Speaker
Description
The high species richness of bats (> 1400 species) is mirrored by the diversity of viral families they harbor. It is likely that SARS-CoV-2, a Betacoronavirus Sarbecovirus responsible for the COVID-19 pandemic, originated in Rhinolophus spp. bats. In this context, it is critical to understand the origins of Sarbecovirus diversity in wildlife and the mechanisms that favor their emergence in other species. Thus, we conducted an extensive longitudinal survey of a Rhinolophus ferrumequinum maternity colony that harbors BBCoV, a SARS-CoV/SARS-CoV-2 sister-clade. Roughly, 2700 fecal samples were collected at a high-frequency rate for 10 years and analyzed with a specific Sarbecovirus RT-qPCR system. An epidemiological compartmental model was generated based on the prevalence data collected during a part of the study period. Samples were deep-sequenced and analyzed via a time-resolved Bayesian phylogeny, and potential presence of recombinants genomes was assessed using RDP4 software.
Selection pressure and intra-host diversity were investigated through the study of SNPs (single nucleotide polymorphism) frequency. Over the study period, 1224 BBCoV-positive individuals were detected. Circulation varies according to the seasonal behavior of the colony (births of juveniles, weaning, migration). The compartmental model confirmed certain hypotheses regarding the transmission patterns of BBCoV, and highlighted the substantial role of juveniles in maintaining the epidemic within the colony. The Bayesian phylogeny shows a gradual emergence of BBCoV, though punctuated by the rooting of recent genomes to 2016 lineages, suggesting the existence of recombination events. Intra-host diversity dynamics is heterogenous across individuals and time, and is subjected to differential selection pressure across the genome. In conclusion, this in-depth study of a SARS-like Sarbecovirus species circulating in Europe provides a robust natural model to explain how circulation of coronaviruses in the first steps of their emergence, can opportunistically lead to the birth of better-fitting variants, that could promote emergence of new lineages, that may spill-over in other species.
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