Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis
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We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.\\n\\nMETHODS AND FINDINGS: We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling.\\n\\nCONCLUSIONS: Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.", "link"=>"http://www.mendeley.com/research/geographic-temporal-trends-molecular-epidemiology-genetic-mechanisms-transmitted-hiv1-drug-resistanc", "reader_count"=>162, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>5, "Librarian"=>2, "Researcher"=>36, "Student > Doctoral Student"=>7, "Student > Ph. D. 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  • {"files"=>["https://ndownloader.figshare.com/files/2007777"], "description"=>"<p>Flow chart showing the derivation of study sets meeting meta-analysis inclusion criteria: studies of representative ARV-naïve populations of 25 or more individuals with published RT sequences with or without protease sequences.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369590, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_chart_showing_the_derivation_of_study_sets_meeting_meta_analysis_inclusion_criteria_studies_of_representative_ARV_na_239_ve_populations_of_25_or_more_individuals_with_published_RT_sequences_with_or_without_protease_sequences_/1369590", "title"=>"Flow chart showing the derivation of study sets meeting meta-analysis inclusion criteria: studies of representative ARV-naïve populations of 25 or more individuals with published RT sequences with or without protease sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007780"], "description"=>"<p>Each study is represented by a circle. The size of the circle is proportional to the number of individuals in the study. The circle color indicates the prevalence of overall TDR in the study: white (<2.5%), pale yellow (2.5% to 4.9%), orange (5.0% to 9.9%), and red (≥10.0%). Each study can also be located on a sidebar, which lists each publication, percent overall TDR, number of individuals, and the country (or countries) where the study was conducted. Clicking on a sidebar row or a study circle in the interactive version of the map at <a href=\"http://hivdb.stanford.edu/surveillance/map/\" target=\"_blank\">http://hivdb.stanford.edu/surveillance/map/</a> generates a pop-up box with additional information including a link to the appropriate PubMed reference, the TDR prevalence by ARV class, the median year of virus sampling, the source of virus isolation, the mechanism of participant recruitment, and the virus subtype distribution (a pop-up box of the study Bila13 is shown as an example). The complete set of data associated with a study can be reviewed by clicking on the “Resistance (%)” link either on the sidebar or within the study circle pop-up menu.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369592, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_snapshot_of_an_interactive_map_plotting_the_prevalence_of_transmitted_drug_resistance_in_111_countries_from_287_studies_between_2000_and_2013_http_hivdb_stanford_edu_surveillance_map_/1369592", "title"=>"A snapshot of an interactive map plotting the prevalence of transmitted drug resistance in 111 countries from 287 studies between 2000 and 2013 (http://hivdb.stanford.edu/surveillance/map/).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007782"], "description"=>"<p>The <i>x</i>-axes represent the number of years since ARV scale-up for each isolate. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of years since ARV scale-up in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369595, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_sub_Saharan_Africa_/1369595", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in sub-Saharan Africa.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007783"], "description"=>"<p>The <i>x</i>-axes represent the number of years since ARV scale-up for each isolate. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of years since ARV scale-up in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369596, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_low_and_middle_income_countries_of_south_and_southeast_Asia_/1369596", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in low- and middle-income countries of south and southeast Asia.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007784"], "description"=>"<p>The <i>x</i>-axes represent the calendar year of the sample. