Genome characterization and traceability analysis of SARS-CoV-2 in a local outbreak
10.3760/cma.j.cn112309-20220210-00041
- VernacularTitle:一起新型冠状病毒暴发疫情的基因组特征与溯源分析
- Author:
Yi LI
1
;
Yun SONG
;
Bicong WU
;
Shidong LU
;
Lin ZHU
;
Dongxiao LI
;
Baifan ZHANG
;
Xiao HU
;
Haiyan WEI
;
Sheng ZHAO
;
Hongxia MA
;
Ying YE
;
Xueyong HUANG
;
Wanshen GUO
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;
Delta variant;
Genome characterization;
Nucleotide mutation;
Amino acid mutation
- From:
Chinese Journal of Microbiology and Immunology
2022;42(4):245-250
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the genome characteristics and variations in nucleotides and amino acids of SARS-CoV-2 causing an outbreak in Henan Province in November 2021 and perform the traceability analysis.Methods:In this study, throat swab specimens from cases in the acute phase were collected and tested for the nucleic acids of SARS-CoV-2 by real-time fluorescent RT-PCR. SARS-CoV-2 nucleic acid-positive samples were subjected to high-throughput genome sequencing and whole-genome alignment analysis.Results:The median Ct values of ORF1ab gene and N gene in 70 positive specimens was 26.41 (15.58 to 39.27) and 24.43 (12.04 to 39.74), respectively. Compared with the sequence of Wuhan-Hu(NC_045512) reference strain, 47 to 49 nucleotide mutations sharing 47 nucleotide mutation and 41 amino acid mutations were found in 63 strains of successfully sequenced SARS-CoV-2. Nine nucleotide mutations and 12 amino acid mutations were found in the spike protein. The index case shared 47 mutations with the Russian imported cases in Henan Province on October 14 and the local cases in Jiangxi Province in October. Moreover, their genomes were highly homologous and they all belonged to the Delta variant (AY.122 evolutionary branch).Conclusions:Continuous monitoring of imported COVID-19 cases and prolonging the period of quarantine were needed to reduce the risk of local outbreak and epidemic caused by imported COVID-19 cases. Analysis of the genomic characteristics of SARS-CoV-2 and the variations in nucleotides and amino acids was conducive to trace the origin of COVID-19 outbreak quickly and provide reference for precise control.
