Whole-genome sequencing and genetic characterization of 200 novel coronavirus cases in Baiyin city in 2023
Objective To analyze the prevalence and genetic variations of SARS-CoV-2 variants in Baiyin city,Gansu province in 2023,and provide scientific basis for epidemic prevention and control and vaccine development.Methods A total of 200 nasal/oropharyngeal swab samples were collected from COVID-19 cases who visited medical institutions,were hospitalized,or under monitoring in Baiyin city,Gansu province from January to September 2023.Next-generation sequencing technology was used for whole-genome sequencing.MGI metargetCOVID software was used for sequence assembly analysis and Pangolin platform for typing.FREEBAYES was used to detect mutation sites,and annotation was performed based on NIRVANA.MAFFT software was used for multiple sequence alignment,and IQTREE was used to construct the phylogenetic tree.GGTREE and GGTREEEXTRA software were used for visualization analysis of the phylogenetic tree and related clinical information.Results From January to September 2023,all detected SARS-CoV-2 in Baiyin city were Omicron variants,with BA.5.2(32 cases,100.00％)in the first quarter(January-March),mainly XBB(56 cases,62.92％)and FL(20 cases,22.47％)families in the second quarter(April-June),and mainly dominated by EG.5.1.1(52 cases,65.82％)in the third quarter(July-September).Forty-two mutation sites were significantly enriched in moderate cases,including 25 mutations in the ORF lab gene,9 mutations in the S gene,3 mutations each in the ORF3a and ORF8 genes,and 2 mutations in the N gene.Conclusion The SARS-CoV-2 genomes circulating in Baiyin city were in different branches from the Wuhan reference strain and were basically consistent with the Pangolin typing lineages and input time.There were genetic associations between different clinical symptoms,and the association of vaccination and previous infection with the phylogenetic tree was not significant.
novel coronaviruswhole-genome sequencinggenetic characterizationmutation siteBaiyin city
NETL
NSTL
万方数据