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of sample year in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369597, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_Latin_America_Caribbean_/1369597", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in Latin America/Caribbean.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007785"], "description"=>"<p>The <i>x</i>-axes represent the calendar year of the sample. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of sample year in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369598, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_North_America_/1369598", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in North America.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007787"], "description"=>"<p>The <i>x</i>-axes represent the calendar year of the sample. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of sample year in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369600, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_upper_income_Asian_countries_/1369600", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in upper-income Asian countries.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007789"], "description"=>"<p>The <i>x</i>-axes represent the calendar year of the sample. The diameter of each circle is proportional to the number of samples sequenced that year. The fitted line shows the fixed effect of sample year in generalized linear mixed model regression.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369602, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_trends_in_the_yearly_proportion_of_individuals_having_one_or_more_surveillance_drug_resistance_mutations_in_Europe_and_Israel_/1369602", "title"=>"Temporal trends in the yearly proportion of individuals having one or more surveillance drug-resistance mutations in Europe (and Israel).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007791"], "description"=>"<p>The Spearman’s rank correlation coefficient (rho) and the <i>p-</i>value are shown in each plot. The number of isolates from NRTI-experienced individuals were 4,522, 2,218, 4,164, and 13,522 for SSA, SSEA, Latin America/Caribbean, and the pooled upper-income countries (UIC; Europe, North America, and upper-income Asian countries), respectively.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369604, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_prevalence_of_each_NRTI_associated_surveillance_drug_resistance_mutation_in_this_meta_analysis_versus_in_NRTI_experienced_individuals_in_the_same_regions_according_to_HIVDB_/1369604", "title"=>"The prevalence of each NRTI-associated surveillance drug-resistance mutation in this meta-analysis versus in NRTI-experienced individuals in the same regions according to HIVDB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007792"], "description"=>"<p>The Spearman’s rank correlation coefficient (rho) and the <i>p-</i>value are shown in each plot. The number of isolates from NNRTI-experienced individuals were 4,959, 1,994, 3,677, and 8,927 for SSA, SSEA, Latin America/Caribbean, and the pooled upper-income countries (UIC; Europe, North America, and upper-income Asian countries), respectively.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369605, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_prevalence_of_each_NNRTI_associated_surveillance_drug_resistance_mutation_in_this_meta_analysis_versus_in_NNRTI_experienced_individuals_in_the_same_regions_according_to_HIVDB_/1369605", "title"=>"The prevalence of each NNRTI-associated surveillance drug-resistance mutation in this meta-analysis versus in NNRTI-experienced individuals in the same regions according to HIVDB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007794"], "description"=>"<p>The Spearman’s rank correlation coefficient (rho) and the <i>p-</i>value are shown in each plot. The number of isolates from PI-experienced individuals were 717, 103, 4,107, and 9,985 for SSA, SSEA, Latin America/Caribbean, and the pooled upper-income countries (UIC; Europe, North America, and upper-income Asian countries), respectively.