Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees
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{"title"=>"Molecular ecology and natural history of Simian foamy virus infection in wild-living chimpanzees", "type"=>"journal", "authors"=>[{"first_name"=>"Weimin", "last_name"=>"Liu", "scopus_author_id"=>"55723580100"}, {"first_name"=>"Michael", "last_name"=>"Worobey", "scopus_author_id"=>"6603603024"}, {"first_name"=>"Yingying", "last_name"=>"Li", "scopus_author_id"=>"35262131400"}, {"first_name"=>"Brandon F.", "last_name"=>"Keele", "scopus_author_id"=>"6701829878"}, {"first_name"=>"Frederic", "last_name"=>"Bibollet-Ruche", "scopus_author_id"=>"6701671843"}, {"first_name"=>"Yuanyuan", "last_name"=>"Guo", "scopus_author_id"=>"24481133900"}, {"first_name"=>"Paul A.", "last_name"=>"Goepfert", "scopus_author_id"=>"7004018810"}, {"first_name"=>"Mario L.", "last_name"=>"Santiago", "scopus_author_id"=>"34573063500"}, {"first_name"=>"Jean Bosco N.", "last_name"=>"Ndjango", "scopus_author_id"=>"6506919104"}, {"first_name"=>"Cecile", "last_name"=>"Neel", "scopus_author_id"=>"15059451700"}, {"first_name"=>"Stephen L.", "last_name"=>"Clifford", "scopus_author_id"=>"16303266200"}, {"first_name"=>"Crickette", "last_name"=>"Sanz", "scopus_author_id"=>"16048109600"}, {"first_name"=>"Shadrack", "last_name"=>"Kamenya", "scopus_author_id"=>"57193985734"}, {"first_name"=>"Michael L.", "last_name"=>"Wilson", "scopus_author_id"=>"36039555900"}, {"first_name"=>"Anne E.", "last_name"=>"Pusey", "scopus_author_id"=>"6701915235"}, {"first_name"=>"Nicole", "last_name"=>"Gross-Camp", "scopus_author_id"=>"6505649270"}, {"first_name"=>"Christophe", "last_name"=>"Boesch", "scopus_author_id"=>"26642873000"}, {"first_name"=>"Vince", "last_name"=>"Smith", "scopus_author_id"=>"55618440400"}, {"first_name"=>"Koichiro", "last_name"=>"Zamma", "scopus_author_id"=>"56049163000"}, {"first_name"=>"Michael A.", "last_name"=>"Huffman", "scopus_author_id"=>"7005058201"}, {"first_name"=>"John C.", "last_name"=>"Mitani", "scopus_author_id"=>"7004596132"}, {"first_name"=>"David P.", "last_name"=>"Watts", "scopus_author_id"=>"7201539616"}, {"first_name"=>"Martine", "last_name"=>"Peeters", "scopus_author_id"=>"7203079647"}, {"first_name"=>"George M.", "last_name"=>"Shaw", "scopus_author_id"=>"7401773516"}, {"first_name"=>"William M.", "last_name"=>"Switzer", "scopus_author_id"=>"7006277806"}, {"first_name"=>"Paul M.", "last_name"=>"Sharp", "scopus_author_id"=>"7402935847"}, {"first_name"=>"Beatrice H.", "last_name"=>"Hahn", "scopus_author_id"=>"7201799232"}], "year"=>2008, "source"=>"PLoS Pathogens", "identifiers"=>{"scopus"=>"2-s2.0-48249095547", "sgr"=>"48249095547", "issn"=>"15537366", "doi"=>"10.1371/journal.ppat.1000097", "pmid"=>"18604273", "isbn"=>"1553-7374 (Electronic)\\n1553-7366 (Linking)", "pui"=>"352076494"}, "id"=>"c39247e7-e018-3d01-9447-3e267e508579", "abstract"=>"Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health, as evidenced by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) and Ebola virus. Simian foamy viruses (SFVs) are ancient retroviruses that infect Old and New World monkeys and apes. Although not known to cause disease, these viruses are of public health interest because they have the potential to infect humans and thus provide a more general indication of zoonotic exposure risks. Surprisingly, no information exists concerning the prevalence, geographic distribution, and genetic diversity of SFVs in wild-living monkeys and apes. Here, we report the first comprehensive survey of SFVcpz infection in free-ranging chimpanzees (Pan troglodytes) using newly developed, fecal-based assays. Chimpanzee fecal samples (n = 724) were collected at 25 field sites throughout equatorial Africa and tested for SFVcpz-specific antibodies (n = 706) or viral nucleic acids (n = 392). SFVcpz infection was documented at all field sites, with prevalence rates ranging from 44% to 100%. In two habituated communities, adult chimpanzees had significantly higher SFVcpz infection rates than infants and juveniles, indicating predominantly horizontal rather than vertical transmission routes. Some chimpanzees were co-infected with simian immunodeficiency virus (SIVcpz); however, there was no evidence that SFVcpz and SIVcpz were epidemiologically linked. SFVcpz nucleic acids were recovered from 177 fecal samples, all of which contained SFVcpz RNA and not DNA. Phylogenetic analysis