Seasonal detection of Sarbecoviruses in bats from North Vietnam – SO-VIET-BAT

Ten months after the first reported cases of Covid-19 in Wuhan, the origin of the SARS-CoV-2 virus still continues to be debated. In order to avoid other epidemics in the future, it appears crucial to identify the different steps that led to the first human contamination by an animal, in particular the evolution and circulation of sarbecoviruses among bat species of the genus Rhinolophus, the natural reservoir host.
The phylogeny based on the viral genomes of the subgenus Sarbecovirus has shown the existence of two divergent lineages in Chinese bats, corresponding respectively to the human viruses SARS-CoV and SARS-CoV-2, that separated several centuries ago. In addition, the phylogeographic analyses suggest that these two viral lineages originated from Yunnan, a province in southwestern China. However, very few field studies have been carried out on bat coronaviruses in Southeast Asian countries. Our project aims to fill this gap by studying bats sampled between April and October 2021 in several caves in North Vietnam. This karst region, which is adjacent to the Yunnan province, is situated in the transition zone between the temperate and intertropical climates. It is the home to roughly 100 recorded bat species, including R. sinicus, the main reservoir host of the SARS-CoV lineage, and the two species of horseshoe bats from which the two viruses closest to SARS-CoV-2 were sequenced (RaTG13 and RmYN02), namely R. affinis and R. malayanus. This suggests that bats of North Vietnam are also likely to host a similar diversity of sarbecoviruses.
Our field studies will aim to better understand the seasonal variations of bat assemblages in several caves in North Vietnam. In other words, we will determine the diversity of bat species nesting in these caves, their relative proportions in terms of individuals, but also the seasonal variations in site occupation. These data are important for understanding how sarbecoviruses can be transmitted among bat species. The mitochondrial Cox1 gene will be sequenced for all the bats examined in order to validate the field species identifications and to study the phylogeography of horseshoe bat species. Bat stools will be used to detect and sequence new sarbecovirus genomes.
The expected outcomes of this research will provide much information on: (1) the seasonal variations in bat assemblages in the caves of North Vietnam; (2) the seasonal detection of sarbecoviruses in bats captured in these sites; (3) the comparative phylogeography of horseshoe bats identified as reservoir hosts of sarbecoviruses; (4) the role of genomic recombination on the barrier jump of host species ; and (5) the potential impact of anthropogenic climate change on the circulation of viruses among bat species. This new knowledge-based information will be core components of disease control and bat conservation programs.