Modern Disease Control and Prevention

Objective To analyze the genomic characteristics of Omicron variant strains of local SARS-CoV-2 in Anyang, and provide scientific evidence for understanding the mutation and change regular pattern of novel coronavirus infection in Anyang.Methods The whole genome sequence of the virus was obtained by third-generation nanopore sequencing of oropharyngeal swabs collected from 13 local reported COVID-19 cases in Anyang in November,2022. The virus type was determined by using an online analysis platform. MEGA 11.0 software was used for sequence alignment and analysis; phylogenetic tree was constructed; specific mutation sites were identified, and the molecular characteristics of viruses were analyzed. Results All of the 13 strains were Omicron variants, with sequence lengths of 29 615 nt-29 752 nt, covering 99.1%-99.7%, and a total of 103nucleotide mutation sites and 94 amino acid mutation sites. The mutation sites were distributed in 8 gene coding regions, 5'terminal non-coding region and 3' terminal non-coding region of the novel coronavirus. Among them, the mutation of S protein had the greatest impact on the mutation of the novel coronavirus. R346T and C1243F were the unique amino acid mutation sites of BF.7.14 on S protein; T883I was the amino acid mutation site unique to BA.5.2.49. Q241K was the unique amino acid mutation site of DY.2; the types of the 13 sequences on the Pangolin database were DY.2, BA.5.2.49 and BF.7.14, respectively,and the Nextclade evolutionary analysis was 22B. Phylogenetic tree analysis showed that the 13 SARS-CoV-2 whole genome sequences and reference sequence construction phylogenetic tree were divided into two major branches, namely BF.7 branch and BA.5.2 branch. Conclusions The genomic variation characteristics of the 13 strains of SARS-CoV-2 in this study showed that S protein mutation sites in the gene coding region had the highest number, and there were also protein mutation sites in other regions. The variation sites can be used to analyze the changes of virus transmission ability, immune escape ability and so on;this analysis has accumulated data for continuous monitoring of SARS-CoV-2 genomic variation in the future.