Literature detail

Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins.

Tommy Tsan-Yuk Lam^1,2 Na Jia³ Ya-Wei Zhang³ Marcus Ho-Hin Shum² Jia-Fu Jiang³ Hua-Chen Zhu^1,2 Yi-Gang Tong⁴ Yong-Xia Shi⁵ Xue-Bing Ni² Yun-Shi Liao² Wen-Juan Li⁴ Bao-Gui Jiang³ Wei Wei⁶ Ting-Ting Yuan³ Kui Zheng⁵ Xiao-Ming Cui³ Jie Li³ Guang-Qian Pei³ Xin Qiang³ William Yiu-Man Cheung² Lian-Feng Li⁷ Fang-Fang Sun⁵ Si Qin³ Ji-Cheng Huang⁵ Gabriel M Leung² Edward C Holmes⁸ Yan-Ling Hu^9,10 Yi Guan^11,12 Wu-Chun Cao¹³

Affiliations 13 institutions

Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China.
State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China.
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China.
Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China.
Guangzhou Customs Technology Center, Guangzhou, P. R. China.
Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China.
School of Information and Management, Guangxi Medical University, Nanning, P. R. China.
Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
Life Sciences Institute, Guangxi Medical University, Nanning, P. R. China. [email protected].
Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, P. R. China. [email protected].
Joint Institute of Virology (Shantou University and The University of Hong Kong), Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, P. R. China. [email protected].
State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, P. R. China. [email protected].
State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, P. R. China. [email protected].

PMID 32218527 2020 Nature eng ppublish

PubMed DOI Browse context

Article

Publication summary

The ongoing outbreak of viral pneumonia in China and across the world is associated with a new coronavirus, SARS-CoV-2<sup>1</sup>. This outbreak has been tentatively associated with a seafood market in Wuhan, China, where the sale of wild animals may be the source of zoonotic infection<sup>2</sup>. Although bats are probable reservoir hosts for SARS-CoV-2, the identity of any intermediate host that may have facilitated transfer to humans is unknown. Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2. The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of new coronaviruses and should be removed from wet markets to prevent zoonotic transmission.

Evolution, Molecular Sequence Homology, Nucleic Acid Amino Acid Sequence Animals Betacoronavirus China Chiroptera Coronavirus Infections COVID-19 Disease Reservoirs Eutheria Genome, Viral Genomics Humans Malaysia Pandemics Phylogeny Pneumonia, Viral

Structured evidence records

Evidence records

4 total

Genomic Evolution 1 records

Genomic Evolution Extraction confidence 0.90

Key finding

Metagenomic and phylogenetic analyses revealed two pangolin coronavirus sub-lineages closely related to SARS-CoV-2, one showing high similarity in the receptor-binding domain.

Virus

Host

Location

Supporting text

Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, including one that exhibits strong similarity in the receptor-binding domain to SARS-CoV-2.

Genes or proteins: receptor-binding domain; Spike Glycoprotein
Analysis methods: metagenomic sequencing; phylogenetic analysis; sequence alignment; comparative genomics

Receptor Usage 1 records

Receptor Usage Extraction confidence 0.80

Key finding

A pangolin-associated coronavirus was found to have strong similarity in its receptor-binding domain to SARS-CoV-2, suggesting potential compatibility with the same receptor and related entry mechanisms.

Virus

Host

Location

Supporting text

Method: metagenomic sequencing
Receptors: receptor-binding domain

Recombination Or Reassortment 1 records

Recombination Or Reassortment Extraction confidence 0.70

Key finding

Pangolin-associated coronaviruses show genetic relationships to SARS-CoV-2 that involve recombination among related betacoronavirus lineages.

Virus

Host

Location

Supporting text

Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses, and the MeSH term 'Recombination, Genetic' indicates analysis of recombination among these lineages.