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369606, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_prevalence_of_each_PI_associated_surveillance_drug_resistance_mutation_in_this_meta_analysis_versus_in_PI_experienced_individuals_in_the_same_regions_according_to_HIVDB_/1369606", "title"=>"The prevalence of each PI-associated surveillance drug-resistance mutation in this meta-analysis versus in PI-experienced individuals in the same regions according to HIVDB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007796"], "description"=>"<p>HIVDB genotypic resistance interpretation program predictions of NRTI, NNRTI, and PI resistance for all virus samples using NRTI, NNRTI, and PI SDRMs, respectively (A). HIVDB program predictions of NRTI, NNRTI, and PI resistance in all samples without an SDRM (B). NRTIs: zidovudine (AZT), abacavir (ABC), lamivudine (3TC), and tenofovir (TDF); NNRTIs: nevirapine (NVP), efavirenz (EFV), rilpivirine (RPV), and etravirine (ETR); PIs: lopinavir (LPVr), atazanavir (ATVr), and darunavir (DRVr). UIC, upper-income countries.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369609, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.g012"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_levels_of_predicted_genotypic_drug_resistance_for_viruses_with_and_without_surveillance_drug_resistance_mutations_/1369609", "title"=>"Estimated levels of predicted genotypic drug resistance for viruses with and without surveillance drug-resistance mutations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007797"], "description"=>"<p>Latin America/Caribbean includes three studies from Caribbean countries. Three studies from North Africa and two studies from Australia are not included in this table but are summarized in <a href=\"http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001810#pmed.1001810.s004\" target=\"_blank\">S1 Table</a>. Country abbreviations: AR, Argentina; BR, Brazil; CA, Canada; CM, Cameroon; CN, China; EE, Estonia; ES, Spain; IN, India; IT, Italy; JP, Japan; KR, Republic of Korea; MX, Mexico; PR, Puerto Rico; RU, Russia; SE, Sweden; TW, Taiwan; UA, Ukraine; UG, Uganda; VN, Viet Nam; ZA, South Africa. Recruitment site abbreviations: ANC, antenatal clinics; BD, blood donation centers; HIVC, HIV clinics; STD, sexually transmitted disease clinics; TB, tuberculosis clinics; VCT, voluntary counseling and testing centers.</p><p>Epidemiologic characteristics in seven geo-economic regions.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369610, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Epidemiologic_characteristics_in_seven_geo_economic_regions_/1369610", "title"=>"Epidemiologic characteristics in seven geo-economic regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007798"], "description"=>"<p>Data are median (IQR) of study-level prevalence of individuals with any (overall) and NRTI-, NNRTI-, and PI-associated SDRMs by region; the number of studies conducted is indicated for each region (<i>n</i>). Latin America/Caribbean includes three studies from Caribbean countries. Three studies from North Africa and two studies from Australia are not included in this table but are summarized in <a href=\"http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.1001810#pmed.1001810.s004\" target=\"_blank\">S1 Table</a>.</p><p>Study-level estimates of transmitted drug resistance in seven geo-economic regions.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369611, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Study_level_estimates_of_transmitted_drug_resistance_in_seven_geo_economic_regions_/1369611", "title"=>"Study-level estimates of transmitted drug resistance in seven geo-economic regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007800"], "description"=>"<p>Three studies from North Africa and two studies from Australia were excluded. Latin America/Caribbean includes three studies from Caribbean countries.</p><p><sup>a</sup>For each region, a generalized linear mixed model was used to assess the yearly change in the odds (OR) of TDR accounting for study heterogeneity using the R package lme4. The model included a categorical outcome variable indicating the presence or absence of TDR and two explanatory variables: years since scale-up (or the sample year) as a fixed-effect term and the study as a random-effect term.</p><p><sup>b</sup>Yearly change in the odds of TDR since ARV scale-up in regions with national ARV scale-up programs and for each sample year in regions without national ARV scale-up; the number of individuals in each region (<i>n</i>) is indicated.</p><p>Yearly change in odds of transmitted drug resistance in generalized linear mixed regression models in geo-economic regions with and without ARV scale-up.</p>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369613, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Yearly_change_in_odds_of_transmitted_drug_resistance_in_generalized_linear_mixed_regression_models_in_geo_economic_regions_with_and_without_ARV_scale_up_/1369613", "title"=>"Yearly change in odds of transmitted drug resistance in generalized linear mixed regression models in geo-economic regions with and without ARV scale-up.