Response to COVID-19 Epidemic
Analysis of the genome and transmission characteristics of an aggregated novel coronavirus infection based on metagenomic next-generation sequencing
Yang Yurong, Wan Hanbing, Kang Yaoxia, Peng Jingxian, Gao Meng, Liu Xin, Guo Xiaokui, Zhu Yongzhang
Published 2023-02-20
Cite as Chin J Endemiol, 2023, 42(2): 152-156. DOI: 10.3760/cma.j.cn231583-20210922-00312
Abstract
ObjectiveTo analyze the viral genome sequence of novel coronavirus infected persons in Baotou City, understand the mutation characteristics of novel coronavirus genome in the process of transmission among cases, and explore the transmission rule of novel coronavirus in the clustered populations.
MethodsNine throat swabs samples (No. 1 - 7, No. 9, and No. 10), two sputum samples (No. 8, No. 11, and No. 11 sample was from No. 10 case), and one surface smear sample (No.12, and No. 12 sample was from No. 10 case) were collected from 10 confirmed cases of novel coronavirus infection in Baotou City from January 25 to February 21, 2020. Samples 1 and 3 were from single cases, and the rest were from clustered cases. The virus genome was sequenced by metagenomic next-generation sequencing (mNGS), and single nucleotide polymorphism (SNP) mutation sites were screened by comparing with NC_045512, a reference strain of novel coronavirus. Combined with relevant epidemiological information, gene mutation, virus typing, and evolutionary traceability analysis were carried out.
ResultsThe results of viral genome mNGS showed that 76 SNP mutation sites were detected in 12 samples compared with the reference strain NC_045512, including 3 (3.95%) transitions and 73 (96.05%) reversals. There were 19 (25.00%) synonymous mutations and 57 (75.00%) non-synonymous mutations. The analysis of nucleotide and amino acid variation sites showed that mutations were found at five sites (T2821C, C6548T, T16464C, G16858A and T251C) in all the clustered cases (cases 2, 4 - 10). In the single cases, sample 1 had mutations at C9245T and A15340T, and sample 3 had mutation at C13T. The virus typing analysis showed that the samples 1 and 3 belonged to the L type of novel coronavirus, while the rest belonged to the S type of novel coronavirus. The results of genomic evolutionary relationship analysis showed that all the samples could be divided into two branches. The branches of sample 1 and 3 belonged to single cases, and the rest belonged to family clustered cases.
ConclusionThe genomic characteristics of the clustered cases of novel coronavirus infection in Baotou City are basically consistent with the epidemiological investigation results, and the transmission of the virus is mainly related to close contact and family gathering.
Key words:
Novel coronavirus infection; Clustered case; Metagenomic next-generation sequencing; Genetic characteristics
Contributor Information
Yang Yurong
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Wan Hanbing
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Kang Yaoxia
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Peng Jingxian
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Gao Meng
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Liu Xin
Microbiology Laboratory, Baotou Center for Disease Control and Prevention, Baotou 014030, China
Guo Xiaokui
School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
Zhu Yongzhang
School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