of partial gag (616 bp), pol-RT (717 bp), and pol-IN (425 bp) sequences identified a diverse group of viruses, which could be subdivided into four distinct SFVcpz lineages according to their chimpanzee subspecies of origin. Within these lineages, there was evidence of frequent superinfection and viral recombination. One chimpanzee was infected by a foamy virus from a Cercopithecus monkey species, indicating cross-species transmission of SFVs in the wild. These data indicate that SFVcpz (i) is widely distributed among all chimpanzee subspecies; (ii) is shed in fecal samples as viral RNA; (iii) is transmitted predominantly by horizontal routes; (iv) is prone to superinfection and recombination; (v) has co-evolved with its natural host; and (vi) represents a sensitive marker of population structure that may be useful for chimpanzee taxonomy and conservation strategies.", "link"=>"http://www.mendeley.com/research/molecular-ecology-natural-history-simian-foamy-virus-infection-wildliving-chimpanzees", "reader_count"=>92, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Librarian"=>4, "Researcher"=>19, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>8, "Other"=>7, "Student > Bachelor"=>7, "Professor"=>6}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Librarian"=>4, "Researcher"=>19, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>24, "Student > Postgraduate"=>4, "Student > Master"=>8, "Other"=>7, "Student > Bachelor"=>7, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Agricultural and Biological Sciences"=>54, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1, "Environmental Science"=>2, "Nursing and Health Professions"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Medicine and Dentistry"=>13, "Psychology"=>1, "Social Sciences"=>4, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>13}, "Social Sciences"=>{"Social Sciences"=>4}, "Psychology"=>{"Psychology"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>54}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Belgium"=>1, "Japan"=>1, "United Kingdom"=>1, "Chile"=>1, "France"=>1, "Germany"=>1, "Spain"=>1, "India"=>1}, "group_count"=>2}

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  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"21"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"25"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"4", "xml_views"=>"1", "html_views"=>"27"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"5", "xml_views"=>"1", "html_views"=>"52"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"30"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"10", "xml_views"=>"1", "html_views"=>"24"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"17"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"15"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"9"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"1"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"3", "html_views"=>"10"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"6"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"17", "xml_views"=>"0", "html_views"=>"9"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"13", "xml_views"=>"1", "html_views"=>"18"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"8"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"10"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"12"}
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  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"19"}
  • {"month"=>"12", "year"=>"2019", "pdf_views"=>"18", "xml_views"=>"2", "html_views"=>"5"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/928051"], "description"=>"<p>Members of the habituated Mitumba and Kasekela communities in Gombe National Park were non-invasively tested for SFVcpz infection and their infection rate (y-axis) plotted by age group (x-axis). Group 1 comprises 4 infants age 2 or younger; group 2 comprises 10 chimpanzees age 2.1 to 9 years; and group 3 comprises 13 adult chimpanzees age 14 to 45.</p>", "links"=>[], "tags"=>["sfvcpz", "rates"], "article_id"=>598469, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Increase_of_SFVcpz_infection_rates_with_age_/598469", "title"=>"Increase of SFVcpz infection rates with age.