{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T12:10:07Z","timestamp":1687954207017},"reference-count":34,"publisher":"Microbiology Society","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:p>The initiation of drug therapy results in a reduction in the human immunodeficiency virus type 1 (HIV-1) population, which represents a potential genetic bottleneck. The effect of this drug-induced genetic bottleneck on the population dynamics of the envelope (Env) regions has been addressed in several<jats:italic>in vivo<\/jats:italic>studies. However, it is difficult to investigate the effect on the<jats:italic>env<\/jats:italic>gene of the genetic bottleneck induced not only by entry inhibitors but also by non-entry inhibitors, particularly<jats:italic>in vivo<\/jats:italic>. Therefore, this study used an<jats:italic>in vitro<\/jats:italic>selection system using unique bulk primary isolates established in the laboratory to observe the effects of the antiretroviral drug-induced bottleneck on the integrase and<jats:italic>env<\/jats:italic>genes. Env diversity was decreased significantly in one primary isolate [KP-1, harbouring both CXCR4 (X4)- and CCR5 (R5)-tropic variants] when passaged in the presence or absence of raltegravir (RAL) during<jats:italic>in vitro<\/jats:italic>selection. Furthermore, the RAL-selected KP-1 variant had a completely different Env sequence from that in the passage control (particularly evident in the gp120, V1\/V2 and V4-loop regions), and a different number of potential<jats:italic>N<\/jats:italic>-glycosylation sites. A similar pattern was also observed in other primary isolates when using different classes of drugs. This is the first study to explore the influence of anti-HIV drugs on bottlenecks in bulk primary HIV isolates with highly diverse Env sequences using<jats:italic>in vitro<\/jats:italic>selection.<\/jats:p>","DOI":"10.1099\/vir.0.047167-0","type":"journal-article","created":{"date-parts":[[2013,1,4]],"date-time":"2013-01-04T05:13:37Z","timestamp":1357276417000},"page":"933-943","source":"Crossref","is-referenced-by-count":4,"title":["Impact of antiretroviral pressure on selection of primary human immunodeficiency virus type 1 envelope sequences in vitro"],"prefix":"10.1099","volume":"94","author":[{"given":"Shigeyoshi","family":"Harada","sequence":"first","affiliation":[{"name":"AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan"},{"name":"Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo\u2010ku, Kumamoto 860-0811, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuhisa","family":"Yoshimura","sequence":"additional","affiliation":[{"name":"AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan"},{"name":"Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo\u2010ku, Kumamoto 860-0811, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aki","family":"Yamaguchi","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo\u2010ku, Kumamoto 860-0811, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samatchaya","family":"Boonchawalit","sequence":"additional","affiliation":[{"name":"AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan"},{"name":"Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo\u2010ku, Kumamoto 860-0811, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keisuke","family":"Yusa","sequence":"additional","affiliation":[{"name":"Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kami-youga, Setagaya-ku, Tokyo 158-8501, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuzo","family":"Matsushita","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Chuo\u2010ku, Kumamoto 860-0811, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"345","reference":[{"key":"r1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0811713106"},{"key":"r2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000548"},{"key":"r3","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.80.5.2472-2482.2006"},{"key":"r4","doi-asserted-by":"crossref","first-page":"2416","DOI":"10.1128\/JVI.72.3.2416-2421.1998","article-title":"Rapid, transient changes at the env locus of plasma human immunodeficiency virus type 1 populations during the emergence of protease inhibitor resistance","volume":"72","author":"Delwart","year":"1998","journal-title":"J Virol"},{"key":"r5","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(93)90047-7"},{"key":"r6","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0803152"},{"key":"r7","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.017426-0"},{"key":"r8","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00911-07"},{"key":"r9","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1099\/0022-1317-81-1-85","article-title":"Human immunodeficiency virus type 1 population bottleneck during indinavir therapy causes a genetic drift in the env quasispecies","volume":"81","author":"Ib\u00e1\u00f1ez","year":"2000","journal-title":"J Gen Virol"},{"key":"r10","doi-asserted-by":"publisher","DOI":"10.1086\/652190"},{"key":"r11","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.16.10627-10637.2005"},{"key":"r12","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2008.06.012"},{"key":"r13","doi-asserted-by":"publisher","DOI":"10.1016\/j.antiviral.2007.11.001"},{"key":"r14","doi-asserted-by":"publisher","DOI":"10.1086\/652189"},{"key":"r15","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1097\/00002030-200216004-00002","article-title":"Genetic recombination and its role in the development of the HIV-1 pandemic","volume":"16","author":"N\u00e1jera","year":"2002","journal-title":"AIDS"},{"key":"r16","article-title":"Pharmacodynamics, safety, and pharmacokinetics of BMS-663068: a potentially first-in-class oral HIV attachment inhibitor","author":"Nettles","year":"2011"},{"key":"r17","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.24.14441"},{"key":"r18","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00083-07"},{"key":"r19","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-5-74"},{"key":"r20","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-77-5-1071"},{"key":"r21","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01544-06"},{"key":"r22","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1177\/135965350701200709","article-title":"Predicting HIV coreceptor usage on the basis of genetic and clinical covariates","volume":"12","author":"Sing","year":"2007","journal-title":"Antivir Ther"},{"key":"r23","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0708975"},{"key":"r24","doi-asserted-by":"publisher","DOI":"10.1021\/jm100978n"},{"key":"r25","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm092"},{"key":"r26","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01109-10"},{"key":"r27","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02237-10"},{"key":"r28","doi-asserted-by":"publisher","DOI":"10.1038\/nature04388"},{"key":"r29","doi-asserted-by":"publisher","DOI":"10.1097\/01.aids.0000247587.31320.fe"},{"key":"r30","first-page":"640","article-title":"Mutations in V4 and C4 regions of the HIV-1 CRF08-BC envelope induced by the in vitro selection of Maraviroc Confer cross-resistance to other CCR5 inhibitors","author":"Yoshimura","year":"2009"},{"key":"r31","article-title":"Two step escape pathway of the HIV-1 subtype C primary isolate induced by the in vitro selection of Maraviroc","author":"Yoshimura","year":"2010a","journal-title":"17th Conference on Retroviruses and Opportunistic Infections"},{"key":"r32","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00227-10"},{"key":"r33","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M414360200"},{"key":"r34","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1128\/JVI.68.1.425-432.1994","article-title":"Persistence of four related human immunodeficiency virus subtypes during the course of zidovudine therapy: relationship between virion RNA and proviral DNA","volume":"68","author":"Zhang","year":"1994","journal-title":"J Virol"}],"container-title":["Journal of General Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.047167-0?crawler=true","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T11:52:20Z","timestamp":1687953140000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/jgv\/10.1099\/vir.0.047167-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,5,1]]},"references-count":34,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2013,5,1]]}},"URL":"https:\/\/doi.org\/10.1099\/vir.0.047167-0","relation":{},"ISSN":["0022-1317","1465-2099"],"issn-type":[{"value":"0022-1317","type":"print"},{"value":"1465-2099","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,5,1]]}}}