{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T21:03:55Z","timestamp":1774559035533,"version":"3.50.1"},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,11,16]],"date-time":"2015-11-16T00:00:00Z","timestamp":1447632000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2015,11,16]],"date-time":"2015-11-16T00:00:00Z","timestamp":1447632000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI097265"],"award-info":[{"award-number":["R01AI097265"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["F32-AI108414"],"award-info":[{"award-number":["F32-AI108414"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Retrovirology"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12977-015-0222-0","type":"journal-article","created":{"date-parts":[[2015,11,16]],"date-time":"2015-11-16T13:50:33Z","timestamp":1447681833000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission"],"prefix":"10.1186","volume":"12","author":[{"given":"Keri B.","family":"Sanborn","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohan","family":"Somasundaran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katherine","family":"Luzuriaga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,11,16]]},"reference":[{"issue":"21","key":"222_CR1","doi-asserted-by":"publisher","first-page":"10674","DOI":"10.1128\/JVI.76.21.10674-10684.2002","volume":"76","author":"SL Liu","year":"2002","unstructured":"Liu SL, Mittler JE, Nickle DC, Mulvania TM, Shriner D, Rodrigo AG, Kosloff B, He X, Corey L, Mullins JI. Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS. J Virol. 2002;76(21):10674\u201384.","journal-title":"J Virol"},{"issue":"5","key":"222_CR2","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1128\/JVI.80.5.2472-2482.2006","volume":"80","author":"C Charpentier","year":"2006","unstructured":"Charpentier C, Nora T, Tenaillon O, Clavel F, Hance AJ. Extensive recombination among human immunodeficiency virus type 1 quasispecies makes an important contribution to viral diversity in individual patients. J Virol. 2006;80(5):2472\u201382.","journal-title":"J Virol"},{"issue":"4","key":"222_CR3","doi-asserted-by":"publisher","first-page":"1573","DOI":"10.1534\/genetics.103.023382","volume":"167","author":"D Shriner","year":"2004","unstructured":"Shriner D, Rodrigo AG, Nickle DC, Mullins JI. Pervasive genomic recombination of HIV-1 in vivo. Genetics. 2004;167(4):1573\u201383.","journal-title":"Genetics"},{"issue":"12","key":"222_CR4","doi-asserted-by":"publisher","first-page":"4204","DOI":"10.1073\/pnas.0306764101","volume":"101","author":"DN Levy","year":"2004","unstructured":"Levy DN, Aldrovandi GM, Kutsch O, Shaw GM. Dynamics of HIV-1 recombination in its natural target cells. Proc Natl Acad Sci USA. 2004;101(12):4204\u20139.","journal-title":"Proc Natl Acad Sci USA"},{"key":"222_CR5","doi-asserted-by":"publisher","first-page":"e1000660","DOI":"10.1371\/journal.pcbi.1000660","volume":"6","author":"RA Neher","year":"2010","unstructured":"Neher RA, Leitner T. Recombination rate and selection strength in HIV intra-patient evolution. PLoS Comput Biol. 2010;6:e1000660.","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"222_CR6","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1016\/j.ympev.2008.08.017","volume":"49","author":"M Salemi","year":"2008","unstructured":"Salemi M, Gray RR, Goodenow MM. An exploratory algorithm to identify intra-host recombinant viral sequences. Mol Phylogenet Evol. 2008;49(2):618\u201328.","journal-title":"Mol Phylogenet Evol"},{"key":"222_CR7","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1017\/S0016672300023958","volume":"51","author":"J Maynard Smith","year":"1988","unstructured":"Maynard Smith J. Selection for recombination in a polygenic model: the mechanism. Genet Res. 1988;51:59\u201363.","journal-title":"Genet Res"},{"issue":"5","key":"222_CR8","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1093\/oxfordjournals.jhered.a111358","volume":"84","author":"AS Kondrashov","year":"1993","unstructured":"Kondrashov AS. Classification of hypotheses on the advantage of amphimixis. J Hered. 