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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
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:
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
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:
The double mutation T76A, T78G has appeared almost solely in France with very sudden occurrence and disappearance:
![image](https://private-user-images.githubusercontent.com/25161793/298406108-27eea764-0c9d-4f70-b577-4aa619609af9.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.HIu1gn8B1GKygLFdjPipbbd8myxgPDJ9HwGIuskdbsQ)
It is very homoplasic, occurring in many clades:
![image](https://private-user-images.githubusercontent.com/25161793/298406189-ac2d0fd0-b24d-432a-85ad-adea536517b9.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.Kr2P37Mq8Kkj6feClxyGaoamzf8r-ms-3w_X2_Gixa0)
See cov-Spectrum
I messaged the submitters through GISAID's "contact submitter" field
Full set of accessions: epi_isls.txt
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