Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

• Published in: Virologica Sinica Vol. 39; no. 4; pp. 565 - 573
• Main Authors: Si, Hao-Rui, Wu, Ke, Su, Jia, Dong, Tian-Yi, Zhu, Yan, Li, Bei, Chen, Ying, Li, Yang, Shi, Zheng-Li, Zhou, Peng
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2024; KeAi Publishing Communications Ltd; Wuhan Institute of Virology, Chinese Academy of Sciences
• Subjects: Alphacoronavirus; Animals; Bacteria; Bat; Bats; China; Chiroptera - virology; Co-infection; Coinfection - microbiology; Coinfection - veterinary; Coinfection - virology; Coronaviruses; Disease Reservoirs - virology; Disease transmission; Genome, Viral - genetics; Genomes; Genomics; Metagenomics; Microbiome; Microbiomes; Microenvironments; Microorganisms; Pandemics; Phylogeny; SARS-related coronavirus; Severe acute respiratory syndrome coronavirus 2; Severe acute respiratory syndrome-related coronavirus - classification; Severe acute respiratory syndrome-related coronavirus - genetics; Severe acute respiratory syndrome-related coronavirus - isolation & purification; Virome; Viruses; China; SARS-related coronavirus; Co-infection; Bat; Alphacoronavirus; Microbiome
• ISSN: 1995-820X; 1674-0769; 1995-820X
• DOI: 10.1016/j.virs.2024.06.008

Bats are the natural reservoir hosts for SARS-related coronavirus (SARSr-CoV) and other highly pathogenic microorganisms. Therefore, it is conceivable that an individual bat may harbor multiple microbes. However, there is limited knowledge on the overall co-circulation of microorganisms in bats. Here, we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative districts. Among these, 76 individual samples were selected for further metagenomics analysis. We found a complex microenvironment characterized by the general co-circulation of microbes from two different sources: mammal-associated viruses or environment-associated microbes. The later includes commensal bacteria, enterobacteria-related phages, and insect or fungal viruses of food origin. Results showed that 25% (19/76) of the samples contained at least one another mammal-associated virus, notably alphacoronaviruses (13/76) such as AlphaCoV/YN2012, HKU2-related CoV and AlphaCoV/Rf-HuB2013, along with viruses from other families. Notably, we observed three viruses co-circulating within a single bat, comprising two coronavirus species and one picornavirus. Our analysis also revealed the potential presence of pathogenic bacteria or fungi in bats. Furthermore, we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples, some of which formed new evolutionary lineages. Collectively, our study reveals the complex microenvironment of bat microbiome, facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission. •Mammal-associated viruses were generally co-circulating with SARS-related coronaviruses in bats .•The general comparison of bat virome was revealed.•Potential pathogenic bacteria or fungi and 25 new viral genomes were found in bats.