Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)r...Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)representing 20 species collected across eight cities in south China between 2018 and 2024.Samples included internal organs,oropharyngeal and anal swabs,and feces.We identified 63 vertebrate-associated viruses,including 34 novel viruses.Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens.Cross-species transmission was observed in 14.3%(9/63)of viruses,shared by at least two host species,with bats,particularly Rhinolophus and Hipposideros,serving as key hubs for viral circulation and zoonotic spillover.Virome composition varied substantially among mammalian species and geographic regions(adonis test,R^(2)=0.50,P=0.001).Generalized linear models quantified the roles of host taxonomy,ecotypes,and meteorological factors in shaping viral diversity,demonstrating host taxonomy(at the order level)as a predominant role(25.70%deviance explained),followed by ecotypes(10.27%deviance explained).Phylogenetic analysis conducted using our betacoronavirus sequences,as well as betacoronavirus sequences derived from 2.0×10^(4) bats sampled in China between July 2013 and March 2024,revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains(e.g.,RaTG13).These findings provide critical insights into virus evolution,transmission,and ecological determinants,which are essential for the prevention of emerging infectious diseases.展开更多
The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.Th...The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health conditions.Herein,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses.In total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and Spinareoviridae.Notably,the presence of rotavirus was recorded in tree shrews for the first time.Three viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(<70%)with previously reported viruses at the whole-genome scale,indicating novelty.Conversely,three other viruses-hepacivirus 2,hepatovirus A and hepevirus-exhibited high similarity(>94%)to known viral strains.Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants.These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.展开更多
基金supported by the 3-year Public Health Program of the Shanghai Municipal Health Commission[grant number GWVI-11.1-10(GC)]the National Key Research and Development Program of China[grant number 2022YFC2602900(GC)]the Shanghai Municipal Health Commission[grant number 2022JC033(GC)].
文摘Mammals are critical reservoirs of human infectious diseases and the spillover of viruses is related to climate conditions.We conducted meta-transcriptomic sequencing of 226 mammals(bats,rodents,hedgehogs,and shrews)representing 20 species collected across eight cities in south China between 2018 and 2024.Samples included internal organs,oropharyngeal and anal swabs,and feces.We identified 63 vertebrate-associated viruses,including 34 novel viruses.Phylogenetic analysis revealed six viruses with potential infection risks to humans or domestic animals due to their close phylogenetic relationships with known pathogens.Cross-species transmission was observed in 14.3%(9/63)of viruses,shared by at least two host species,with bats,particularly Rhinolophus and Hipposideros,serving as key hubs for viral circulation and zoonotic spillover.Virome composition varied substantially among mammalian species and geographic regions(adonis test,R^(2)=0.50,P=0.001).Generalized linear models quantified the roles of host taxonomy,ecotypes,and meteorological factors in shaping viral diversity,demonstrating host taxonomy(at the order level)as a predominant role(25.70%deviance explained),followed by ecotypes(10.27%deviance explained).Phylogenetic analysis conducted using our betacoronavirus sequences,as well as betacoronavirus sequences derived from 2.0×10^(4) bats sampled in China between July 2013 and March 2024,revealed that no betacoronaviruses exhibited closer phylogenetic relationships to SARS-CoV-2 than the known strains(e.g.,RaTG13).These findings provide critical insights into virus evolution,transmission,and ecological determinants,which are essential for the prevention of emerging infectious diseases.
基金supported by the National Key R&D Program of China (2021YFC2300900,2021YFC2301300)Academic Promotion Programme of Shandong First Medical University (2019QL006)+2 种基金Natural Science Foundation of Shandong Province (ZR2020QH274)Yunnan Key Research and Development Program (202103AQ100001,202102AA310055)Key Program of Chinese Academy of Sciences (KJZD-SW-L11)。
文摘The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health conditions.Herein,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses.In total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and Spinareoviridae.Notably,the presence of rotavirus was recorded in tree shrews for the first time.Three viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(<70%)with previously reported viruses at the whole-genome scale,indicating novelty.Conversely,three other viruses-hepacivirus 2,hepatovirus A and hepevirus-exhibited high similarity(>94%)to known viral strains.Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants.These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.