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:21:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/928694"], "description"=>"<p>(A) The maximum clade credibility (MCC) topology of <i>pol</i>-IN sequences is shown, with branch lengths as described in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figure 6</a>. Brackets indicate the number of distinct SFVcpz strains that are present in samples DP157 and MF1279, respectively. Bulk PCR derived sequences are shown in red; SGA derived sequences are shown in blue. Numbers on nodes indicate posterior probabilities expressed as percentages (only values of 90% or higher are shown). The scale bar represents 0.009 substitutions per site. (B) Maximum clade credibility (MCC) topologies of <i>gag</i> sequences in two adjacent fragments are shown. Viruses that exhibit discordant branching patterns are highlighted. Numbers on nodes indicate percentage posterior probabilities. The scale bars represent 0.02 substitutions per site.</p>", "links"=>[], "tags"=>["recombination"], "article_id"=>599110, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g009", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coinfection_and_recombination_in_SFVcpz_/599110", "title"=>"Coinfection and recombination in SFVcpz.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:31:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/927665"], "description"=>"<p>Field sites are shown in relation to the ranges of the four proposed chimpanzee subspecies. White circles indicate forest areas where fecal samples were collected for prevalence studies (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-t003\" target=\"_blank\">Table 3</a>). These were located in Cote d'Ivoire (TA), Cameroon (MF, WE, MP, MT, DG, DP, BQ, CP, EK, BB, MB, LB), the Central African Republic (ME), Gabon (LP), Republic of Congo (GT), Democratic Republic of Congo (BD, WL, WK), Uganda (KB), Rwanda (NY), and Tanzania (GM-MT, GM-KK, GM-KL, MH). Black circles indicate forest sites where eight ancillary samples (BA432, BF1167, EP479, EP486, KS310, UB446, WA466, WA543) were collected. International borders and major rivers are shown.</p>", "links"=>[], "tags"=>["chimpanzee"], "article_id"=>598087, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_wild_chimpanzee_study_sites_/598087", "title"=>"Location of wild chimpanzee study sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:14:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/928320"], "description"=>"<p><i>Gag</i> (616 bp) sequences were analyzed as described in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figure 6</a>. The <i>gag</i> tree was rooted using a relaxed clock. Posterior probabilities are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g001\" target=\"_blank\">Figure 1</a>). Representative strains from the database are shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s003\" target=\"_blank\">Table S2</a>). Sample WE464 (boxed) was collected in the <i>P. t. vellerosus</i> range, but has a <i>P. t. troglodytes</i> mtDNA haplotype (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s001\" target=\"_blank\">Figure S1</a>). The scale bar represents 0.02 substitutions per site.</p>", "links"=>[], "tags"=>["relationships", "derived", "sfvcpz", "strains"], "article_id"=>598732, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_of_newly_derived_SFVcpz_strains_in_the_gag_region_/598732", "title"=>"Evolutionary relationships of newly derived SFVcpz strains in the <i>gag</i> region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:25:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/928819"], "description"=>"<p>The maximum clade credibility (MCC) topology of <i>pol</i>-IN sequences is shown, with branch lengths as described in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figure 6</a>. The chimpanzee SFV strain LB309 (red box) significantly clusters within a group of SFVs previously derived from captive L'Hoest's (LHO), Hamlyn's (HAM), mustached (MUS), DeBrazza's (DEB), mona (MON), Sykes's (SYK) and blue (BLU) monkeys (GenBank accession numbers are indicated in parentheses), thus strongly suggesting a <i>Cercopithecus</i> monkey origin. Newly derived SFV sequences from a bonobo (LM183), gorilla (LP5), mandrill (LP47) and DeBrazza's monkey (CNE01) are also shown (blue) in relation to reference sequences from <i>Chlorocebus</i> and <i>Mandrillus</i> species (black). Numbers on nodes indicate posterior probabilities expressed as percentages (only 90% or higher are shown). The scale bar represents 0.08 substitutions per site.