Genome characterization and traceability analysis of SARS-CoV-2 in a local outbreak
Chinese Journal of Microbiology and Immunology (China)
; 42(4):245-250, 2022.
Article
in Chinese
| EMBASE | ID: covidwho-1928717
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.
article; controlled study; coronavirus disease 2019; epidemic; genetic susceptibility; major clinical study; nonhuman; polymerase chain reaction; quarantine; risk assessment; SARS-CoV-2 Delta; Severe acute respiratory syndrome coronavirus 2; throat swab; amino acid; endogenous compound; nucleic acid; nucleotide; virus spike protein
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Databases of international organizations
Database:
EMBASE
Language:
Chinese
Journal:
Chinese Journal of Microbiology and Immunology (China)
Year:
2022
Document Type:
Article
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