Objective:To identify the genome-wide characteristics and variations of the novel coronavirus 2019(2019-nCoV) by combining high-throughput sequencing and bioinformatics techniques, to type and trace the virus.Methods:Pharyngeal swab sample of one 2019-nCoV infection case imported from Weihai city was selected for 2019-nCoV whole-genome sequence capture and NGS high-throughput sequencing. The obtained sequencing data were sequenced and analyzed using virus mutation analysis software, we classify viruses and build phylogenetic trees to track their potential sources.Results:The complete genome sequence of 2019-nCoV was obtained, with a total length of 29 808 bp and an average sequencing depth of 5 013.11×. A total of 51 nucleotide mutations were found in 8 coding regions (ORF1ab, S, ORF3a, E, M, ORF6, ORF7a and N). The result of virus typing showed that the virus belonged to Omicron BA.2. Evolutionary analysis showed that the virus sequence was in the same clade as the reference strains from Japan.Conclusions:The sequencing method and analysis result established in this study can be used for mutation analysis of 2019-nCoV and case tracing, which is of great significance for the prevention and control of COVID-19.

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.