Analysis of the Hosts and Transmission Paths of SARS-CoV-2 in the COVID-19 Outbreak.

Rui Dong,Shaojun Pei,Rong Lucy He,Changchuan Yin,Stephen S-T Yau

doi:10.3390/genes11060637

Rui Dong, Shaojun Pei + Show 3 more

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https://doi.org/10.3390/genes11060637

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Abstract

The severe respiratory disease COVID-19 was initially reported in Wuhan, China, in December 2019, and spread into many provinces from Wuhan. The corresponding pathogen was soon identified as a novel coronavirus named SARS-CoV-2 (formerly, 2019-nCoV). As of 2 May, 2020, over 3 million COVID-19 cases had been confirmed, and 235,290 deaths had been reported globally, and the numbers are still increasing. It is important to understand the phylogenetic relationship between SARS-CoV-2 and known coronaviruses, and to identify its hosts for preventing the next round of emergency outbreak. In this study, we employ an effective alignment-free approach, the Natural Vector method, to analyze the phylogeny and classify the coronaviruses based on genomic and protein data. Our results show that SARS-CoV-2 is closely related to, but distinct from the SARS-CoV branch. By analyzing the genetic distances from the SARS-CoV-2 strain to the coronaviruses residing in animal hosts, we establish that the most possible transmission path originates from bats to pangolins to humans.

Highlights

Coronaviruses (CoVs) are members of the subfamily Coronavirinae in the family Coronaviridae and the order Nidovirales
//platform.gisaid.org/epi3/frontend) on 23 February, 2020, which were collected from patients at the early stage of the outbreak in Wuhan, China. 731 known human coronavirus complete genomes were downloaded from NCBI directly, which consist of 29 HCoV-229E strains, 52 HCoV-NL63 strains, 34 HCoV-HKU1 strains, 153 HCoV-OC43 strains, 214 SARS-CoVs and 249 MERS-CoVs
The phylogenetic tree based on the SARS-CoV-2 strains and 731 complete genomes of human coronaviruses (HCovs) is shown in Figure 2, in which different colors represent different virus types

Summary

Introduction

Coronaviruses (CoVs) are members of the subfamily Coronavirinae in the family Coronaviridae and the order Nidovirales. They can cause respiratory and intestinal infections in animals and humans [1], and are considered to be highly pathogenic to humans since the outbreak of SARS (severe acute respiratory syndrome) in Guangzhou, China in 2003 [2]. Another highly pathogenic coronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), emerged ten years after. Among the six human coronaviruses, HCoV-229E and HCoV-NL63 are alpha-coronaviruses, while the other four

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