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We optimised a multiassay algorithm (MAA) and assessed HIV incidence, correlates of recent infections, viral diversity, plus transmission clusters among participants screened for Kisumu Incidence Cohort Study (KICoS1) (2007\u20132009). We performed BED-CEIA, Limiting antigen (LAg) avidity, Biorad avidity, and viral load (VL) tests on HIV-positive samples. Genotypic analyses focused on HIV-1 <jats:italic>pol<\/jats:italic> gene. Correlates of testing recent by MAA were assessed using logistic regression model. Overall, 133 (12%, 95% CI: 10.2\u201314.1) participants were HIV-positive, of whom 11 tested recent by MAA (BED-CEIA OD-n\u2009&lt;\u20090.8\u2009+\u2009LAg avidity OD-n\u2009&lt;\u20091.5\u2009+\u2009VL\u2009&gt;\u20091000 copies\/mL), giving an incidence of 1.46% (95% CI: 0.58\u20132.35) per year. This MAA-based incidence was similar to longitudinal KICoS1 incidence. Correlates of testing recent included sexually transmitted infection (STI) treatment history (OR\u2009=\u20093.94, 95% CI: 1.03\u201315.07) and syphilis seropositivity (OR\u2009=\u200910.15, 95% CI: 1.51\u201368.22). Overall, HIV-1 subtype A (63%), D (15%), C (3%), G (1%) and recombinants (18%), two monophyletic dyads and intrinsic viral mutations (V81I, V81I\/V, V108I\/V and K101Q) were observed. Viral diversity mirrored known patterns in this region, while resistance mutations reflected likely non-exposure to antiretroviral drugs. Management of STIs may help address ongoing HIV transmission in this region.<\/jats:p>","DOI":"10.1038\/srep37964","type":"journal-article","created":{"date-parts":[[2016,11,29]],"date-time":"2016-11-29T10:28:21Z","timestamp":1480415301000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Viral and Host Characteristics of Recent and Established HIV-1 Infections in Kisumu based on a Multiassay Approach"],"prefix":"10.1038","volume":"6","author":[{"given":"Newton","family":"Otecko","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seth","family":"Inzaule","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Collins","family":"Odhiambo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valarie","family":"Opollo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Morwabe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kennedy","family":"Were","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth","family":"Ndiege","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fredrick","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea A.","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clement","family":"Zeh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,11,29]]},"reference":[{"key":"BFsrep37964_CR1","unstructured":"UNAIDS. 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