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Origin and cross-species transmission of bat coronaviruses in China

Author

Listed:
  • Alice Latinne

    (EcoHealth Alliance
    Health Program)

  • Ben Hu

    (Chinese Academy of Sciences)

  • Kevin J. Olival

    (EcoHealth Alliance)

  • Guangjian Zhu

    (EcoHealth Alliance)

  • Libiao Zhang

    (Guangdong Academy of Sciences)

  • Hongying Li

    (EcoHealth Alliance)

  • Aleksei A. Chmura

    (EcoHealth Alliance)

  • Hume E. Field

    (EcoHealth Alliance
    The University of Queensland)

  • Carlos Zambrana-Torrelio

    (EcoHealth Alliance)

  • Jonathan H. Epstein

    (EcoHealth Alliance)

  • Bei Li

    (Chinese Academy of Sciences)

  • Wei Zhang

    (Chinese Academy of Sciences)

  • Lin-Fa Wang

    (Duke-NUS Medical School)

  • Zheng-Li Shi

    (Chinese Academy of Sciences)

  • Peter Daszak

    (EcoHealth Alliance)

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 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.

Suggested Citation

  • Alice Latinne & Ben Hu & Kevin J. Olival & Guangjian Zhu & Libiao Zhang & Hongying Li & Aleksei A. Chmura & Hume E. Field & Carlos Zambrana-Torrelio & Jonathan H. Epstein & Bei Li & Wei Zhang & Lin-Fa, 2020. "Origin and cross-species transmission of bat coronaviruses in China," Nature Communications, Nature, vol. 11(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17687-3
    DOI: 10.1038/s41467-020-17687-3
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    Cited by:

    1. Jun-Yu Si & Yuan-Mei Chen & Ye-Hui Sun & Meng-Xue Gu & Mei-Ling Huang & Lu-Lu Shi & Xiao Yu & Xiao Yang & Qing Xiong & Cheng-Bao Ma & Peng Liu & Zheng-Li Shi & Huan Yan, 2024. "Sarbecovirus RBD indels and specific residues dictating multi-species ACE2 adaptiveness," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    2. Yelin Han & Panpan Xu & Yuyang Wang & Wenliang Zhao & Junpeng Zhang & Shuyi Zhang & Jianwei Wang & Qi Jin & Zhiqiang Wu, 2023. "Panoramic analysis of coronaviruses carried by representative bat species in Southern China to better understand the coronavirus sphere," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    3. Magdalena Meyer & Dominik W. Melville & Heather J. Baldwin & Kerstin Wilhelm & Evans Ewald Nkrumah & Ebenezer K. Badu & Samuel Kingsley Oppong & Nina Schwensow & Adam Stow & Peter Vallo & Victor M. Co, 2024. "Bat species assemblage predicts coronavirus prevalence," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Cecilia A. Sánchez & Hongying Li & Kendra L. Phelps & Carlos Zambrana-Torrelio & Lin-Fa Wang & Peng Zhou & Zheng-Li Shi & Kevin J. Olival & Peter Daszak, 2022. "A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    5. Renata L. Muylaert & David A. Wilkinson & Tigga Kingston & Paolo D’Odorico & Maria Cristina Rulli & Nikolas Galli & Reju Sam John & Phillip Alviola & David T. S. Hayman, 2023. "Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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