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Related Experiment Video

Updated: Jun 2, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

Martin Däumer1, Rolf Kaiser, Rolf Klein

  • 1Institute of Immunology and Genetics, Pfaffplatz 10, 67655 Kaiserslautern, Germany.

BMC Medical Informatics and Decision Making
|May 17, 2011
PubMed
Summary

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Massively parallel sequencing (MPS) significantly improves the prediction of CXCR4-using (X4) viral variants in HIV patients. This sensitive method detects minor variants, enhancing genotypic tropism prediction accuracy compared to bulk sequencing.

Area of Science:

  • Virology
  • Genetics
  • Infectious Diseases

Background:

  • Genotypic inference of viral tropism is a cost-effective alternative to phenotypic testing.
  • Standard bulk sequencing lacks sensitivity for detecting minor CXCR4-using (X4) variants in clinical isolates.
  • Massively parallel sequencing (MPS) offers enhanced sensitivity for detecting minor viral clones.

Purpose of the Study:

  • To improve the accuracy of genotypic prediction of HIV coreceptor usage.
  • To evaluate the utility of MPS for detecting minor CXCR4-using (X4) variants.
  • To enhance the sensitivity of tropism prediction in clinical isolates.

Main Methods:

  • Plasma samples from 55 HIV patients were analyzed using standard bulk sequencing and MPS.
  • Coreceptor usage was determined using the Monogram Trofile Assay.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

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Last Updated: Jun 2, 2026

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3
11:10

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
05:53

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

  • Tropism was predicted using the geno2pheno[coreceptor] algorithm.

    • Main Results:

    • Bulk sequencing showed 59.1% sensitivity and 90.9% specificity for tropism prediction.
    • MPS detected minor CXCR4-using (X4) variants in all analyzed isolates.
    • Using MPS with a 5% minority cutoff achieved high concordance with phenotypic testing.

    Conclusions:

    • Combining MPS with genotypic prediction provides a sensitive and accurate alternative to phenotypic tropism assays.
    • The presence of minor X4 variants is significant for treatment outcomes.
    • This approach may enable better prediction of response to CCR5-antagonists.