Paper - WANFANG MED ONLINE

You Position: Home > Paper

Virome diversity of ticks feeding on domestic mammals in China

( views:5, downloads:0 )

Author:: No author available

Journal Title:: Virologica Sinica

Issue:: 2

DOI:: No doi available

Key Word:: Central and western China;Viral metagenomes;Tick-borne virus;Phylogenetic analysis;Domestic mammals;Tick virome

Abstract： Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses.From 2017 to 2018,640 ticks were collected in eight different provinces in central and western China.Six species were detected,including H.longicornis,De.everestianus,Rh.microplus,Rh.turanicus,Rh.sangui-neous,and Hy.asiaticum.Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform,resulting in 13.44 G(5.88×107)of 250-bp-end reads,in which 2,437,941 are viral reads.We found 27 nearly complete genome sequences,including 16 genome sequences encoding entire protein-coding regions(lack of 3'or 5'end non-coding regions)and complete viral genomes,distributed in the arboviral family(Chuviridae,Rhab-doviridae,Nairoviridae,Phenuiviridae,Flaviviridae,Iflaviridae)as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans.In addition,13 virus sequences found in Chuviridae,Nairoviridae,Flavi-viridae,Iflaviridae,Hepeviridae,Parvoviridae,and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera.Besides,an epidemiological survey shows a high prevalence(9.38％and 15.63％)of two viruses(Ovine Copiparvovirus and Bovine parvovirus 2)in the tick cohort.

