Fragments of different origins mobile genetic elements in the genome of coronavirus SARS-CoV-2

Abstract

Aims. To analyze the presence of fragments of mobile genetic elements (MGE) of pro- and eukaryotic origin in the nucleotide sequence of the new human coronavirus SARS-CoV-2. Methods. The homology between nucleotide sequences was determined by BLAST 2.6.1. The results of the search and identification of MGE were performed using the ISfinder and CENSOR programs. Results. In the genome of the human coronavirus SARS-CoV-2, fragments of 11 bacterial IS elements (0.68% of the viral genome) and 23 eukaryotic MGEs (4.6%) have been identified. Of the 11 SARS-CoV-2 genes, fragments of IS-elements are present in two genes (ORF1ab and M) and in 3’UTR. Fragments of MGE eukaryotes have been detected within four genes (ORF1ab, S, N, and ORF7b) and in 3’UTR. The highest percentage of MGE was found in the ORF7b gene and in 3’UTR. Analyzing the insertion profiles of IS fragments on the example of known human coronaviruses and their intermediate hosts, we have been concluded that the possibility of using fragments of prokaryotic MGE for phylogenetic studies of the new human coronavirus SARS-CoV-2. Conclusions. Based on the obtained results, we have been suggested that fragments of MGE of pro- and eukaryotic origin may play a role in the evolution of the SARS-CoV-2 genome, in particular in the formation of viral genes. They could also be informative phylogenetic markers.Keywords: human coronaviruses, SARS-CoV-2, MGE, IS-elements, phylogenetic markers