1993;84(5):372\u201387.","journal-title":"J Hered"},{"issue":"5385","key":"222_CR9","doi-asserted-by":"publisher","first-page":"1986","DOI":"10.1126\/science.281.5385.1986","volume":"281","author":"NH Barton","year":"1998","unstructured":"Barton NH, Charlesworth B. Why sex and recombination? Science. 1998;281(5385):1986\u201390.","journal-title":"Science"},{"issue":"8","key":"222_CR10","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nrmicro2614","volume":"9","author":"E Simon-Loriere","year":"2011","unstructured":"Simon-Loriere E, Holmes EC. Why do RNA viruses recombine? Nat Rev Microbiol. 2011;9(8):617\u201326.","journal-title":"Nat Rev Microbiol"},{"key":"222_CR11","doi-asserted-by":"crossref","DOI":"10.5962\/bhl.title.27468","volume-title":"The general theory of natural selection","author":"RA Fisher","year":"1930","unstructured":"Fisher RA. The general theory of natural selection. Oxford: Clarendon; 1930."},{"key":"222_CR12","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1086\/280418","volume":"66","author":"HJ Muller","year":"1932","unstructured":"Muller HJ. Some aspects of sex. Am Nat. 1932;66:118\u201338.","journal-title":"Am Nat"},{"key":"222_CR13","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1086\/282389","volume":"99","author":"JF Crow","year":"1965","unstructured":"Crow JF, Kimura M. Evolution in sexual and asexual populations. Am Nat. 1965;99:439\u201350.","journal-title":"Am Nat"},{"issue":"2","key":"222_CR14","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1093\/genetics\/78.2.737","volume":"78","author":"J Felsenstein","year":"1974","unstructured":"Felsenstein J. The evolutionary advantage of recombination. Genetics. 1974;78(2):737\u201356.","journal-title":"Genetics"},{"issue":"3","key":"222_CR15","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.meegid.2008.01.002","volume":"8","author":"RE Michod","year":"2008","unstructured":"Michod RE, Bernstein H, Nedelcu AM. Adaptive value of sex in microbial pathogens. Infect Genet Evol. 2008;8(3):267\u201385.","journal-title":"Infect Genet Evol"},{"issue":"21","key":"222_CR16","doi-asserted-by":"publisher","first-page":"12089","DOI":"10.1073\/pnas.211214298","volume":"98","author":"FA Kondrashov","year":"2001","unstructured":"Kondrashov FA, Kondrashov AS. Multidimensional epistasis and the disadvantage of sex. Proc Natl Acad Sci USA. 2001;98(21):12089\u201392.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"222_CR17","doi-asserted-by":"publisher","first-page":"e1004439","DOI":"10.1371\/journal.pgen.1004439","volume":"10","author":"D Moradigaravand","year":"2014","unstructured":"Moradigaravand D, Kouyos R, Hinkley T, Haddad M, Petropoulos CJ, Engelstadter J, Bonhoeffer S. Recombination accelerates adaptation on a large-scale empirical fitness landscape in HIV-1. PLoS Genet. 2014;10(6):e1004439.","journal-title":"PLoS Genet"},{"key":"222_CR18","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/BF00170462","volume":"37","author":"EG Shpaer","year":"1993","unstructured":"Shpaer EG, Mullins JI. Rates of amino acid change in the envelope protein correlate with pathogenicity of primate lentiviruses. J Mol Evol. 1993;37:57\u201365.","journal-title":"J Mol Evol"},{"key":"222_CR19","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1126\/science.1546316","volume":"255","author":"SM Wolinsky","year":"1992","unstructured":"Wolinsky SM, Wike CM, Korber BTM, Hutto C, Parks WP, Rosenblum LL, Kunstman KJ, Furtado MR, Munoz JL. Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science. 