Ref Seqs for VOCs (especially 5'UTRs)

General
1

Hey just wondering if anyone can point me to full-length sequences (or at least sequences which include all of 5’UTR) of a representative for each SARS-CoV-2 VOC: Alpha (this one (WA-1) is easily findable in GenBank), Beta, Gamma, Delta, Omicron, Omicron BA.5… Other major sublineages (especially within Omicron) would also be of interest> but mostly am just looking for consensus Reference Sequences specifically for 5’UTR of the major VOC swarms. Any advice (e.g. GenBank #s!) would be most appreciated.
Dave

2

Hi @dave, welcome. I can’t speak to the presence/absence of the 5’UTRs in these sequences, but you may find what you want in the GenBank sequences used in the https://nextstrain.org/ncov/open/reference build.

3

Thanks for the response. I apologize in advance for my comprehensive ignorance! So I guess there aren’t GenBank-type sequence reads per say to represent each of the major VOCs-- but rather some strain of each VOC is represented by a list of mutations compared to an ancestor. Is that correct? Is the ancestor always WA-1 sequence (that does appear in GenBank as NC_045512)? How to access mutation list for each VOC? I am a little concerned about the mutation lists because it is hard to tell if the 5’-most genomic sequence is included. Thanks for your advice, Dave

4

I see now. The GenBank #'s are present thru the detailed info on the Phylogeny chart. Cool! But one prob is that many of the 5’UTRs appear incomplete-- they too short. So am still left to wonder if there is a recognized GenBank Ref Seq for each major VOC> that includes verified (or at least approx correct length of ~250+ nt) complete 5’UTR. Any further info would be much appreciated (I am kind of new to this genomics stuff). Thanks, Dave