Sequence Analysis and Variations in the 5’ UTR genomic regions of Coronaviruses

The 5’UTR genomic regions of coronaviruses were analysed regarding sequence variations, nucleotide constituents, and patterns of evolutionary course. The 5ʹ UTR of the viral genome highly conserved that appeared clearly between the closely related viruses. It possessed variable sites of varied nucleotides.
          The 5’UTRs revealed long highly conserved regions (nt61 to nt107, nt211- nt236, nt262 to nt277). The longest one (nt61 to nt107) possessed nearly half of the core leader sequence (nt 61 to nt93) confirming its existence in viral genomes. The nucleotides composition exhibited favouritism towards AT(U) contents against GC contents which potentially is necessary   for viral origin and replication activity. The length of 5′ UTR varies in studied cronaviruses, ranging from 245 bp (SARS coronavirus BJ01, AY278488.2) to 283 bp (hCoV-19_Chile, gaisd-EPI_ISL_445295). Additionally, the 5’ UTR region of Chile, EPI_ISL_445295 isolate included a foremost 18 nucleotides, these are not found in other isolates.
            Phylogenetic analysis of 5’ UTR regions using the maximum likelihood method confirmed the close evolutionary distance and origin of betacronoviruses analysed. The most genetic closely isolates to the SARS-CoV-2 Wuhan-Hu-1 is the Bat coronavirus RaTG13. The SARS coronaviruses BJ01 and GD01 displayed the most distant betacronoviruses to SARS-CoV-2 that confirm their early arisen lineage. Finally, phylogenetic clustering in 5’ UTR regions for studied betacronoviruses revealed the genetic diversity of betacronoviruses and their high tendency towards frequent genetic mutations and gene recombination. This potentially leads to increased risk of interspecies transmission with viral evolution and accumulation of mutations.