Epidemiological and Genomic Analysis of SARS-CoV-2 in 10 Patients From a Mid-Sized City Outside of Hubei, China in the Early Phase of the COVID-19 Outbreak

Frontiers in Public Health

article

Jinkun Chen¹  Jialiang Tang¹  Shangxin Yang²  Evann E. Hilt²  Fan Li⁴  Huan Wu⁵  Zhuojing Jiang¹  Qinchao Zhang¹  Jiling Wang¹  Yifang Wang⁵  Ziqin Li³ 

[1] Shaoxing Center for Disease Control and Prevention;Department of Pathology and Laboratory Medicine, University of California, United States;Zhejiang-California International Nanosystems Institute, Zhejiang University;Inc., United States;IngeniGen XunMinKang Biotechnology Inc.

关键词: 2019-nCoV;    COVID-19;    genotype;    metagenomic sequencing;    mutation rate;    transmission;    genomic epidemiology;    SARS-CoV-2;   

DOI  :  10.3389/fpubh.2020.567621

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

A novel coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. In this study, we performed a comprehensive epidemiological and genomic analysis of SARS-CoV-2 genomes from 10 patients in Shaoxing (Zhejiang Province), a mid-sized city outside of the epicenter Hubei province, China, during the early stage of the outbreak (late January to early February, 2020). We obtained viral genomes with >99% coverage and a mean depth of 296X demonstrating that viral genomic analysis is feasible via metagenomics sequencing directly on nasopharyngeal samples with SARS-CoV-2 Real-time PCR C t values <28. We found that a cluster of four patients with travel history to Hubei shared the exact same virus with patients from Wuhan, Taiwan, Belgium, and Australia, highlighting how quickly this virus spread to the globe. The virus from another cluster of two family members living together without travel history but with a sick contact of a confirmed case from another city outside of Hubei accumulated significantly more mutations (9 SNPs vs. average 4 SNPs), suggesting a complex and dynamic nature of this outbreak. Our findings add to the growing knowledge of the epidemiological and genomic characteristics of SARS-CoV-2 and offers a glimpse into the early phase of this viral infection outside of Hubei, China.

【 授权许可】

CC BY