I was alerted by my colleagues that a newly sequenced SARS-CoV-2 sample had multiple novel deletions in the starting amino acids of the Spike protein.
Bracing for another variant of concern, I ran the sequencing data through my own pipeline (bwa-mem2+iVar) and submitted both to nextclade.
Nextclade identified large Spike deletions in both sequences:
However, I could not find a single indication of these deletions outside of the nextclade results.
Both consensus sequences had the Spike start codon fully in-tact.
My variant caller (iVar) found no such deletions, save for the well known ones further down the gene (69-70 and so forth).
Other tools, such as the GISAID CoVsurver and cov-glue, didn’t find anything out of the ordinary either.
Do you have any idea what happened here?
Thanks in advance,