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Here, we describe the in-depth analysis of HIV-1 over time in a patient twice superinfected with HIV-1, first with a subtype B (B2) strain and then with CRF01_AE after initial infection with a subtype B (B1) strain.<\/jats:p>\n          <jats:p>The nucleotide evolution of <jats:italic>gag<\/jats:italic> and <jats:italic>env<\/jats:italic>-V3 of the three strains followed a similar pattern: a very low substitution rate in the first 2\u20133 years of infection, with an increase in synonymous substitutions thereafter. Convergent evolution at the protein level was rare: only a single amino acid in a <jats:italic>gag<\/jats:italic> p24 epitope showed convergence in the subtype B strains. Reversal of CTL-epitope mutations were also rare, and did not converge. Recombinant viruses were observed between the two subtype B strains. Luciferase-assays suggested that the CRF01_AE long terminal repeat (LTR) constituted the strongest promoter, but this was not reflected in the plasma viral load. Specific real-time PCR assays based upon the <jats:italic>env<\/jats:italic> gene showed that strain B2 and CRF01_AE RNA was present in equal amounts, while levels of strain B1 were 100-fold lower.<\/jats:p>\n          <jats:p>All three strains were detected in seminal plasma, suggesting that simultaneous transmission is possible.<\/jats:p>","DOI":"10.1186\/1742-4690-4-59","type":"journal-article","created":{"date-parts":[[2007,8,23]],"date-time":"2007-08-23T18:13:13Z","timestamp":1187892793000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["HIV-1 sequence evolution in vivo after superinfection with three viral strains"],"prefix":"10.1186","volume":"4","author":[{"given":"Karolina","family":"Kozaczynska","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marion","family":"Cornelissen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Reiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fokla","family":"Zorgdrager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antoinette C","family":"van der Kuyl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,8,23]]},"reference":[{"key":"788_CR1","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/418144a","volume":"418","author":"A Jung","year":"2002","unstructured":"Jung A, Maier R, Vartanian JP, Bocharov G, Jung V, Fischer U, Meese E, Wain-Hobson S, Meyerhans A: Multiply infected spleen cells in HIV patients. 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