1992;255:1134\u20137.","journal-title":"Science"},{"issue":"5125","key":"222_CR20","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1126\/science.8356453","volume":"261","author":"T Zhu","year":"1993","unstructured":"Zhu T, Mo H, Wang N, Nam DS, Cao Y, Koup RA, Ho DD. Genotypic and phenotypic characterization of HIV-1 patients with primary infection. Science. 1993;261(5125):1179\u201381.","journal-title":"Science"},{"key":"222_CR21","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1073\/pnas.90.5.1721","volume":"90","author":"G Scarlatti","year":"1993","unstructured":"Scarlatti G, Leitner T, Halapi E, Wahlberg J, Marchisio P, Clerici-Schoeller MA, Wigzell H, Feny\u00f6 EM, Albert J, Uhl\u00e9n M, et al. Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers. Proc Natl Acad Sci USA. 1993;90:1721\u20135.","journal-title":"Proc Natl Acad Sci USA"},{"key":"222_CR22","doi-asserted-by":"crossref","first-page":"10489","DOI":"10.1128\/JVI.73.12.10489-10502.1999","volume":"73","author":"R Shankarappa","year":"1999","unstructured":"Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol. 1999;73:10489\u2013502.","journal-title":"J Virol"},{"issue":"12","key":"222_CR23","doi-asserted-by":"publisher","first-page":"e1000240","DOI":"10.1371\/journal.pcbi.1000240","volume":"4","author":"HY Lee","year":"2008","unstructured":"Lee HY, Perelson AS, Park SC, Leitner T. Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput Biol. 2008;4(12):e1000240.","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"222_CR24","doi-asserted-by":"publisher","first-page":"e21747","DOI":"10.1371\/journal.pone.0021747","volume":"6","author":"H Skar","year":"2011","unstructured":"Skar H, Gutenkunst RN, Wilbe Ramsay K, Alaeus A, Albert J, Leitner T. Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality. PLoS One. 2011;6(8):e21747.","journal-title":"PLoS One"},{"issue":"1","key":"222_CR25","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1128\/JVI.71.1.663-677.1997","volume":"71","author":"S Ganeshan","year":"1997","unstructured":"Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol. 1997;71(1):663\u201377.","journal-title":"J Virol"},{"key":"222_CR26","doi-asserted-by":"publisher","first-page":"1709","DOI":"10.1097\/00002030-199714000-00007","volume":"11","author":"E Halapi","year":"1997","unstructured":"Halapi E, Leitner T, Jansson M, Scarlatti G, Orlandi P, Plebani A, Romiti L, Albert J, Wigzell H, Rossi P. Correlation between HIV sequence evolution, specific immune response and clinical outcome in vertically infected infants. AIDS. 1997;11:1709\u201317.","journal-title":"AIDS"},{"issue":"3","key":"222_CR27","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1093\/molbev\/msi029","volume":"22","author":"S Williamson","year":"2005","unstructured":"Williamson S, Perry SM, Bustamante CD, Orive ME, Stearns MN, Kelly JK. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol Biol Evol. 2005;22(3):456\u201368.","journal-title":"Mol Biol Evol"},{"issue":"10","key":"222_CR28","doi-asserted-by":"crossref","first-page":"7498","DOI":"10.1128\/JVI.71.10.7498-7508.1997","volume":"71","author":"EL Delwart","year":"1997","unstructured":"Delwart EL, Pan H, Sheppard HW, Wolpert D, Neumann AU, Korber B, Mullins JI. Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J Virol. 1997;71(10):7498\u2013508.","journal-title":"J Virol"},{"key":"222_CR29","doi-asserted-by":"publisher","first-page":"9434","DOI":"10.1073\/pnas.89.20.9434","volume":"89","author":"T Shioda","year":"1992","unstructured":"Shioda T, Levy JA, Cheng-Mayer C. Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci USA. 1992;89:9434\u20138.","journal-title":"Proc Natl Acad Sci USA"},{"key":"222_CR30","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1126\/science.272.5261.537","volume":"272","author":"SM Wolinsky","year":"1996","unstructured":"Wolinsky SM, Korber BTM, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT, et al. Adaptive evolution of human immunodeficiency virus type1 during the natural course of infection. Science. 