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AIDS Research and Human Retroviruses
A New Perspective on V3 Phenotype Prediction
To cite this article:
Satish Pillai, Benjamin Good, Douglas Richman, Jacques Corbeil.
AIDS Research and Human Retroviruses.
February 2003,
19(2): 145-149.
doi:10.1089/088922203762688658.
Satish Pillai University of California, San Diego, La Jolla, California 92093 Benjamin Good Veterans Administration, San Diego Healthcare System, San Diego, California 92161 Douglas Richman University of California, San Diego, La Jolla, California 92093 and Veterans Administration, San Diego Healthcare System, San Diego, California 92161 Jacques Corbeil University of California, San Diego, La Jolla, California 92093 and Veterans Administration, San Diego Healthcare System, San Diego, California 92161 The particular coreceptor used by a strain of HIV-1 to enter a host cell is highly indicative of its pathology. HIV-1 coreceptor usage is primarily determined by the amino acid sequences of the V3 loop region of the viral envelope glycoprotein. The canonical approach to sequence-based prediction of coreceptor usage was derived via statistical analysis of a less reliable and significantly smaller data set than is presently available. We aimed to produce a superior phenotypic classifier by applying modern machine learning (ML) techniques to the current database of V3 loop sequences with known phenotype. The trained classifiers along with the sequence data are available for public use at the supplementary website: http://genomiac2.ucsd.edu:8080/wetcat/v3.html  This paper was cited by:Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing John Archer, Michael S Braverman, Bruce E Taillon, Brian Desany, Ian James, P Richard Harrigan, Marilyn Lewis, David L Robertson AIDS. Jul 2009, Vol. 23, No. 10: 1209-1218 CrossRef Improvement in the determination of HIV-1 tropism using the V3 gene sequence and a combination of bioinformatic tools Natalia Chueca, Carolina Garrido, Marta Álvarez, Eva Poveda, Juan de Dios Luna, Natalia Zahonero, José Hernández-Quero, Vicente Soriano, Carmen Maroto, Carmen de Mendoza, Federico García Journal of Medical Virology. Jun 2009, Vol. 81, No. 5: 763-767 CrossRef Design and validation of new genotypic tools for easy and reliable estimation of HIV tropism before using CCR5 antagonists E. Poveda, E. Seclen, M. d. M. Gonzalez, F. Garcia, N. Chueca, A. Aguilera, J. J. Rodriguez, J. Gonzalez-Lahoz, V. Soriano Journal of Antimicrobial Chemotherapy. Apr 2009, Vol. 63, No. 5: 1006-1010 CrossRef Relationship Between HIV Coreceptor Tropism and Disease Progression in Persons With Untreated Chronic HIV Infection Matthew Bidwell Goetz, Robert Leduc, Jay R Kostman, Ann M Labriola, Yolanda Lie, Jodi Weidler, Eoin Coakley, Michael Bates, Roberta Luskin-Hawk JAIDS Journal of Acquired Immune Deficiency Syndromes. Apr 2009, Vol. 50, No. 3: 259-266 CrossRef Current tests to evaluate HIV-1 coreceptor tropism Justine D Rose, Ariel M Rhea, Jan Weber, Miguel E Quiñones-Mateu Current Opinion in HIV and AIDS. Apr 2009, Vol. 4, No. 2: 136-142 CrossRef Robust Supervised and Unsupervised Statistical Learning for HIV Type 1 Coreceptor Usage Analysis Mattia C.F. Prosperi, Iuri Fanti, Giovanni Ulivi, Alessandro Micarelli, Andrea De Luca, Maurizio Zazzi AIDS Research and Human Retroviruses. Mar 2009, Vol. 25, No. 3: 305-314 Abstract | Full Text PDF | Reprints & PermissionsCXCR4-Using HIV Type 1 Variants Are More Commonly Found in Peripheral Blood Mononuclear Cell DNA Than in Plasma RNA Chris Verhofstede, Linos Vandekerckhove, Veerle Van Eygen, Els Demecheleer, Ina Vandenbroucke, Bart Winters, Jean Plum, Dirk Vogelaers, Lieven Stuyver JAIDS Journal of Acquired Immune Deficiency Syndromes. Mar 2009, Vol. 50, No. 2: 126-136 CrossRef HIV rebounds from latently infected cells, rather than from continuing