Infectome analysis of #bat #kidneys from #Yunnan province, #China, reveals novel #henipaviruses related to #Hendra and #Nipah viruses and prevalent bacterial and eukaryotic microbes

Abstract

Bats are natural reservoirs for a wide range of microorganisms, including many notable zoonotic pathogens. However, the composition of the infectome (i.e., the collection of viral, bacterial and eukaryotic microorganisms) within bat kidneys remains poorly understood. To address this gap, we performed meta-transcriptomic sequencing on kidney tissues from 142 bats, spanning ten species sampled at five locations in Yunnan province, China. This analysis identified 22 viral species, including 20 novel viruses, two of which represented newly discovered henipaviruses closely related to the highly pathogenic Hendra and Nipah viruses. These henipaviruses were found in the kidneys of bats inhabiting an orchard near villages, raising concerns about potential fruit contamination via bat urine and transmission risks to livestock or humans. Additionally, we identified a novel protozoan parasite, tentatively named Klossiella yunnanensis, along with two highly abundant bacterial species, one of which is a newly discovered species—Flavobacterium yunnanensis. These findings broaden our understanding of the bat kidney infectome, underscore critical zoonotic threats, and highlight the need for comprehensive, full-spectrum microbial analyses of previously understudied organs to better assess spillover risks from bat populations.

Author summary

Although extensive investigations have been conducted on the bat virome, most studies have focused on fecal samples, leaving other tissues, such as the kidney, largely unexplored. However, the kidney can harbor important zoonotic pathogens, including the highly pathogenic Hendra and Nipah viruses, and genomic evidence of henipaviruses in bats from China has remained undocumented. In this study, we report the first detection of two novel henipavirus genomes from bat kidneys in China, one of which is the closest known relative of pathogenic henipaviruses identified to date. Beyond virome analysis, our study also examined highly prevalent bacteria and eukaryotic microbes, identifying those potentially relevant to bat infections. Overall, these findings provide valuable insights into the infectome of the bat kidney, highlighting the need for broader microbial surveillance beyond the gastrointestinal tract.

Source: PLoS Pathogens, https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1013235

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