Genetic variations among SARS-CoV-2 strains isolated in China

Abstract

The rapid spread of COVID-19, which has led to a global pandemic, has placed public health systems under severe pressure. Identifying variations in SARS-CoV-2 strains from different regions is a key factor for understanding the pathogenic mechanisms, aid in diagnosis, prevention and therapy of this disease. The present study is an analytical descriptive study aimed to determine genetic variations among SARS-CoV-2 strains isolated in China. Sixty six complete genome sequences of the virus were retrieved from NCBI, the sequence of original Wuhan strain accession number NC 045512 was used as the reference sequence. Each genome sequence was blasted against the original Wuhan strain; the analysis was done using NCBI Nucleo-blast. The collected sequences showed 10 different variants. One hundred and thirty four mutations were identified among the variants of SARS-CoV-2 in this study; most of them 52.2% (70/134) were missense point mutation, majority of the mutations 65.7% (88/134) occurred in the open reading frame a/b (ORFab), few mutations occurred in the structural viral genome, each of spike (S) gene and nucleocapsid (N) gene showed 4 mutations; 2 silent point mutations and 2 missense point mutations occurred in each gene whereas membrane (M) gene showed silent point mutation and no mutation observed in the envelope E gene. The remarkable observation in this study showed by Yunnan variant accession number MT226610 which exhibited high incidence of mutations, it displayed 28 different point mutations; only 3(10.7%) of them were silent mutations while the rest were missense mutations. Our analysis showed several mutations including spike S gene and membrane M gene which may be responsible for a change in the structures of target proteins.