low-level replication B. Joos, M. Fischer, H. Kuster, S. K. Pillai, J. K. Wong, J. Boni, B. Hirschel, R. Weber, A. Trkola, H. F. Gunthard Proceedings of the National Academy of Sciences. Nov 2008, Vol. 105, No. 43: 16725-16730 CrossRef Antiretroviral Drug Resistance Testing in Adult HIV‐1 Infection: 2008 Recommendations of an International AIDS Society–USA Panel Martin S. Hirsch, Huldrych F. Günthard, Jonathan M. Schapiro, Françoise Brun‐Vézinet, Bonaventura Clotet, Scott M. Hammer, Victoria A. Johnson, Daniel R. Kuritzkes, John W. Mellors, Deenan Pillay, Patrick G. Yeni, Donna M. Jacobsen, Douglas D. Richman Clinical Infectious Diseases. Aug 2008, Vol. 47, No. 2: 266-285 CrossRef Performance of a Population-Based HIV-1 Tropism Phenotypic Assay and Correlation With V3 Genotypic Prediction Tools in Recent HIV-1 Seroconverters Carmen de Mendoza, Kurt Van Baelen, Eva Poveda, Evelien Rondelez, Natalia Zahonero, Lieven Stuyver, Carolina Garrido, Jorge Villacian, Vincent Soriano JAIDS Journal of Acquired Immune Deficiency Syndromes. Aug 2008, Vol. 48, No. 3: 241-244 CrossRef Characterization of a chemokine receptor CCR5-negative T cell line and its use in determining human immunodeficiency virus type 1 phenotype Dorothea Binninger-Schinzel, Daniela Müller, Timo Wolf, Birgit Krause, Britta Meye, Gudrun Winskowsky, Sylvia Raupp, Stephen Norley, Reinhard Brodt, Albrecht Werner Journal of Medical Virology. Mar 2008, Vol. 80, No. 2: 192-200 CrossRef CD4-Dependent Characteristics of Coreceptor Use and HIV Type 1 V3 Sequence in a Large Population of Therapy-Naive Individuals Andrew J. Low, David Marchant, Chanson J. Brumme, Zabrina L. Brumme, Winnie Dong, Tobias Sing, Robert S. Hogg, Julio S.G. Montaner, Vikram Gill, Peter K. Cheung, P. Richard Harrigan AIDS Research and Human Retroviruses. Feb 2008, Vol. 24, No. 2: 219-228 Abstract | Full Text PDF | Reprints & PermissionsBioinformatics prediction of HIV coreceptor usage Thomas Lengauer, Oliver Sander, Saleta Sierra, Alexander Thielen, Rolf Kaiser Nature Biotechnology. Jan 2008, Vol. 25, No. 12: 1407-1410 CrossRef Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates Andrew J Low, Winnie Dong, Dennison Chan, Tobias Sing, Ronald Swanstrom, Mark Jensen, Satish Pillai, Benjamin Good, P Richard Harrigan AIDS. Oct 2007, Vol. 21, No. 14: F17-F24 CrossRef Prevalence of X4 tropic HIV-1 variants in patients with differences in disease stage and exposure to antiretroviral therapy Eva Poveda, Verónica Briz, Carmen de Mendoza, José Miguel Benito, Angélica Corral, Natalia Zahonero, Sara Lozano, Juan González-Lahoz, Vincent Soriano Journal of Medical Virology. Sep 2007, Vol. 79, No. 8: 1040-1046 CrossRef Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use Eva Poveda, Ver??nica Briz, Vanessa Roulet, Mar??a del Mar Gonz??lez, Jean-Louis Faudon, Katharina Skrabal, Vincent Soriano AIDS. Aug 2007, Vol. 21, No. 11: 1487-1490 CrossRef HIV tropism: diagnostic tools and implications for disease progression and treatment with entry inhibitors Eva Poveda, Ver??nica Briz, Miguel Qui??ones-Mateu, Vincent Soriano AIDS. Jul 2006, Vol. 20, No. 10: 1359???1367 CrossRef Genotypic and Phenotypic Correlates of the HIV Type 1 env Gene Evolution in Infected Children with Discordant Response to Antiretroviral Therapy Patrizia Bagnarelli, Manuela Vecchi, Nicoletta Burighel, Domenico Bellanova, Stefano Menzo, Massimo Clementi, Anita De Rossi AIDS Research and Human Retroviruses. Dec 2004, Vol. 20, No. 12: 1306-1313 Abstract | Full Text PDF | Reprints & PermissionsClinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy Zabrina L Brumme, Winnie WY Dong, Benita Yip, Brian Wynhoven, Noah G Hoffman, Ronald Swanstrom, Mark A Jensen, James I Mullins, Robert S Hogg, Julio SG Montaner, P Richard Harrigan AIDS. Apr 2004, Vol. 18, No. 4: F1-F9 CrossRef |
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