Analysis of genetic characteristics and risk factors of the first SARS-CoV-2 subtype XBB.1.16 in Sanya City
Objective To analyze the genetic characteristics and risk factors of the first case of SARS-CoV-2 subtype XBB.1.16 in Sanya City,in order to provide scientific basis for the prevention and control of epidemic.Methods The throat swab samples of 260 patients infected SARS-CoV-2 from August 2022 to April 2023 in Sanya were collect-ed,RT-qPCR was used to detect SARS-CoV-2 nucleic acid,the samples with ORF1ab and N genes Ct value less than 32 were sequenced using Nanopore third-generation sequencing.Based on the sequencing results the patients were divided into XBB.1.16 and other SARS-CoV-2 evolutionary clade positive patients.The risk factors including age,gender,social and economic risk index(SERI),demographics,health behavior variables were collected,univariate and multivariate logistic regression were used to infer the association between SARS-CoV-2 positive and independent variables.Variable selection using forward and backward stepwise Chichi Information Guidelines(AIC).Results The gene sequencing showed that the first XBB.1.16 NextStrain in Sanya was typed 23B,with a coverage rate of 100％.Compared with Wuhan reference strain(NC_045512.2),there were 101 nucleotide mutation sites and 63 amino acid mutations.The mutation frequency of XBB.1,XBB.1.5 and XBB.1.16 was above 0.9,and the mutation regions were NSP6,NSP14,Spike and ORF8,respectively.Close contact with cases,unvaccinated and high-risk SERI census tracts were risk factors for SARS-CoV-2 infection.Conclusion Reducing close contact with patients and vaccination could reduce SARS-CoV-2 infection.
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