Abstract
SARS-CoV-2 is a member of the subgenus Sarbecovirus and thus contains the genetic element s2m. We have extensively mined nucleotide data in GenBank in order to obtain a comprehensive list of s2m sequences both in the four virus families where s2m has previously been described and in other groups of organisms. Surprisingly, there seems to be a xenologue of s2m in a large number of insect species. The function of s2m is unknown, but our data show a very high degree of sequence conservation both in insects and in viruses and that the version of s2m found in SARS-CoV-2 has unique features, not seen in any other virus or insect strains.
Highlights
SARS-CoV-2 is a member of the subgenus Sarbecovirus and contains the genetic element s2m
We have previously reported the presence of a 41–43 nt long hairpin-forming element, referred to as stem-loop II-like motif (s2m) [1], in several families of positive-s ense ssRNA [(+)ssRNA] viruses [2]
To further characterize the specific s2m sequence found in SARS-CoV-2, blastn [8] with word size 11 was used to search the entire virus section of GenBank using all s2m sequences reported in the literature (n=97) [1,2,3, 7] as query sequences
Summary
SARS-CoV-2 is a member of the subgenus Sarbecovirus and contains the genetic element s2m. The presence of s2m in the SARS-CoV-2 genome (GenBank accession MN908947, position 29 727–29 768; Figs 1 and 2) and other members of this group is probably the result of a single horizontal transfer event, pre-dating the divergence of SARS-related viruses [2, 7].
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