Whole-genome characterization and traceability analysis of the first COVID-19 outbreak caused by Omicron variant in Henan Province
10.3760/cma.j.cn112309-20220823-00269
- VernacularTitle:河南省首起奥密克戎COVID-19疫情全基因组特征与溯源分析
- Author:
Yun SONG
1
;
Shidong LU
;
Xiao HU
;
Lin ZHU
;
Baifan ZHANG
;
Jingjing PAN
;
Dongxiao LI
;
Haiyan WEI
;
Yi LI
;
Sheng ZHAO
;
Haifeng WANG
;
Ying YE
;
Xueyong HUANG
;
Hongxia MA
Author Information
1. 河南省疾病预防控制中心传染病预防控制所，河南省传染病病原生物重点实验室，郑州 450016
- Keywords:
SARS-CoV-2;
Omicron variant;
Genome characteristics
- From:
Chinese Journal of Microbiology and Immunology
2023;43(4):271-278
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the whole genome of Omicron variants causing the first local Omicron outbreak in Henan Province and to investigate the mutations in the SARS-CoV-2 genome for source tracing.Methods:Respiratory tract samples from COVID-19 cases in the Omicron outbreak in Henan Province from January 7 to 29, 2022 were subjected to whole-genome sequencing and sequence alignment analysis. Whole-genome identity, variations and evolution of the Omicron variants were analyzed.Results:Through high-throughput sequencing, the whole-genome sequences of SARS-CoV-2 were obtained from 120 cases, which accounted for 25.64% (120/468) of all COVID-19 cases in Anyang during the same period. Compared with the genome of Wuhan reference strain (NC_045512.2), there were 57-59 nucleotide mutation sites in the 120 whole genome sequences, and one or two nucleotide mutation sites were added to the shared 57 nucleotide sites. All of the 120 strains were VOC/Omicron (BA.1.1) variants and shared high homology. The whole-genome sequence obtained from the first case A contained 57 nucleotide mutation sites, while apart from the 57 identical nucleotide mutation sites, one specific mutation site (C1594T) was found in the whole-genome sequence obtained from the first case B, suggesting that the two cases were in the same transmission chain. After comparing with the database of domestic and imported cases by the Chinese Center for Disease Control and Prevention and the Henan Provincial Center for Disease Control and Prevention, it was found that the current outbreak was linked with the same transmission chain as the existing local epidemics in other provinces. Moreover, epidemiological investigation showed that on January 2, case A had come into contact with her cousin and his family who returned from an affected area outside the province.Conclusions:Based on the gene sequencing results and epidemiological investigation, the COVID-19 outbreak in Anyang city, Henan Province was a local epidemic and the source of it was a college student who returned to Anyang city from other province on December 28, 2021. These infections were linked to the same transmission chain as the existing local infection in other provinces.
