Dynamic Analysis on Spike Mutation and Genetic Characteristics of SARS-CoV-2 Omicron Strains in Quanzhou,China,from 2022 to 2023
To understand the genotype distribution and genetic characteristics of SARS-CoV-2 in Quanzhou,China,and to dynamic surveillance the mutation on key domain of spike protein.The whole genome sequence of SARS-CoV-2 from surveillance cases in Quanzhou,China from 2022 to 2023 were detected by nanopore sequencing.A total of 641 sequences post quality control were genotyped,alignmented and dynamic analysed on the key mutation of spike protein by cluster heatmap.The influence of mutations on viral transmission and adaptability was evaluated by VarEPS.All the 641 cases were Omicron variants of SARS-CoV-2 shown as turnover of BA.2-BA.5-XBB lineage,in according with the national epidemic trend during the corresponding period.The numbers of mutations in nucleotides and amino acids were 81(79～84)and 57(55～62)with gradual growth.Turnovers of various amino acid substitutions were shown in Receptor binding motif region of spike protein,such as G446V to G446S,T478K to T478R/N and F486I/V to F486S/P.High-frequency amino acid substitutions in N-terminal domain region of BA.2.75 were detected during the non-BA.2.75 epidemic,such as W152R,F157L and I210V.Various amino acid substitutions in the region of the Furin cleavage site and the S2 subunit were detected in various periods,associated with genotypic turnover.The stability of S protein binding to neutralizing antibodies was reduced accompanying all of these amino acid mutations,while hardly reduced binding to ACE2,and they were mostly neutral mutations.The dynamic surveillance on mutations of SARS-CoV-2 by genetic level can show the genotype characteristics and the evolution of virus,help to explore the effects of variation on viral transmission and adaptation,and give warning on the key mutations in time.
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