Optimization of a genotypic assay applicable to all human immunodeficiency virus type 1 protease and reverse transcriptase subtypes.

Genotypic assays are used often to guide clinicians in decisions concerning the treatment of patients. An optimized sequence-based genotypic assay was used to determine the whole protease and reverse transcriptase (RT) gene, including the gag cleavage site region and RNase H region. Since non-B subtypes are increasing in countries where subtype B was the most prevalent subtype, and treatment becomes more available in developing countries where the epidemic is characterized by a high prevalence of non-B subtypes, it was important that the genotypic test was evaluated using a panel of different subtypes. Amplification was successful for different subtypes: A, B, C, D, F, G, H, J, CRF01_AE, CRF02_AG, CRF11_cpx, CRF13_cpx and an uncharacterized recombinant sample. The detection limit of the PCR was 1000 copies/ml, except for 1 subtype C sample (PL3) and 1 CRF02_AG sample (PL8). The detection limit for these samples was 5000 copies/ml. A sequence could be obtained in both directions for most of the samples.

[1]  F. Liégeois,et al.  The Senegalese government's highly active antiretroviral therapy initiative: an 18-month follow-up study , 2002, AIDS.

[2]  B. Schmidt,et al.  Rapid, phenotypic HIV-1 drug sensitivity assay for protease and reverse transcriptase inhibitors. , 1999, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[3]  Victoria A Johnson,et al.  Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA Panel. , 2003, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[4]  Hsinyi Tsang,et al.  Amino Acid Substitutions in Gag Protein at Non-cleavage Sites Are Indispensable for the Development of a High Multitude of HIV-1 Resistance against Protease Inhibitors* , 2002, The Journal of Biological Chemistry.

[5]  E. De Clercq,et al.  Phenotypic assays and sequencing are less sensitive than point mutation assays for detection of resistance in mixed HIV-1 genotypic populations. , 1999, Journal of Acquired Immune Deficiency Syndromes.

[6]  P. Harrigan,et al.  Human Immunodeficiency Virus Type 1 Protease Cleavage Site Mutations Associated with Protease Inhibitor Cross-Resistance Selected by Indinavir, Ritonavir, and/or Saquinavir , 2001, Journal of Virology.

[7]  A. Telenti,et al.  Resistance to Nucleoside Analog Reverse Transcriptase Inhibitors Mediated by Human Immunodeficiency Virus Type 1 p6 Protein , 2001, Journal of Virology.

[8]  M. Moroni,et al.  Increasing prevalence of non-clade B HIV-1 strains in heterosexual men and women, as monitored by analysis of reverse transcriptase and protease sequences. , 2001 .

[9]  M. Peeters,et al.  Resistance to Antiretroviral Treatment in Gabon: Need for Implementation of Guidelines on Antiretroviral Therapy Use and HIV‐1 Drug Resistance Monitoring in Developing Countries , 2002, Journal of acquired immune deficiency syndromes.

[10]  J Desmyter,et al.  Evaluating Clinical Isolates for Their Phenotypic and Genotypic Resistance Against Anti-HIV Drugs. , 2000, Methods in molecular medicine.

[11]  M. Zwahlen,et al.  high Frequency of Non-b Subtypes in Newly Diagnosed Hiv-1 Infections in Switzerland , 1999 .

[12]  Diana D. Huang,et al.  Underestimation of HIV type 1 drug resistance mutations: results from the ENVA-2 genotyping proficiency program. , 2002, AIDS research and human retroviruses.

[13]  J. Saba,et al.  Virologic and immunologic outcomes and programmatic challenges of an antiretroviral treatment pilot project in Abidjan, Côte d'Ivoire , 2003, AIDS.

[14]  R K Craig,et al.  Methods in molecular medicine. , 1987, British medical journal.

[15]  M. Peeters,et al.  Identification of all HIV type 1 group M subtypes in Senegal, a country with low and stable seroprevalence. , 2000, AIDS research and human retroviruses.

[16]  J. Falloon,et al.  Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites , 1997, Journal of virology.

[17]  Soriano,et al.  Clinical and laboratory guidelines for the use of HIV-1 drug resistance testing as part of treatment management: recommendations for the European setting. The EuroGUidelines Group for HIV resistance. , 2001, AIDS.

[18]  A. Vandamme,et al.  Rising Prevalence of HIV-1 Non-B Subtypes in Belgium: 1983–2001 , 2004, Journal of acquired immune deficiency syndromes.

[19]  G. Satten,et al.  Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. , 1998, The New England journal of medicine.

[20]  S. Sarafianos,et al.  Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Pillonel,et al.  Increasing diversity of HIV‐1M serotypes in French blood donors over a 10‐year period (1985–1995) , 1997, AIDS.

[22]  M. Van Ranst,et al.  Performance of ViroSeq HIV-1 Genotyping System in routine practice at a Belgian clinical laboratory. , 2004, Journal of virological methods.

[23]  E. De Clercq,et al.  Evaluation of two commercial kits for the detection of genotypic drug resistance on a panel of HIV type 1 subtypes A through J. , 2001, Journal of acquired immune deficiency syndromes.

[24]  B. Schmidt,et al.  Quality Control Trial for Human Immunodeficiency Virus Type 1 Drug Resistance Testing Using Clinical Samples Reveals Problems with Detecting Minority Species and Interpretation of Test Results , 2003, Journal of Clinical Microbiology.

[25]  K. Hertogs,et al.  Performance of drug resistance assays in testing HIV-1 non-B subtypes. , 2003, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[26]  L. Jagodzinski,et al.  Performance Characteristics of Human Immunodeficiency Virus Type 1 (HIV-1) Genotyping Systems in Sequence-Based Analysis of Subtypes Other than HIV-1 Subtype B , 2003, Journal of Clinical Microbiology.

[27]  K. Hertogs,et al.  Clinical and laboratory guidelines for the use of HIV-1 drug resistance testing as part of treatment management: recommendations for the European setting , 2001 .

[28]  JD Lundgren,et al.  Changing patterns of mortality across Europe in patients infected with HIV-1 , 1998, The Lancet.

[29]  P. Sharp,et al.  A Comprehensive Panel of Near-Full-Length Clones and Reference Sequences for Non-Subtype B Isolates of Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.

[30]  J. Nkengasong,et al.  The puzzle of HIV‐1 subtypes in Africa , 1997, AIDS.