| Emerging infectious diseases(EIDs)pose a great threat to global public health.Severe infectious diseases will lead to people panic and make an impact on social stabilty and economic development.Therefore,prevention and control of infectious disease has become a one of the goals of society.More than 60%of the EIDs is the animal origin.Rodentia is the largest group of mammalian species,accounting for about 43%of all mammalian species and widely distributed through the world and intimately interacted with humans and livestock.The virome has an important impact on the health of human and mammals as the source for traditional viral pathogens.Rodents are considered natural carriers of a large variety of viruses.Recently,more and more attention is focused on the wildlife original pathogen offered by domestic and overseas researchers and many rodents original viral pathogen has been identified,such as hantavirus,arenavirus,etc.These are only a few reports of systematic etiology about rodents as the natural reservoir of virus in worldwide.In the main land of china,screening the natural reservoir of original viruses in multiple regions in variety rodents species remains lacking.Therefore,as a parts of the china rodents virome studied by our team,my PhD studies focus on the rodents virome surveys of Arenaviridae,Flaviviridae,Picornaviridae,Hepeviridae,Astroviridae,Circoviridae,Parvovirinae,and the characteristic of genomic organization,phylogenetic analysis,the host range,the geographical evolution.We trying to surveys the presence of known zoonotic viruses in rodents with extensive contacts with humans can be used to monitor for EIDs.Over 6,000 pharyngeal and anal swabs samples were taken from a total of 3,005 animal individuals in 20 provinces throughout China(sampled by Chinese center for disease control and prevention).The animal individuals belonged to 51 species in the order of Rodentina,4 species in Lagomorpha and Soricomorpha that reside in urban,rural,and wild areas throughout China.Samples from the same species and from the same sampling site were then pooled together and processed with viral particle-protected nucleic acid purification.Totally pools of samples were subjected to viral nucleic acid library construction,next-generation sequencing,metagenomic analysis and taxonomic assignments,and obtained 12,073,729 reads with best match to viral proteins available in the NR database.The virus-associated reads of each lane were assigned into 70 families.By further screening out the non-mammalian viruses such as insect viruses,fungal viruses,plant viruses,and phages,the rest viral reads were assigned into families of mammalian viruses.3,298,152 sequence reads classified as the seven virus family of Arenaviridae,Flaviviridae,Picornaviridae,etc,by MEGAN 4 were extracted.Metagenomic analysis show that Arenaviridae distributed in 16 animal hosts species from 10 province,Flaviviridae distributed in 12 animal hosts species from 8 province,Astroviridae distributed in 51 animal hosts species from 17 province,Herpesviridae distributed in 36 animal hosts species from 16 province,Picornaviridae distributed in 23 animal hosts species from 20 province,Circoviridae distributed in 55 animal hosts species from 20 province,Parvovirinae distributed in 52 animal hosts species from 20 province.Based on the partial genomic sequences of the viruses obtained by the metagenomic analyses,we designed specific nested primers for PCR or RT-PCR to screen for each virus in individual samples.Representative positive samples for each virus were selected for genome sequencing.The remaining genomic sequences were determined using inverse PCR,genome walking,and 5'-and 3'-rapid amplification of cDNA ends(RACE).Here,a total of 138 rodent and Sorex araneus carried viral sequences were identified,included 65 complete genome sequencing of mammalian viruses.Seven new virus lineage and 55 new virus strain are prorosed as new genus or new species in different virus family.Novel AreVs found in Rattus species from Zhejiang,Hunan,Yunnan which clustered with WENV and its human-infected variants reported previously reveals the broad geographic distribution of these potential zoonotic viruses(87%-89%aa identities for L,93%aa 154 identities for G,95%aa identities for N).We identified diverse Arenaviridae,Flaviviridae,Parvoviruses located in different phylogenetic position which indicate the presence of novel viruses in new hosts such as AreV in the Dipus,Pestiviruses in the rodents.This study extends the host range for members of each viral family and the viral taxa to include many new viral genera and species,reveals unique ecological and evolutionary characteristics of rodent-and shrew-borne viruses.Here,We outlined the rodent and small mammal viromes and the basic ecological and genetic characteristics of many novel viruses in China.These results suggest that there is a likely high diversity of viruses awaiting discovery in rodent species in Asia.These findings,greatly increase our knowledge of the viral community in wildlife in a densely-populated country in an emerging disease hotspot.All of these data could offer a meaningful basis for the identification and tracking of potential rodent-origin EIDs and providing a baseline of the viruses present to help detect future changes associated with disease outbreaks. |
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