{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T06:44:21Z","timestamp":1773470661161,"version":"3.50.1"},"reference-count":31,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,3,1]],"date-time":"2021-03-01T00:00:00Z","timestamp":1614556800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T00:00:00Z","timestamp":1613088000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010877","name":"ViiV Healthcare","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010877","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Clinical Virology"],"published-print":{"date-parts":[[2021,3]]},"DOI":"10.1016\/j.jcv.2021.104755","type":"journal-article","created":{"date-parts":[[2021,2,9]],"date-time":"2021-02-09T20:49:54Z","timestamp":1612903794000},"page":"104755","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia"],"prefix":"10.1016","volume":"136","author":[{"given":"Nina","family":"Marty","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siriphan","family":"Saeng-Aroon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eva","family":"Heger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Thielen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2511-9553","authenticated-orcid":false,"given":"Martin","family":"Obermeier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nico","family":"Pfeifer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rolf","family":"Kaiser","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4945-6511","authenticated-orcid":false,"given":"Thomas","family":"Klimkait","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.jcv.2021.104755_bib0005","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.tim.2005.04.005","article-title":"The HIV coreceptor switch: a population dynamical perspective","volume":"13","author":"Regoes","year":"2005","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.jcv.2021.104755_bib0010","first-page":"125","article-title":"How HIV changes its tropism: evolution and adaptation?","volume":"4","author":"Mosier","year":"2009","journal-title":"Curr. Opin. HIV AIDS"},{"key":"10.1016\/j.jcv.2021.104755_bib0015","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1586\/14787210.2013.852469","article-title":"Determination of HIV tropism and its use in the clinical practice","volume":"11","author":"Perez-Olmeda","year":"2013","journal-title":"Expert Rev. Anti. Ther."},{"key":"10.1016\/j.jcv.2021.104755_bib0020","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1038\/s41598-018-20814-2","article-title":"Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa","volume":"8","author":"Siddik","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jcv.2021.104755_bib0025","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1016\/S1473-3099(10)70319-4","article-title":"European guidelines on the clinical management of HIV-1 tropism testing","volume":"11","author":"Vandekerckhove","year":"2011","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.jcv.2021.104755_bib0030","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1128\/JCM.02762-14","article-title":"A diagnostic HIV-1 tropism system based on sequence relatedness","volume":"53","author":"Edwards","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.jcv.2021.104755_bib0035","doi-asserted-by":"crossref","first-page":"3850","DOI":"10.1093\/nar\/gkg575","article-title":"Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes","volume":"31","author":"Beerenwinkel","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jcv.2021.104755_bib0040","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1038\/nbt1371","article-title":"Bioinformatics prediction of HIV coreceptor usage","volume":"25","author":"Lengauer","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jcv.2021.104755_bib0045","doi-asserted-by":"crossref","DOI":"10.1097\/QAD.0b013e32833e6cfb","article-title":"Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies","volume":"24","author":"McGovern","year":"2010","journal-title":"AIDS"},{"key":"10.1016\/j.jcv.2021.104755_bib0050","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1093\/cid\/cir493","article-title":"Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc","volume":"53","author":"Swenson","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.jcv.2021.104755_bib0055","doi-asserted-by":"crossref","first-page":"1570","DOI":"10.1038\/s41598-017-01858-2","article-title":"HIV-1 CRF01_AE strain is associated with faster HIV\/AIDS progression in Jiangsu Province, China","volume":"7","author":"Chu","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jcv.2021.104755_bib0060","doi-asserted-by":"crossref","first-page":"e15738","DOI":"10.1371\/journal.pone.0015738","article-title":"Increased rate of CD4+ T-Cell decline and faster time to antiretroviral therapy in HIV-1 subtype CRF01_AE infected seroconverters in Singapore","volume":"6","author":"Ng","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.jcv.2021.104755_bib0065","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1097\/COH.0b013e328356eaa7","article-title":"HIV population genotypic tropism testing and its clinical significance","volume":"7","author":"Obermeier","year":"2012","journal-title":"Curr. Opin. HIV AIDS"},{"key":"10.1016\/j.jcv.2021.104755_bib0070","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1128\/JCM.02328-12","article-title":"Genotypic prediction of HIV-1 CRF01-AE tropism","volume":"51","author":"Raymond","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.jcv.2021.104755_bib0075","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1111\/hiv.12108","article-title":"Coreceptor tropism determined by genotypic assay in HIV-1 circulating in Thailand, where CRF01_AE predominates","volume":"15","author":"Phuphuakrat","year":"2014","journal-title":"HIV Med."