{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T13:06:58Z","timestamp":1649164018930},"reference-count":57,"publisher":"Microbiology Society","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,11,1]]},"abstract":"<jats:p>Human immunodeficiency virus intra-host recombination has never been studied<jats:italic>in vivo<\/jats:italic>both during early infection and throughout disease progression. The CD8-depleted rhesus macaque model of neuroAIDS was used to investigate the impact of recombination from early infection up to the onset of neuropathology in animals inoculated with a simian immunodeficiency virus (SIV) swarm. Several lymphoid and non-lymphoid tissues were collected longitudinally at 21 days post-infection (p.i.), 61 days p.i. and necropsy (75\u2013118 days p.i.) from four macaques that developed SIV-encephalitis or meningitis, as well as from two animals euthanized at 21 days p.i. The number of recombinant sequences and breakpoints in different tissues and over time from each primate were compared. Breakpoint locations were mapped onto predicted RNA and protein secondary structures. Recombinants were found at each time point and in each primate as early as 21 days p.i. No association was found between recombination rates and specific tissue of origin. Several identical breakpoints were identified in sequences derived from different tissues in the same primate and among different primates. Breakpoints predominantly mapped to unpaired nucleotides or pseudoknots in RNA secondary structures, and proximal to glycosylation sites and cysteine residues in protein sequences, suggesting selective advantage in the emergence of specific recombinant sequences. Results indicate that recombinant sequences can become fixed very early after infection with a heterogeneous viral swarm. Features of RNA and protein secondary structure appear to play a role in driving the production of recombinants and their selection in the rapid disease model of neuroAIDS.<\/jats:p>","DOI":"10.1099\/vir.0.055335-0","type":"journal-article","created":{"date-parts":[[2013,8,21]],"date-time":"2013-08-21T03:42:09Z","timestamp":1377056529000},"page":"2469-2479","source":"Crossref","is-referenced-by-count":3,"title":["Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS"],"prefix":"10.1099","volume":"94","author":[{"given":"Susanna L.","family":"Lamers","sequence":"first","affiliation":[{"name":"BioInfoExperts LLC, Thibodaux, LA 70301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David J.","family":"Nolan","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA"},{"name":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha L.","family":"Strickland","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA"},{"name":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mattia","family":"Prosperi","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA"},{"name":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary B.","family":"Fogel","sequence":"additional","affiliation":[{"name":"Natural Selection Inc., San Diego, CA 92121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maureen M.","family":"Goodenow","sequence":"additional","affiliation":[{"name":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Salemi","sequence":"additional","affiliation":[{"name":"Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA"},{"name":"Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"r1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000178"},{"key":"r2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-3-91"},{"key":"r3","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(03)00784-8"},{"key":"r4","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.105.048975"},{"key":"r5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000842"},{"key":"r6","first-page":"243","article-title":"A procedure for RNA pseudoknot prediction","volume":"8","author":"Chen","year":"1992","journal-title":"Comput Appl Biosci"},{"key":"r7","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.14.9337-9340.2005"},{"key":"r8","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-42-1-1"},{"key":"r9","doi-asserted-by":"publisher","DOI":"10.1126\/science.7824947"},{"key":"r10","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.16.7435-7452.2001"},{"key":"r11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq429"},{"key":"r12","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2500605"},{"key":"r13","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1089\/aid.2011.0176","article-title":"HIV type 1 genetic variation in foreskin and blood from subjects in Rakai, Uganda","volume":"28","author":"Galiwango","year":"2012","journal-title":"AIDS Res Hum Retroviruses"},{"key":"r14","doi-asserted-by":"crossref","first-page":"7013","DOI":"10.1128\/JVI.70.10.7013-7029.1996","article-title":"The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A\/E) recombinant of African origin","volume":"70","author":"Gao","year":"1996","journal-title":"J