title: Comparison of susceptibility of HIV-1 variants to antiretroviral drugs by genotypic and recombinant virus phenotypic analyses.
abstract: OBJECTIVE
  This study utilized genotypic and in-house recombinant virus phenotypic assays to examine HIV-1 variant susceptibility to antiretroviral (ARV) drugs; comparisons were made between the analyses.
  
  
  METHODS
  A nested PCR was employed to amplify the HIV-1 gag-pol gene, which comprised the entire PR gene (codons 1-99) and the former RT gene (codons 1-312). Genetic resistance was determined by submitting the sequences to the Stanford University Network HIV-1 Database. Phenotypic susceptibilities to six ARV drugs were measured using a high-throughput, multi-cycle, recombinant virus phenotypic assay. Results were expressed in terms of the IC50 (half maximal inhibitory concentration) and fold-change values. The relationship between phenotypic drug resistance and genetic polymorphisms was determined.
  
  
  RESULTS
  Nineteen fragment sequences for which recombinant viruses were successfully constructed were translated and compared with the consensus B sequences in the Stanford University Network HIV-1 Database. No recognizable genotypic resistance-associated mutations were noted, except in one sample. Each homologous replication-competent recombinant viral fold-change in the presence of six ARV drugs used widely in China was measured. According to the clinical and statistical criteria, 16 of the 19 samples were susceptible to the six drugs tested. The majority of phenotypic and genotypic results obtained were in agreement, with a concordance rate of 97.4%. Both phenotypic and genotypic assays suggested that sample HN2009001 was resistant to all drugs tested. All phenotypic and genotypic results obtained regarding the susceptibility of the 19 recombinant viruses to nucleoside reverse transcriptase inhibitors (NRTIs) were in agreement. With regard to the genotypic results for the non-nucleoside reverse transcriptase inhibitors (NNRTIs), 7.9% (3/38) were inconsistent with the phenotypic results.
  
  
  CONCLUSIONS
  The in-house recombinant virus phenotypic assay was able to provide a straightforward quantitative assessment of resistance. In most cases, the genotypic and novel phenotypic assays yielded similar results. The disparity in HIV-1 susceptibility indicates a need to further investigate the clinical outcomes of antiretroviral therapy in certain individuals.
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Chang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Daomin
authors.initials: D
authors.lastname: Zhuang
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Jingyun
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Siyang
authors.initials: S
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Hanping
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Jingwan
authors.initials: J
authors.lastname: Han
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Yongjian
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Zuoyi
authors.initials: Z
authors.lastname: Bao
authors.affiliation: State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Science, Beijing, China.
authors.forename: Tianyi
authors.initials: T
authors.lastname: Li
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China. Electronic address: hongbinsong@263.net.
authors.forename: Hongbin
authors.initials: H
authors.lastname: Song
authors.affiliation: Institute of Disease Control and Prevention, Academy of Military Medical Science, Beijing, 100071, China. Electronic address: zhangwf@nic.bmi.ac.cn.
authors.forename: Wenfu
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000163:Acquired Immunodeficiency Syndrome / Q000821:virology; D019380:Anti-HIV Agents / Q000494:pharmacology*; D024882:Drug Resistance, Viral; D005260:Female; D005838:Genotype; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D009154:Mutation; D010641:Phenotype; D011110:Polymorphism, Genetic; D018894:Reverse Transcriptase Inhibitors / Q000494:pharmacology
chemical_list: D019380:Anti-HIV Agents; D018894:Reverse Transcriptase Inhibitors
keywords: Antiretroviral therapy; Genetic mutations; HIV/AIDS; Phenotypic drug resistance