Analysis Of Digestive Virus Community And Genetic Characteristics Research Of Novel Viruses Related To Human And Animal Health In Birds

In recent years,with the continuous emergence of new pathogens,new infectious diseases have become epidemic in outbreaks worldwide,causing great threats to zoonotic life health.Birds,as one of the most abundant species in nature,are important natural hosts for many pathogenic viruses.Viruses carried by wild birds undergo longrange transmission with migration,causing new outbreaks in animals or humans.The digestive tract of birds is one of the microenvironments in which the most viral taxa are carried by birds,and the viruses present in the digestive tract will be eliminated with excretion into the birds,which can cause pollution of water sources,soil,food or even air within the flight range of birds,forming an infectious source.In addition to carrying a large number of known viruses,birds may harbor novel or recombinant viruses that are potentially pathogenic to humans,livestock,and other wildlife,which are less readily detected and more harmful.Traditional viral detection methods have many limitations in the detection of unknown viruses or highly variable recombinant viruses,and a new viral metagenomics method that does not rely on viral gene information and cell culture for rapid virus detection helps us solve the problems encountered in studying the virome resolution of bird digestive tract,Unknown novel viruses hidden from the digestive tract of birds can be rapidly and effectively discovered.To elucidate the viral community of the digestive tract of birds and discover the viral taxa of the digestive tract of birds that are potentially harmful to public health and safety,in this study,we collected bird cloacal swab samples on a large scale,constructed viral metagenomic libraries based on the theory of viral metagenomics,and used the Illumina Nova Seq sequencing platform to obtain next-generation sequencing big data,In turn,using bioinformatics to dissect the viral community composition and diversity of the digestive tract of birds and mine potential novel viruses,It is also important to analyze their genetic characteristics and potential genomic homologous recombination events to provide technical support and genetic data for preventing and preventing early warning and diagnosis and treatment of outbreaks of emerging viral infectious diseases of avian origin in China.It is also of great significance for the protection of rare birds in our country.The main content and results of this study are as follows:1.Analysis of viral communities in the digestive tract of birdsViral communities were analyzed from 2689 avian cloacal swab samples collected from different orders,different sampling sites,different habitats(wild and breeding)and different behavioral feature(resident and migratory)and were grouped at the overall level of the family as follows: Parvoviridae(31.15%),Dicistroviridae(22.60%),Picornaviridae(15.40%),Filoviridae(11.56%),unclassified riboviria(10.80%),genomoviridae(4.03%),astroviridae(1.90%),unclassified picornavirales(0.97%),coronaviridae(0.34%),Polycipiviridae(0.34%),Nodaviridae(0.34%)and other viridae(0.57%).The composition of the avian digestive virus community shows the following remarkable characteristics:(1)the composition of the avian digestive virus community shows a high diversity.(2)The dominant viral taxa of this virus community were composed of Parvoviridae,Dicistroviridae and Picornaviridae,which accounted for69.15% of all viruses.(3)At the bird order level,the virus diversity of Galliforme birds was higher than that of the other nine orders.Among the different sampling sites,the virus community in the cloacal swab samples of birds at the Xinqing bird banding station in Heilongjiang province had a higher diversity than the other sampling sites.There were no obvious differences in viral community diversity between migratory and resident birds.From the point of view of bird breeding modes,the viral diversity of wild birds is higher than breeding birds,and some of these viruses(such as Dicistroviridae and Iflaviridae)show different distribution patterns between breeding and wild birds.2.Genetic characterization of a novel virus potentially threatening zoonotic health in the digestive tract of birdsIn this study,553 viral genome sequences with complete viral coding regions(CDS)were obtained from 182 avian virus libraries constructed.The 553 viral genomes belong to 21 distinct virus families and unclassified virus groups,with 424 genomes belonged to RNA viruses and 129 to DNA viruses.486 viral genomes were from wild birds,and 67 viral genomes were from breeding birds.395 virus genomes were from migratory birds,and 158 virus genomes were from resident birds.A blastx search within public databases based on 553 whole genome sequences revealed that 301 of these genomes shared < 60% amino acid sequence homology with the best matching strains in Gen Bank.In turn,the 553 viruses were analyzed for relevant genetic features such as genome structure,taxonomic status,phylogenetic characteristics,and gene recombination.Results:(1)the study found 182 novel viral whole genomes potentially infecting mammals and birds,which taxonomically included 33 astroviruses,6coronaviruses(all belong to deltacoronavirus),3 retroviruses,6 caliciviruses,32 small RNA viruses,82 parvoviruses,14 circoviruses whole and 6 adenoviruses.(2)Fifteen novel phages within the gut of birds with smaller genome sequences and potential as indicative markers of phage composition in the digestive tract of birds were discovered in the study,including four filamentous phages and 11 microphages.(3)Picornavirus and coronavirus genome sequences exhibit extensive gene recombination.(4)Several members within astroviruses and caliciviruses have potential transmission characteristics across different host species.(5)The prevalence of deltacoronavirus in passerine birds was 0.75%(16/2140).Conclusions: The viral metagenomics method was used to analyze viral communities in the digestive tract of birds,the distribution of viruses varied between hosts at different orders levels,different sampling sites,and different habitats(wild and breeding),whereas no significant differences were observed in the distribution of different behavioural characteristics of the hosts(resident and migratory).In addition,553 viral genome sequences with complete CDS were assembled and identified from within the avian viral community data,including 182 novel viral genome sequences potentially infecting birds and mammals and 15 novel phage whole genomes that could serve as indicators of avian digestive tract phages.The taxonomic status of the 553 virus strains,the phenomenon of genetic recombination and cross species infection potential of some of the viruses were elucidated in detail,and a virus epidemiology screen of deltacoronavirus in gallinaceous birds was completed.The results of this study have important implications for the future diagnosis,and prevention of zoonotic emerging infectious disease outbreaks caused by avian associated viruses.