A #Genomic #Perspective on the #Origin and #Emergence of #SARS-CoV-2 (Cell, abstract)

[Source: Cell Press, full page: (LINK). Abstract, edited.]

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

Yong-Zhen Zhang, Edward C. Holmes

Open Access | Published: March 26, 2020 | DOI: https://doi.org/10.1016/j.cell.2020.03.035

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Abstract

The ongoing pandemic of a new human coronavirus, SARS-CoV-2, has generated enormous global concern. We and others in China were involved in the initial genome sequencing of the virus. Herein, we describe what genomic data reveal about the emergence SARS-CoV-2 and discuss the gaps in our understanding of its origins.

Keywords: SARS-CoV-2; COVID-19; Wildlife; China.

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#Genetic #Evolution Analysis of 2019 Novel #Coronavirus and Coronavirus From Other Species (Infect Genet Evol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Infect Genet Evol, 104285 2020 Mar 10 [Online ahead of print]

Genetic Evolution Analysis of 2019 Novel Coronavirus and Coronavirus From Other Species

Chun Li 1, Yanling Yang 2, Linzhu Ren 3

Affiliations: 1 The Chinese Peoples’ Liberation Army 964 Hospital, Changchun, China. 2 Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China. Electronic address: m18043213639@163.com. 3 College of Animal Sciences, Jilin University, Changchun 130062, China. Electronic address: renlz@jlu.edu.cn.

PMID: 32169673 DOI: 10.1016/j.meegid.2020.104285

 

Abstract

The Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a Public Health Emergency of International Concern. However, so far, there are still controversies about the source of the virus and its intermediate host. Here, we found the novel coronavirus was closely related to coronaviruses derived from five wild animals, including Paguma larvata, Paradoxurus hermaphroditus, Civet, Aselliscus stoliczkanus and Rhinolophus sinicus, and was in the same branch of the phylogenetic tree. However, genome and ORF1a homology show that the virus is not the same coronavirus as the coronavirus derived from these five animals, whereas the virus has the highest homology with Bat coronavirus isolate RaTG13.

Keywords: 2019 Coronavirus disease (COVID-19); Genetic evolution; Genome; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Structural protein.

Copyright © 2019. Published by Elsevier B.V.

Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Keywords: SARS-CoV-2; COVID-19; Bats.

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2019 novel #Coronavirus: Rapid #Classification of #Betacoronaviruses and Identification of #TCM as Potential Origin of #Zoonotic Coronaviruses (Lett Appl Microbiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Lett Appl Microbiol 2020 Feb 14 [Online ahead of print]

2019_nCoV: Rapid Classification of Betacoronaviruses and Identification of Traditional Chinese Medicine as Potential Origin of Zoonotic Coronaviruses

Trudy M Wassenaar 1, Ying Zou 2

Affiliations: 1 Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576, Zotzenheim, Germany. 2 SciPaperEdit, Chuangkexing, 17# Wenzhi Street, Hongshan District, Wuhan, Hubei Province, China.

PMID: 32060933 DOI: 10.1111/lam.13285

 

Abstract

The current outbreak of a novel SARS-like coronavirus, 2019_nCoV, illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of whole-genome sequence comparisons, we demonstrate that the non-coding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream non-coding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Further, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics.

Keywords: Sarbecovirus; Coronavirus; Traditional Chinese Medicine; bats; epidemic; whole-genome comparison; zoonosis.

This article is protected by copyright. All rights reserved.

Keywords: Betacoronavirus; Sarbecovirus; SARS-CoV-2; COVID-19; Bats.

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The #Global #Spread of 2019 novel #Coronavirus: A #Molecular #Evolutionary Analysis (Pathog Glob Health, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Pathog Glob Health, 1-4 2020 Feb 12 [Online ahead of print]

The Global Spread of 2019-nCoV: A Molecular Evolutionary Analysis

Domenico Benvenuto 1, Marta Giovanetti 2, Marco Salemi 3 4, Mattia Prosperi 3 4, Cecilia De Flora 1, Luiz Carlos Junior Alcantara 2, Silvia Angeletti 5, Massimo Ciccozzi 2

Affiliations: 1 Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy. 2 Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil. 3 Department of Epidemiology, University of Florida, Gainesville, FL, USA. 4 Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. 5 Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Italy.

PMID: 32048560 DOI: 10.1080/20477724.2020.1725339

 

Abstract

The global spread of the 2019-nCoV is continuing and is fast moving, as indicated by the WHO raising the risk assessment to high. In this article, we provide a preliminary phylodynamic and phylogeographic analysis of this new virus. A Maximum Clade Credibility tree has been built using the 29 available whole genome sequences of 2019-nCoV and two whole genome sequences that are highly similar sequences from Bat SARS-like Coronavirus available in GeneBank. We are able to clarify the mechanism of transmission among the countries which have provided the 2019-nCoV sequence isolates from their patients. The Bayesian phylogeographic reconstruction shows that the 2019-2020 nCoV most probably originated from the Bat SARS-like Coronavirus circulating in the Rhinolophus bat family. In agreement with epidemiological observations, the most likely geographic origin of the new outbreak was the city of Wuhan, China, where 2019-nCoV time of the most recent common ancestor emerged, according to molecular clock analysis, around November 25th, 2019. These results, together with previously recorded epidemics, suggest a recurring pattern of periodical epizootic outbreaks due to Betacoronavirus. Moreover, our study describes the same population genetic dynamic underlying the SARS 2003 epidemic, and suggests the urgent need for the development of effective molecular surveillance strategies of Betacoronavirus among animals and Rhinolophus of the bat family.

