229E- and NL63-like coronaviruses in phyllostomid bats, Belize

Abstract

Coronaviruses (CoVs) are a diverse group of RNA viruses that infect a broad range of hosts, including many bat species. The emergence of several CoVs, specifically α-CoVs and β-coVs causing significant human and domestic animal diseases, has been linked to bats. Characterizing the evolutionary relationships and host associations of bat-borne CoVs is crucial for understanding and mitigating zoonotic risks. While most bat CoV research has focused on the Eastern Hemisphere, the diversity of CoVs in Neotropical bats remains relatively understudied. Here, we report novel and previously identified α-CoV diversity in three phyllostomid bats (Desmodus rotundus, Carollia sowelli, and Sturnira parvidens) in Belize. Our analysis targeting the partial RNA-dependent RNA polymerase gene revealed varying prevalence (22.22 - 36.36 %) across these species. Our phylogenetic analysis suggests strong similarity between two Neotropical bat α-CoV lineages and human CoVs (229E and NL63), illustrating new evolutionary relationships compared to prior bat α-CoVs.

Keywords: Alphacoronavirus; Neotropical; One Health; Surveillance; Virus discovery.

Fig. 1

A) Map showing the sampling location in Belize (blue point) with the distribution of Desmodus rotundus, Sturnira parvidens, and Carollia sowelli. The dark reddish-brown areas indicate regions where all three species distributions overlap B) Species-level CoV prevalence based on positivity in at least one sample type tested per individual. C) CoV prevalence by sample type: feces (FC), oral swabs (OS), rectal swabs (RS), and urine (UR). FC and UR were only collected from S. parvidens. Point estimates of CoV prevalence are scaled by sample size. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Maximum likelihood phylogeny displaying the evolutionary relationships among bat α-CoVs, HCoVs 229E and NL63, and the alpaca α-CoV using partial RdRp sequences. GTR + G nucleotide substitution model with 1000 bootstrap replicates was used to infer tree topology and assess node support. The phylogeny was rooted with two bat β-CoV sequences. Sequences generated from Belize bats here are highlighted. Nodes are colored by bootstrap support (values <50 % are not shown).