Origin and cross-species transmission of bat coronaviruses in China

• Published in: Nature communications Vol. 15; no. 1; pp. 10705 - 16
• Main Authors: Latinne, Alice, Hu, Ben, Olival, Kevin J., Zhu, Guangjian, Zhang, Li-Biao, Li, Hongying, Chmura, Aleksei A., Field, Hume E., Zambrana-Torrelio, Carlos, Epstein, Jonathan H., Li, Bei, Zhang, Wei, Wang, Lin-Fa, Shi, Zheng-Li, Daszak, Peter
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.12.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 45; 45/77; 45/91; 631/326/596/2078; 631/326/596/2562; 692/308/174; 692/699/255/2514; Alphacoronavirus - classification; Alphacoronavirus - genetics; Alphacoronavirus - isolation & purification; Animals; Bayes Theorem; Bayesian analysis; Betacoronavirus - classification; Betacoronavirus - genetics; Betacoronavirus - isolation & purification; Biodiversity hot spots; China - epidemiology; Chiroptera - virology; Coronaviridae; Coronavirus - classification; Coronavirus - genetics; Coronavirus - isolation & purification; Coronavirus Infections - epidemiology; Coronavirus Infections - transmission; Coronavirus Infections - veterinary; Coronavirus Infections - virology; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - transmission; COVID-19 - virology; Disease hot spots; Disease Reservoirs - virology; Disease transmission; Evolution, Molecular; Host Specificity; Humanities and Social Sciences; Humans; Macroevolution; multidisciplinary; Phylogenetics; Phylogeny; Rhinolophus; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Taxa; Zoonoses; China
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-55384-7

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. Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.