</p>", "links"=>[], "tags"=>["sfv"], "article_id"=>599246, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g010", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cross_species_transmission_of_SFV_in_the_wild_/599246", "title"=>"Cross-species transmission of SFV in the wild.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:34:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/928520"], "description"=>"<p><i>Pol</i>-RT (718 bp) sequences were analyzed as described in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figure 6</a>. The tree was rooted using LM183 as an outgroup. Posterior probabilities are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g001\" target=\"_blank\">Figure 1</a>). One representative strain from the database (HFV) is shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s003\" target=\"_blank\">Table S2</a>). Sample WE464 (boxed) was collected in the <i>P. t. vellerosus</i> range, but has a <i>P. t. troglodytes</i> mtDNA haplotype (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s001\" target=\"_blank\">Figure S1</a>). Arrows identify distinct SFVcpz strains (termed A or B) that were found in the same sample. The scale bar represents 0.02 substitutions per site.</p>", "links"=>[], "tags"=>["relationships", "derived", "sfvcpz", "strains"], "article_id"=>598932, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_of_newly_derived_SFVcpz_strains_in_the_pol_RT_region_/598932", "title"=>"Evolutionary relationships of newly derived SFVcpz strains in the <i>pol</i>-RT region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:28:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/928142"], "description"=>"<p><i>Pol</i>-IN (425 bp) sequences were analyzed using the Bayesian Markov chain Monte Carlo (BMCMC) method implemented in BEAST. Sequence LM183 (from a wild bonobo) was included as an outgroup. The maximum clade credibility (MCC) tree topology inferred using TreeAnnotator v1.4.7 is shown, with branch lengths depicting the mean value for that branch in the upper half of the MCMC sample. Posterior probabilities (expressed as percentages) are indicated on well-supported nodes, either as asterisks (100%) or filled circles (90%–99%). Newly identified SFVcpz strains are color coded according to their subspecies of origin (as shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g001\" target=\"_blank\">Figure 1</a>). Representative strains from the database are shown in black. Plus signs (+) denote sequences that represent placeholders of multiple viruses with identical sequences (a complete list is provided in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s003\" target=\"_blank\">Table S2</a>). Sample WE464 (boxed) was collected in the <i>P. t. vellerosus</i> range, but has a <i>P. t. troglodytes</i> mtDNA haplotype (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097.s001\" target=\"_blank\">Figure S1</a>). Arrows identify distinct SFVcpz strains (termed A or B) that were found in the same sample. The scale bar represents 0.02 substitutions per site.</p>", "links"=>[], "tags"=>["relationships", "derived", "sfvcpz", "strains"], "article_id"=>598552, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_relationships_of_newly_derived_SFVcpz_strains_in_the_pol_IN_region_/598552", "title"=>"Evolutionary relationships of newly derived SFVcpz strains in the <i>pol</i>-IN region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/928917"], "description"=>"a<p>Only collection sites with known numbers of infected individuals were included in this analysis.</p>", "links"=>[], "tags"=>["sfvcpz", "sivcpz", "infections", "chimpanzee", "communities", "harboring"], "article_id"=>599321, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.t004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_SFVcpz_and_SIVcpz_Infections_in_Chimpanzee_Communities_Harboring_Both_Viruses_/599321", "title"=>"Number of SFVcpz and SIVcpz Infections in Chimpanzee Communities Harboring Both Viruses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-04 02:35:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/927879"], "description"=>"<p>Amplification products are shown in relation to the corresponding regions in the SFVcpz genome, with the length of the amplified fragments indicated. The genomic organization of SFVcpz is shown on the top (structural and accessory genes are drawn to scale) <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097-Peters1\" target=\"_blank\">[79]</a>.