Identification and characterization of novel Alphacoronaviruses in Tadarida brasiliensis (Chiroptera) from Argentina: first genomes reported in family Molossidae in the Americas

AGUSTINA CERRI; ELISA BOLATTI; TOMAZ ZOREC; MARÍA EUGENIA MONTANI; AGUSTINA RIMONDI; LEA HONSJAK; PABLO CASAL; VIOLETA DI DOMENICA; RUBÉN BARQUEZ; MARIO POLJAK; ADRIANA GIRI

Stellenbosch

Workshop; Virus Evolution and Molecular Epidemiology Workshop (VEME) 2023; 2023

STIAS-Stellenbosch Institute for Advanced Study, Stellenbosch, South Africa

Bats harbor the largest number of coronavirus species among mammals. Due to their large genome size, high recombination rates, and genomic plasticity, coronaviruses can jump between bat species or to different mammalian hosts, including humans. Herein, coronavirus infection of three bat species (Tadarida brasiliensis, Eumops bonariensis, Molossus molossus) of family Molossidae from Argentina was explored using a metagenomic approach. Fecal samples of 47 individuals living in three semi-urban or highly urbanized areas of Santa Fe province were investigated. After a viral particle enrichment procedure, RNA was sequenced using Illumina NextSeq 550, and the reads were cleaned-up and analyzed using several bioinformatic approaches. Three novel Alphacoronavirus (AlphaCoV) genomes (isolates Tb1, Tb2 and Tb3) and six partial sequences were identified in T. brasiliensis and M. molossus samples. The Maximum Likelihood phylogenomic analysis showed two lineages, Tb1 and Tb2/Tb3, circulating in the T. brasiliensis colony outside the 15 officially recognized AlphaCoV subgenera. Isolate Tb1 was related to subgenus Myotacovirus while Tb2/Tb3 lineage was close to the Colacovirus subgenus and seems to constitute a persistent infection.By performing pairwise amino acid comparisons of the polyprotein pp1ab conserved domains, and according to the current ICTV demarcation criteria, we concluded that Tb2/Tb3 could be considered as prototype of a novel species within the AlphaCoV genus, while Tb1 might be conspecific with AlphaCoVs previously detected in Eptesicus bats. Since Spike protein phylogenetic analysis revealed tree topologies changes, we use RDP analysis in order to explore whether the new viruses might have participated in past recombination events. Interestingly, a statistically significant recombination event involving Tb1 genome was found and confirmed by phylogenetic incongruence analysis, where the putative recombinant and major parent were AlphaCoVs isolated in Eptesicus fuscus bats from the USA, while Tb1 was recognized as putative minor parent. The recombinant region represented a 1,618 nt fragment within the Spike gene, which has previously been reported as a recombination hotspot in AlphaCoV genus. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights on recombination as an additional mechanism for the evolution of coronaviruses in the cross-species transmission process.