},{"key":"10.1016\/j.jcv.2021.104755_bib0080","doi-asserted-by":"crossref","first-page":"e60566","DOI":"10.1371\/journal.pone.0060566","article-title":"HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRF01_AE and CRF02_AG [corrected]","volume":"8","author":"Mulinge","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jcv.2021.104755_bib0085","doi-asserted-by":"crossref","first-page":"264","DOI":"10.7883\/yoken.JJID.2017.482","article-title":"Performance evaluation of a genotypic tropism test using HIV-1 CRF01_AE isolates in Japan","volume":"71","author":"Matsuda","year":"2018","journal-title":"Jpn. J. Infect. Dis."},{"key":"10.1016\/j.jcv.2021.104755_bib0090","doi-asserted-by":"crossref","first-page":"e89462","DOI":"10.1371\/journal.pone.0089462","article-title":"Evidence that HIV-1 CRF01_AE is associated with low CD4+T cell count and CXCR4 co-receptor usage in recently infected young men who have sex with men (MSM) in Shanghai, China","volume":"9","author":"Li","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.jcv.2021.104755_bib0095","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1097\/QAD.0000000000000125","article-title":"CRF01_AE subtype is associated with X4 tropism and fast HIV progression in Chinese patients infected through sexual transmission","volume":"28","author":"Li","year":"2014","journal-title":"AIDS"},{"key":"10.1016\/j.jcv.2021.104755_bib0100","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1089\/aid.2015.0371","article-title":"Circulation of HIV-1 multiple complexity recombinant forms among female sex workers recently infected with HIV-1 in Thailand","volume":"32","author":"Saeng-aroon","year":"2016","journal-title":"AIDS Res. Hum. Retroviruses"},{"key":"10.1016\/j.jcv.2021.104755_bib0105","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1479-5876-9-14","article-title":"Replicative phenotyping adds value to genotypic resistance testing in heavily pre-treated HIV-infected individuals - the Swiss HIV Cohort Study","volume":"9","author":"Fehr","year":"2011","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.jcv.2021.104755_bib0110","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1007\/s007050050447","article-title":"Dissecting the mode of action of various HIV-inhibitor classes in a stable cellular system","volume":"143","author":"Klimkait","year":"1998","journal-title":"Arch. Virol."},{"key":"10.1016\/j.jcv.2021.104755_bib0115","doi-asserted-by":"crossref","first-page":"6583","DOI":"10.1128\/JVI.00600-16","article-title":"HIV-1 Gag, envelope, and extracellular determinants cooperate to regulate the stability and turnover of virological synapses","volume":"90","author":"Gardiner","year":"2016","journal-title":"J. Virol."},{"key":"10.1016\/j.jcv.2021.104755_bib0120","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/s41467-017-00515-6","article-title":"Envelope glycoprotein mobility on HIV-1 particles depends on the virus maturation state","volume":"8","author":"Chojnacki","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jcv.2021.104755_bib0125","doi-asserted-by":"crossref","first-page":"5448","DOI":"10.1128\/jvi.64.11.5448-5456.1990","article-title":"Env and Vpu proteins of human immunodeficiency virus type 1 are produced from multiple bicistronic mRNAs","volume":"64","author":"Schwartz","year":"1990","journal-title":"J. Virol."},{"key":"10.1016\/j.jcv.2021.104755_bib0130","doi-asserted-by":"crossref","first-page":"8047","DOI":"10.1128\/JVI.00252-06","article-title":"Contribution of Vpu, Env, and Nef to CD4 down-modulation and resistance of human immunodeficiency virus type 1-infected T cells to superinfection","volume":"80","author":"Wildum","year":"2006","journal-title":"J. Virol."},{"key":"10.1016\/j.jcv.2021.104755_bib0135","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/j.compbiolchem.2019.05.006","article-title":"HIVCoR: a sequence-based tool for predicting HIV-1 CRF01_AE coreceptor usage","volume":"80","author":"Hongjaisee","year":"2019","journal-title":"Comput. Biol. Chem."},{"key":"10.1016\/j.jcv.2021.104755_bib0140","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.jcv.2017.12.014","article-title":"Performance of genotypic algorithms for predicting tropism for HIV-1 CRF01_AE recombinant","volume":"99-100","author":"Soulie","year":"2018","journal-title":"J. Clin. Virol."},{"key":"10.1016\/j.jcv.2021.104755_bib0145","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/infdis\/jiq030","article-title":"Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients","volume":"203","author":"Swenson","year":"2011","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.jcv.2021.104755_bib0150","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":"10.1016\/j.jcv.2021.104755_bib0155","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1097\/QAD.0000000000001981","article-title":"Rapid CD4+ T-cell decline is associated with coreceptor switch among MSM primarily infected with HIV-1 CRF01_AE in Northeast China","volume":"33","author":"Cui","year":"2019","journal-title":"AIDS"}],"container-title":["Journal of Clinical Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1386653221000226?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1386653221000226?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T03:13:49Z","timestamp":1761362029000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1386653221000226"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3]]},"references-count":31,"alternative-id":["S1386653221000226"],"URL":"https:\/\/doi.org\/10.1016\/j.jcv.2021.104755","relation":{},"ISSN":["1386-6532"],"issn-type":[{"value":"1386-6532","type":"print"}],"subject":[],"published":{"date-parts":[[2021,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia","name":"articletitle","label":"Article Title"},{"value":"Journal of Clinical Virology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcv.2021.104755","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"104755"}}