Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, Botswana
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{"title"=>"Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana", "type"=>"journal", "authors"=>[{"first_name"=>"Vladimir", "last_name"=>"Novitsky", "scopus_author_id"=>"7004689873"}, {"first_name"=>"Hermann", "last_name"=>"Bussmann", "scopus_author_id"=>"6603702950"}, {"first_name"=>"Andrew", "last_name"=>"Logan", "scopus_author_id"=>"56006855900"}, {"first_name"=>"Sikhulile", "last_name"=>"Moyo", "scopus_author_id"=>"13407981700"}, {"first_name"=>"Erik", "last_name"=>"Van Widenfelt", "scopus_author_id"=>"14065440900"}, {"first_name"=>"Lillian", "last_name"=>"Okui", "scopus_author_id"=>"37041431300"}, {"first_name"=>"Mompati", "last_name"=>"Mmalane", "scopus_author_id"=>"36459956000"}, {"first_name"=>"Jeannie", "last_name"=>"Baca", "scopus_author_id"=>"35175550400"}, {"first_name"=>"Lauren", "last_name"=>"Buck", "scopus_author_id"=>"56006454400"}, {"first_name"=>"Eleanor", "last_name"=>"Phillips", "scopus_author_id"=>"56005985200"}, {"first_name"=>"David", "last_name"=>"Tim", "scopus_author_id"=>"56006734500"}, {"first_name"=>"Mary Fran", "last_name"=>"McLane", "scopus_author_id"=>"35413246700"}, {"first_name"=>"Quanhong", "last_name"=>"Lei", "scopus_author_id"=>"56006776900"}, {"first_name"=>"Rui", "last_name"=>"Wang", "scopus_author_id"=>"56154254500"}, {"first_name"=>"Joseph", "last_name"=>"Makhema", "scopus_author_id"=>"6504162014"}, {"first_name"=>"Shahin", "last_name"=>"Lockman", "scopus_author_id"=>"6603692731"}, {"first_name"=>"Victor", "last_name"=>"DeGruttola", "scopus_author_id"=>"7004328863"}, {"first_name"=>"M.", "last_name"=>"Essex", "scopus_author_id"=>"7103043787"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84892618660", "doi"=>"10.1371/journal.pone.0080589", "issn"=>"19326203", "pui"=>"372134068", "isbn"=>"1932-6203", "pmid"=>"24349005", "scopus"=>"2-s2.0-84892618660"}, "id"=>"e78c5f71-4127-3355-bd2f-a521f357b035", "abstract"=>"BACKGROUND: Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.\\n\\nMETHODS: To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits.\\n\\nRESULTS: The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.\\n\\nCONCLUSIONS: The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.", "link"=>"http://www.mendeley.com/research/phylogenetic-relatedness-circulating-hiv1c-variants-mochudi-botswana", "reader_count"=>25, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>7, "Veterinary Science and Veterinary Medicine"=>1, "Social Sciences"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Vietnam"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1311785"], "description"=>"<p>Axis <i>x</i> shows cluster size as the number of members per cluster. Axis <i>y</i> shows the number of identified clusters. <b>A:</b> ML<sub>FastTree2</sub>. <b>B:</b> ML<sub>FastTree2</sub> + ML<sub>PhyML</sub>. <b>C:</b> ML<sub>FastTree2</sub> + ML<sub>RAxML</sub>. <b>D:</b> ML<sub>FastTree2</sub> + ME<sub>MCL</sub>. Note: The cluster with 55 members was identified in the ML<sub>FastTree2</sub> analysis only, and was not confirmed in the second-step analysis by the ML or ME phylogeny.</p>", "links"=>[], "tags"=>["followed"], "article_id"=>875200, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_uniform_cluster_size_distribution_followed_the_power_law_/875200", "title"=>"The uniform cluster size distribution followed the power law.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311783"], "description"=>"<p>A total of 11,934 non-recombinant HIV-1C <i>env</i> sequences spanning at least 1,000 bp within the gp120 V1–C5 region were selected from the LANL HIV Database. After initial on-line filtering, 3,170 sequences were selected. The applied manual filtering left 1,334 sequences. Together with 885 new Botswana sequences including 785 sequences known to be from Mochudi, a total of 2,219 HIV-1C <i>env</i> sequences were included in analysis.</p>", "links"=>[], "tags"=>["sequences", "included"], "article_id"=>875198, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HIV_1C_env_sequences_included_in_analysis_/875198", "title"=>"HIV-1C <i>env</i> sequences included in analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311797"], "description"=>"<p>The tree was generated by ML<sub>PhyML</sub> with 968 HIV-1C <i>env</i> sequences from Botswana. Clustered sequences with bootstrap support of splits ≥80% are shown in red. The incident HIV-1C cases from Mochudi are highlighted by circles: clustered seroconverters are indicated with filled red circles, while non-clustered seroconverters are shown with open circles.