Analysis of the whole genome traceability and transmission path simulation experiment of the local cluster COVID-19 epidemic.

Yun SONG; Shi Dong LU; Xiao HU; Bi Cong WU; Wei FAN; Hong Xia MA; Ying YE; Dong Xiao LI; Yi LI; Bai Fan ZHANG; Sheng ZHAO; Hai Yan WEI; Jing Jing PAN; Da Cheng GUO; Dong Yang ZHAO; Wan Shen GUO; Xue Yong HUANG

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Analysis of the whole genome traceability and transmission path simulation experiment of the local cluster COVID-19 epidemic.

VernacularTitle:河南省一起新型冠状病毒肺炎本地聚集性疫情全基因组溯源及传播路径模拟实验分析
Author: Yun SONG ¹ ; Shi Dong LU ¹ ; Xiao HU ¹ ; Bi Cong WU ¹ ; Wei FAN ¹ ; Hong Xia MA ¹ ; Ying YE ¹ ; Dong Xiao LI ¹ ; Yi LI ¹ ; Bai Fan ZHANG ¹ ; Sheng ZHAO ² ; Hai Yan WEI ¹ ; Jing Jing PAN ¹ ; Da Cheng GUO ¹ ; Dong Yang ZHAO ¹ ; Wan Shen GUO ¹ ; Xue Yong HUANG ¹
Author Information

1. Henan Provincial Center for Disease Control and Prevention,Infectious Disease Control and Prevention Institute,Henan Provincial Key Laboratory of Infectious Disease Pathogens,Zhengzhou 450016, China.
2. Henan Provincial Center for Disease Control and Prevention, Institute of Immunization Prevention and Planning, Zhengzhou 450016, China.
Publication Type:Journal Article
MeSH: Humans; COVID-19; SARS-CoV-2/genetics*; Genome, Viral; Epidemics; Phylogeny
From: Chinese Journal of Preventive Medicine 2022;56(12):1795-1802
CountryChina
Language:Chinese
Abstract: Objective: To trace and characterize the whole genome of SARS-CoV-2 of confirmed cases in the outbreak of COVID-19 on July 31, 2021 in Henan Province. Method: Genome-wide sequencing and comparative analysis were performed on positive nucleic acid samples of SARS-CoV-2 from 167 local cases related to the epidemic on July 31, 2021, to analyze the consistency and evolution of the whole genome sequence of virus. Results: Through high-throughput sequencing, a total of 106 cases of SARS-CoV-2 whole genome sequences were obtained. The results of genome analysis showed that the whole genome sequences of 106 cases belonged to the VOC/Delta variant strain (B.1.617.2 clade), and the whole genome sequences of 106 cases were shared with the genomes of 3 imported cases from Myanmar admitted to a hospital in Zhengzhou. On the basis of 45 nucleotide sites, 1-5 nucleotide variation sites were added, and the genome sequence was highly homologous. Conclusion: Combined with the comprehensive analysis of viral genomics, transmission path simulation experiments and epidemiology, it is determined that the local new epidemic in Henan Province is caused by imported cases in the nosocomial area, and the spillover has caused localized infection in the community. At the same time, it spills over to some provincial cities and results in localized clustered epidemics.