Whole-genome sequencing of SARS-CoV-2 Gamma variant first discovered in Chinese mainland / 中华微生物学和免疫学杂志

ABSTRACT

Objective:To investigate the whole genome of SARS-CoV-2 causing COVID-19 in Rongcheng city of Shandong Province in May 2022 and to further analyze the nucleotide and amino acid variations for source tracing.Methods:High-throughput sequencing was used to sequence the SARS-CoV-2 genome in 15 nasopharyngeal swab samples from COVID-19 cluster infections and three environmental samples related to an aquatic product import company. Whole-genome sequence splicing, variant site analysis and sequence typing were performed on the raw sequencing data using virus sequence and variant analysis software. A phylogenetic tree was constructed by evolutionary analysis software. Epidemiological investigation was used to trace the potential source of infection.Results:Thirteen whole genome sequences of SARS-CoV-2 with the length ranging from 29 653 bp to 29 780 bp were successfully obtained from the nasopharyngeal swab samples. The average sequencing depth was 1 756-6 565 X and the genome coverage was 99.20%-99.63%. The results of Pangolin typing showed that the 13 genomes belonged to the VOC/Gamma (P.1.15) evolutionary branch. Compared with the Wuhan reference strain (NC_045512.2), the 13 genome sequences had 40-41 nucleotide mutation sites. There were 23-24 amino acid variation sites in seven protein domains (ORF1a, ORF1b, S, ORF3a, ORF8, ORF9b and N proteins). Evolutionary analysis showed that the viral sequence was grouped to the same subclade as the reference strain from Argentina (EPI_ISL_4082233).Conclusions:In this study, the whole genome sequences of 13 Gamma variant strains were obtained from COVID-19 cluster infections associated with imported cold-chain aquatic products in Rongcheng city, and the imported seafood from South America in 2021 was found to be the source of the virus in a timely manner. This study provided reference for the SARS-CoV-2 variant analysis and case tracing and also suggested that the survival and transmission ability of SARS-CoV-2 on the surface of cold-chain products should not be underestimated and needed further investigation.