BF.7 Sublineage with ORF1a:S1307N, ORF1a:A4016V (597 seq)

[ryhisner]

Description

Sub-lineage of: BF.7
Earliest sequence: 2022-8-12, Germany — EPI_ISL_14517718
Most recent sequence: 2022-12-3, Denmark — EPI_ISL_16063730, EPI_ISL_16063121, EPI_ISL_16063138
Countries circulating: Germany (197), Denmark (87), USA (77), UK (15), Belgium (12), France (10), Netherlands (9), Spain (9), Luxembourg (8), Switzerland (8), etc.
Number of Sequences: 482
GISAID Query: NSP3_G489N, NSP8_A74V + Nucleotide query: C7528T, A27038G
CovSpectrum Query: Nextcladepangolineage:BA.5.2.1* & C7528T & ORF1a:S1307N & ORF1a:A4016V
Substitutions on top of BF.7:
ORF1a: S1307N, A4060V
Nucleotide: G4185A, C12312T

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/BF.7%20%2B%20ORF1aS1307N%20%2B%20ORF1aA4016V%20-%20subtreeAuspice1_genome_32715_683120.json

Evidence
ORF1a:S1307N (NSP3_G489N) involves a second nucleotide substitution at this residue. This is usually a sign selection is at work. BF.7 is a dying lineage, but I thought this worth proposing due to the rare two-nucleotide AA change in ORF1a which appears to confer a substantial growth advantage.

In this case, the mutation, together with ORF1a:V4016V, appears to confer a 15-20% growth advantage (CI: 14-22%) to this lineage over all other BF.7* in Europe (where the majority of sequences are from) and about a 30% weekly growth advantage relative to BF.7* in the United States (both figures over the past three months).

Geno
BF.7 + ORF1aS1307N + ORF1aA4016V - GISAID_hcov-19_ids_2022_12_12_01_40.csv
mes

[ryhisner]

This one's really just a curiosity I suppose, so I'm closing. Just wanted to get the 2-nuc ORF1a:S1307N mutation, which appears to be advantageous, on the record somehow.