Hello,
I tried to get the sequences of the variants for SARS-CoV-2. I can find what should be 'alpha' that is the "NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome" from GenBank. But when I try with "Severe acute respiratory syndrome coronavirus 2 beta variant" I get "OL689430.1" and "OL675863", both "Enhanced fitness of SARS-CoV-2 variant of concern Alpha, but not Beta".
Where are the variant sequences (complete genome) stored?
I got an answer from NCBI:
```
Dear colleague,
We do not have RefSeq sequences for variants of SARS-CoV-2. Indeed, we only have a single RefSeq genome, the NC_045512.2 you identified.
To find GenBank records from a particular variant, you can search the variant's lineage on our NCBI Virus page using the "Pango Lineage" section: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049
```
Dear Dr Luigi Marongiu,
I found an article that may help you:
https://www.doh.wa.gov/Portals/1/Documents/1600/coronavirus/data-tables/420-316-SequencingAndVariantsReport.pdf
Best regerads,
Pr Hambaba
Thank you very nice. There are just missing the nu, xi, omicron codes but it helps a lot.
NCBI also gave me a link to the official store of C0V-2 variants' names:
https://cov-lineages.org/lineage_list.html
You can try various databases for mining data/sequences of SARS-CoV-2 variants, including:
NCBI SARS-CoV-2 Resources: https://www.ncbi.nlm.nih.gov/sars-cov-2/
GISAID: https://www.gisaid.org/
PANGO Lineages/CoV lineages: https://cov-lineages.org/
Further on the subject, it is nice to see that the WHO must have spent a pretty penny on slick graphics as here https://cov-lineages.org/resources.html but then one needs weeks to find the fasta of the variants since it looks like they are store nowhere (at least publicly).
To facilitate the understanding, I made a table of variants' names.
I am also interested to find out right answer for this good Question
It looks like the official repository of CoV sequences is this: https://www.gisaid.org/
It requires an institutional email and takes time to be accepted.
I have found that this paper Article Mechanisms of SARS-CoV-2 entry into cells
gives a nice list of the SARS variables in table 1.