Genomic characteristics of 2019 novel coronavirus from imported cases of coronavirus disease 2019 in Henan Province / 中华传染病杂志

ABSTRACT

Objective:To analyze the evolutionary characteristics and variations of 2019 novel coronavirus (2019-nCoV) strains imported from abroad in Henan Province.Methods:A total of 16 imported cases of coronavirus disease 2019 (COVID-19) reported in Henan Province from May to December 2020 were enrolled. The throat swab specimens from the patients were collected and sent to the Henan Provincial Center for Disease Control and Prevention for whole genome sequencing. Taking SARS-CoV-2 Wuhan-Hu-1 published in Global Initiative on Sharing All Influenza Data (GISAID) as the reference sequence, the sequences were aligned and analyzed by MEGA X, and the phylogenetic tree was constructed by the maximum likelihood method.Results:Among 16 cases, 13 cases were imported from Russia, two cases were imported from Myanmar, and one case was imported from Ukraine. A total of 16 strains of 2019-nCoV genomes with the lengths of 29 804 bp to 29 882 bp were obtained. A total of 145 nucleotide mutations and 80 amino acid mutations were detected. Nucleotide variations of C241T, C3037T, C14408T, A23403G and the amino acid variation of D614G in spike protein were detected in all sequences. Meanwhile, insertion A at the site of 29704 was found in BetaCov/HEN02/Human/2020, BetaCov/HEN04/Human/2020 and BetaCov/HEN05/Human/2020. Deletion variation was not found. Phylogenetic analysis showed that there was no correlation between the 16 strains and currently epidemic variants of concern (VOC) .Conclusion:From May to December 2020, the detection of viral genome mutations in the imported cases of Henan Province shows randomness and diversity, while the strains are not VOC.