Genomic Epidemiology of SARS-CoV-2 From Mainland China With Newly Obtained Genomes From Henan Province.

Ning Song,Guang-Lin Cui,Qing-Lei Zeng

doi:10.3389/fmicb.2021.673855

Abstract

Even though the COVID-19 epidemic in China has been successfully put under control within a few months, it is still very important to infer the origin time and genetic diversity from the perspective of the whole genome sequence of its agent, SARS-CoV-2. Yet, the sequence of the entire virus genome from China in the current public database is very unevenly distributed with reference to time and place of collection. In particular, only one sequence was obtained in Henan province, adjacent to China's worst-case province, Hubei Province. Herein, we used high-throughput sequencing techniques to get 19 whole-genome sequences of SARS-CoV-2 from 18 severe patients admitted to the First Affiliated Hospital of Zhengzhou University, a provincial designated hospital for the treatment of severe COVID-19 cases in Henan province. The demographic, baseline, and clinical characteristics of these patients were described. To investigate the molecular epidemiology of SARS-CoV-2 of the current COVID-19 outbreak in China, 729 genome sequences (including 19 sequences from this study) sampled from Mainland China were analyzed with state-of-the-art comprehensive methods, including likelihood-mapping, split network, ML phylogenetic, and Bayesian time-scaled phylogenetic analyses. We estimated that the evolutionary rate and the time to the most recent common ancestor (TMRCA) of SARS-CoV-2 from Mainland China were 9.25 × 10−4 substitutions per site per year (95% BCI: 6.75 × 10−4 to 1.28 × 10−3) and October 1, 2019 (95% BCI: August 22, 2019 to November 6, 2019), respectively. Our results contribute to studying the molecular epidemiology and genetic diversity of SARS-CoV-2 over time in Mainland China.

Highlights

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the severe respiratory disease coronavirus disease 2019 (COVID-19), which was first reported in Wuhan city, Hubei Province, China in December 2019 (Wu et al, 2020a; Zhou et al, 2020; Zhu et al, 2020), subsequently turning into a pandemic with devastating effects
We only investigated the 18 severe or critically ill patients with COVID-19, for whom sequences of SARSCoV-2 were successfully assembled with coverage of more than 90% by the aforementioned method
For a better understanding of the impact of the minority viral population on SARS-CoV-2 evolution and transmission, more studies are needed to uncover the in-host variability of the virus during the course of the infection

Summary

Introduction

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the severe respiratory disease coronavirus disease 2019 (COVID-19), which was first reported in Wuhan city, Hubei Province, China in December 2019 (Wu et al, 2020a; Zhou et al, 2020; Zhu et al, 2020), subsequently turning into a pandemic with devastating effects. Henan Province, which borders with Hubei Province to the north, has the third-largest population in China (94 m people). It contains many large cities, including Zhengzhou (10 million people), Nanyang (10 million people), Zhoukou (8 million people), Shangqiu (7 million people), and Zhumadian (7 million people). By December 30, 2020, Henan Province had reported 1,273 local confirmed cases of COVID-19, including 22 deaths. Almost all of the cases in Henan Province were reported in January and February 2020, as described by our previous studies (Zeng et al, 2020a,b)

Methods

Results

Conclusion