Covid variant sequences

Question

[elisheva]

Hi everyone,

I am trying to compare private mutations of different patients.
Therefore I have to get rid of the known Omicron/Delta mutations which are common between the patients. (and other known variants as well).
Does anyone know where can I find the sequence of those variants or alternatively a VCF file containing the known mutations?

TIA

[GenoMax]

COVID variants:
https://covariants.org/variants
https://covdb.stanford.edu/page/mutation-viewer/

Answer 1

[jv]

GISAID has been the primary repository for SARS-CoV-2 genome sequences that I have used in my COVID-19 related work.

I have yet to see an established reference sequence for any of the major variants like delta and omicron. Your best bet is to define a set of reference mutations for delta and omicron based on the literature and to use that for your comparison to the mutations in your patient samples. Many papers will cite the specific GISAID accession(s) for the sequence(s) that they used to represent delta or omicron in their work but these will vary from study.