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

Genes
Rui DongStephen S-T Yau

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.

References

Apr 12, 2003·The New England Journal of Medicine·Christian DrostenHans Wilhelm Doerr
Sep 20, 2005·Proceedings of the National Academy of Sciences of the United States of America·Susanna K P LauKwok-Yung Yuen
Oct 1, 2005·Science·Wendong LiLin-Fa Wang
Feb 10, 2009·Nature Reviews. Microbiology·Lanying DuShibo Jiang
Feb 26, 2009·Emerging Infectious Diseases·Suxiang TongCharles E Rupprecht
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·Se-Ran JunSung-Hou Kim
Jul 19, 2011·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Meriadeg Ar GouilhJean-Claude Manuguerra
Jun 7, 2013·Emerging Infectious Diseases·Li YangQi Jin
Sep 21, 2013·Emerging Infectious Diseases·Ndapewa Laudika ItheteWolfgang Preiser
Feb 4, 2014·Journal of Theoretical Biology·Chenglong YuStephen S-T Yau
Jun 10, 2014·Journal of Theoretical Biology·Changchuan YinStephen S-T Yau
Aug 31, 2014·Molecular Phylogenetics and Evolution·Hsin-Hsiung HuangStephen S-T Yau
Mar 25, 2015·DNA and Cell Biology·Hui ZhengStephen S-T Yau
Apr 18, 2015·Virology Journal·Supaporn WacharapluesadeeThiravat Hemachudha
Jul 2, 2015·Molecular Biology and Evolution·Vincent LefortOlivier Gascuel
Dec 10, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Audrey LacroixPhilippe Buchy
Jan 9, 2018·Evolutionary Bioinformatics Online·Rui DongStephen St Yau
Dec 7, 2018·Journal of Biomolecular Structure & Dynamics·Kun TianStephen Yau
Dec 12, 2018·Nature Reviews. Microbiology·Jie CuiZheng-Li Shi
Aug 7, 2019·Computational and Structural Biotechnology Journal·Shaojun PeiStephen S-T Yau
Jan 23, 2020·Journal of Medical Virology·Wei JiXingguang Li
Feb 25, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Tung Phan
Mar 29, 2020·Nature·Tommy Tsan-Yuk LamWu-Chun Cao
Mar 31, 2020·Journal of Medical Virology·Andrés E CastilloJorge Fernández
Apr 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Peter ForsterMichael Forster
Apr 15, 2020·Nature Medicine·Kristian G AndersenRobert F Garry
Apr 22, 2020·Current Biology : CB·Tao ZhangZhigang Zhang

❮ Previous
Next ❯

Citations

Sep 29, 2020·Transboundary and Emerging Diseases·Saverio PaltrinieriStefania Lauzi
Oct 27, 2020·Frontiers in Microbiology·Jie ZhaoBao-Ping Tian
Aug 7, 2020·Travel Medicine and Infectious Disease·Kuldeep DhamaAlfonso J Rodriguez-Morales
Apr 23, 2021·Briefings in Bioinformatics·Abozar GhorbaniThomas P Karbanowicz
Apr 27, 2021·Acta Mathematica Scientia = Shu Xue Wu Li Xue Bao·Shaojun Pei, Stephen S-T Yau
May 24, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Yuyan ZhangGuizhi Li

❮ Previous
Next ❯

Methods Mentioned

BETA
GISAID

Software Mentioned

ClustalX2
BioNJ
FigTree
MATLAB
NJ
FastME

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases
Yuyan ZhangGuizhi Li
Molecular Biology and Evolution
Thomas Leitner, Sudhir Kumar
© 2022 Meta ULC. All rights reserved