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

Jinkun Chen, Evann E. Hilt, Fan Li, Huan Wu, Zhuojing Jiang, Qinchao Zhang, Jiling Wang, Yifang Wang, Ziqin Li, Jialiang Tang, Shangxin Yang

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

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 Ct 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.

Original languageEnglish (US)
Article number567621
JournalFrontiers in Public Health
Volume8
DOIs
StatePublished - Sep 18 2020
Externally publishedYes

Bibliographical note

Funding Information:
This study was funded by Shaoxing IngeniGen XMK Biotechnologies, Inc.

Funding Information:
We would like to thank Yong-Zhen Zhang (Fudan University) and Eddie Holmes (University of Sydney) for sharing the sequence of the first SARS-CoV-2 isolate in a very timely manner. We would also like to thank Fanchao Meng, Bin Hu, Haihao Shou, and Yuanyuan Cai from Shaoxing IngeniGen XMK Biotechnologies, Inc. for their technical assistance. This manuscript has been released as a pre-print at MedRxiv: Chen et al. (26). Funding. This study was funded by Shaoxing IngeniGen XMK Biotechnologies, Inc.

Funding Information:
Conflict of Interest: HW and YW were employed by the company Shaoxing IngeniGen XMK Biotechnologies. FL was the Chief Executive Officer of the company Three Coin Analytics. The authors declare that this study received funding from Shaoxing IngeniGen XMK Biotechnologies. The funder had the following involvement with this study: providing sequencing data and preliminary bioinformatics analysis.

Publisher Copyright:
© Copyright © 2020 Chen, Hilt, Li, Wu, Jiang, Zhang, Wang, Wang, Li, Tang and Yang.

Keywords

  • 2019-nCoV
  • COVID-19
  • SARS-CoV-2
  • genomic epidemiology
  • genotype
  • metagenomic sequencing
  • mutation rate
  • transmission

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