Genomic characterization of a novel SARS-CoV-2

Gene Rep. 2020 Jun;19:100682. doi: 10.1016/j.genrep.2020.100682. Epub 2020 Apr 16.

Abstract

A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of Wuhan in China. Our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of SARS-CoV-2 using bioinformatics programs. Information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. To understand the genomic structure and variations of the SARS-CoV-2. The study analyzed 95 SARS-CoV-2 complete genome sequences available in GenBank, National MicrobiologyData Center (NMDC) and NGDC Genome Warehouse from December-2019 until 05 of April-2020. The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.

Keywords: BLAST, Basic Local Alignment Search Tool; CDC, Centers of Disease Control and Prevention; COVID-19; COVID-19, Coronavirus disease 2019; EMBOSS, The European Molecular Biology Open Software Suite; Genomic characterization; MERS, Middle East Respiratory Syndrome; Mutation; NCBI, National Center for Biotechnology Information; NGDC, National Genomics Data Center; NMDC, National Microbiology Data Center; NSP, nonstructural protein; ORF, Open Reading Frame; SARS-CoV-2; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; UTR, Untranslated region; WHO, World Health Organization.