{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T04:28:42Z","timestamp":1760243322290,"version":"build-2065373602"},"reference-count":167,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2014,9,24]],"date-time":"2014-09-24T00:00:00Z","timestamp":1411516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM105876","T32 AI083196"],"award-info":[{"award-number":["R01 GM105876","T32 AI083196"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Retrovirus population diversity within infected hosts is commonly high due in part to elevated rates of replication, mutation, and recombination. This high genetic diversity often complicates the development of effective diagnostics, vaccines, and antiviral drugs. This review highlights the diverse vectors and approaches that have been used to examine mutation and recombination in retroviruses. Retroviral vectors for these purposes can broadly be divided into two categories: those that utilize reporter genes as mutation or recombination targets and those that utilize viral genes as targets of mutation or recombination. Reporter gene vectors greatly facilitate the detection, quantification, and characterization of mutants and\/or recombinants, but may not fully recapitulate the patterns of mutagenesis or recombination observed in native viral gene sequences. In contrast, the detection of mutations or recombination events directly in viral genes is more biologically relevant but also typically more challenging and inefficient. We will highlight the advantages and disadvantages of the various vectors and approaches used as well as propose ways in which they could be improved.<\/jats:p>","DOI":"10.3390\/v6093612","type":"journal-article","created":{"date-parts":[[2014,9,24]],"date-time":"2014-09-24T08:58:34Z","timestamp":1411549114000},"page":"3612-3642","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Retroviral Vectors for Analysis of Viral Mutagenesis  and Recombination"],"prefix":"10.3390","volume":"6","author":[{"given":"Jonathan","family":"Rawson","sequence":"first","affiliation":[{"name":"Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242,  515 Delaware St SE, Minneapolis, MN 55455, USA"},{"name":"Molecular, Cellular, Developmental Biology & Genetics Graduate Program,  University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Louis","family":"Mansky","sequence":"additional","affiliation":[{"name":"Institute for Molecular Virology, University of Minnesota, Moos Tower 18-242,  515 Delaware St SE, Minneapolis, MN 55455, USA"},{"name":"Molecular, Cellular, Developmental Biology & Genetics Graduate Program,  University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA"},{"name":"Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware St SE, Minneapolis, MN 55455, USA"},{"name":"Department of Microbiology, University of Minnesota, 420 Delaware St SE, Minneapolis,  MN 55455, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2014,9,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.3390\/v3091650","article-title":"Mechanisms and factors that influence high frequency retroviral recombination","volume":"3","author":"Galli","year":"2011","journal-title":"Viruses"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1016\/j.virusres.2012.06.015","article-title":"The origin of genetic diversity in hiv-1","volume":"169","author":"Smyth","year":"2012","journal-title":"Virus Res."},{"doi-asserted-by":"crossref","unstructured":"Hu, W.S., and Hughes, S.H. 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