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The country\u2019s primary challenge is identifying people living with HIV who are unaware of their status. We evaluated factors associated with undiagnosed HIV infection using HIV-1 phylogenetic, behavioural, and demographic data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>As part of the Botswana Combination Prevention Project, 20% of households in 30 villages were tested for HIV and followed from 2013 to 2018. A total of 12,610 participants were enrolled, 3596 tested HIV-positive at enrolment, and 147 participants acquired HIV during the trial. Extensive socio-demographic and behavioural data were collected from participants and next-generation sequences were generated for HIV-positive cases. We compared three groups of participants: (1) those previously known to be HIV-positive at enrolment (n\u2009=\u20092995); (2) those newly diagnosed at enrolment (n\u2009=\u2009601) and (3) those who tested HIV-negative at enrolment but tested HIV-positive during follow-up (n\u2009=\u2009147). We searched for differences in demographic and behavioural factors between known and newly diagnosed group using logistic regression. We also compared the topology of each group in HIV-1 phylogenies and used a genetic diversity-based algorithm to classify infections as recent (&lt;\u20091\u00a0year) or chronic (\u2265\u20091\u00a0year).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Being male (aOR\u2009=\u20092.23) and younger than 35\u00a0years old (aOR\u2009=\u20098.08) was associated with undiagnosed HIV infection (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.001), as was inconsistent condom use (aOR\u2009=\u20091.76). Women were more likely to have undiagnosed infections if they were married, educated, and tested frequently. For men, being divorced increased their risk. The genetic diversity-based algorithm classified most incident infections as recent (75.0%), but almost none of known infections (2.0%). The estimated proportion of recent infections among new diagnoses was 37.0% (<jats:italic>p<\/jats:italic>\u2009&lt;\u20090.001).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Our results indicate that those with undiagnosed infections are likely to be young men and women who do not use condoms consistently. Among women, several factors were predictive: being married, educated, and testing frequently increased risk. Men at risk were more difficult to delineate. A sizeable proportion of undiagnosed infections were recent based on a genetic diversity-based classifier. In the era of \u201ctest and treat all\u201d, pre-exposure prophylaxis may be prioritized towards individuals who self-identify or who can be identified using these predictors in order to halt onward transmission in time.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12879-022-07698-4","type":"journal-article","created":{"date-parts":[[2022,8,28]],"date-time":"2022-08-28T07:02:32Z","timestamp":1661670152000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Epidemiological and viral characteristics of undiagnosed HIV infections in Botswana"],"prefix":"10.1186","volume":"22","author":[{"given":"Lynnette","family":"Bhebhe","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sikhulile","family":"Moyo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simani","family":"Gaseitsiwe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Molly","family":"Pretorius-Holme","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Etienne K.","family":"Yankinda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kutlo","family":"Manyake","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Coulson","family":"Kgathi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mompati","family":"Mmalane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Refeletswe","family":"Lebelonyane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tendani","family":"Gaolathe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pamela","family":"Bachanas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Faith","family":"Ussery","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mpho","family":"Letebele","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"Makhema","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kathleen E.","family":"Wirth","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shahin","family":"Lockman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Max","family":"Essex","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vlad","family":"Novitsky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manon","family":"Ragonnet-Cronin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,8,28]]},"reference":[{"issue":"6","key":"7698_CR1","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1097\/COH.0000000000000580","volume":"14","author":"M Essex","year":"2019","unstructured":"Essex M, Makhema J, Lockman S. 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Demography. 2008;45(2):303\u201322.","journal-title":"Demography"}],"container-title":["BMC Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12879-022-07698-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12879-022-07698-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12879-022-07698-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,28]],"date-time":"2022-08-28T08:05:19Z","timestamp":1661673919000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcinfectdis.biomedcentral.com\/articles\/10.1186\/s12879-022-07698-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,8,28]]},"references-count":51,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["7698"],"URL":"https:\/\/doi.org\/10.1186\/s12879-022-07698-4","relation":{},"ISSN":["1471-2334"],"issn-type":[{"type":"electronic","value":"1471-2334"}],"subject":[],"published":{"date-parts":[[2022,8,28]]},"assertion":[{"value":"14 March 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 August 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 August 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The BCPP study was approved by the Human Research Development Committee (HPDME 13\/18\/1) (the Institutional Review Board based at the Botswana Ministry of Health and Wellness), and the US Centers for Disease Control and Prevention (Protocol 6475). The study is registered at ClinicalTrials.gov (NCT01965470). All participants provided written informed consent and participants aged 16 to 18\u00a0years provided written assent (with parental or guardian written permission). The data collection procedures were performed in accordance with the Declaration of Helsinki.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"SM is an editorial Board Member for BMC Infectious Diseases. All other authors report no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"710"}}