Metagenomic Profile of the Viral Communities in Rhipicephalus spp. Ticks from Yunnan, China
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{"title"=>"Metagenomic profile of the viral communities in rhipicephalus spp. ticks from Yunnan, China", "type"=>"journal", "authors"=>[{"first_name"=>"Han", "last_name"=>"Xia", "scopus_author_id"=>"36480775000"}, {"first_name"=>"Cheng", "last_name"=>"Hu", "scopus_author_id"=>"57198697373"}, {"first_name"=>"Dake", "last_name"=>"Zhang", "scopus_author_id"=>"35365606400"}, {"first_name"=>"Shuang", "last_name"=>"Tang", "scopus_author_id"=>"55293899100"}, {"first_name"=>"Zhong", "last_name"=>"Zhang", "scopus_author_id"=>"55721916900"}, {"first_name"=>"Zheng", "last_name"=>"Kou", "scopus_author_id"=>"10640966700"}, {"first_name"=>"Zhaojun", "last_name"=>"Fan", "scopus_author_id"=>"12802465800"}, {"first_name"=>"Dennis", "last_name"=>"Bente", "scopus_author_id"=>"8864079300"}, {"first_name"=>"Changqing", "last_name"=>"Zeng", "scopus_author_id"=>"8236325500"}, {"first_name"=>"Tianxian", "last_name"=>"Li", "scopus_author_id"=>"55855621500"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84925738673", "sgr"=>"84925738673", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25799057", "doi"=>"10.1371/journal.pone.0121609", "pui"=>"603282160"}, "id"=>"fa354ddc-d4ca-3b03-95c6-d3852d70bf6f", "abstract"=>"Besides mosquitoes, ticks are regarded as the primary source of vector-borne infectious diseases. Indeed, a wide variety of severe infectious human diseases, including those involving viruses, are transmitted by ticks in many parts of the world. To date, there are no published reports on the use of next-generation sequencing for studying viral diversity in ticks or discovering new viruses in these arthropods from China. Here, Ion-torrent sequencing was used to investigate the presence of viruses in three Rhipicephalus spp. tick pools (NY-11, NY-13, and MM-13) collected from the Menglian district of Yunnan, China. The sequencing run resulted in 3,641,088, 3,106,733, and 3,871,851 reads in each tick pool after trimming. Reads and assembled contiguous sequences (contigs) were subject to basic local alignment search tool analysis against the GenBank database. Large numbers of reads and contigs related to known viral sequences corresponding to a broad range of viral families were identified. Some of the sequences originated from viruses that have not been described previously in ticks. Our findings will facilitate better understanding of the tick virome, and add to our current knowledge of disease-causing viruses in ticks living under natural conditions.", "link"=>"http://www.mendeley.com/research/metagenomic-profile-viral-communities-rhipicephalus-spp-ticks-yunnan-china", "reader_count"=>52, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>5, "Student > Master"=>8, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>5, "Student > Master"=>8, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>10, "Agricultural and Biological Sciences"=>30, "Veterinary Science and Veterinary Medicine"=>2, "Decision Sciences"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Decision Sciences"=>{"Decision Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Cameroon"=>1, "Czech Republic"=>1, "Brazil"=>2, "Italy"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1980659"], "description"=>"<p><i>De novo</i> assembly of three tick viromes.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349571, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.t001", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_novo_assembly_of_three_tick_viromes_/1349571", "title"=>"<i>De novo</i> assembly of three tick viromes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980658"], "description"=>"<p>(a) Schematic representation of the large polymerase protein of rhabdovirus. The green bar represents the contig sequence from NY-13. (b) Phylogenetic analysis of the selected contig related to rhabdovirus is based on an alignment with an 889 amino acid sequence from the large polymerase protein region of rhabdovirus. All nine <i>Rhabdoviridae</i> genera are indicated on the right of the tree.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349570, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.g005", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_tick_rhabdovirus_related_sequences_/1349570", "title"=>"Phylogenetic analysis of tick rhabdovirus-related sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980652"], "description"=>"<p><i>(a) Classified by viral host</i>. Breakdown of the viral sequences into seven categories: vertebrate-human-invertebrate, vertebrate-human, vertebrates, invertebrates, plants, algae, and protozoa viruses. <i>(b) Classified by viral family</i>. Viral metagenomic sequences were compared with the viral protein database in GenBank. Comparisons were performed with the BLASTx algorithm using an E-value cutoff 1e-04. The MEGAN5 program (<a href=\"http://ab.inf.uni-tuebingen.de/software/megan5/\" target=\"_blank\">http://ab.inf.uni-tuebingen.de/software/megan5/</a>) was used for acceptance of the output of a BLAST enquiry based on the lowest-common-ancestor algorithm taxonomy analysis.