</p>", "links"=>[], "tags"=>["rt-pcr", "derived", "amplicons", "sfvcpz"], "article_id"=>598298, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_RT_PCR_derived_amplicons_in_the_SFVcpz_genome_/598298", "title"=>"Location of RT-PCR derived amplicons in the SFVcpz genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:18:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/459022", "https://ndownloader.figshare.com/files/459193", "https://ndownloader.figshare.com/files/459281"], "description"=>"<div><p>Identifying microbial pathogens with zoonotic potential in wild-living primates can be important to human health, as evidenced by human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2) and Ebola virus. Simian foamy viruses (SFVs) are ancient retroviruses that infect Old and New World monkeys and apes. Although not known to cause disease, these viruses are of public health interest because they have the potential to infect humans and thus provide a more general indication of zoonotic exposure risks. Surprisingly, no information exists concerning the prevalence, geographic distribution, and genetic diversity of SFVs in wild-living monkeys and apes. Here, we report the first comprehensive survey of SFVcpz infection in free-ranging chimpanzees (<em>Pan troglodytes</em>) using newly developed, fecal-based assays. Chimpanzee fecal samples (n = 724) were collected at 25 field sites throughout equatorial Africa and tested for SFVcpz-specific antibodies (n = 706) or viral nucleic acids (n = 392). SFVcpz infection was documented at all field sites, with prevalence rates ranging from 44% to 100%. In two habituated communities, adult chimpanzees had significantly higher SFVcpz infection rates than infants and juveniles, indicating predominantly horizontal rather than vertical transmission routes. Some chimpanzees were co-infected with simian immunodeficiency virus (SIVcpz); however, there was no evidence that SFVcpz and SIVcpz were epidemiologically linked. SFVcpz nucleic acids were recovered from 177 fecal samples, all of which contained SFVcpz RNA and not DNA. Phylogenetic analysis of partial <em>gag</em> (616 bp), <em>pol</em>-RT (717 bp), and <em>pol</em>-IN (425 bp) sequences identified a diverse group of viruses, which could be subdivided into four distinct SFVcpz lineages according to their chimpanzee subspecies of origin. Within these lineages, there was evidence of frequent superinfection and viral recombination. One chimpanzee was infected by a foamy virus from a <em>Cercopithecus</em> monkey species, indicating cross-species transmission of SFVs in the wild. These data indicate that SFVcpz (i) is widely distributed among all chimpanzee subspecies; (ii) is shed in fecal samples as viral RNA; (iii) is transmitted predominantly by horizontal routes; (iv) is prone to superinfection and recombination; (v) has co-evolved with its natural host; and (vi) represents a sensitive marker of population structure that may be useful for chimpanzee taxonomy and conservation strategies.</p></div>", "links"=>[], "tags"=>["molecular", "ecology", "simian", "foamy", "wild-living", "chimpanzees"], "article_id"=>150427, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000097.s001", "https://dx.doi.org/10.1371/journal.ppat.1000097.s002", "https://dx.doi.org/10.1371/journal.ppat.1000097.s003"], "stats"=>{"downloads"=>13, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Ecology_and_Natural_History_of_Simian_Foamy_Virus_Infection_in_Wild_Living_Chimpanzees/150427", "title"=>"Molecular Ecology and Natural History of Simian Foamy Virus Infection in Wild-Living Chimpanzees", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-07-04 00:07:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/927968"], "description"=>"<p>Fecal viral RNA (x-axis) and antibody (y-axis) detection sensitivities are plotted for field sites with known numbers of infected chimpanzees (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-t002\" target=\"_blank\">Table 2</a>). The size of the circle is directly proportional to the number of samples tested (results from the three Gombe communities were combined). Color coding and corresponding two letter codes are as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g001\" target=\"_blank\">Figure 1</a>. Test sensitivities are significantly inversely correlated (P<0.001).