Potential misdating (is: 2023, should: 2022) of 32 German RKI sequences
corneliusroemer opened this issue · 1 comments
Release data: 2023-11-03, 2023-11-05, 2024-01-15
Submitter: Brinkmann,A.,Kohl,C.,Schrick,L.,Michel,J.,Schaade,L.,Nitsche,A.
Submitting institution: Robert Koch Institut
Country: Germany
NCBI virus link: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Monkeypox%20virus,%20taxid:10244&Authors_idx%20q.op%3DAND=viscardi&CreateDate_dt=2024-01-09T00:00:00.00Z%20TO%202024-01-20T23:59:59.00Z
Example Genbank: https://www.ncbi.nlm.nih.gov/nuccore/OR743494
Status: Submitter contacted (2024-01-21), submitter double checked and confirmed dates are correct (2024-01-22)
List of Genbank accessions
OR743494
OR743495
OR743497
OR743498
OR777671
OR777672
OR777673
OR777675
OR777676
OR777678
OR777679
OR777680
OR777681
PP093697
PP093698
PP093699
PP093700
PP093701
PP093702
PP093703
PP093705
PP093706
PP093708
PP093712
PP093715
PP093716
PP093717
PP093719
PP093722
PP093723
PP093724
PP093727
I noticed a potential year-off-by-one date error in 32 recently submitted German sequences. Off-by-one year errors have been regularly observed in SARS-CoV-2 sequences from a range of labs, so it is not unexpected that this can also happen in mpox sequences.
The common ancestor of the 32 sequences has only 1 extra SNP compared to summer 2022 sequences. Yet all sequences are supposed to be collected more than 1 year later. With a clock rate of around 12 SNPs/year, this indicates a likely date entry error.
Other sequences from the same submitters dated to 2023 are in line with the clock and cluster with other 2023 sequences from other labs. This is notably not the case here: no other lab has submitted sequences from this putative 2023 lineage.
The submitter kindly confirmed that the dates are correct and not a typo. So there isn't any misdating!