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. 2020 Jun 9;11(6):637.
doi: 10.3390/genes11060637.

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

Rui Dong  1 , Shaojun Pei  1 , Changchuan Yin  2 , Rong Lucy He  3 , Stephen S-T Yau  1
Affiliations

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

Rui Dong et al. Genes (Basel). .

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.

Keywords: COVID-19; Natural Vector method; SARS-CoV-2; transmission path.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The genomic structures of SARS-CoV-2, SARS-CoV, bat-CoV and pangolin-CoV. The genomic structures of SARS-CoV-2 (NC_045512), SARS-CoV (NC_004718) and bat-CoV (MN_996532) were drawn according to their annotations in NCBI GenBank. The genomic structure of pangolin-CoV was drawn in [8].
Figure 2
Figure 2
The phylogenetic tree of 95 SARS-CoV-2 and 731 known coronaviruses based on BioNJ and Natural Vector algorithm. Different colors represent different types of coronaviruses that can infect humans.
Figure 3
Figure 3
The phylogenetic tree of 38 coronavirus genomes based on BioNJ and Natural Vector algorithm.
Figure 4
Figure 4
The phylogenetic tree of 95 SARS-CoV-2 strains where different colors represent the SARS-CoV-2 strains sampled from different countries.
Figure 5
Figure 5
The phylogenetic BioNJ tree based on the Hausdorff distance between SARS-CoV-2 strains group and 13 possible host groups.
Figure 6
Figure 6
The natural graph of 13 possible host sources and SARS-CoV-2 group. The blue arrows represent the first-level relationship while the red ones represent the second-level relationships. First level indicates closer relationship.
See this image and copyright information in PMC

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