XBB.1.16 with orf9b:T24S started in India(293 seqs, 31 countries )

[aviczhl2]

Sub-lineage of: XBB.1.16
Mutations on top of XBB.1.16: A28353T (orf9b:T24S, N:N27I) , C29386T
GISAID query: T28297C, A28353T
No. of seqs: 16(India 16)
First seq: EPI_ISL_17236461 (India) 2023-3-1
Latest seq: EPI_ISL_17326218(India) 2023-3-17
Sequences:
EPI_ISL_17236461, EPI_ISL_17236463, EPI_ISL_17269904,
EPI_ISL_17269908, EPI_ISL_17269927, EPI_ISL_17269939,
EPI_ISL_17269950, EPI_ISL_17269993, EPI_ISL_17270042,
EPI_ISL_17270044, EPI_ISL_17326043, EPI_ISL_17326169,
EPI_ISL_17326190, EPI_ISL_17326218, EPI_ISL_17326224,
EPI_ISL_17326236

Usher shows that there is a major branch with some singlets hiding in artefact reversion branches.
usher

this paper says orf9b:24 is one of the variable site among the residues involved in the formation of dimeric orf9b.

Of the 15 residues involved in the formation of dimeric ORF9b, only six (A22/T24/P51/N55/R58/K59) were variable, while the others were highly conserved.

Orf9b:T24 mutations occurred in many previous seqs, but T24S was very rare, and have negative fitness score on previous backbones. However, this mutation always groups up with other orf9b mutations in previous seqs. (P10S, D16G or P60A) So it may make a difference given XBB.1.16's orf9b being different from original.

[aviczhl2]

17 seqs and detected in USA

[aviczhl2]

62 seqs now, massive upload from Gujarat. (43/606 of 4-10 batch)

[aviczhl2]

66 seqs and detected in Switzerland.

[aviczhl2]

Wow, 45% growth advantage against XBB.1.16 in India.

[aviczhl2]

77 and detected in Malaysia.

[aviczhl2]

116 now and in Canada. The 3 new USA seqs one is airport and one is from India.

@corneliusroemer I think this one satisfies a designation now? Compared with others it grows faster inside India but appears less frequently outside India.

[aviczhl2]

135 seqs, massive upload from Canada and detected in Thailand and Poland.

[aviczhl2]

152 seqs and in China and Japan.

[aviczhl2]

157 seqs, Austria, France and Portugal, UK.

[aviczhl2]

248, Croatia

[aviczhl2]

256, Sweden

[FedeGueli]

New leaders coming and this not so much to do : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=T28297C%2CA28353T&analysisMode=CompareToBaseline&

[aviczhl2]

266, Grenada

[aviczhl2]

274, Italy

[aviczhl2]

279, Albania

[aviczhl2]

283, Australia

[aviczhl2]

286, Oman

[FedeGueli]

Thanks for tracking it! this lasted through october with no Spike mutation over original xbb.1.16. As we already saw in BA.5.1 in japan Orf9b mutations alone sometimes allow persistance of apparently outdated lineages. cc @ryhisner.