Event type: recombination
Genes or segments: receptor-binding domain

Zoonotic Surveillance 1 records

Zoonotic Surveillance Extraction confidence 0.95

Key finding

SARS-CoV-2-related coronaviruses were detected in Malayan pangolins through metagenomic sequencing, indicating active viral surveillance of pangolin hosts in southern China.

Virus

Host

Location

Supporting text

Here we report the identification of SARS-CoV-2-related coronaviruses in Malayan pangolins (Manis javanica) seized in anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin-associated coronaviruses that belong to two sub-lineages of SARS-CoV-2-related coronaviruses.

Method: metagenomic sequencing
Geographic raw: southern China
Country inferred: China

Citation context

References

39 references

Reference network

Force-directed citation graph. OmniVira-indexed references are prioritized and recursively expanded up to three steps.

153 nodes · 192 links

Drag nodes to explore citation neighborhoods


-	A new coronavirus associated with human respiratory disease in China	Wu	2020
-	Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding	Lu	2020
-	Coronavirus disease 2019 (COVID-19) Situation Report – 101	World Health Organization	2020
-	Mining coronavirus genomes for clues to the outbreak’s origins	Cohen	2020
-	SARS-CoV infection in a restaurant from palm civet	Wang	2005
-	A pneumonia outbreak associated with a new coronavirus of probable bat origin	Zhou	2020
-	Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica)	Liu	2019
-	Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus	Hon	2008
PMID 31996437 In OmniVira	Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus.	Wan	2020
-	The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade	Coutard	2020
-	The Global Trafficking of Pangolins: A Comprehensive Summary of Seizures and Trafficking Routes from 2010–2015 (TRAFFIC, 2017)	Heinrich	2017
PMID 28637760	Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses	Wang	2017
-	M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph	Li	2015
-	Fast and accurate long-read alignment with Burrows–Wheeler transform	Li	2010
-	M., Standley, D. M. & Katoh, K. MAFFT-DASH: integrated protein sequence and structural alignment	Rozewicki	2019
-	RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies	Stamatakis	2014
-	Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination	Lole	1999
-	Analysis of multimerization of the SARS coronavirus nucleocapsid protein	He	2004
-	Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage	Snijder	2003
PMID 12730501	The genome sequence of the SARS-associated coronavirus	Marra	2003
-	Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human	Song	2005
-	Identification of diverse bat alphacoronaviruses and betacoronaviruses in China provides new insights into the evolution and origin of coronavirus-related diseases	Han	2019
-	Complete genome sequence of a severe acute respiratory syndrome-related coronavirus from Kenyan bats	Tao	2019
-	Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats	Hu	2018
-	Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus	Hu	2017
-	ORF8-related genetic evidence for Chinese horseshoe bats as the source of human severe acute respiratory syndrome coronavirus	Wu	2016
-	Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases	Wu	2016
PMID 23739658	Novel SARS-like betacoronaviruses in bats, China, 2011	Yang	2013
-	Detection and characterization of diverse alpha- and betacoronaviruses from bats in China	Xu	2016
-	Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China	He	2014
-	Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor	Ge	2013
-	Bats are natural reservoirs of SARS-like coronaviruses	Li	2005
-	Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences	Drexler	2010
-	Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events	Lau	2010
-	Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans	Yuan	2010
-	Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China	Guan	2003
-	Prevalence and genetic diversity of coronaviruses in bats from China	Tang	2006
-	Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: molecular epidemiology and genome evolution	Yeh	2004
-	Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003	Vega	2004

Evidence overview

Evidence 4

Types 4

Virus 2

Host 1

Evidence types

Genomic Evolution 1 Receptor Usage 1 Recombination Or Reassortment 1 Zoonotic Surveillance 1

Linked entities

Viruses

Hosts

Locations

Publication metadata

Journal: Nature
Volume / Issue / Pages: 583 / 7815 / 282-285
ISSN: 1476-4687
Journal country: England
DOI: 10.1038/s41586-020-2169-0