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-07 03:56:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2007805", "https://ndownloader.figshare.com/files/2007806", "https://ndownloader.figshare.com/files/2007807", "https://ndownloader.figshare.com/files/2007809", "https://ndownloader.figshare.com/files/2007810", "https://ndownloader.figshare.com/files/2007811", "https://ndownloader.figshare.com/files/2007812", "https://ndownloader.figshare.com/files/2007813", "https://ndownloader.figshare.com/files/2007814", "https://ndownloader.figshare.com/files/2007815", "https://ndownloader.figshare.com/files/2007816", "https://ndownloader.figshare.com/files/2007817", "https://ndownloader.figshare.com/files/2007818"], "description"=>"<div><p>Background</p><p>Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes.</p><p>Methods and Findings</p><p>We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05–1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06–1.25), North America (OR = 1.19; 95% CI: 1.12–1.26), Europe (OR = 1.07; 95% CI: 1.01–1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12–1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92–1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions—a proxy for recent infection—yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs—K101E, K103N, Y181C, and G190A—accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling.</p><p>Conclusions</p><p>Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.</p></div>", "links"=>[], "tags"=>["transcriptase inhibitor", "19 sequence pairs", "Asian countries", "nnrti", "genotypic resistance testing", "sdrm", "nrti", "region", "ssa", "ci", "103N", "190A", "sampling.ConclusionsMost TDR strains", "hiv", "181C", "arv", "ssea"], "article_id"=>1369617, "categories"=>["Biological Sciences"], "users"=>["Soo-Yon Rhee", "Jose Luis Blanco", "Michael R. Jordan", "Jonathan Taylor", "Philippe Lemey", "Vici Varghese", "Raph L. Hamers", "Silvia Bertagnolio", "Tobias F. Rinke de Wit", "Avelin F. Aghokeng", "Jan Albert", "Radko Avi", "Santiago Ávila-Ríos", "Pascal O. Bessong", "James I. Brooks", "Charles A. B. Boucher", "Zabrina L. Brumme", "Michael P. Busch", "Hermann Bussmann", "Marie-Laure Chaix", "Bum Sik Chin", "Toni T. D’Aquin", "Cillian F. De Gascun", "Anne Derache", "Diane Descamps", "Alaka K. Deshpande", "Cyrille F. Djoko", "Susan H. Eshleman", "Hervé Fleury", "Pierre Frange", "Seiichiro Fujisaki", "P. Richard Harrigan", "Junko Hattori", "Africa Holguin", "Gillian M. Hunt", "Hiroshi Ichimura", "Pontiano Kaleebu", "David Katzenstein", "Sasisopin Kiertiburanakul", "Jerome H. Kim", "Sung Soon Kim", "Yanpeng Li", "Irja Lutsar", "Lynn Morris", "Nicaise Ndembi", "Kee Peng Ng", "Ramesh S. Paranjape", "Martine Peeters", "Mario Poljak", "Matt A. Price", "Manon L. Ragonnet-Cronin", "Gustavo Reyes-Terán", "Morgane Rolland", "Sunee Sirivichayakul", "Davey M. Smith", "Marcelo A. Soares", "Vincent V. Soriano", "Deogratius Ssemwanga", "Maja Stanojevic", "Mariane A. Stefani", "Wataru Sugiura", "Somnuek Sungkanuparph", "Amilcar Tanuri", "Kok Keng Tee", "Hong-Ha M. Truong", "David A. M. C. van de Vijver", "Nicole Vidal", "Chunfu Yang", "Rongge Yang", "Gonzalo Yebra", "John P. A. Ioannidis", "Anne-Mieke Vandamme", "Robert W. Shafer"], "doi"=>["https://dx.doi.org/10.1371/journal.pmed.1001810.s001", "https://dx.doi.org/10.1371/journal.pmed.1001810.s002", "https://dx.doi.org/10.1371/journal.pmed.1001810.s003", "https://dx.doi.org/10.1371/journal.pmed.1001810.s004", "https://dx.doi.org/10.1371/journal.pmed.1001810.s005", "https://dx.doi.org/10.1371/journal.pmed.1001810.s006", "https://dx.doi.org/10.1371/journal.pmed.1001810.s007", "https://dx.doi.org/10.1371/journal.pmed.1001810.s008", "https://dx.doi.org/10.1371/journal.pmed.1001810.s009", "https://dx.doi.org/10.1371/journal.pmed.1001810.s010", "https://dx.doi.org/10.1371/journal.pmed.1001810.s011", "https://dx.doi.org/10.1371/journal.pmed.1001810.s012", "https://dx.doi.org/10.1371/journal.pmed.1001810.s013"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_and_Temporal_Trends_in_the_Molecular_Epidemiology_and_Genetic_Mechanisms_of_Transmitted_HIV_1_Drug_Resistance_An_Individual_Patient_and_Sequence_Level_Meta_Analysis_/1369617", "title"=>"Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-07 03:56:10"}

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