RESUMO
Objective:To 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.Methods:Nine 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.Results:The 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.Conclusion:The 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.
RESUMO
ObjectiveTo characterize a cluster epidemic of coronavirus disease 2019 （COVID-19）on campus in Baotou city and provide evidence for the prevention and control of COVID-19 in universities. MethodsField epidemiological investigation was conducted to determine the confirmed cases and close contacts in the cluster epidemic of COVID-19 in a university of western China in 2022. Descriptive analysis was utilized to illustrate the epidemic timeline and schematic diagram. Real-time quantitative fluorescent PCR（RT-PCR） was used to detect the nucleic acid of SARS-CoV-2 in the collected samples. ResultsA total of eight students were infected in the cluster epidemic on campus， including 2 confirmed cases and 6 asymptomatic cases. Case A1 infected other 7 students in the same dormitory or on the same floor by close contact. After a 10-day quarantine and medical observation， no further case was reported. The overall incidence rate was 1.22% and the incidence rate among close contacts was 2.24%. ConclusionThis cluster epidemic of COVID-19 is characterized by strong and fast transmission. Repeated contact with no personal protection in confined space is highly vulnerable to cluster epidemic. Prevention of cluster epidemics on campus remains crucial to contain the epidemic. Therefore， it is necessary to strengthen the management of campus containment， interrupt the transmission route， identify close contacts and implement quarantine management as early as possible to avoid the cluster epidemics on campus.