OmniVira

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].
PMID39702450 DOI10.1038/s41467-024-55384-7 Year2024 Journal Nature communications Nat Commun Languageeng Publication statusActive
Active Last checked 2026-10-01 03:31:09 Source: NCBI PubMed

Abstract

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.

Supporting text Virus Host Location
Bayes Theorem 33 Chiroptera 376 COVID-19 427 Phylogeny 826 SARS-CoV-2 456 Alphacoronavirus 29 Animals 1981 Betacoronavirus 79 China 234 Coronavirus 93 Coronavirus Infections 172 Disease Reservoirs 149 Evolution, Molecular 178 Host Specificity 135 Humans 1455

Evidence records

4 total
Zoonotic Surveillance
1 records · 1 evidence types
Evidence type Viral Detection
1 records
OVE8687 Viral Detection
Key finding

A large set of 589 novel bat coronavirus sequences was detected from bat samples collected in China through sequencing-based surveillance.

Virus
Coronaviridae
Host
bats Chiroptera Natural host
Location
China
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.

Method
sequencing | Bayesian statistical framework | genomic analysis
Sample type
bat samples
Geographic raw
China
Country inferred
CHN
Genomic Evolution
3 records · 1 evidence types
Evidence type Phylogenetic Evolution
3 records
OVE8690 Phylogenetic Evolution
Key finding

Phylogenetic analysis places SARS-CoV-2 within lineages from Rhinolophus spp. bats, indicating an evolutionary origin in these bats.

Virus
Severe acute respiratory syndrome coronavirus 2
Host
Rhinolophus Natural host
Location
Not specified
Supporting text

Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Analysis methods
phylogenetic analysis
OVE8688 Phylogenetic Evolution
Key finding

Alpha-CoVs showed more frequent cross-species transmission among bat families and genera than beta-CoVs in China.

Virus
Alphacoronavirus Coronaviridae
Host
bats Chiroptera Natural host
Location
China
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. 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.

Analysis methods
Bayesian phylogenetic analysis
OVE8689 Phylogenetic Evolution
Key finding

Inter-family and inter-genus transmission of bat coronaviruses occurred most frequently within Rhinolophidae and the genus Rhinolophus in China.

Virus
Coronaviridae
Host
horseshoe bats Rhinolophidae Natural host Rhinolophus Natural host
Location
China
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. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus.

Analysis methods
Bayesian phylogenetic analysis