Whole genome sequencing on SARS-CoV-2 strains isolated among local COVID-19 patients during an Omicron epidemic in Tianshui city

Abstract

ObjectiveTo analyze the genomic characteristics and variation of severe acute respiratory disease coronavirus 2 (SARS-CoV-2) strains prevalent in a local epidemic of coronavirus disease 2019 (COVID-19) in Tianshui city of Gansu province. MethodsPharyngeal swab samples were collected from 136 severe COVID-19 cases in Tianshui city during December 2022. Nucleic acid detection was performed on the isolated SARS-CoV-2 strains with mutant nucleic acid detection kits; whole genome sequencing of the isolated strains was performed using second generation sequencing technology; virus lineage and type were determined with Pangolin and Nextclade platforms and MAFFT software was used for multiple sequences comparison; a phylogenetic tree was constructed using MEGA software with neighbor-joining method. ResultsWhole genome sequences of 32 isolated SARS-CoV-2 strains were obtained. Pangolin typing analysis showed that of the 32 isolated strains, 31 belonged to Omicron variant BA.5.2 evolutionary branch and only one belonged to Omicron variant BF.7 evolutionary branch. Totally 68 nucleotide mutation sites and 32 amino acid mutation sites were identified. The S494P and A522S variants exist in the key sites of the receptor binding domain (RBD) of the S protein. ConclusionThere were multiple coding region mutations for the SARS-CoV-2 Omicron virus variants isolated from local COVID-19 patients in Tianshui city and the mutations could affect the pathogenicity, infectivity and immune escape of the prevalent viral stains.

Keywords

• sars-cov-2
• omicron variant
• amino acid mutation
• nucleotide mutation
• tianshui city