Literature DB >> 12624021

Performance characteristics of human immunodeficiency virus type 1 (HIV-1) genotyping systems in sequence-based analysis of subtypes other than HIV-1 subtype B.

Linda L Jagodzinski1, John D Cooley, Mark Weber, Nelson L Michael.   

Abstract

Given the diversity of human immunodeficiency virus type 1 (HIV-1) subtypes and the emergence of subtypes other than HIV-1 subtype B in the United States, genotypic assays must be capable of delivering sequence data on diverse HIV-1 subtypes. We evaluated the performance of Visible Genetics TRUGENE HIV-1 genotyping kit and Applied Biosystems ViroSeq HIV-1 genotyping system on a panel of 34 well-characterized HIV-1 viral stocks (subtypes A through H). Both assays perform well on diverse HIV-1 subtypes despite being designed for HIV-1 subtype B. The TRUGENE assay produced sequence data for 31 isolates but not for one C and two G isolates. The TRUGENE assay using prototype 1.5 RT-PCR primers and the ViroSeq assay were both successful for all variants tested, although five isolates lacked double-strand sequence coverage in the ViroSeq assay. The availability of standardized HIV-1 genotyping kits that perform reliably with all HIV subtypes will facilitate broad implementation of HIV-1 resistance testing.

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Year:  2003        PMID： 12624021      PMCID： PMC150292          DOI： 10.1128/JCM.41.3.998-1003.2003

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


  22 in total

1.  Prevalence of genotypic and phenotypic resistance to anti-retroviral drugs in a cohort of therapy-naïve HIV-1 infected US military personnel.

Authors:  S A Wegner; S K Brodine; J R Mascola; S A Tasker; R A Shaffer; M J Starkey; A Barile; G J Martin; N Aronson; W W Emmons; K Stephan; S Bloor; J Vingerhoets; K Hertogs; B Larder
Journal:  AIDS       Date:  2000-05-26       Impact factor: 4.177

2.  Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J.

Authors:  E Fontaine; C Riva; M Peeters; J C Schmit; E Delaporte; K Van Laethem; K Van Vaerenbergh; J Snoeck; E Van Wijngaerden; E De Clercq; M Van Ranst; A M Vandamme
Journal:  J Acquir Immune Defic Syndr       Date:  2001-11-01       Impact factor: 3.731

3.  Drug resistance patterns, genetic subtypes, clinical features, and risk factors in military personnel with HIV-1 seroconversion.

Authors:  S K Brodine; R A Shaffer; M J Starkey; S A Tasker; J L Gilcrest; M K Louder; A Barile; T C VanCott; M T Vahey; F E McCutchan; D L Birx; D D Richman; J R Mascola
Journal:  Ann Intern Med       Date:  1999-10-05       Impact factor: 25.391

4.  Performance of Applied Biosystems ViroSeq HIV-1 Genotyping System for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda.

Authors:  M Mracna; G Becker-Pergola; J Dileanis; L A Guay; S Cunningham; J B Jackson; S H Eshleman
Journal:  J Clin Microbiol       Date:  2001-12       Impact factor: 5.948

5.  Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods.

Authors:  M Erali; S Page; L G Reimer; D R Hillyard
Journal:  J Clin Microbiol       Date:  2001-06       Impact factor: 5.948

6.  Presence of human immunodeficiency virus (HIV) type 1, group M, non-B subtypes, Bronx, New York: a sentinel site for monitoring HIV genetic diversity in the United States.

Authors:  P J Weidle; C E Ganea; K L Irwin; D Pieniazek; J P McGowan; N Olivo; A Ramos; C Schable; R B Lal; S D Holmberg; J A Ernst
Journal:  J Infect Dis       Date:  2000-02       Impact factor: 5.226

7.  Protease sequences from HIV-1 group M subtypes A-H reveal distinct amino acid mutation patterns associated with protease resistance in protease inhibitor-naive individuals worldwide. HIV Variant Working Group.

Authors:  D Pieniazek; M Rayfield; D J Hu; J Nkengasong; S Z Wiktor; R Downing; B Biryahwaho; T Mastro; A Tanuri; V Soriano; R Lal; T Dondero
Journal:  AIDS       Date:  2000-07-28       Impact factor: 4.177

8.  Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel.

Authors:  M S Hirsch; F Brun-Vézinet; R T D'Aquila; S M Hammer; V A Johnson; D R Kuritzkes; C Loveday; J W Mellors; B Clotet; B Conway; L M Demeter; S Vella; D M Jacobsen; D D Richman
Journal:  JAMA       Date:  2000-05-10       Impact factor: 56.272

9.  Genetic diversity of protease and reverse transcriptase sequences in non-subtype-B human immunodeficiency virus type 1 strains: evidence of many minor drug resistance mutations in treatment-naive patients.

