Use of drug resistance sequence data for the systematic detection of non-B human immunodeficiency virus type 1 (HIV-1) subtypes: how to create a sentinel site for monitoring the genetic diversity of HIV-1 at a country scale.
To assess the molecular epidemiology of human immunodeficiency virus type 1 (HIV-1), a screening method was developed for identification of non-B subtypes from sequence data obtained for resistance testing. The method is based on the evaluation of the percentage of divergence of a given sequence from the reference B subtype HXB2. Analysis of 1720 reverse-transcriptase (RT) and 1824 protease sequences stored in a database allowed for the determination of a threshold level of divergence from HXB2 above which a non-B subtype could be unambiguously characterized regardless of the pattern of resistance mutations (>8.6% for RT; >10.8% for protease). This conclusion was validated by phylogenetic analysis of RT, protease, and env genes. Overall, 72 (4.2%) and 73 (4.0%) non-B sequences were identified in the RT and protease coding regions, respectively. This method allows for the rapid detection of non-B subtypes among retrospective, recent, and future RT and/or protease sequence databases.
Yahi
N
N
Laboratoire de Virologie, Faculté des Sciences, CHRU La Timone, Rue saint Pierre 13005, Marseille, France.
Fantini
J
J
Tourres
C
C
Tivoli
N
N
Koch
N
N
Tamalet
C
C
D000293:Adolescent; D000328:Adult; D000368:Aged; D016000:Cluster Analysis; D015331:Cohort Studies; D004351:Drug Resistance / Q000235:genetics; D005260:Female; D005602:France / Q000453:epidemiology; D015752:Genes, env / Q000235:genetics; D014644:Genetic Variation; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D016333:HIV Protease / Q000032:analysis / Q000235:genetics*; D054303:HIV Reverse Transcriptase / Q000032:analysis / Q000235:genetics*; D015497:HIV-1 / Q000145:classification / Q000201:enzymology / Q000235:genetics; D006801:Humans; D016130:Immunophenotyping; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D017421:Sequence Analysis
D054303:HIV Reverse Transcriptase; D016333:HIV Protease