Literature DB >> 21734029

High concordance between the position-specific scoring matrix and geno2pheno algorithms for genotypic interpretation of HIV-1 tropism: V3 length as the major cause of disagreement.

Eduardo Seclén1, Vicente Soriano, María M González, Sagrario Gómez, Alexander Thielen, Eva Poveda.   

Abstract

The agreement between the position-specific scoring matrix (PSSM) and geno2pheno as tools for genotypic interpretation of HIV-1 tropism using 800 clinical specimens was assessed. There was an overall concordance of 88%. Disagreement was found mostly in specimens with short V3 lengths (<35 amino acids). Thus, consideration of V3 lengths should improve the predictability of HIV-1 tropism using genotypic algorithms.

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Year:  2011        PMID： 21734029      PMCID： PMC3165608          DOI： 10.1128/JCM.00908-11

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  9 in total

Review 1.  Genotypic determination of HIV tropism - clinical and methodological recommendations to guide the therapeutic use of CCR5 antagonists.

Authors:  Eva Poveda; José Alcamí; Roger Paredes; Juan Córdoba; Félix Gutiérrez; Josep María Llibre; Rafael Delgado; Federico Pulido; José Antonio Iribarren; Miguel García Deltoro; José Hernández Quero; Santiago Moreno; Federico García
Journal:  AIDS Rev       Date:  2010 Jul-Sep       Impact factor: 2.500

2.  Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

Authors:  Rachel A McGovern; Alexander Thielen; Theresa Mo; Winnie Dong; Conan K Woods; Douglass Chapman; Marilyn Lewis; Ian James; Jayvant Heera; Hernan Valdez; P Richard Harrigan
Journal:  AIDS       Date:  2010-10-23       Impact factor: 4.177

3.  Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use.

Authors:  Eva Poveda; Verónica Briz; Vanessa Roulet; María Del Mar González; Jean-Louis Faudon; Katharina Skrabal; Vincent Soriano
Journal:  AIDS       Date:  2007-07-11       Impact factor: 4.177

4.  High sensitivity of specific genotypic tools for detection of X4 variants in antiretroviral-experienced patients suitable to be treated with CCR5 antagonists.

Authors:  Eduardo Seclén; Carolina Garrido; María del Mar González; Juan González-Lahoz; Carmen de Mendoza; Vincent Soriano; Eva Poveda
Journal:  J Antimicrob Chemother       Date:  2010-04-28       Impact factor: 5.790

Review 5.  European guidelines on the clinical management of HIV-1 tropism testing.

Authors:  L P R Vandekerckhove; A M J Wensing; R Kaiser; F Brun-Vézinet; B Clotet; A De Luca; S Dressler; F Garcia; A M Geretti; T Klimkait; K Korn; B Masquelier; C F Perno; J M Schapiro; V Soriano; A Sönnerborg; A-M Vandamme; C Verhofstede; H Walter; M Zazzi; C A B Boucher
Journal:  Lancet Infect Dis       Date:  2011-03-21       Impact factor: 25.071

6.  Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates.

Authors:  Andrew J Low; Winnie Dong; Dennison Chan; Tobias Sing; Ronald Swanstrom; Mark Jensen; Satish Pillai; Benjamin Good; P Richard Harrigan
Journal:  AIDS       Date:  2007-09-12       Impact factor: 4.177

7.  Design and validation of new genotypic tools for easy and reliable estimation of HIV tropism before using CCR5 antagonists.

Authors:  Eva Poveda; Eduardo Seclén; María del Mar González; Federico García; Natalia Chueca; Antonio Aguilera; Jose Javier Rodríguez; Juan González-Lahoz; Vincent Soriano
Journal:  J Antimicrob Chemother       Date:  2009-03-03       Impact factor: 5.790

8.  Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type 1 subtypes.

Authors:  Carolina Garrido; Vanessa Roulet; Natalia Chueca; Eva Poveda; Antonio Aguilera; Katharina Skrabal; Natalia Zahonero; Silvia Carlos; Federico García; Jean Louis Faudon; Vincent Soriano; Carmen de Mendoza
Journal:  J Clin Microbiol       Date:  2008-01-16       Impact factor: 5.948

9.  Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences.