</p>", "links"=>[], "tags"=>["fecal", "antibody", "viral", "rna", "detection"], "article_id"=>598382, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inverse_correlation_of_fecal_antibody_and_viral_RNA_detection_at_different_field_sites_/598382", "title"=>"Inverse correlation of fecal antibody and viral RNA detection at different field sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:19:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/929056"], "description"=>"a<p>Western blot strips were prepared using an infectious molecular clone (pMod-1) of SFVcpz<i>Pts</i> (see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#s4\" target=\"_blank\">Methods</a>).</p>b<p>RT-PCR was performed using SFVcpz specific <i>pol</i>-IN primers.</p>c<p>Sensitivities of SFVcpz antibody and viral RNA detection were determined for captive (YK) as well as wild-living chimpanzees at different field sites (TA, DP, EK, BB, MB, LB, GT, GM, MH).</p>d<p>SFVcpz infection in captive chimpanzees was confirmed by demonstrating virus specific antibodies in their blood; SFVcpz infection of wild-living chimpanzees was determined by demonstrating virus specific antibodies or viral RNA in at least one fecal sample.</p>e<p>The sensitivities of fecal antibody and viral RNA detection were calculated for each site based on the total number of samples collected from infected chimpanzees at that site (with 95% confidence intervals [CI]); the specificity of fecal antibody detection was determined by testing fecal samples from uninfected human volunteers (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-t001\" target=\"_blank\">Table 1</a>) and determined to be 1.00 (0.87–1.00); the specificity of virion RNA detection was set to 1.00 since all amplification products were sequence confirmed.</p>", "links"=>[], "tags"=>["antibody", "viral", "rna", "detection", "fecal", "samples", "captive"], "article_id"=>599471, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sensitivities_of_Antibody_and_Viral_RNA_Detection_in_Fecal_Samples_From_Captive_and_Wild_Chimpanzees_/599471", "title"=>"Sensitivities of Antibody and Viral RNA Detection in Fecal Samples From Captive and Wild Chimpanzees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-04 02:37:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/928993"], "description"=>"a<p>All individuals were members of the Mitumba and Kasekela communities.</p><p>nd; not done.</p>", "links"=>[], "tags"=>["mother-offspring", "pairs", "gombe"], "article_id"=>599408, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.t005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SFVcpz_Infection_in_Three_Mother_Offspring_Pairs_in_Gombe_National_Park_/599408", "title"=>"SFVcpz Infection in Three Mother-Offspring Pairs in Gombe National Park.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-04 02:36:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/929201"], "description"=>"a<p>All chimpanzees were housed at the Yerkes Primate Research Center; SFVcpz infection was confirmed by demonstrating virus specific (anti-Gag) antibodies in their blood.</p><p>The phylogenetic relationships of SFVcpz strains YK2-YK32 strains are shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figures 6</a>–<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g007\" target=\"_blank\"></a><a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g008\" target=\"_blank\">8</a>.</p>b<p>n/a, not available.</p>c<p>nd, not done.</p>", "links"=>[], "tags"=>["fecal-based", "antibody", "nucleic", "detection", "assays", "samples", "sfvcpz", "infected", "captive", "chimpanzees", "uninfected"], "article_id"=>599602, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.t001", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_Fecal_Based_Antibody_and_Nucleic_Acid_Detection_Assays_Using_Samples_from_SFVcpz_Infected_Captive_Chimpanzees_and_Uninfected_Human_Volunteers_/599602", "title"=>"Validation of Fecal-Based Antibody and Nucleic Acid Detection Assays Using Samples from SFVcpz Infected Captive Chimpanzees and Uninfected Human Volunteers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-04 02:40:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/927779"], "description"=>"<p>Enhanced chemiluminescent (ECL) Western blot analysis of fecal extracts from (A) human volunteers and captive chimpanzees, and (B) SFVcpz infected wild chimpanzees representing four different chimpanzee subspecies. Strips were prepared using an infectious molecular clone (pMod-1) of SFVcpz<i>Pts</i> (see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#s4\" target=\"_blank\">Methods</a>). Samples are numbered, with letters indicating the species (panel A) or collection site (panel B) of origin. Molecular weights of SFVcpz specific Gag and Bet proteins are shown. The banding pattern of plasma from an SFVcpz infected chimpanzee (used at a 1∶100,000 dilution) and an uninfected human are shown as positive (Pos) and negative (Neg) controls, respectively.