Analysis Of Gastrointestinal Virus Community And Genetic Characteristics Of Novel Viruses In Wild Birds

In recent years,emerging infectious diseases,as a common type of public health emergencies,have broken out frequently around the world,making the global ecology operate at a high level and seriously threatening the lives and health of human and animals.Wild birds are the natural hosts of many pathogenic viruses,and more and more emerging virus diseases to be identified associated with wild birds included avian influenza virus and West Nile virus.In addition,due to its large-scale gathering and seasonal migration,it has greatly increased the risk of virus transmission among wild bird populations.Furthermore,the virus spreads widely along the migration routes and even causes diseases in other animals and humans.Therefore,it is of great public health significance to understand and master the situation of viruses carried by different wild birds,excavate novel viruses and analyze their genetic characteristics.With the development of next generation sequencing technology and the evolution of viral metagenomics,a new method that does not rely on cell culture and known sequences for traditional PCR amplification-viral metagenomics has emerged.This method takes all viral nucleic acids in the sample as the research object,which can detect the composition of all viral communities in the sample,and provide theoretical and technical support for the diagnosis of emerging infectious diseases and the exploration of potential pathogens.In order to understand the composition of the intestinal virus community of the main migratory birds in China and to explore the genetic characteristics of the new viruses.This study used viral metagenomics methods to construct corresponding libraries of cloaca swabs samples from four different birds,including wildgeese,egrets,cranes and finches from Qinghai Lake,the station of Xinqing bird ringing,Maoershan Nature Reserve in Heilongjiang Province,Changbai Mountain in Jilin Province and Hangzhou Wetland Park in Zhejiang Province.The main contents and conclusions of this study are as follows1.Analysis of four avian enterovirus communitiesThe wildgeese enterovirus community mainly includes: Parvoviridae(26.20%),None(18.13%),Papillomaviridae(16.28%),Dicistroviridae(15.29%),Bidnaviridae(6.15%),Adenoviridae(5.10%),Picornaviridae(4.06%),Other(8.79%).There are a variety of viruses from vertebrate account for the largest proportion 66.48%.The egrets enterovirus community mainly includes: Iridoviridae(25.18%),None(17.23%),Dicistroviridae(16.28%),Poxviridae(13.06%),Papillomaviridae(6.21%),Caliciviridae(4.60%),Nanoviridae(3.55%),Iflaviridae(3.97%),Flaviviridae(1.73%),Retroviridae(1.63%),Microviridae(1.49%),Others(5.07%).There are a variety of viruses from invertebrate account for the largest proportion 58.23%.The cranes enterovirus community mainly includes: Dicistroviridae(25.67%),Parvoviridae(20.66%),Papillomaviridae(15.70%),None(12.31%),Baculoviridae(7.98%),Iflaviridae(4.91%),Caliciviridae(3.37%),Nodaviridae(2.95%),Partitiviridae(2.72%),Others(3.73%).There are a variety of viruses from vertebrate account for the largest proportion 52.40%.The finches enterovirus community mainly includes: Dicistroviridae(35.20%),Iflaviridae(24.54%),Parvoviridae(15.70%),Unclassified RNA viruses(11.82%),Astroviridae(6.92%),Picornaviridae(3.28%),Others(2.54%),There are a variety of viruses from invertebrate account for the largest proportion 31.70%.2.Identification and genetic characteristics analysis of novel genomovirusesIn this study,we characterized 40 novel genomovirus genomes,including 8 ones from wildgeese,3 from egrets,9 from cranes,as well as 20 from finches in four different types of cloacal swabs of wild birds sampled in Qinghai Lake,the station of Xinqing bird ringing,Maoershan Nature Reserve in Heilongjiang Province,Changbai Mountain in Jilin Province,and Hangzhou Wetland Park in Zhejiang Province.Based on the sequence of nucleic acid and protein,we predicted and analyzed the genome structure,protein basic physicochemical properties,secondary structure,tertiary structure,conserved motif and domain to expand our understanding of the new viruses.In addition,based on BLASTn search results,using phylogenetic analysis of Rep protein and the currently accepted threshold of species classification of Genomoviridae(78%),all 40 full-length genome sequences were divided into different virus genera and corresponding new species classification.Conclusion: The viral metagenomics method was used to analyze the composition of the enterovirus communities of four different wild birds of wildgeese,egrets,cranes and finches.We found that the enteroviruses of four infected birds are similar in composition,but the host source is slightly different.The host of the large bird enterovirus community in wildgeese and cranes is mainly from vertebrate,while that of egrets and finches enterovirus is mainly from invertebrate.In addition,40 new genomoviruses have been identified in this study,ranging in size from 2003 nt to2359nt and dividing into 8 different virus genera within the family Genomoviridae.The Rep proteins of different viral genera showed hydrophilic characteristics and contained a conserved domain: a replication initiator protein associated with rolling-circle replication(Gemini?AL1;Pfam: PF00799).The corresponding species classification studies show that wildgeese associated genomoviruses represent 7species(5 of which are new),egrets represent 2 species(2 of which are new),cranes represent 9 species(6 of which are new),finches represent 20 species(13 of which are new).Based on the prediction results of Cap and Rep protein conserved motifs,there is significant difference between them and the identified conserved motifs of corrseponding virus genus proteins,which proves the possibility of new species.