Mary Wilson
Well-known member
Dec 26, 2022
Proposal for a sublineage of BF.7
Earliest seq: 2022-09-27 (Inner Mongolia, China)
Countries detected: China (15 seq, from Beijing and Inner Mongolia), Singapore (8, including 4 travellers from China), Cambodia (1), Italy (1)
Mutations on top of BF.7:
ORF7a:H47Y, then ORF1b:L238F, then S:C1243F, ORF1a:V274L, C29632T
GISAID query: Spike_C1243F, NSP2_V94L + nuc mutation C29632T
We've got a Christmas present: actual sequences from China! Based on these, and samples from travellers arriving in Singapore and Japan, there appear to be two main lineages circulating in China, and this is one of them (the other is a BA.5.2+ORF1b:T1050N, see #1471). It was circulating in Inner Mongolia as early as late September, well before the abandonment of the zero-Covid policy, so its high prevalence in China is presumably due to a founder effect; however, the selection pressure from immune escape is much lower in China than elsewhere, so we should not necessarily expect a rapid takeover by BQ.1* and XBB*.
Note that Nextclade calls some of the Singapore sequences as BA.5.2.1 due to what looks like a sequencing artefact at the deletion in the N protein. ...
https://github.com/cov-lineages/pango-designation/issues/1470
Proposal for a sublineage of BF.7
Earliest seq: 2022-09-27 (Inner Mongolia, China)
Countries detected: China (15 seq, from Beijing and Inner Mongolia), Singapore (8, including 4 travellers from China), Cambodia (1), Italy (1)
Mutations on top of BF.7:
ORF7a:H47Y, then ORF1b:L238F, then S:C1243F, ORF1a:V274L, C29632T
GISAID query: Spike_C1243F, NSP2_V94L + nuc mutation C29632T
We've got a Christmas present: actual sequences from China! Based on these, and samples from travellers arriving in Singapore and Japan, there appear to be two main lineages circulating in China, and this is one of them (the other is a BA.5.2+ORF1b:T1050N, see #1471). It was circulating in Inner Mongolia as early as late September, well before the abandonment of the zero-Covid policy, so its high prevalence in China is presumably due to a founder effect; however, the selection pressure from immune escape is much lower in China than elsewhere, so we should not necessarily expect a rapid takeover by BQ.1* and XBB*.
Note that Nextclade calls some of the Singapore sequences as BA.5.2.1 due to what looks like a sequencing artefact at the deletion in the N protein. ...
https://github.com/cov-lineages/pango-designation/issues/1470