1996;272:537\u201342.","journal-title":"Science"},{"issue":"5728","key":"222_CR31","doi-asserted-by":"publisher","first-page":"1582","DOI":"10.1126\/science.1112489","volume":"308","author":"TC Quinn","year":"2005","unstructured":"Quinn TC, Overbaugh J. HIV\/AIDS in women: an expanding epidemic. Science. 2005;308(5728):1582\u20133.","journal-title":"Science"},{"issue":"1","key":"222_CR32","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s12977-014-0081-0","volume":"11","author":"TT Immonen","year":"2014","unstructured":"Immonen TT, Leitner T. Reduced evolutionary rates in HIV-1 reveal extensive latency periods among replicating lineages. Retrovirology. 2014;11(1):81.","journal-title":"Retrovirology"},{"issue":"4","key":"222_CR33","doi-asserted-by":"publisher","first-page":"2665","DOI":"10.1534\/genetics.105.048975","volume":"172","author":"TC Bruen","year":"2006","unstructured":"Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172(4):2665\u201381.","journal-title":"Genetics"},{"key":"222_CR34","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1126\/science.1083338","volume":"300","author":"D Lecossier","year":"2003","unstructured":"Lecossier D, Bouchonnet F, Clavel F, Hance AJ. Hypermutation of HIV-1 DNA in the absence of the Vif protein. Science. 2003;300:1112.","journal-title":"Science"},{"key":"222_CR35","doi-asserted-by":"publisher","first-page":"1385","DOI":"10.1016\/j.cub.2004.06.050","volume":"14","author":"M Liddament","year":"2004","unstructured":"Liddament M, Brown W, Schumacher A, Harris R. APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr Biol. 2004;14:1385\u201391.","journal-title":"Curr Biol"},{"key":"222_CR36","doi-asserted-by":"publisher","first-page":"10752","DOI":"10.1073\/pnas.96.19.10752","volume":"96","author":"T Leitner","year":"1999","unstructured":"Leitner T, Albert J. The molecular clock of HIV-1 unveiled through analysis of a known transmission history. Proc Natl Acad Sci USA. 1999;96:10752\u20137.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"222_CR37","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.1093\/molbev\/msu179","volume":"31","author":"E Romero-Severson","year":"2014","unstructured":"Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol. 2014;31(9):2472\u201382.","journal-title":"Mol Biol Evol"},{"key":"222_CR38","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/1742-4690-8-67","volume":"8","author":"M Kishko","year":"2011","unstructured":"Kishko M, Somasundaran M, Brewster F, Sullivan JL, Clapham PR, Luzuriaga K. Genotypic and functional properties of early infant HIV-1 envelopes. Retrovirology. 2011;8:67.","journal-title":"Retrovirology"},{"issue":"6","key":"222_CR39","doi-asserted-by":"publisher","first-page":"1273","DOI":"10.1084\/jem.20090378","volume":"206","author":"JF Salazar-Gonzalez","year":"2009","unstructured":"Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, et al. Genetic identity, biological phenotype, and evolutionary pathways of transmitted\/founder viruses in acute and early HIV-1 infection. J Exp Med. 2009;206(6):1273\u201389.","journal-title":"J Exp Med"},{"issue":"5666","key":"222_CR40","doi-asserted-by":"publisher","first-page":"2019","DOI":"10.1126\/science.1093137","volume":"303","author":"CA Derdeyn","year":"2004","unstructured":"Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science. 