ArticleJournal of clinical microbiology2013
Genotypic prediction of HIV-1 CRF01-AE tropism.
Article in Journal of clinical microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Frequent Detection of HIV-1 Variants With Mixed Coreceptor Usage Among People Who Inject Drugs Infected With CRF01_AE: Possible Association With Coreceptor Switch.Open forum infectious diseases · 2026Article
- Prediction of the Co-receptor usage of the main worldwide HIV-1 subtypes, CRF, and CRF35-AD in Iranian patients via the five genotypic tools.Biochemistry and biophysics reports · 2025Article
- Critical amino acid residues and potential N-linked glycosylation sites contribute to circulating recombinant form 01_AE pathogenesis in Northeast China.AIDS (London, England) · 2019Article
- Novel Strategy To Adapt Simian-Human Immunodeficiency Virus E1 CarryingJournal of virology · 2018Article
- Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use.Scientific reports · 2017Article
- Possible involvement of distinct phylogenetic clusters of HIV-1 variants in the discrepancies between coreceptor tropism predictions based on viral RNA and proviral DNA.Journal of pharmaceutical health care and sciences · 2016Article
- Position-specific automated processing of V3 env ultra-deep pyrosequencing data for predicting HIV-1 tropism.Scientific reports · 2015Article
- Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate.BMC infectious diseases · 2015Article
- Antiretroviral-Experienced HIV-1-Infected Patients Treated with Maraviroc: Factors Associated with Virological Response.AIDS research and human retroviruses · 2015Observational
- Reliable genotypic tropism tests for the major HIV-1 subtypes.Scientific reports · 2015Article
- High proportion of HIV serodiscordance among HIV-affected married couples in northern Vietnam.PloS one · 2015Article
- Bioinformatic analysis of HIV-1 entry and pathogenesis.Current HIV research · 2014Review
- Article
- Algorithm-based prediction of HIV-1 subtype D coreceptor use.Journal of clinical microbiology · 2013Article
- Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HIV-1 subtype CRF01-AE predominates in south Asia and has spread throughout the world. The virus tropism must be determined before using CCR5 antagonists. Genotypic methods could be used, but the prediction algorithms may be inaccurate for non-B subtypes like CRF01-AE and the correlation with the phenotypic approach has not been assessed. We analyzed 61 CRF01-AE V3 clonal sequences of known phenotype from the GenBank database. The sensitivity of the Geno2pheno10 genotypic algorithm was 91%, but its specificity was poor (54%). In contrast, the combined 11/25 and net charge rule was highly specific (98%) but rather insensitive (64%). We thus identified subtype CRF01-AE determinants in the V3 region that are associated with CXCR4 use and developed a new simple rule for optimizing the genotypic prediction of CRF01-AE tropism. The concordance between the predicted CRF01-AE genotype and the phenotype was 95% for the clonal data set. We then validated this algorithm by analyzing the data from 44 patients infected with subtype CRF01-AE, whose tropism was determined using a recombinant phenotypic entry assay and V3-loop bulk sequencing. The CRF01-AE genotypic tool was 70% sensitive and 96% specific for predicting CXCR4 use, and the concordance between genotype and phenotype was 84%, approaching the concordance obtained for predicting the tropism of HIV-1 subtype B. Genotypic predictions that use a subtype CRF01-AE-specific algorithm appear to be preferable for characterizing coreceptor usage both in pathophysiological studies and for ensuring the appropriate use of CCR5 antagonists.
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