Zoology/Biology session

Bats play a crucial role as natural reservoirs for various viral families, many of which can infect other mammals, including humans. Several bat-origin viruses are listed on the WHO's priority list of diseases (e.g., COVID-19, Nipah, Ebola), as well as "Disease X," which refers to unknown, naturally occurring diseases with pandemic potential. Our aim was to discover and genetically characterize new viruses from Vietnamese bat samples, contributing to viral diversity understanding and potentially informing effective prevention strategies.

Metagenomics is a powerful method for discovering new viruses, as in some cases, the complete viral genome can be assembled from the short Illumina reads. In our study, we analyzed sequences from bat guano samples collected in Vietnam in 2017. The samples were sequenced individually, allowing the results to be linked to individual bats. A total of 55 samples were included, and we identified new viruses from various families, including coronaviruses, adenoviruses, circoviruses, hepatitis B virus, hepatitis E viruses, herpesviruses, picornaviruses, genomoviruses, and parvoviruses.

We focused on two viral groups in detail. Among the coronaviruses, most were alphacoronaviruses, but one sarbecovirus (related to SARS-CoV-1, SARS-CoV-2, and MERS) was also detected. Although we could only assemble about 60% of the sarbecovirus genome from Illumina reads, we completed the missing sections using amplicon-based Nanopore sequencing. One of the alphacoronaviruses was closely related to a swine coronavirus that causes epidemic diarrhea and death among pigs. We also identified two Hepatitis E viruses, one with a complete and another with a nearly complete genome. Hepatitis E viruses infect over 20 million people globally each year, causing tens of thousands of deaths. Only a few bat-origin Hepeviruses are known, and their zoonotic potential is suspected. Our findings suggest that Hepeviruses may be more widespread in bats than previously thought and might show relative host specificity. These results contribute to a better understanding of coronavirus and Hepevirus diversity and emphasize that many undiscovered viruses are likely circulating in bats.