Potential BF.7.4 sublineage with C9365T, T21180C, and ORF1b:P1427S (333 good-quality seqs as of 2022-10-27; North America, Europe, Asia, Australia)

[alurqu]

There may be a BF.7.4 sublineage with C9365T, T21180C, and ORF1b:P1427S (C17746T) first detected in Massachusetts, USA.

As of 2022-10-25, Cov-Spectrum reports 271 BF.7.4+ORF1b:1427S+21180C+9365T sequences (259 with good quality control scores).
Source: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?variantQuery=nextcladePangoLineage%3ABF.7.4+%26+ORF1b%3AP1427S+%26+T21180C+%26+C9365T&nextcladeQcOverallScoreTo=29&

This sublineage shows a growth advantage over both BF.7* and BF.7.4*.

The defining non-synonymous mutation for this sublineage is similar to but different from the defining mutation ORF1b:P1427L of BF.7.5.

As of 2022-10-25, UShER shows all of the GenBank and CoV-Spectrum samples are on a single subtree:

To visualize on UShER: https://nextstrain.org/fetch/github.com/alurqu/pango-designation-support-alurqu/raw/main/2022/10/subtreeAuspice1_genome_genbank_BF.7.4%2BORF1b_1427S%2B21180C%2B9365T.json?branchLabel=aa%20mutations&c=gt-ORF1ab_5828&label=nuc%20mutations:T21483C

To visualize on UShER: https://nextstrain.org/fetch/github.com/alurqu/pango-designation-support-alurqu/raw/main/2022/10/subtreeAuspice1_genome_cov-spectrum_BF.7.4%2BORF1b_1427S%2B21180C%2B9365T.json?branchLabel=aa%20mutations&c=gt-ORF1ab_5828&label=nuc%20mutations:C9365T

First GenBank sequence: Massachusetts, USA 2022-08-04

Most Recent GenBank sequence: New Jersey, USA 2022-10-09

A zip archive of GenBank-formatted and derived metadata and FASTA files plus UShER output files for these sequences is available at
Support_BF.7.4+ORF1b_1427S+21180C+9365T.zip.

The CoV-Spectrum contributors spreadsheet with the GISAID identifiers of good-quality sequences is at
CoV-Spectrum_sequences_BF.7.4+ORF1b_1427S+21180C+9365T_good.csv.

[alurqu]

The current GISAID query is lineage BF.7 with substitutions NS8_H17Y, NSP13_P504S.

First collection date for a GISAID sequence currently shows as 2022-08-03 (Netherlands). Note: This is a day before the first GenBank sequence from Massachusetts, USA.
Eighth collection date for a GISAID sequence currently shows as 2022-08-07 (also Netherlands).

[InfrPopGen]

Thanks for submitting. We've added lineage BF.7.4.1 with 28 newly designated sequences, and 27 updated designations from BF.7.4. Defining mutation C17746T (ORF1b:P1427S) (following T21180C).