Analysis Of Genital Tract Viral Communities And Their Novel Viruses From Dairy Cow And Human

In recent years,with the deepening research of microbial we have found that the relationship between microbes and the occurrence,development of clinical diseases.As a member of microorganism,virus also poses a threat to the health of animals and humans.Due to the developing of the society,human activities,ecnomic and trade exchanges,the risk of virus especially new virus and strains ourtbreak is increasing.Researches confirmed that some viruses,such as human immunodeficiency virus(HIV),can persist in animals for a long time without symptoms.However,once they transmit from animals to humans,they will cause more serious clinical symptoms.Therefore,it is very important to analyze the composition of animals and human virome,the differences between the two groups,and the new viruses in the viromes.At present,the traditional methods of virus analysis such as cell culture,electron microscopy,PCR,ELISA,et al,have great limitations for the study of new viruses.With the development of next-generation sequencing technologies and bioinformatics,viral metagenomics have became a powerful research tool especially in the new virus identification and virome analysis.Viral metagenomics can be defined as the characterization of viral genetic information directly from given samples,including all eukaryotic and prokaryotic(phage)nucleic acids.It is a sequence-and culture-independent approach that does not rely on the presence of sequence,shape,antibody or antigen.This method can analyze the microbial diversity,population structure,comprehensive research on interactions and functional activity of the environmental samples without the techniques of organism culture.To analyze the composition of the bovine and human genital tract virome and genetic characteristic of novel virus.we used a viral metagenomics approach to perform the current research.as follows:The main contents of this research include:1.Research on the bovine genital tract viromeThe composition of the bovine genital tract swab virome at the family level:ds DNA virus: Adenoviridae 0.0797%?Ascoviridae 0.5503%?Baculoviridae 0.3068%?Herpesviridae 5.7212%(which contains Alloherpesviridae 0.0746%)?Papillomaviridae1.1159%?Polyomaviridae 0.1029%?Poxviridae 38.4279%.Picobirnaviridae 0.0771%.Retroviridae 0.7688%.ss DNA virus: Circoviridae 8.6781%?Genomoviridae 7.035%?Parvoviridae 0.2237%?Smacoviridae 8.3027%?Unclassified ss DNA Virius 27.1657%.ss RNA virus: Astroviridae 0.0180% ? Coronaviridae 1.2162% ? Picornaviridae0.0103%.Unclassified RNA Virius 0.198%.The characteristics of the bovine genital tract virome:(1)The abundance of the virus group is big.(2)Mammalian virus accounts for up to 65.2945%.(3)We found a new papillomavirus in the CattleS02 library(4)We found the presence of bovine polyomaviruses in the Cattle S05 library.(5)We also found 6 new CRESS-DNA viruses.2.Research on the human genital tract viromeThe composition of the human genital tract swab virome at the family level:ds DNA virus:Ascoviridae 0.1173% ? Baculoviridae 0.2346% ? Herpesviridae 0.2346% ?Papillomaviridae 51.1928%?Poxviridae 2.3465%.Retroviridae 15.4869%.Hepadnaviridae 0.0782%.ss DNA virus: Anelloviridae 29.2912%?Parvoviridae 0.0391%.ss RNA virus: Astroviridae 0.0391%?Picornaviridae 0.8604%?Unclassified ss DNA Virius 0.0391%.Unclassified RNA Viriuses 0.0391%.The characteristics of the human genital tract virome:(1)The abundance of the virome is great.(2)Mammalian virus accounts for up to 99.6872%.(3)A new human Papillomavirus was detected in the LVS02 library.(4)We also found 3 new anellovirius3.Comparison of bovine and human genital tract virusThe bovine and human genital tract virus groups are similar in composition,but there are significant differences in some viral families,such as the Anvilviridae.Some of the same virus families have significant differences in abundance.4.Discovery of novel viruses and their phylogenetic analysis(1)Novel PapillomavirusA new type of papillomavirus was found in the cattle genital swab CattleS02 library and the human genital tract swab LVS02 library.Papillomaviridae is highly diverse,papillomavirus is a double-stranded circular DNA virus with a size of approximately 8 kb and a highly conserved open reading frame(ORF)L1 region.It can infect various of mammals,including cattle,birds,etc,of which human-hosted papillomavirus is called Human papillomavirus(HPV).The novel papillomavirus in the Cattle S02 library was named bovine papillomavirus ujs-21015,which is 7398 bp in length and contains the early genes E6(1-426 bp),E7(428-751 bp),E1(738-2564 bp),and E2(2506).-3747bp)and late genes L1(5376-6887),L2(3828-5369bp)and long-chain non-coding region LCR(6888-7389),which are new species within the genus Dyoxipapillomavirus.The novel papillomavirus in the LVS02 library was named new HPV with a full length of 7554 bp and contains the early genes E7(195-494),E1(475-2379),E2(2321-3487)and late gene L2(3551-5164).)L1(5085-6710)is a new species within the genus Gammapapillomavirus.(2)Novel CRESS-DNA virusCRESS-DNA virus is a kind of circular single-stranded DNA virus.It mainly encodes proteins such as Rep protein and Cap protein.The CRESS-DNA virus contains Circoviridae,Geminiviridae,Nanoviridae,etc.We found 6 new CRESS-DNA viruses in the bovine genital tract virus library,named as C0101(2,255 bp)?C05001(2,562 bp)?C042793(2,958 bp)?C021765(2,727 bp)?C025899(2,734bp)?C013782(3,085bp),C0101?C05001 and C042793 are similar to some viruses in the Circoviridae family.C021765 and C025899 are similar to ring viruses.C013782 is similar to gemycircularvirus in Genomoviridae(3)PolyomavirusIn the cattle genital swab,CattleS05 library,we found the sequences of polyomavirus BPy V1(KM496323)and BPy V2(KX455486).Polyomaviruses are widely distributed among mammalian and avian species.Many mammalian polyomaviruses cause asymptomatic infections with life-long persistence in immunocompetent hosts.Only some of the polyomaviruses have been described to cause disease in immunocompromised hosts.In this study,BPy V1 and BPy V2 were detected in ground beef samples.Whether they are also present in the other tissues is currently unknown.Indicating a possible mode of transmission.(4)Novel AnelloviriusIn this study,we obtained a partial genome of three Anelloviriuses,which were named as ujs0601,ujs0801,and ujs0804.After comparison,these three strains were all novel Anelloviriuses.Anelloviruses,which are all single-strand circular DNA viruses.The genome consists of a coding region of three major overlapping open reading frames(ORF).ORF1 encodes the largest protein,which is considered to play a role in the replication of the circular genome.Most of these viruses are detected in the body fluid from the majority of human populations,although their disease associations are still elusive.that need to clarify its association with genital tract-related diseases in future epidemiological studies based on specific diseases.