Keywords: 2019-nCoV; SARS; molecular Epidemiology; phylogeny.

Keywords: SARS-CoV-2; COVID-19; Bats; Zoonoses.

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Emerging Novel #Coronavirus (2019-nCoV) – Current #Scenario, #Evolutionary #Perspective Based on #Genome Analysis and Recent Developments (Vet Q., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Vet Q, 1-12 2020 Feb 8 [Online ahead of print]

Emerging Novel Coronavirus (2019-nCoV) – Current Scenario, Evolutionary Perspective Based on Genome Analysis and Recent Developments

Yashpal Singh Malik 1, Shubhankar Sircar 1, Sudipta Bhat 1, Khan Sharun 2, Kuldeep Dhama 3, Maryam Dadar 4, Ruchi Tiwari 5, Wanpen Chaicumpa 6

Affiliations: 1 Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 2 Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 3 Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 4 Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran; 5 Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura 281 001, India; 6 Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.

PMID: 32036774 DOI: 10.1080/01652176.2020.1727993

 

Abstract

Coronaviruses are the well-known cause of severe respiratory, enteric and systemic infections in a wide range of hosts including man, mammals, fish, and avian. The scientific interest on coronaviruses increased after the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) outbreaks in 2002-2003 followed by Middle East Respiratory Syndrome CoV (MERS-CoV). This decade’s first CoV, named 2019-nCoV, emerged from Wuhan, China, and declared as “Public Health Emergency of International Concern” on January 30th, 2020 by the World Health Organization (WHO). As on February 4, 2020, 425 deaths reported in China only and one death outside China (Philippines). In a short span of time, the virus spread has been noted in 24 countries. The zoonotic transmission (animal-to-human) is suspected as the route of disease origin. The genetic analyses predict bats as the most probable source of 2019-nCoV though further investigations needed to confirm the origin of the novel virus. The ongoing nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses as well. The successful virus isolation attempts have made doors open for developing better diagnostics and effective vaccines helping in combating the spread of the virus to newer areas.

Keywords: 2019-nCoV; Coronavirus; Middle East Respiratory Syndrome CoV; Public Health Emergency; Severe Acute Respiratory Syndrome CoV; genetic analyses; reservoir host; therapeutics; vaccines; zoonoses.

Keywords: 2019-nCoV; Bats; Wildlife.

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Full- #genome #evolutionary #analysis of the novel #corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent #recombination event (Infect Genet Evol., abstract)

[Source: Infection, Genetics & Evolution, full page: (LINK). Abstract, edited.]

Infection, Genetics and Evolution / Volume 79, April 2020, 104212 / Short communication

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

D. Paraskevis a, E.G. Kostaki a, G. Magiorkinis a, G. Panayiotakopoulos b, G. Sourvinos c, S. Tsiodras d

{a} Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; {b} National Public Health Organization (NPHO), Athens, Greece; {c} Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece; {d} Medical School, National and Kapodistrian University of Athens, Athens, Greece

Received 27 January 2020, Accepted 28 January 2020, Available online 29 January 2020. DOI: https://doi.org/10.1016/j.meegid.2020.104212

 

Highlights

  • Full-genomic sequence analysis of the novel corona virus (2019-nCoV).
  • Phylogenetic and recombination analysis within the subgenus of sarbecovirus.
  • Evidence that the 2019-nCoV shows discordant clustering with the Bat_SARS-like coronavirus sequences.
  • Evidence that the hypothesis of emergence of 2019-nCoV as a result of a recent recombination event is rejected.

 

Abstract

Background

A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.

Methods

Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods.

Results

Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5′-part spanning the first 11,498 nucleotides and the last 3′-part spanning 24,341–30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3′-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch.

Conclusions

The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.

Keywords: Novel coronavirus  – Genomic sequence analysis – Phylogenetic analysis – Recombination – Origin – Molecular epidemiology

Keywords: 2019-nCoV; Genetics; Bats; Evolution; Betacoronavirus; Sarbecovirus.

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#Evolutionary #Perspectives on Novel #Coronaviruses Identified in #Pneumonia Cases in #China (Nat Sci Rev., abstract)

[Source: National Science Review, full page: (LINK). Abstract, edited.]

PERSPECTIVE

Evolutionary Perspectives on Novel Coronaviruses Identified in Pneumonia Cases in China

Xiaoman Wei1,2,3, Xiang Li1,3, Jie Cui1,2,*

1 CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China. 2 Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, China. 3 University of Chinese Academy of Sciences, Beijing, China.

*Corresponding author (email: jcui@ips.ac.cn)

 

Abstract

Coronaviruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), are highly transmissible pathogens, and they can be lethal in humans. Bats are believed to be the original sources of these lethal pathogens. In December 2019, a cluster of pneumonia cases was reported in Wuhan and a novel coronavirus (2019-nCoV) has been linked to the causative agent. Early studies indicated that the new virus was genetically similar to a bat betacoronavirus, providing evidence for bat origin of the third human-infecting coronavirus in less than 20 years. We here highlight the potential for viral spillover from animals to humans and discuss evolutionary mechanisms leading to the outbreaks.

Keywords: Coronavirus; 2019-nCoV; China.

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