Typing of alpha and beta coronaviruses by DNA barcoding of NSP12 gene

Abstract

Since the spread of the COVID-19 pandemic, the world paid attention to coronaviruses (CoVs) evolution and their diverged lineages because many researches studies supposed that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is evolutionarily developed from a lineage of bats CoVs. This is due to the ability of some mutant CoVs to transmit from a host to different hosts. For this reason, there are many fears about the pathogenicity of the upcoming variants of CoVs. Thus, it is important to get a rapid and economic technique for typing a wide range of human and animal CoVs species for following up their mutant transmission. Therefore, the present study aims at approaching a simple design of DNA barcoding of a wide range of mammals' CoVs (including alpha and beta CoVs), by universal amplification of a species-specific sequence inside a conserved gene (NSP12) followed by amplicon sequencing. The in silico evaluation involved 96 nucleotide sequences of different CoVs (18 alpha CoVs and 78 beta CoVs), and was applied experimentally into the lab on 5 human CoVs isolates; 3 of them belong to beta CoVs (OC43, MERS, and SARS-CoV-2) and 2 are alpha CoVs (229E and NL63). The results indicated that the designed universal primers are able to amplify 332 bp of a taxonomic region inside the NSP12 coding sequence that facilitates the identification and classification of mammals' CoVs upon the resulting phylogenetic tree.