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The<jats:italic>nef<\/jats:italic>locus also represents one of the most genetically variable regions in the HIV genome, and<jats:italic>nef<\/jats:italic>sequences undergo substantial evolution within a single individual over the course of infection. Few studies however have simultaneously characterized the impact of within-host<jats:italic>nef<\/jats:italic>sequence evolution on Nef protein function over prolonged timescales. Here, we isolated 50 unique Nef clones by single-genome amplification over an 11-year period from the plasma of an individual who was largely na\u00efve to antiretroviral treatment during this time. Together, these clones harbored nonsynonymous substitutions at 13% of<jats:italic>nef\u2019<\/jats:italic>s codons. We assessed their ability to downregulate cell-surface CD4, HLA and SERINC5 and observed that all three Nef functions declined modestly over time, where the reductions in CD4 and HLA downregulation (an average of 0.6% and 2.0% per year, respectively) achieved statistical significance. The results from this case study support all three Nef activities as being important to maintain throughout untreated HIV infection, but nevertheless suggest that, despite<jats:italic>nef\u2019<\/jats:italic>s mutational plasticity, within-host viral evolution can compromise Nef function, albeit modestly, over prolonged periods.<\/jats:p>","DOI":"10.1186\/s12977-019-0510-1","type":"journal-article","created":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T15:02:57Z","timestamp":1578582177000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study"],"prefix":"10.1186","volume":"17","author":[{"given":"Hanwei","family":"Sudderuddin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie N.","family":"Kinloch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven W.","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel L.","family":"Miller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bradley R.","family":"Jones","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chanson J.","family":"Brumme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey B.","family":"Joy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark A.","family":"Brockman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8157-1037","authenticated-orcid":false,"given":"Zabrina L.","family":"Brumme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,1,9]]},"reference":[{"issue":"3","key":"510_CR1","first-page":"125","volume":"8","author":"P Lemey","year":"2006","unstructured":"Lemey P, Rambaut A, Pybus OG. 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