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Literature detail

Origin and cross-species transmission of bat coronaviruses in China.

Alice Latinne1,2,3 Ben Hu4 Kevin J Olival1 Guangjian Zhu1 Libiao Zhang5 Hongying Li1 Aleksei A Chmura1 Hume E Field1,6 Carlos Zambrana-Torrelio1 Jonathan H Epstein1 Bei Li4 Wei Zhang4 Lin-Fa Wang7 Zheng-Li Shi8 Peter Daszak9
Affiliations 9 institutions
  1. EcoHealth Alliance, New York, USA.
  2. Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Viet Nam
  3. Wildlife Conservation Society, Health Program, Bronx, NY, USA.
  4. Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
  5. Guangdong Institute of Applied Biological Resources, Guangdong Academy of Sciences, Guangzhou, China.
  6. School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia.
  7. Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
  8. Key Laboratory of Special Pathogens And Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China. [email protected].
  9. EcoHealth Alliance, New York, USA. [email protected].
PMID 32843626 2020 Nat Commun eng epublish
PubMed DOI Browse context

Article

Publication summary

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Evolution, Molecular Animals Bayes Theorem Betacoronavirus Biodiversity China Chiroptera Coronavirus Coronavirus Infections COVID-19 Humans Pandemics Phylogeny Phylogeography Pneumonia, Viral SARS-CoV-2 Zoonoses

Structured evidence records

Evidence records

3 total
Cross Species Transmission 1 records
Cross Species Transmission Extraction confidence 1.00
Key finding

Phylogenetic analysis of bat coronaviruses in China indicates frequent inter-family and inter-genus host switching among bats, particularly within Rhinolophidae and Rhinolophus.

Location
China China
Supporting text

We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus.

Method
Bayesian statistical framework; phylogenetic analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 0.95
Key finding

Phylogenetic analysis of bat coronavirus sequences indicated a likely origin of SARS-CoV-2 in Rhinolophus spp. bats.

Virus
SARS-CoV-2
Location
Not specified
Supporting text

Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal... Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Genes or proteins
whole genome
Analysis methods
phylogenetic analysis; Bayesian statistical framework
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.90
Key finding

A large sequencing dataset from bats in China identified coronavirus lineages and host taxa defining hotspots that inform targeted bat-CoV surveillance.

Host
Chiroptera
Location
China China
Supporting text

We use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China ... that could help target bat-CoV discovery for proactive zoonotic disease surveillance.

Method
Bayesian statistical framework; sequence data analysis
Geographic raw
China
Country inferred
China