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Despite this, the magnitude of this population bottleneck is unclear.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We use coalescent methods to quantify the bottleneck in a single case of homosexual transmission and find that over 99% of the<jats:italic>env<\/jats:italic>and<jats:italic>gag<\/jats:italic>diversity present in the donor is lost. This was consistent with the diversity present at seroconversion in nine other horizontally infected individuals. Furthermore, we estimated viral diversity at birth in 27 infants infected through vertical transmission and found there to be no difference between the two modes of transmission.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Assuming the bottleneck at transmission is selectively neutral, such a severe reduction in genetic diversity has important implications for adaptation in HIV-1, since beneficial mutations have a reduced chance of transmission.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2148-6-28","type":"journal-article","created":{"date-parts":[[2006,4,6]],"date-time":"2006-04-06T12:49:20Z","timestamp":1144327760000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":61,"title":["Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1"],"prefix":"10.1186","volume":"6","author":[{"given":"Charles TT","family":"Edwards","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edward C","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel J","family":"Wilson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raphael P","family":"Viscidi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elaine J","family":"Abrams","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodney E","family":"Phillips","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexei J","family":"Drummond","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,3,23]]},"reference":[{"key":"213_CR1","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1097\/00002030-200201250-00007","volume":"16","author":"E Delwart","year":"2002","unstructured":"Delwart E, Magierowska M, Royz M, Foley B, Peddada L, Smith R, Heldebrant C, Conrad A, Busch M: Homogeneous quasispecies in 16 out of 17 individuals during very early HIV-1 primary infection. 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