Reference

[1]Yong-Zhen Zhang,Yan-Mei Chen,Wen Wang.Annual Review of VirologyExpanding the RNA Virosphereby Unbiased Metagenomics[J].2019,6.
[2]Peñalver Enrique,Arillo Antonio,Delclòs Xavier,etc.Ticks parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages[J].2017,8(1).
[3]Natapong Jupatanakul,Shuzhen Sim.The Insect Microbiome Modulates Vector Competence for Arboviruses.[J].2014,6(11).
[4]Qi J,Auch AF,Huson DH,etc.MEGAN analysis of metagenomic data.[J].2007,17(3).
[5]Boxiao, Wang,Xiao-Feng, Tan,Stephanie, Thurmond,etc.The structure of Zika virus NS5 reveals a conserved domain conformation.[J].2017,8(Spec ).
[6]Siddell, Stuart G.,Walker, Peter J.,Lefkowitz, Elliot J.,etc.Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018)[J].2019,164(3).
[7]Wen Zhang,Linlin Li,Xutao Deng,etc.Viral nucleic acids in human plasma pools[J].2016,56(9).
[8]Moradpour,D.,Penin,F..Hepatitis C virus proteins: From structure to function[J].2013,369.
[9]Ci-Xiu, Li,Mang, Shi,Jun-Hua, Tian,etc.Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses.[J].2015,4.
[10]Buchfink, Benjamin,Xie, Chao,Huson, Daniel H..Fast and sensitive protein alignment using DIAMOND[J].2015,12(1).
[11]Johne R,Garcea RL,Imperiale MJ,etc.Taxonomical developments in the family Polyomaviridae.[J].2011,156(9).
[12]Shennan,Lu,Jiyao,Wang,Farideh,Chitsaz,etc.CDD/SPARCLE: the conserved domain database in 2020.[J].2020,48(D1).
[13]Simmonds, Peter,Becher, Paul,Bukh, Jens,etc.ICTV Virus Taxonomy Profile: Flaviviridae[J].2017,98(Pt.1).
[14]Fagrouch, Z.,Sarwari, R.,Lavergne, A.,etc.Novel polyomaviruses in South American bats and their relationship to other members of the family Polyomaviridae[J].2012,93(12).
[15]Katoh, Kazutaka,Standley, Daron M..MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability[J].2013,30(4).
[16]Beate I. Marczinke,Stuart T. Nichol.Nairobi Sheep Disease Virus, an Important Tick-Borne Pathogen of Sheep and Goats in Africa, Is Also Present in Asia[J].2002,303(1).
[17]Bera AK,Wu JH,Kuhn RJ,etc.Structure of the flavivirus helicase: Implications for catalytic activity, protein interactions, and proteolytic processing[J].2005,79(16).
[18]Tanca Alessandro,Abbondio Marcello,Palomba Antonio,etc.Potential and active functions in the gut microbiota of a healthy human cohort[J].2017,5(1).
[19]Edgar RC.MUSCLE: multiple sequence alignment with high accuracy and high throughput.[J].2004,32(5).
[20]T M, Rivers,F F, Schwentker.Louping Ill in MAN.[J].1934,59(5).
[21]Magnarelli LA,Anderson JF.Biology of ticks.[J].2008,22(2).
[22]Peter J, Walker,Cadhla, Firth,Steven G, Widen,etc.Evolution of genome size and complexity in the rhabdoviridae.[J].2015,11.
[23]Holmes, Edward C.,Shi, Mang,Zhang, Yong-Zhen.Using Metagenomics to Characterize an Expanding Virosphere[J].2018,172(6).
[24]Baoyu, Zhao,Guanghui, Yi,Fenglei, Du,etc.Structure and function of the Zika virus full-length NS5 protein.[J].2017,8(Spec ).
[25]Ronquist, Fredrik,Teslenko, Maxim,van der Mark, Paul,etc.MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space[J].2012,61(3).
[26]Fikrig E,Sukumaran B,Narasimhan S,etc.An Ixodes scapularis protein required for survival of Anaplasma phagocytophilum in tick salivary glands.[J].2006,203(6).
[27]Tingting Zhao,Haiyan Gong,Xiaojuan Shen,etc.Comparison of Viromes in Ticks from Different Domestic Animals in China[J].2020,(4).
[28]Moore PS,Chang Y,Shuda M,etc.Clonal integration of a polyomavirus in human Merkel cell carcinoma.[J].2008,319(5866).
[29]Shi, Mang,Lin, Xian-Dan,Tian, Jun-Hua,etc.Redefining the invertebrate RNA virosphere[J].2016,540(Dec.22 TN.7634).
[30]Calisher, Charles H.,Kurath, Gael,Ben Longdon,etc.ICTV Virus Taxonomy Profile: Rhabdoviridae[J].2018,99(Pt.4).
[31]John P. Huelsenbeck,Fredrik Ronquist.MRBAYES: Bayesian inference of phylogenetic trees[J].2001,17(8).
[32]Calvignac-Spencer, Sebastien,Feltkamp, Mariet C. W.,Daugherty, Matthew D.,etc.A taxonomy update for the family Polyomaviridae[J].2016,161(6).
[33]Wen Zhang,Linlin Li,Xutao Deng,etc.Faecal virome of cats in an animal shelter[J].2014,95(11).
[34]Krumbholz, Andi,Bininda-Emonds, Olaf R. P.,Wutzler, Peter,etc.Phylogenetics, evolution, and medical importance of polyomaviruses[J].2009,9(5).
[35]Carter, J.J.,Daugherty, M.D.,Qi, X.,etc.Identification of an overprinting gene in Merkel cell polyomavirus provides evolutionary insight into the birth of viral genes[J].2013,110(31).
[36]Valles, S. M.,Chen, Y.,Firth, A. E.,etc.ICTV Virus Taxonomy Profile: Iflaviridae[J].2017,98(Pt.4).
[37]Moens, Ugo,Calvignac-Spencer, Sebastien,Lauber, Chris,etc.ICTV Virus Taxonomy Profile: Polyomaviridae[J].2017,98(Pt.6).
[38]Lindquist L,Vapalahti O.Tick-borne encephalitis.[J].2008,371(9627).
[39]Jaenson Thomas GT,Jaenson David GE,Eisen Lars,etc.Changes in the geographical distribution and abundance of the tick Ixodes ricinus during the past 30 years in Sweden[J].2012,5(1).
[40]Parola, Philippe,Raoult, Didier.Ticks and Tickborne Bacterial Diseases in Humans: An Emerging Infectious Threat.[J].2001,32(6).
[41]Zhang Wen,Yang Shixing,Shan Tongling,etc.Virome comparisons in wild-diseased and healthy captive giant pandas[J].2017,5(1).
[42]Yadav, Pragya D.,Vincent, Martin J.,Khristova, Marina,etc.Genomic analysis reveals Nairobi sheep disease virus to be highly diverse and present in both Africa, and in India in the form of the Ganjam virus variant[J].2011,11(5).
[43]M, Labuda,P A, Nuttall.Tick-borne viruses.[J].2004,129 Suppl.
[44]Wang, Hao,Ling, Yu,Shan, Tongling,etc.Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae[J].2019,5(1).
[45]Cotmore, Susan F.,Agbandje-McKenna, Mavis,Canuti, Marta,etc.ICTV Virus Taxonomy Profile: Parvoviridae[J].2019,100(3).
[46].Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data[J].2020,15(3).
[47]Lasecka,L.,Baron,M.D..The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses[J].2014,159(6).
[48].Nosocomial infections caused by Crimean-Congo haemorrhagic fever virus[J].2020,105(1).
[49]Hao Li,Lei-Ke Zhang,Shu-Fen Li,etc.Calcium channel blockers reduce severe fever with thrombocytopenia syndrome virus (SFTSV) related fatality[J].2019,29(9).