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

作　　者：Hao-Rui Si Ke Wu Jia Su Tian-Yi Dong Yan Zhu Bei Li Ying Chen Yang Li Zheng-Li Shi Peng Zhou 

机构地区：[1]Wuhan Institute of Virology,Chinese Academy of Sciences,Wuhan 43000,China [2]Guangzhou National Laboratory,Guangzhou International Bio Island,Guangzhou 510005,China [3]University of Chinese Academy of Sciences,Beijing 100000,China [4]State Key Laboratory of Respiratory Disease,The First Affiliated Hospital of Guangzhou Medical School,Guangzhou 510005,China

出　　处：《Virologica Sinica》2024年第4期565-573,共9页中国病毒学（英文版）

基　　金：supported by the National Key R&D Program of China(2021YFC2300901 to P.Z.);China Natural Science Foundation for outstanding scholars(82325032 to P.Z.);the Self-Supporting Program of Guangzhou Laboratory(SRPG22-001 to P.Z.;GZNL2023A01001 to ZLS).

摘　　要：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 cocirculation 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.

关 键 词：Bat Microbiome SARS-related coronavirus CO-INFECTION Alphacoronavirus 

分 类 号：R373[医药卫生—病原生物学] S852.6[医药卫生—基础医学]