Authors:  L Vergne; M Peeters; E Mpoudi-Ngole; A Bourgeois; F Liegeois; C Toure-Kane; S Mboup; C Mulanga-Kabeya; E Saman; J Jourdan; J Reynes; E Delaporte
Journal:  J Clin Microbiol       Date:  2000-11       Impact factor: 5.948

10.  Antiretroviral-drug resistance among patients recently infected with HIV.

Authors:  Susan J Little; Sarah Holte; Jean-Pierre Routy; Eric S Daar; Marty Markowitz; Ann C Collier; Richard A Koup; John W Mellors; Elizabeth Connick; Brian Conway; Michael Kilby; Lei Wang; Jeannette M Whitcomb; Nicholas S Hellmann; Douglas D Richman
Journal:  N Engl J Med       Date:  2002-08-08       Impact factor: 91.245
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  11 in total

1.  Prevalence of Rilpivirine and Etravirine Resistance Mutations in HIV-1 Subtype C-Infected Patients Failing Nevirapine or Efavirenz-Based Combination Antiretroviral Therapy in Botswana.

Authors:  Thabo Diphoko; Simani Gaseitsiwe; Ishmael Kasvosve; Sikhulile Moyo; Harriet Okatch; Rosemary Musonda; Mark Wainberg; Joseph Makhema; Richard Marlink; Vladimir Novitsky; Max Essex
Journal:  AIDS Res Hum Retroviruses       Date:  2018-06-12       Impact factor: 2.205

2.  Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent.

Authors:  Joke Snoeck; Rami Kantor; Robert W Shafer; Kristel Van Laethem; Koen Deforche; Ana Patricia Carvalho; Brian Wynhoven; Marcelo A Soares; Patricia Cane; John Clarke; Candice Pillay; Sunee Sirivichayakul; Koya Ariyoshi; Africa Holguin; Hagit Rudich; Rosangela Rodrigues; Maria Belen Bouzas; Françoise Brun-Vézinet; Caroline Reid; Pedro Cahn; Luis Fernando Brigido; Zehava Grossman; Vincent Soriano; Wataru Sugiura; Praphan Phanuphak; Lynn Morris; Jonathan Weber; Deenan Pillay; Amilcar Tanuri; Richard P Harrigan; Ricardo Camacho; Jonathan M Schapiro; David Katzenstein; Anne-Mieke Vandamme
Journal:  Antimicrob Agents Chemother       Date:  2006-02       Impact factor: 5.191

3.  Use of sequence data generated in the Bayer Tru Gene genotyping assay to recognize and characterize non-subtype-b human immunodeficiency virus type 1 strains.

Authors:  Diane L Hirigoyen; Charles P Cartwright
Journal:  J Clin Microbiol       Date:  2005-10       Impact factor: 5.948

4.  Field evaluation of a broadly sensitive HIV-1 in-house genotyping assay for use with both plasma and dried blood spot specimens in a resource-limited country.

Authors:  Seth Inzaule; Chunfu Yang; Alex Kasembeli; Lillian Nafisa; Jully Okonji; Boaz Oyaro; Richard Lando; Lisa A Mills; Kayla Laserson; Timothy Thomas; John Nkengasong; Clement Zeh
Journal:  J Clin Microbiol       Date:  2012-12-05       Impact factor: 5.948

5.  Genotyping of B and non-B subtypes of human immunodeficiency virus type 1.

Authors:  C Y W Tong; J Mullen; R Kulasegaram; A De Ruiter; S O'Shea; I L Chrystie
Journal:  J Clin Microbiol       Date:  2005-09       Impact factor: 5.948

6.  Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains.

Authors:  Susan H Eshleman; John Hackett; Priscilla Swanson; Shawn P Cunningham; Birgit Drews; Catherine Brennan; Sushil G Devare; Léopold Zekeng; Lazare Kaptué; Natalia Marlowe
Journal:  J Clin Microbiol       Date:  2004-06       Impact factor: 5.948

7.  Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system.

Authors:  Christian Paar; Christina Palmetshofer; Karin Flieger; Maria Geit; Rolf Kaiser; Herbert Stekel; Jörg Berg
Journal:  J Clin Microbiol       Date:  2008-10-22       Impact factor: 5.948

8.  Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.

Authors:  Zhiyong Zhou; Nick Wagar; Joshua R DeVos; Erin Rottinghaus; Karidia Diallo; Duc B Nguyen; Orji Bassey; Richard Ugbena; Nellie Wadonda-Kabondo; Michelle S McConnell; Isaac Zulu; Benson Chilima; John Nkengasong; Chunfu Yang
Journal:  PLoS One       Date:  2011-11-23       Impact factor: 3.240

9.  Prevalence of Drug Resistance and Associated Mutations in a Population of HIV-1(+) Puerto Ricans: 2006-2010.

Authors:  Lycely Del C Sepúlveda-Torres; Alexandra De La Rosa; Luz Cumba; Nawal Boukli; Eddy Ríos-Olivares; Luis A Cubano
Journal:  AIDS Res Treat       Date:  2012-04-24

10.  Performance of an in-house human immunodeficiency virus type 1 genotyping system for assessment of drug resistance in Cuba.

Authors:  Yoan Alemán; Lore Vinken; Vivian Kourí; Lissette Pérez; Alina Álvarez; Yeissel Abrahantes; Carlos Fonseca; Jorge Pérez; Consuelo Correa; Yudira Soto; Yoeri Schrooten; Anne-Mieke Vandamme; Kristel Van Laethem
Journal:  PLoS One       Date:  2015-02-11       Impact factor: 3.240
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