SARS-CoV-2 genetic characterization of the first cases from 12 local epidemics in border areas of Yunnan province caused by Omicron variant
10.3760/cma.j.cn112866-20220708-00157
- VernacularTitle:奥密克戎BA.2引起的12起云南省边境地区本土疫情首例病例新冠病毒基因特征分析
- Author:
Meiling ZHANG
1
;
Xiaoqing FU
;
Yong ZHANG
;
Chunrui LUO
;
Zhaosheng LIU
;
Xiaonan ZHAO
;
Jienan ZHOU
Author Information
1. 云南省疾病预防控制中心，昆明 650022
- Keywords:
severe acute respiratory syndrome coronavirus 2;
Virus genome;
Omicron variant;
Mutation site;
Source of virus infection
- From:
Chinese Journal of Experimental and Clinical Virology
2023;37(1):13-19
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To understand the characteristics of the local Coronavirus Disease 2019 (COVID-19) epidemic in the border areas of Yunnan province, and to analyze and trace the genome variation of the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2).Methods:The basic information and samples of the first cases of 12 local epidemics in the border areas of Yunnan province from mid-February to April 2022 were collected. The virus genomes, genotypes and mutations were determined by the whole genome sequencing technology, the Pangolin COVID-19 Lineage Assigner and MEGA software. The sources of virus infection were estimated based on the contents of epidemiological investigations.Results:The first cases from 12 local epidemics in the border areas of Yunnan province had diverse occupations, and none of them had ever left the local area. The virus genomes of 12 first cases were Omicron (BA.2) variants and every two of them further belonged to the evolutionary clades BA.2.10 and BA.2.3.2, respectively. The genome-wide nucleotide-level mutation analysis showed that there were 1 or more specific nucleotide mutation sites in 10 first cases of the local epidemics. Combined with the epidemiological investigations, it was suggested that there might be different sources of virus infection in all 12 local epidemics. Further analysis of amino acid mutations revealed that in addition to the representative mutation sites of evolutionary clades, there were also specific amino acid mutation sites (such as S: E1188 D) in the genome sequences between the cases, which also deserved attention. The result of phylogenetic tree analysis were consistent with Pangolin Assigner and mutation analysis.Conclusions:The 12 local epidemics in Yunnan may have different sources of virus infection, which indicates that the COVID-19 epidemic in the border areas of Yunnan province is extremely complicated. Strengthening the frequency of nucleic acid screening and the scope of key populations and monitoring the variation of SARS-CoV-2 are of great significance for the precise prevention and control of the epidemic.