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349564, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Taxonomic_classification_overview_of_metagenomic_sequences_from_the_three_tick_viromes_/1349564", "title"=>"Taxonomic classification overview of metagenomic sequences from the three tick viromes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980650"], "description"=>"<p><i>(a)</i> In the Menglian district, tick pools NY-11 and NY-13 were collected from Nayun, while MM-13 was collected from Mengma <i>(b)</i> A tick representing the Rhipicephalus genus from this region.Ticks were collected by the Menglian Center for Disease Control and Prevention (China) using a standard dragging method.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349561, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tick_species_and_sample_collection_map_/1349561", "title"=>"Tick species and sample collection map.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980660", "https://ndownloader.figshare.com/files/1980661", "https://ndownloader.figshare.com/files/1980662"], "description"=>"<div><p>Besides mosquitoes, ticks are regarded as the primary source of vector-borne infectious diseases. Indeed, a wide variety of severe infectious human diseases, including those involving viruses, are transmitted by ticks in many parts of the world. To date, there are no published reports on the use of next-generation sequencing for studying viral diversity in ticks or discovering new viruses in these arthropods from China. Here, Ion-torrent sequencing was used to investigate the presence of viruses in three <i>Rhipicephalus</i> spp. tick pools (NY-11, NY-13, and MM-13) collected from the Menglian district of Yunnan, China. The sequencing run resulted in 3,641,088, 3,106,733, and 3,871,851 reads in each tick pool after trimming. Reads and assembled contiguous sequences (contigs) were subject to basic local alignment search tool analysis against the GenBank database. Large numbers of reads and contigs related to known viral sequences corresponding to a broad range of viral families were identified. Some of the sequences originated from viruses that have not been described previously in ticks. Our findings will facilitate better understanding of the tick virome, and add to our current knowledge of disease-causing viruses in ticks living under natural conditions.</p></div>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349572, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0121609.s001", "https://dx.doi.org/10.1371/journal.pone.0121609.s002", "https://dx.doi.org/10.1371/journal.pone.0121609.s003"], "stats"=>{"downloads"=>7, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Metagenomic_Profile_of_the_Viral_Communities_in_Rhipicephalus_spp_Ticks_from_Yunnan_China/1349572", "title"=>"Metagenomic Profile of the Viral Communities in <i>Rhipicephalus</i> spp. Ticks from Yunnan, China", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980657"], "description"=>"<p>(a) Schematic representation of three ORFs for <i>Thetatorquevirus</i>. The orange bar represents the contig sequence from NY-11. (b) Phylogenetic analysis of the selected contig related to <i>Thetatorquevirus</i> is based on an alignment with the predicted 440 amino acid sequence of ORF1. <i>Thetatorquevirus</i> and three other genera from the <i>Anelloviridae</i> family are indicated on the right of the tree.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349569, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.g004", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_tick_thetatorquevirus_related_sequences_/1349569", "title"=>"Phylogenetic analysis of tick thetatorquevirus-related sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:57:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1980655"], "description"=>"<p>(a) Schematic representation of the S segment encoded nucleoprotein (∼480 amino acids) of <i>Nairovirus</i>. The orange and green bars represent the contig sequences from NY-11 and NY-13. (b) Phylogenetic analysis of the selected contigs related to <i>Nairovirus</i> is based on alignments with 480 amino acids of the nucleoprotein. All five <i>Bunyaviridae</i> genera are indicated on the right of the tree. NP denotes nucleoprotein.</p>", "links"=>[], "tags"=>["Rhipicephalus spp", "contig", "sequence", "yunnan", "ny", "alignment search tool analysis", "sequencing", "virus", "tick", "pool", "mm"], "article_id"=>1349567, "categories"=>["Biological Sciences"], "users"=>["Han Xia", "Cheng Hu", "Dake Zhang", "Shuang Tang", "Zhong Zhang", "Zheng Kou", "Zhaojun Fan", "Dennis Bente", "Changqing Zeng", "Tianxian Li"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0121609.g003", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_nairovirus_related_sequences_from_ticks_/1349567", "title"=>"Phylogenetic analysis of nairovirus-related sequences from ticks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-23 02:57:48"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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