2004;303(5666):2019\u201322.","journal-title":"Science"},{"issue":"6","key":"222_CR41","doi-asserted-by":"publisher","first-page":"578","DOI":"10.2174\/157016207782418461","volume":"5","author":"CA Blish","year":"2007","unstructured":"Blish CA, Blay WM, Haigwood NL, Overbaugh J. Transmission of HIV-1 in the face of neutralizing antibodies. Curr HIV Res. 2007;5(6):578\u201387.","journal-title":"Curr HIV Res"},{"issue":"4","key":"222_CR42","doi-asserted-by":"publisher","first-page":"e1000365","DOI":"10.1371\/journal.ppat.1000365","volume":"5","author":"RM Troyer","year":"2009","unstructured":"Troyer RM, McNevin J, Liu Y, Zhang SC, Krizan RW, Abraha A, Tebit DM, Zhao H, Avila S, Lobritz MA, et al. Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog. 2009;5(4):e1000365.","journal-title":"PLoS Pathog"},{"issue":"2","key":"222_CR43","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1128\/JVI.69.2.669-674.1995","volume":"69","author":"P Kellam","year":"1995","unstructured":"Kellam P, Larder BA. Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance. J Virol. 1995;69(2):669\u201374.","journal-title":"J Virol"},{"issue":"12","key":"222_CR44","doi-asserted-by":"publisher","first-page":"6106","DOI":"10.1073\/pnas.93.12.6106","volume":"93","author":"L Moutouh","year":"1996","unstructured":"Moutouh L, Corbeil J, Richman DD. Recombination leads to the rapid emergence of HIV-1 dually resistant mutants under selective drug pressure. Proc Natl Acad Sci USA. 1996;93(12):6106\u201311.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"Pt 10","key":"222_CR45","doi-asserted-by":"publisher","first-page":"2601","DOI":"10.1099\/0022-1317-76-10-2601","volume":"76","author":"Z Gu","year":"1995","unstructured":"Gu Z, Gao Q, Faust EA, Wainberg MA. Possible involvement of cell fusion and viral recombination in generation of human immunodeficiency virus variants that display dual resistance to AZT and 3TC. J Gen Virol. 1995;76(Pt 10):2601\u20135.","journal-title":"J Gen Virol"},{"key":"222_CR46","first-page":"143","volume":"176","author":"J Coffin","year":"1992","unstructured":"Coffin J. Genetic diveristy and evolution of retroviruses. Curr Top Microbiol Immunol. 1992;176:143\u201364.","journal-title":"Curr Top Microbiol Immunol"},{"key":"222_CR47","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1126\/science.3008335","volume":"232","author":"J Coffin","year":"1986","unstructured":"Coffin J, Hasse A, Levy JA, Montagnier L, Oroszlan S, Teich N, Temin H, Toyoshima K, Varmus H, Weiss R. Human immunodeficiency viruses. Science. 1986;232:697.","journal-title":"Science"},{"key":"222_CR48","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1038\/374124b0","volume":"374","author":"DL Robertson","year":"1995","unstructured":"Robertson DL, Sharp PM, McCutchan FE, Hahn BH. Recombination in HIV-1. Nature. 1995;374:124\u20136.","journal-title":"Nature"},{"issue":"1","key":"222_CR49","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1006\/viro.1995.1237","volume":"209","author":"T Leitner","year":"1995","unstructured":"Leitner T, Escanilla D, Marquina S, Wahlberg J, Brostrom C, Hansson HB, Uhlen M, Albert J. Biological and molecular characterization of subtype D, G, and A\/D recombinant HIV-1 transmissions in Sweden. Virology. 1995;209(1):136\u201346.","journal-title":"Virology"},{"key":"222_CR50","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/1742-4690-7-25","volume":"7","author":"M Zhang","year":"2010","unstructured":"Zhang M, Foley B, Schultz AK, Macke JP, Bulla I, Stanke M, Morgenstern B, Korber B, Leitner T. The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology. 2010;7:25.","journal-title":"Retrovirology"},{"issue":"12","key":"222_CR51","doi-asserted-by":"publisher","first-page":"6024","DOI":"10.1128\/JVI.00131-11","volume":"85","author":"RJ Brown","year":"2011","unstructured":"Brown RJ, Peters PJ, Caron C, Gonzalez-Perez MP, Stones L, Ankghuambom C, Pondei K, McClure CP, Alemnji G, Taylor S, et al. Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors. J Virol. 