</p>", "links"=>[], "tags"=>["sfvcpz", "antibodies", "chimpanzee", "fecal"], "article_id"=>598197, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_SFVcpz_antibodies_in_chimpanzee_fecal_samples_/598197", "title"=>"Detection of SFVcpz antibodies in chimpanzee fecal samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-04 02:16:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/929127"], "description"=>"a<p>Location of sites is shown in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g001\" target=\"_blank\">Figure 1</a>.</p>b<p><i>P.t.v.</i>, <i>P. t. verus</i>; <i>P.t.vl.</i>, <i>P. t. vellerosus</i>; <i>P.t.t.</i>, <i>P. t. troglodytes</i>; <i>P.t.s.</i>, <i>P. t. schweinfurthii</i>.</p>c<p>Number of fecal samples tested for SFVcpz antibodies and/or viral RNA, with brackets indicating those tested by Western blot (WB) and those tested by RT-PCR, respectively.</p>d<p>Number of fecal samples positive for SFVcpz antibodies and/or viral RNA, with brackets indicating those positive by WB and those positive by RT-PCR, respectively (the phylogenetic relationships of these newly derived SFVcpz strains are depicted in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g006\" target=\"_blank\">Figures 6</a>–<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g007\" target=\"_blank\"></a><a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat-1000097-g008\" target=\"_blank\">8</a>).</p>e<p>For four habituated communities (TA, GM-MT, GM-KK, MH) the number of tested chimpanzees was known; for seven non-habituated communities (GT, DP, EK, BB, MB, LB, GM-KL) the number of tested chimpanzees was determined by microsatellite analysis of fecal DNA <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#ppat.1000097-Keele1\" target=\"_blank\">[33]</a>.</p>f<p>For sites where the number of chimpanzees was known, SFVcpz prevalence rates (%, with brackets indicating 95% confidence intervals) were estimated based on the proportion of infected individuals, taking into account the “field sensitivities” of the antibody and virion RNA detection tests. For sites where the number of chimpanzees was not known, prevalence rates were estimated based on the number of fecal samples tested, assuming that a fraction (17%) was partially degraded and that any given chimpanzee was sampled on average 1.72 times (see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000097#s4\" target=\"_blank\">Methods</a> for details).</p>g<p>Based on mtDNA analysis, 24 samples were of <i>P. t. vellerosus</i> and 2 of <i>P. t. troglodytes</i> origin.</p>h<p>–; not available.</p>i<p>For this prevalence estimate, two WB indeterminant samples (reacting only with the Bet protein) were counted as negative.</p>", "links"=>[], "tags"=>["rates", "sfvcpz", "chimpanzees", "equatorial"], "article_id"=>599541, "categories"=>["Microbiology", "Ecology", "Medicine"], "users"=>["Weimin Liu", "Michael Worobey", "Yingying Li", "Brandon F. Keele", "Frederic Bibollet-Ruche", "Yuanyuan Guo", "Paul A. Goepfert", "Mario L. Santiago", "Jean-Bosco N. Ndjango", "Cecile Neel", "Stephen L. Clifford", "Crickette Sanz", "Shadrack Kamenya", "Michael L. Wilson", "Anne E. Pusey", "Nicole Gross-Camp", "Christophe Boesch", "Vince Smith", "Koichiro Zamma", "Michael A. Huffman", "John C. Mitani", "David P. Watts", "Martine Peeters", "George M. Shaw", "William M. Switzer", "Paul M. Sharp", "Beatrice H. Hahn"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000097.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_Rates_of_SFVcpz_Infection_in_Wild_Chimpanzees_throughout_Equatorial_Africa_/599541", "title"=>"Prevalence Rates of SFVcpz Infection in Wild Chimpanzees throughout Equatorial Africa.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-04 02:39:01"}

PMC Usage Stats | Further Information

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