Virome analysis of bats in Hong Kong unveils diverse mammalian viruses

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the coronavirus disease 2019 (COVID-19) pandemic highlights the importance of understanding viral diversity in wildlife, including bats, which are recognized reservoirs of many zoonotic viruses. Following the identification of bats as the origin of the SARS epidemic, surveillance in Hong Kong revealed diverse bat coronaviruses, yet comprehensive virome data remain limited. Here, we used next-generation sequencing (NGS) to analyse the viromes of nine bat species in Hong Kong. We identified coronaviruses from six subgenera (Decacovirus, Minunacovirus, Myotacovirus, Merbecovirus, Sarbecovirus, and Rhinacovirus) across seven bat species. Viruses from nine additional families were also detected, indicating broad viral diversity. Notably, bat coronavirus HKU4 was identified for the first time in Chinese horseshoe bats, expanding the known host range of this virus and warranting further investigation into its potential zoonotic significance. Coronaviridae, Picornaviridae, and Parvoviridae were the most abundant families, accounting for 65.0%, 17.0%, and 12.3% of mammalian viral reads, respectively. These viral families were also detected across seven bat species. Lesser bent-winged bats, Horsfield’s bats, and Rickett’s big-footed bats showed the greatest viral diversity, harbouring sequence reads from eight viral families. Using a reference database generated through an artificial intelligence (AI)-assisted approach, we identified nearly one million additional sequence reads representing putative viral species from four mammalian virus supergroups, as well as over 5,000 reads belonging to two unclassified viral supergroups, which remain unclassified by International Committee on Taxonomy of Viruses (ICTV). These findings provide comprehensive insights into the bat viromes of Hong Kong and demonstrate the value of integrating NGS with AI-assisted approach to enhance viral discovery and support future wildlife surveillance efforts.