{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T17:40:42Z","timestamp":1775151642887,"version":"3.50.1"},"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2014,1,9]],"date-time":"2014-01-09T00:00:00Z","timestamp":1389225600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003430","type":"journal-article","created":{"date-parts":[[2014,1,9]],"date-time":"2014-01-09T21:21:34Z","timestamp":1389302494000},"page":"e1003430","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data"],"prefix":"10.1371","volume":"10","author":[{"given":"Nicole Bohme","family":"Carnegie","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rui","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vladimir","family":"Novitsky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"De Gruttola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2014,1,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1097\/00002030-200111230-00010","article-title":"Acute HIV infection: impact on the spread of HIV and transmission of drug resistance","volume":"15","author":"S Yerly","year":"2001","journal-title":"AIDS"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1097\/QAD.0b013e3283121c90","article-title":"Transmission networks of drug resistance acquired in primary\/early stage HIV infection","volume":"22","author":"BG Brenner","year":"2008","journal-title":"AIDS"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e1000590","DOI":"10.1371\/journal.ppat.1000590","article-title":"Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom","volume":"5","author":"GJ Hughes","year":"2009","journal-title":"PLoS Pathogens"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1097\/QAD.0b013e32831d2a81","article-title":"A public health model for the molecular surveillance of HIV transmission in San Diego, California","volume":"23","author":"DM Smith","year":"2009","journal-title":"AIDS"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/cid\/cis612","article-title":"Characterizing HIV trans- mission networks across the United States","volume":"55","author":"JL Aldous","year":"2012","journal-title":"Clinical Infectious Diseases"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1093\/infdis\/jis231","article-title":"Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California","volume":"205","author":"SR Mehta","year":"2012","journal-title":"Journal of Infectious Diseases"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"e1002552","DOI":"10.1371\/journal.pcbi.1002552","article-title":"Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection","volume":"8","author":"EM Volz","year":"2012","journal-title":"PLoS Computational Biology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1097\/QAD.0b013e32835cffd9","article-title":"Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions","volume":"27","author":"B Brenner","year":"2013","journal-title":"AIDS"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1186\/1471-2334-10-262","article-title":"Epidemiological study of phylogenetic transmission clusters in a local HIV-1 epidemic reveals distinct differences between subtype B and non-B infections","volume":"10","author":"K Chalmet","year":"2010","journal-title":"BMC Infectious Diseases"},{"key":"ref10","unstructured":"Datz T (2011) Harvard School of Public Health awarded $20 million CDC grant to study HIV prevention in Botswana. HSPH News September 20, 2011."},{"key":"ref11","first-page":"1","article-title":"Sample size considerations in the design of cluster randomized trials of combination HIV prevention","volume":"161","author":"R Wang","year":"2013","journal-title":"Harvard University BiostatisticsWorking Paper Series"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1093\/biomet\/85.2.487","article-title":"A note on generating correlated binary variables","volume":"85","author":"A Lunn","year":"1998","journal-title":"Biometrika"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1126\/science.8235655","article-title":"Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes","volume":"262","author":"EL Delwart","year":"1993","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.virol.2008.09.017","article-title":"Evolution of proviral gp120 over the first year of HIV-1 subtype C infection","volume":"383","author":"V Novitsky","year":"2009","journal-title":"Virology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"ref17","first-page":"235","article-title":"Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees","volume":"13","author":"A Rambaut","year":"1997","journal-title":"Computational Applied Biosciences"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Molecular Biology and Evolution"},{"key":"ref19","unstructured":"R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.R-project.org\" xlink:type=\"simple\">http:\/\/www.R-project.org<\/ext-link>. ISBN 3-900051-07-0."},{"key":"ref20","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"E Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e10148","DOI":"10.1371\/journal.pone.0010148","article-title":"HIV-1 subtype C-infected individuals maintaining high viral load as potential targets for the test-and-treat approach to reduce HIV transmission","volume":"5","author":"V Novitsky","year":"2010","journal-title":"PLoS ONE"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1080\/106351598260897","article-title":"Phylogenetic analysis and intraspecific variation: Performance of parsimony, likelihood, and distance methods","volume":"47","author":"JJ Wiens","year":"1998","journal-title":"Systematic Biology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e1001250","DOI":"10.1371\/journal.pmed.1001250","article-title":"HIV treatment as prevention: considerations in the design, conduct, and analysis of cluster randomized controlled trials of combination HIV prevention","volume":"9","author":"MC Boily","year":"2012","journal-title":"PLoS Medicine"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003430","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T19:19:51Z","timestamp":1539976791000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003430"}},"subtitle":[],"editor":[{"given":"Christophe","family":"Fraser","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,1,9]]},"references-count":23,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,1,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003430","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,9]]}}}