国内首起新型冠状病毒Gamma变异株的全基因组测序分析

Whole-genome sequencing of SARS-CoV-2 Gamma variant first discovered in Chinese mainland

目的对引发2022年5月山东省荣成市COVID-19疫情的SARS-CoV-2进行全基因组测序,分析核苷酸和氨基酸变异情况并进行溯源。方法应用高通量测序技术对15份来源于某水产进口公司相关COVID-19聚集性病例鼻咽拭子样本和3份环境样本进行病毒全基因组测序。使用病毒序列和变异分析软件,对测序原始数据进行全基因组序列拼接和变异位点分析并对病毒进行分型,利用进化分析软件构建系统发育树,并结合病例流行病学调查结果,追溯病毒的潜在来源。结果成功获得13条来源于病例样本的SARS-CoV-2全基因组序列,长度为29653~29780 bp,平均测序深度为1756~6565 X,基因组覆盖度为99.20%~99.63%;Pangolin分型结果显示13个SARS-CoV-2基因组均属于VOC/Gamma(P.1.15)分支;与武汉参考株(NC_045512.2)相比,13条SARS-CoV-2全基因组序列分别存在40~41个核苷酸突变位点;在7个蛋白质结构域(ORF1a、ORF1b、S、ORF3a、ORF8、ORF9b及N蛋白),存在23~24个氨基酸变异位点。进化分析显示该病毒序列与来自阿根廷的参考株(EPI_ISL_4082233)共处于同一子分支上。结论本研究从荣成市一起冷链进口水产关联的COVID-19聚集性疫情病例样本中测序获得13个Gamma变异株全基因组序列,及时将病毒来源指向于2021年的南美进口海鲜。本研究所采用的测序方法和分析结果可以为SARS-CoV-2的变异分析和病例溯源提供参考,也提示我们SARS-CoV-2在冷链物品表面的存活与传播能力不容小觑,有待进一步探索。

Objective To investigate the whole genome of SARS-CoV-2 causing COVID-19 in Rongcheng city of Shandong Province in May 2022 and to further analyze the nucleotide and amino acid variations for source tracing.Methods High-throughput sequencing was used to sequence the SARS-CoV-2 genome in 15 nasopharyngeal swab samples from COVID-19 cluster infections and three environmental samples related to an aquatic product import company.Whole-genome sequence splicing,variant site analysis and sequence typing were performed on the raw sequencing data using virus sequence and variant analysis software.A phylogenetic tree was constructed by evolutionary analysis software.Epidemiological investigation was used to trace the potential source of infection.Results Thirteen whole genome sequences of SARS-CoV-2 with the length ranging from 29653 bp to 29780 bp were successfully obtained from the nasopharyngeal swab samples.The average sequencing depth was 1756-6565 X and the genome coverage was 99.20%-99.63%.The results of Pangolin typing showed that the 13 genomes belonged to the VOC/Gamma(P.1.15)evolutionary branch.Compared with the Wuhan reference strain(NC_045512.2),the 13 genome sequences had 40-41 nucleotide mutation sites.There were 23-24 amino acid variation sites in seven protein domains(ORF1a,ORF1b,S,ORF3a,ORF8,ORF9b and N proteins).Evolutionary analysis showed that the viral sequence was grouped to the same subclade as the reference strain from Argentina(EPI_ISL_4082233).Conclusions In this study,the whole genome sequences of 13 Gamma variant strains were obtained from COVID-19 cluster infections associated with imported cold-chain aquatic products in Rongcheng city,and the imported seafood from South America in 2021 was found to be the source of the virus in a timely manner.This study provided reference for the SARS-CoV-2 variant analysis and case tracing and also suggested that the survival and transmission ability of SARS-CoV-2 on the surface of cold-chain products should not be underestimated and needed further investigation.