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.
Highlights
1, 1, Bei Li2, 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
We generated 630 partial sequences (440 nt) of the RNA-dependent RNA polymerase (RdRp) gene from bat rectal swabs collected in China and added 608 bat-CoV and 8 pangolin-CoV sequences from China available in GenBank or GISAID to our datasets
Our phylogenetic analysis shows a high diversity of CoVs from bats sampled in China, with most bat genera included in this study (10/16) infected by both α- and β-CoVs
Summary
1, 1, Bei Li2, 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. All CoVs known to infect humans are zoonotic, or of animal origin, with many thought to originate in bat hosts[1,2] Due to their large genome size (the largest nonsegmented RNA viral genome), frequent recombination, and high genomic plasticity, CoVs are prone to cross-species transmission and are able to rapidly adapt to new hosts[1,3]. In 2019, a novel CoV (SARS-CoV-2) causing respiratory illness (COVID-19) was first reported in Wuhan, Hubei province, China This emerging human virus is closely related to SARS-CoV, and appears to have originated in horseshoe bats20,21—with its full genome 96% similar to a viral sequence reported from Rhinolophus affinis[20]. Bat-CoV diversity seems to be correlated with host taxonomic diversity globally, with the highest CoV diversity being found in areas with the highest bat species richness[32]
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