PriSeT: Efficient De Novo Primer Discovery

Marie Hoffmann; Michael T. Monaghan; Knut Reinert

nucleotide collection (nt/nr) online 15 . The first query was run on the complete nt/nr data set and the second on the complete nt/nr data set except SARS-CoV-2 (taxid 2697049) to ensure that we did not miss relevant matches with non SARS-CoV-2 entries. None of the primer pairs produced amplicons with 100 % identity and 100 % coverage for non Sarbecoviruses. Of the 114 primer pairs 5 pairs had 100 % sequence identity with a single accession of a Sarbecovirus isolated from the 15 on 3rd of April 2020 pangolin, but no other relevant matches. There were 109 primer pairs producing amplicons with no other occurrences. Out of the 109 primer pairs, there were 12 pairs with amplicons that were distant from even closely related viruses, i.e. sequence identity < 97 %, and 97 had a proximity (but not identity) to at most two other accessions, namely, two Sarbecovirus species isolated from a bat and the pangolin. The first one is associated with the recent pneumonia outbreak (Zhou et al., 2020) .