISL_16340729, EPI_ISL_16340741, EPI_ISL_16340805, EPI_ISL_16340910, EPI_ISL_16340994, EPI_ISL_16341100, EPI_ISL_16341144, EPI_ISL_16341264, EPI_ISL_16341339, EPI_ISL_16341457, EPI_ISL_16341485, EPI_ISL_16341488, EPI_ISL_16341510, EPI_ISL_16341556, EPI_ISL_16341562, EPI_ISL_16342044, EPI_ISL_16342072, EPI_ISL_16342366, EPI_ISL_16342375, EPI_ISL_16342388, EPI_ISL_16342419, EPI_ISL_16342421, EPI_ISL_16342428, EPI_ISL_16342726, EPI_ISL_16344676, EPI_ISL_16347015, EPI_ISL_16347277, EPI_ISL_16352264, EPI_ISL_16353616, EPI_ISL_16353868, EPI_ISL_16359036, EPI_ISL_16359298, EPI_ISL_16359359, EPI_ISL_16359374, EPI_ISL_16359582, EPI_ISL_16360513, EPI_ISL_16360528, EPI_ISL_16360530, EPI_ISL_16360544, EPI_ISL_16364226, EPI_ISL_16370161, EPI_ISL_16370659, EPI_ISL_16372196, EPI_ISL_16374747, EPI_ISL_16376673, EPI_ISL_16377095, EPI_ISL_16377108, EPI_ISL_16377955, EPI_ISL_16378818, EPI_ISL_16379434

[HugonetX]

Covspectrum gives me 10 of those, recent, in France.
With added :

N:S413R: Omicron frequent mutation seemingly doing nothing (Hossain A. et al, 2022, doi: 10.1016/j.micpath.2022.105699)

S:G142D: A very popular Delta infectivity, nab and remdevisir evading mutation (Lishuan Cheng et al, 2021, DOI:10.1101/2021.09.12.21263475)

[FedeGueli]

@HugonetX N:S413R is defining mutation in all BA.2/4/5
S:142 usually is not real .

[FedeGueli]

521 as today (540 counting the sequences with orf7b:41 further mutated to L) with 67 viruses uploaded in the last thre days from Japan and South Korea but also Canada , Denmark, SIngapore , Usa.
i think its prevalence in SK will go up when last samples will be counted by covspectrum.

https://cov-spectrum.org/explore/South%20Korea/AllSamples/Past3M/variants?aaMutations=ORF1a%3AM3627I%2CORF1a%3AH110Y%2COrf7b%3AC41W&nextcladePangoLineage=BN.1.3&aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

[FedeGueli]

684 sequences as today @thomasppeacock @InfrPopGen @corneliusroemer i think this one is pretty interesting one starting to spreading beyond South Korea and Japan to Singapore and Australia.

Plus its prevalence in South Korea in december trended up around 2,5% with the typical curve we tend to evaluate as important in the pre growth rate tools era.

[FedeGueli]

To be noticed further that two recent singaporean samples have travel history from Vietnam and Thailand and also samples have been taken of this lineage in ML Vietnam: exactly 19 samples out of 449 sequenced in Vietnam since October 1st. suggesting a 5% prevalence in the last months there.
And 23 more samples have Vietnam as travel history on Gisaid Metadata

[FedeGueli]

805 sequences, it is spreading globally, England, Netherlands , Germany , Usa, California and yesterday also one sequence from Shandong China. @thomasppeacock

[FedeGueli]

1030 sequences on Usher: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15071_b89040.json?c=country&label=id:node_8110554

[InfrPopGen]

Thanks for submitting. We've added lineage BN.1.3.5 with 601 newly designated sequences, and 0 updated. Defining mutation T27878G (ORF7b:C41W) (following C7390A).

[FedeGueli]

Thx @InfrPopGen !