Scientists pinpoint regions and species fueling coronavirus evolution in bats

By Vijay Kumar MalesuReviewed by Susha Cheriyedath, M.Sc.Jan 1 2025

Delving deep into bat habitats, scientists uncover how coronaviruses evolve, migrate, and cross-species, shedding light on pandemic origins and future risks.

Study: Origin and cross-species transmission of bat coronaviruses in China. Image Credit: Carl Allen / Shutterstock

In a recent study published in the journal Nature Communications, a group of researchers investigated the evolution, cross-species transmission, and dispersal of bat coronaviruses (CoVs) in China, identified hotspots of evolutionary diversity, and traced the origins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Background

CoVs are Ribonucleic Acid (RNA) viruses causing respiratory and enteric diseases in humans and animals, with all human-infecting CoVs being zoonotic in origin, often from bats. Their large genome size, high recombination rates, and genomic plasticity facilitate cross-species transmission and rapid adaptation, leading to outbreaks such as SARS-CoV, Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and SARS-CoV-2. Bats, particularly genus Rhinolophus, host diverse Alpha-CoVs (α-CoV) and Beta-CoVs (β-CoV), with hotspots in regions like China, where rich bat fauna and unique biogeography amplify spillover risks. The study highlights that these evolutionary traits, combined with the ecological context of Southern and Southwestern China, make these regions particularly important for understanding CoV dynamics. Further research on bat-CoV macroevolution and transmission dynamics is crucial for understanding zoonotic potential and enhancing pandemic prevention through targeted surveillance and preparedness strategies.

About the Study

In the present study, between 2010 and 2015, bat oral and rectal swabs and fecal pellets were collected across Chinese provinces, including Anhui, Beijing, Hainan, Hubei, Guangdong, Guangxi, Yunnan, and others. Non-lethal sampling was conducted using mist nets, with bats released immediately after collection. Wing punches were taken for Deoxyribonucleic Acid (DNA) barcoding. Bat-handling protocols adhered to Institutional Animal Care and Use Committees (IACUC) guidelines from Tufts University and the Wuhan Institute of Virology, Chinese Academy of Sciences. Samples were preserved at −80 degrees Celsius.

RNA was extracted using the High Pure Viral RNA Kit (Roche), and a one-step hemi-nested reverse transcription-polymerase chain reaction (RT-PCR) targeted the RNA-dependent RNA polymerase (RdRp) gene for CoV detection. PCR products were sequenced and confirmed through cloning or barcoding, ensuring data reliability. The dataset included 589 novel sequences and 616 from the Genetic Sequence Database (GenBank) and the Global Initiative on Sharing Avian Influenza Data (GISAID).

Sequences were aligned and analyzed phylogenetically using Bayesian Evolutionary Analysis Sampling Trees (BEAST) software. Based on mammalian diversity, sampling locations were grouped into six zoogeographic regions. Ancestral states for host family, genus, and region were reconstructed, and significant host or region transitions were assessed using Bayes factors. The study acknowledges that relying on partial RdRp sequences, while effective, limits the depth of phylogenetic analysis and may exclude highly divergent CoV variants.

Phylogenetic diversity metrics revealed regional and host-specific patterns of CoV diversity, with Mantel tests highlighting correlations between viral genetic differentiation, host phylogeny, and geographic isolation.

Study Results

A total of 589 partial sequences of the RdRp gene were generated from bat rectal swabs collected across China and combined with 608 bat CoV and 8 pangolin-CoV sequences from public databases, including the GenBank and the GISAID. Two datasets were prepared: one based on host taxa and the other on sampling locations, categorized into six zoogeographic regions reflecting mammalian diversity rather than administrative boundaries. These regions included South Western (SW), Northern (NO), Central (CE), Southern (SO), Central Northern (CN), and Hainan Island (HI).

The host dataset contained 676 α-CoV sequences from 40 bat species and 503 β-CoV sequences from 29 bat species. The geographic dataset included sequences from 21 provinces for α-CoVs and 20 provinces for β-CoVs. Analyses were also conducted on random subsets of sequences to reduce sampling bias and ensure uniform representation.

Bayesian phylogenetic analysis suggested that α-CoVs likely originated in rhinolophid (horseshoe bats) and vespertilionid (evening bats) species, while β-CoVs were linked to vespertilionid and pteropodid (fruit bats) species. Frequent cross-species transmission events were observed, with α-CoVs exhibiting higher rates of inter-family and inter-genus host switching compared to β-CoVs. Rhinolophidae and Miniopteridae (long-fingered bats) were the most frequent donors for α-CoVs, whereas Rhinolophidae dominated as donors and receivers for β-CoVs.

Spatiotemporal analyses revealed significant dispersal routes for both α-CoVs and β-CoVs within China. The SO emerged as a significant hub of CoV migration, with the highest outbound and inbound movements. α-CoVs demonstrated higher migration rates than β-CoVs, with the SW and HI regions exhibiting distinct endemic diversity. Southern and Southwestern China were identified as refugia during glacial periods, contributing to the long-term persistence and diversification of bat-CoVs in these regions.

Phylogenetic clustering, assessed using mean phylogenetic distance (MPD) and mean nearest taxon distance (MNTD), highlighted strong structuring among bat families and zoogeographic regions. The SW and HI regions showed the highest evolutionary distinctiveness for both CoV genera. Mantel tests revealed significant correlations between genetic differentiation and geographic distance for both α-CoVs and β-CoVs, with β-CoVs also showing correlations with host phylogeny.

Conclusions

The phylogenetic analysis of CoVs from bats sampled in China revealed significant diversity, with 11 out of 17 bat genera hosting both α-CoVs and β-CoVs. SARS-CoV-2 likely originated from a clade of viruses found in horseshoe bats (Rhinolophus spp.), predominantly in Yunnan province. However, the study notes that sampling limitations and the proximity of collection sites to international borders suggest that progenitor viruses could also originate from Myanmar, Laos, or other neighboring countries.

The findings highlight the urgent need for targeted surveillance in Southern China and Southeast Asia, especially focusing on Rhinolophus and Hipposideros bats, which are central to cross-species transmission events. The study also emphasizes the importance of understanding the biological characteristics of α-CoVs, which show a higher host-switching potential and zoonotic risk than β-CoVs.