2011;85(12):6024\u201337.","journal-title":"J Virol"},{"issue":"1","key":"222_CR52","first-page":"21","volume":"4","author":"K Luzuriaga","year":"2002","unstructured":"Luzuriaga K, Sullivan JL. Pediatric HIV-1 infection: advances and remaining challenges. AIDS Rev. 2002;4(1):21\u20136.","journal-title":"AIDS Rev"},{"issue":"6929","key":"222_CR53","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1038\/nature01470","volume":"422","author":"X Wei","year":"2003","unstructured":"Wei X, Decker JM, Wang S, Hui H, Kappes JC, Wu X, Salazar-Gonzalez JF, Salazar MG, Kilby JM, Saag MS, et al. Antibody neutralization and escape by HIV-1. Nature. 2003;422(6929):307\u201312.","journal-title":"Nature"},{"issue":"4","key":"222_CR54","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1093\/bib\/bbn013","volume":"9","author":"K Katoh","year":"2008","unstructured":"Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 2008;9(4):286\u201398.","journal-title":"Brief Bioinform"},{"key":"222_CR55","unstructured":"Gaschen B. GeneCutter. In: LANL, Los Alamos: T-10, HIV database; 2003."},{"issue":"2","key":"222_CR56","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1093\/molbev\/msp259","volume":"27","author":"M Gouy","year":"2010","unstructured":"Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010;27(2):221\u20134.","journal-title":"Mol Biol Evol"},{"key":"222_CR57","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1089\/aid.1995.11.1413","volume":"11","author":"AC Siepel","year":"1995","unstructured":"Siepel AC, Halpern AL, Macken C, Korber B. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retrovirus. 1995;11:1413\u20136.","journal-title":"AIDS Res Hum Retrovirus"},{"issue":"Web Server issu","key":"222_CR58","doi-asserted-by":"publisher","first-page":"W557","DOI":"10.1093\/nar\/gki352","volume":"33","author":"S Guindon","year":"2005","unstructured":"Guindon S, Lethiec F, Duroux P, Gascuel O. PHYML Online\u2014a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005;33(Web Server issue):W557\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"222_CR59","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1093\/bioinformatics\/14.1.68","volume":"14","author":"DH Huson","year":"1998","unstructured":"Huson DH. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics. 1998;14(1):68\u201373.","journal-title":"Bioinformatics"},{"key":"222_CR60","volume-title":"R: a language and environment for statistical computing","author":"R Development Core Team.","year":"2003","unstructured":"R Development Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2003."},{"issue":"4","key":"222_CR61","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1080\/10635150600755453","volume":"55","author":"M Anisimova","year":"2006","unstructured":"Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 2006;55(4):539\u201352.","journal-title":"Syst Biol"}],"container-title":["Retrovirology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12977-015-0222-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12977-015-0222-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12977-015-0222-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12977-015-0222-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,26]],"date-time":"2022-05-26T06:49:28Z","timestamp":1653547768000},"score":1,"resource":{"primary":{"URL":"https:\/\/retrovirology.biomedcentral.com\/articles\/10.1186\/s12977-015-0222-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,16]]},"references-count":61,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["222"],"URL":"https:\/\/doi.org\/10.1186\/s12977-015-0222-0","relation":{},"ISSN":["1742-4690"],"issn-type":[{"value":"1742-4690","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,11,16]]},"assertion":[{"value":"3 August 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 November 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 November 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"96"}}