三亚市首例新冠病毒进化分支XBB.1.16的基因特征及风险因素分析

Analysis of genetic characteristics and risk factors of the first SARS-CoV-2 subtype XBB.1.16 in Sanya City

目的分析三亚市首例新冠病毒(SARS-CoV-2)XBB.1.16的基因特征并评估风险因素,为预防和控制疫情提供科学依据。方法收集三亚市2022年8月—2023年4月的260例新冠病毒感染者咽拭子样本,用RT-PCR方法检测SARS-CoV-2核酸,对ORF1ab和N基因检测Ct值小于32的样本使用Nanopore三代测序进行全基因组测序。根据测序结果将感染者分为XBB.1.16和其他进化分支,以感染者年龄、性别、社会和经济风险指数(SERI)等,人口统计和健康行为,作为风险因素,使用单变量和多变量逻辑回归推断SARS-CoV-2阳性与自变量之间的关联,并使用向前和向后逐步赤池信息准则(AIC)进行变量选择。结果基因测序显示三亚首例XBB.1.16感染者NextStrain分型为23B,覆盖率为100%。同武汉参考株(NC_045512.2)相比,核苷酸变异位点101个,氨基酸变异63个,XBB.1、XBB.1.5和XBB.1.16的突变频率>0.9,突变区为NSP6、NSP14、Spike和ORF8等。与病例密切接触、未接种疫苗和高风险社会和经济风险指数普查区是感染的危险因素。结论减少与患者密接并接种疫苗可以减少XBB.1.16等SARS-CoV-2感染。

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 collected,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.