</p>", "links"=>[], "tags"=>["relationships", "mochudi"], "article_id"=>875212, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g009", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_between_Mochudi_seroconverters_/875212", "title"=>"Phylogenetic relationships between Mochudi seroconverters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311794"], "description"=>"<p>The estimated p-values by Wilcoxon test are shown above each graph. <b>A:</b> The entire set of ART-naïve individuals. <b>B:</b> ART-naïve males. <b>C:</b> ART-naïve females.</p>", "links"=>[], "tags"=>["hiv-1", "rna", "clustered", "non-clustered", "sequences"], "article_id"=>875209, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g008", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_HIV_1_RNA_load_within_clustered_and_non_clustered_sequences_in_ART_na_239_ve_individuals_/875209", "title"=>"Comparison of HIV-1 RNA load within clustered and non-clustered sequences in ART-naïve individuals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311792"], "description"=>"<p>The HIV-1C <i>env</i> gp120 V1–C5 signature sequences across 22 clusters with 3+ members, VESPA analysis.</p>", "links"=>[], "tags"=>["hiv-1c", "gp120", "sequences", "22", "clusters", "vespa"], "article_id"=>875207, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g007", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_HIV_1C_env_gp120_V1_C5_signature_sequences_across_22_clusters_with_3_members_VESPA_analysis_/875207", "title"=>"The HIV-1C <i>env</i> gp120 V1–C5 signature sequences across 22 clusters with 3+ members, VESPA analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311788"], "description"=>"<p>Mean pairwise p-distances for 22 clusters with 3+ members are denoted as red circles on the left shoulder of overall distribution. The position of mean pairwise distances is only relevant to the p-distances on the <i>x</i> axis.</p>", "links"=>[], "tags"=>["pairwise", "p-distances", "hiv-1c", "gp120"], "article_id"=>875203, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_pairwise_p_distances_within_the_analyzed_set_of_HIV_1C_env_gp120_V1_C5_region_n_2_219_/875203", "title"=>"Distribution of pairwise p-distances within the analyzed set of HIV-1C <i>env</i> gp120 V1–C5 region, n = 2,219.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311805", "https://ndownloader.figshare.com/files/1311806"], "description"=>"<div><p>Background</p><p>Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.</p><p>Methods</p><p>To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C <i>env</i> sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010–2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C <i>env</i> sequences and bootstrap support of splits.</p><p>Results</p><p>The overall proportion of clustered HIV-1C <i>env</i> sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.</p><p>Conclusions</p><p>The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.</p></div>", "links"=>[], "tags"=>["relatedness", "circulating", "hiv-1c", "variants"], "article_id"=>875220, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0080589.s001", "https://dx.doi.org/10.1371/journal.pone.0080589.s002"], "stats"=>{"downloads"=>9, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Relatedness_of_Circulating_HIV_1C_Variants_in_Mochudi_Botswana_/875220", "title"=>"Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, Botswana", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311802"], "description"=>"<p>Selected countries representation of HIV-1C <i>env</i> sequences included in analysis.</p>", "links"=>[], "tags"=>["countries", "hiv-1c", "sequences", "included"], "article_id"=>875217, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.t001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_countries_representation_of_HIV_1C_env_sequences_included_in_analysis_/875217", "title"=>"Selected countries representation of HIV-1C <i>env</i> sequences included in analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311787"], "description"=>"<p>The identified clusters with bootstrap support of ≥80% are collapsed. The collapsed clusters shown in red represent Mochudi-unique clusters; in blue, Mochudi mixed clusters with other Botswana sequences; in orange, non-Mochudi clusters with Botswana sequences; and in green, non-Botswana clusters. Clusters with mother-infant pairs from two MTCT studies in Malawi are shown by asterisks <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080589#pone.0080589-Russell1\" target=\"_blank\">[78]</a> and green circle <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080589#pone.0080589-Kumar1\" target=\"_blank\">[79]</a>.