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Literature detail

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

Alice Latinne1,2 Ben Hu3 Kevin J Olival1 Guangjian Zhu1 Li-Biao Zhang4 Hongying Li1 Aleksei A Chmura1 Hume E Field1 Carlos Zambrana-Torrelio1 Jonathan H Epstein1 Bei Li3 Wei Zhang3 Lin-Fa Wang5 Zheng-Li Shi6 Peter Daszak7
Affiliations 7 institutions
  1. EcoHealth Alliance, New York, New York, USA.
  2. Wildlife Conservation Society, Melanesia Program, Suva, Fiji.
  3. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
  4. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China.
  5. Programme in Emerging Infectious Disease, Duke-NUS Medical School, Singapore, Singapore.
  6. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China. [email protected].
  7. EcoHealth Alliance, New York, New York, USA. [email protected].
PMID 39702450 2024 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 589 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.

Bayes Theorem Chiroptera COVID-19 Phylogeny SARS-CoV-2 Alphacoronavirus Animals Betacoronavirus China Coronavirus Coronavirus Infections Disease Reservoirs Evolution, Molecular Host Specificity Humans

Structured evidence records

Evidence records

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

Bat alphacoronaviruses and betacoronaviruses undergo frequent host switching between different bat families and genera, particularly among Rhinolophidae and Rhinolophus species in China.

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; large sequence data set analysis
Study design
phylogenetic analysis
Transmission direction
animal-to-animal
Geographic raw
China
Country inferred
China
Genomic Evolution 1 records
Genomic Evolution Extraction confidence 1.00
Key finding

Phylogenetic analysis of 589 bat coronavirus genomes identified frequent host-switching events and suggested a likely origin of SARS-CoV-2 in Rhinolophus 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 589 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
Bayesian statistical framework; phylogenetic analysis
Reservoir Ecology 1 records
Reservoir Ecology Extraction confidence 0.80
Key finding

Rhinolophus spp. bats in China are identified as likely reservoirs of SARS-CoV-2 and other diverse coronaviruses, with specific host taxa and geographic regions serving as hotspots of viral evolutionary diversity.

Virus
SARS-CoV-2
Location
China China
Supporting text

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2... Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China... Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Method
Bayesian statistical framework; phylogenetic analysis
Geographic raw
China
Country inferred
China
Zoonotic Surveillance 1 records
Zoonotic Surveillance Extraction confidence 0.85
Key finding

Bat coronavirus sequences collected in China revealed host and regional hotspots of viral diversity that can inform targeted surveillance for potential zoonotic coronaviruses.

Host
Chiroptera
Location
China China
Supporting text

We use a large sequence data set from bat-CoVs (including 589 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. 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.

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