Virol"},{"key":"r15","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn188"},{"key":"r16","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1991.7.495"},{"key":"r17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/14.1.68"},{"key":"r18","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj030"},{"key":"r19","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.3.1234-1240.2000"},{"key":"r20","doi-asserted-by":"publisher","DOI":"10.1007\/s11908-005-0051-8"},{"key":"r21","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1093\/genetics\/156.3.1393","article-title":"Maximum likelihood estimation of recombination rates from population data","volume":"156","author":"Kuhner","year":"2000","journal-title":"Genetics"},{"key":"r22","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1996.12.1169"},{"key":"r23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005065"},{"key":"r24","doi-asserted-by":"publisher","DOI":"10.3109\/13550281003735709"},{"key":"r25","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0306764101"},{"key":"r26","doi-asserted-by":"publisher","DOI":"10.1023\/A:1026662618911"},{"key":"r27","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.21.10187-10199.2001"},{"key":"r28","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3410\/B2-8","article-title":"RNA pseudoknots: folding and finding","volume":"2","author":"Liu","year":"2010","journal-title":"F1000 Biol Rep"},{"key":"r29","doi-asserted-by":"publisher","DOI":"10.1086\/344938"},{"key":"r30","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01295-06"},{"key":"r31","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.92.15.6971"},{"key":"r32","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2010.0364"},{"key":"r33","doi-asserted-by":"publisher","DOI":"10.1126\/science.276.5320.1857"},{"key":"r34","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.1.406-413.2005"},{"key":"r35","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.241370698"},{"key":"r36","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0684.2011.00475.x"},{"key":"r37","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm258"},{"key":"r38","doi-asserted-by":"crossref","first-page":"6340","DOI":"10.1128\/JVI.68.10.6340-6346.1994","article-title":"Identification of human immunodeficiency virus type 1 envelope genes recombinant between subtypes B and F in two epidemiologically linked individuals from Brazil","volume":"68","author":"Sabino","year":"1994","journal-title":"J Virol"},{"key":"r39","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2008.08.017"},{"key":"r40","volume-title":"The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing","author":"Salemi","year":"2009"},{"key":"r41","doi-asserted-by":"publisher","DOI":"10.1089\/aid.1995.11.1423"},{"key":"r42","doi-asserted-by":"publisher","DOI":"10.1016\/S1369-5266(99)80010-7"},{"key":"r43","doi-asserted-by":"publisher","DOI":"10.1126\/science.283.5403.857"},{"key":"r44","first-page":"22","article-title":"AIDS in Africa. A global responsibility","volume":"84","author":"Sellman","year":"2001","journal-title":"Minn Med"},{"key":"r45","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.103.023382"},{"key":"r46","doi-asserted-by":"crossref","first-page":"5840","DOI":"10.1128\/JVI.64.12.5840-5850.1990","article-title":"Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1","volume":"64","author":"Simmonds","year":"1990","journal-title":"J Virol"},{"key":"r47","doi-asserted-by":"publisher","DOI":"10.1261\/rna.968808"},{"key":"r48","doi-asserted-by":"publisher","DOI":"10.1089\/aid.2011.0100"},{"key":"r49","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.039586-0"},{"key":"r50","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.15.7171-7178.2000"},{"key":"r51","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030134"},{"key":"r52","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-8510(99)00051-2"},{"key":"r53","doi-asserted-by":"publisher","DOI":"10.1038\/nature08237"},{"key":"r54","doi-asserted-by":"publisher","DOI":"10.1007\/s11481-011-9330-3"},{"key":"r55","doi-asserted-by":"crossref","first-page":"4137","DOI":"10.1002\/j.1460-2075.1994.tb06731.x","article-title":"Pseudoknot-dependent read-through of retroviral gag termination codons: importance of sequences in the spacer and loop 2","volume":"13","author":"Wills","year":"1994","journal-title":"EMBO J"},{"key":"r56","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000414"},{"key":"r57","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/9.1.133"}],"container-title":["Journal of General Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.055335-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,4]],"date-time":"2022-03-04T11:04:52Z","timestamp":1646391892000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.055335-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,1]]},"references-count":57,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2013,11,1]]}},"URL":"https:\/\/doi.org\/10.1099\/vir.0.055335-0","relation":{},"ISSN":["0022-1317","1465-2099"],"issn-type":[{"value":"0022-1317","type":"print"},{"value":"1465-2099","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,1]]}}}