</p>", "links"=>[], "tags"=>["relatedness", "hiv-1c", "sequences"], "article_id"=>875202, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g004", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relatedness_of_HIV_1C_env_sequences_based_on_the_ML_FastTree2_ML_PhyML_analysis_/875202", "title"=>"Phylogenetic relatedness of HIV-1C <i>env</i> sequences based on the ML<sub>FastTree2</sub> + ML<sub>PhyML</sub> analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311801"], "description"=>"<p><sup></sup> post-seroconversion, p/s.</p>", "links"=>[], "tags"=>["prospective", "cohort", "individuals", "hiv-1c", "botswana", "seroconveters"], "article_id"=>875215, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.t005", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CD4_levels_in_the_prospective_cohort_of_individuals_with_primary_HIV_1C_infection_in_Botswana_and_seroconveters_in_this_study_/875215", "title"=>"CD4 levels in the prospective cohort of individuals with primary HIV-1C infection in Botswana and seroconveters in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311799"], "description"=>"<p>Pairwise p-distances within clusters with 3+ members.</p>", "links"=>[], "tags"=>["p-distances", "clusters"], "article_id"=>875214, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.t004", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_p_distances_within_clusters_with_3_members_/875214", "title"=>"Pairwise p-distances within clusters with 3+ members.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311790"], "description"=>"<p>The relevant patient-specific data (prevalent or incident HIV infection, gender, age, HIV-1 RNA, CD4 count and ART status) are connected by dotted lines with the tree branches corresponding to genotyped subjects. Note: Subjects reported receiving ART through the National ARV program during the household surveys. <b>A:</b> Mochudi-unique cluster #125 with 11 members. Subjects cohabited in the same household are indicated with asterisks. <b>B:</b> Mochudi-unique cluster #162 with 11 members. <b>C:</b> Mochudi-unique cluster #84 with 6 members. <b>D:</b> Mochudi-mixed cluster#151 with 6 members. Viral sequences from Mochudi are shown as yellow squares, while sequences from outside of Mochudi are denoted by orange circles. <b>E:</b> Mochudi-unique cluster #94 with 5 members. <b>F:</b> Mochudi unique cluster #120 with 5 members.</p>", "links"=>[], "tags"=>["clusters"], "article_id"=>875205, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_individual_clusters_with_3_members_/875205", "title"=>"Examples of individual clusters with 3+ members.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311804"], "description"=>"<p>Proportion of clustered HIV-1C <i>env</i> sequences in clusters with 3+ members.</p>", "links"=>[], "tags"=>["clustered", "hiv-1c", "sequences", "clusters"], "article_id"=>875219, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.t003", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_clustered_HIV_1C_env_sequences_in_clusters_with_3_members_/875219", "title"=>"Proportion of clustered HIV-1C <i>env</i> sequences in clusters with 3+ members.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311803"], "description"=>"<p>Proportion of clustered HIV-1C <i>env</i> sequences.</p>", "links"=>[], "tags"=>["clustered", "hiv-1c"], "article_id"=>875218, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proportion_of_clustered_HIV_1C_env_sequences_/875218", "title"=>"Proportion of clustered HIV-1C <i>env</i> sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-11 04:04:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1311784"], "description"=>"<p>A total of 2,219 HIV-1C <i>env</i> sequences were included. After re-alignment of variable loops, the first step ML analysis was implemented by FastTree2, which selected 969 sequences based on the Shimodira-Hasegawa test for splits support ≥0.98. Two ML analyses implemented by PhyML and RAxML, and ME analysis using MCL model, were performed in the second step. Clusters were identified based on bootstrap support of ≥80% in at least 2 of 3 methods in the second step.</p>", "links"=>[], "tags"=>[], "article_id"=>875199, "categories"=>["Biological Sciences"], "users"=>["Vladimir Novitsky", "Hermann Bussmann", "Andrew Logan", "Sikhulile Moyo", "Erik van Widenfelt", "Lillian Okui", "Mompati Mmalane", "Jeannie Baca", "Lauren Buck", "Eleanor Phillips", "David Tim", "Mary Fran McLane", "Quanhong Lei", "Rui Wang", "Joseph Makhema", "Shahin Lockman", "Victor DeGruttola", "M. Essex"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0080589.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_of_cluster_analysis_/875199", "title"=>"Flow of cluster analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-11 04:04:33"}

PMC Usage Stats | Further Information

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Relative Metric

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