Conserved amino acids in HCoV-HKU1 and SARS-Cov2 at RNA-dependent RNA polymerase (RdRp) motifs

Abstract

A novel and related to severe acute respiratory syndrome associated coronavirus (SARS-CoV2) has been identified as an infectious coronavirus originating from a Wuhan seafood market and rapidly spreading into and beyond China. While non-conserved regions of viral genome can lead to novel coronavirus subtypes, conserved regions are also very important for drug and vaccine researches. In our study, together with SARS-CoV showing high sequence similarity with SARS-Cov2, also genome and protein sequence alignments of non-lethal OC43 and HCoV-HKU1 viruses for SARS-CoV2 were performed in the regions shown as drug targets. The genomic sequence similarities of SARS-CoV2 with SARS-CoV are 79% between 6-1923 bp, 82% between 3956-21577 bp, 80% between 22539-27910 bp and 90% between 28257-29894 bp, respectively. Major similar region of OC43 spike protein with SARS-Cov2 is located in the C terrminus, 2 other conserved regions with lower similarity were detected in N- terminus of S protein. HCoV-HKU1, has a 73% similarity between 14348-15992 bp in the genomic sequence of SARS-CoV2 RNA-dependent RNA polymerase (RdRp). Similar regions of relatively harmless HCoV-HKU1 with SARS-CoV2 for RdRp can contribute understanding active sites of RdRp and developing a specific drug target. Antiviral approaches to the conserved regions of the RdRp protein have the potential to protect against existing and possible novel coronavirus species. Although lethal coronaviruses contain a large number of non-conserved regions compared to relatively harmless respiratory pathogens, existance of the conserved regions for replication and understanding functional importance of these regions may be vital to develop effective treatment methods.

Keywords

• COVID19
• HCoV-HKU1
• OC43
• RdRp

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