Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries

Abdullah Shah; Farooq Rashid; Abdul Aziz; Amin Ullah Jan; Muhammad Suleman

doi:10.1016/j.genrep.2020.100886

Genetic characterization of structural and open reading Fram-8 proteins of SARS-CoV-2 isolates from different countries

Gene Rep. 2020 Dec:21:100886. doi: 10.1016/j.genrep.2020.100886. Epub 2020 Sep 14.

Authors

Abdullah Shah¹, Farooq Rashid², Abdul Aziz³, Amin Ullah Jan¹, Muhammad Suleman⁴

Affiliations

¹ Department of Biotechnology, Shaheed Benazir Bhutto University Sheringal, Dir, Pakistan.
² School of Public Health, Department of Epidemiology, Southern Medical University, Dermatology Hospital, Guangzhou, China.
³ Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China.
⁴ Centre for Biotechnology and Microbiology, University of Swat, Pakistan.

Abstract

Since December 2019, a severe pandemic of pneumonia, COVID-19 associated with a novel coronavirus (SARS-CoV-2), have emerged in Wuhan, China and spreading throughout the world. As RNA viruses have a high mutation rate therefore we wanted to identify whether this virus is also prone to mutations. For this reason we selected four major structural (Spike protein (S), Envelope protein (E), Membrane glycoprotein (M), Nucleocapsid phosphoprotein (N)) and ORF8 protein of 100 different SARS-CoV-2 isolates of fifteen countries from NCBI database and compared these to the reference sequence, Wuhan NC_045512.2, which was the first isolate of SARS-CoV-2 that was sequenced. By multiple sequence alignment of amino acids, we observed substitutions and deletion in S protein at 13 different sites in the isolates of five countries (China, USA, Finland, India and Australia) as compared to the reference sequence. Similarly, alignment of N protein revealed substitutions at three different sites in isolates of China, Spain and Japan. M protein exhibits substitution only in one isolates from USA, however, no mutation was observed in E protein of any isolate. Interestingly, in ORF8 substitution of Leucine, a nonpolar to Serine a polar amino acid at same position (aa84 L to S) in 23 isolates of five countries i.e. China, USA, Spain, Taiwan and India were observed, which may affect the conformation of peptides. Thus, we observed several mutations in the isolates thereafter the first sequencing of SARS-CoV-2 isolate, NC_045512.2, which suggested that this virus might be a threat to the whole world and therefore further studies are needed to characterize how these mutations in different proteins affect the functionality and pathogenesis of SARS-CoV-2.

Keywords: COVID-2; Mutation; Name, Abbreviations; Phosphorylation; SARS-CoV-2; Serine/Threonine kinases; Severe Acute Respiratory Syndrome-Coronavirus-2, SARS-CoV-2; World Health Organization, WHO; angiotensin converting enzyme 2, ACE2; coronavirus disease of 2019, COVID-19; envelope protein, E; membrane glycoprotein, M; nonstructual proteins, NSPs; nucleocapsid phosphoprotein, N; open reading frame, ORF; surface glycoprotein, S.