Authors:  Mark A Jensen; Fu-Sheng Li; Angélique B van 't Wout; David C Nickle; Daniel Shriner; Hong-Xia He; Sherry McLaughlin; Raj Shankarappa; Joseph B Margolick; James I Mullins
Journal:  J Virol       Date:  2003-12       Impact factor: 5.103
  9 in total
  14 in total

1.  Viral tropism and antiretroviral drug resistance in HIV-1 subtype C-infected patients failing highly active antiretroviral therapy in Johannesburg, South Africa.

Authors:  Irene Ketseoglou; Azwidowi Lukhwareni; Kim Steegen; Sergio Carmona; Wendy S Stevens; Maria A Papathanasopoulos
Journal:  AIDS Res Hum Retroviruses       Date:  2013-12-13       Impact factor: 2.205

2.  Next generation sequencing reveals a high frequency of CXCR4 utilizing viruses in HIV-1 chronically infected drug experienced individuals in South Africa.

Authors:  Nontokozo D Matume; Denis M Tebit; Laurie R Gray; Marie-Louise Hammarskjold; David Rekosh; Pascal O Bessong
Journal:  J Clin Virol       Date:  2018-02-15       Impact factor: 3.168

3.  A diagnostic HIV-1 tropism system based on sequence relatedness.

Authors:  Suzanne Edwards; Heinz Stucki; Joëlle Bader; Vincent Vidal; Rolf Kaiser; Manuel Battegay; Thomas Klimkait
Journal:  J Clin Microbiol       Date:  2014-12-10       Impact factor: 5.948

4.  Evolution of HIV-1 coreceptor usage and coreceptor switching during pregnancy.

Authors:  Doris G Ransy; Alena Motorina; Natacha Merindol; Bertine S Akouamba; Johanne Samson; Yolanda Lie; Laura A Napolitano; Normand Lapointe; Marc Boucher; Hugo Soudeyns
Journal:  AIDS Res Hum Retroviruses       Date:  2013-10-25       Impact factor: 2.205

5.  Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism.

Authors:  Jan Weber; Ana C Vazquez; Dane Winner; Richard M Gibson; Ariel M Rhea; Justine D Rose; Doug Wylie; Kenneth Henry; Alison Wright; Kevin King; John Archer; Eva Poveda; Vicente Soriano; David L Robertson; Paul D Olivo; Eric J Arts; Miguel E Quiñones-Mateu
Journal:  J Clin Microbiol       Date:  2013-03-13       Impact factor: 5.948

6.  Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects.

Authors:  Ron M Kagan; Erik P Johnson; Martin F Siaw; Ben Van Baelen; Richard Ogden; Jamie L Platt; Rick L Pesano; Eric Lefebvre
Journal:  AIDS Res Hum Retroviruses       Date:  2013-08-14       Impact factor: 2.205

7.  Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism.

Authors:  John Archer; Jan Weber; Kenneth Henry; Dane Winner; Richard Gibson; Lawrence Lee; Ellen Paxinos; Eric J Arts; David L Robertson; Larry Mimms; Miguel E Quiñones-Mateu
Journal:  PLoS One       Date:  2012-11-14       Impact factor: 3.240

8.  A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients.

Authors:  Ron M Kagan; Erik P Johnson; Martin Siaw; Pinaki Biswas; Douglass S Chapman; Zhaohui Su; Jamie L Platt; Rick L Pesano
Journal:  PLoS One       Date:  2012-09-27       Impact factor: 3.240

9.  Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.

Authors:  Richard M Gibson; Ashley M Meyer; Dane Winner; John Archer; Felix Feyertag; Ezequiel Ruiz-Mateos; Manuel Leal; David L Robertson; Christine L Schmotzer; Miguel E Quiñones-Mateu
Journal:  Antimicrob Agents Chemother       Date:  2014-01-27       Impact factor: 5.191

10.  HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants.

Authors:  Mariano M Sede; Franco A Moretti; Natalia L Laufer; Leandro R Jones; Jorge F Quarleri
Journal:  PLoS One       Date:  2014-07-17       Impact factor: 3.240
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