Likely artefactual SNPs T76A, T78G in ~4k sequences from CNR Virus des Infections Respiratoires, France from 2022-10 to 2023-12

[corneliusroemer]

Collection date range: October 2022 to December 2023
Submission date range: 2022-11-01 to 2023-12-22
Submitter: Hadrien Regue
Submitting institution: CNR Virus des Infections Respiratoires, France SUD
Country: France
Total number affected: ~4100
Status: Submitter has been contacted via GISAID message (2023-12-02)
GISAID query: 76A,78G

Small subset of GISAID accessions

EPI_ISL_15810455
EPI_ISL_15810437
EPI_ISL_15810436
EPI_ISL_15810434
EPI_ISL_15810433
EPI_ISL_15810432
EPI_ISL_15810431
EPI_ISL_15810429
EPI_ISL_15810402
EPI_ISL_15810400
EPI_ISL_15810397
EPI_ISL_15810396
EPI_ISL_15810393
EPI_ISL_15810392
EPI_ISL_15810391
EPI_ISL_15810387
EPI_ISL_15810385
EPI_ISL_15810384
EPI_ISL_15810382
EPI_ISL_15810381
EPI_ISL_15810371
EPI_ISL_15810368
EPI_ISL_15810355
EPI_ISL_15810354
EPI_ISL_15810353
EPI_ISL_15810352
EPI_ISL_15810351
EPI_ISL_15810350
EPI_ISL_15810349
EPI_ISL_15810346
EPI_ISL_15810345
EPI_ISL_15810344
EPI_ISL_15810343
EPI_ISL_15810342
EPI_ISL_15810334
EPI_ISL_15810331
EPI_ISL_15810326
EPI_ISL_18676891
EPI_ISL_18676901
EPI_ISL_18676904
EPI_ISL_18676907
EPI_ISL_18676908
EPI_ISL_18676912
EPI_ISL_18676930
EPI_ISL_18676934
EPI_ISL_18676942
EPI_ISL_18676947
EPI_ISL_18676952
EPI_ISL_18676972
EPI_ISL_18676984
EPI_ISL_18677004

During routine sequence review, I noticed that a lot of sequences across many lineages had a double nuc mutation T76A, T78G.

This double mutation is likely a sequencing artefact for the following reasons:

• It appears almost solely in sequences from one particular submitting lab, were it real, it would appear in a variety of labs
• It appears and disappears fairly suddenly, which is typical of artefacts as they don't grow and disappear like normal lineages. They can appear suddenly with a new primer set or assembly software and disappear when those are changed.
• It appears across the entire phylogenetic tree, i.e. is very homoplasic. Were the double SNP real, it would occur concentrated in one or a few lineages.

The double mutation T76A, T78G has appeared almost solely in France with very sudden occurrence and disappearance:

It is very homoplasic, occurring in many clades:

See cov-Spectrum

I messaged the submitters through GISAID's "contact submitter" field

Full set of accessions: epi_isls.txt