High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C: Implications for use of whole blood DNA in resource-limited settings

Soham Gupta, Ujjwal Neogi, Hiresave Srinivasa, Anita Shet

Research output: Contribution to journalArticle

Abstract

Objectives: Genotypic tropism testing (GTT) of HIV is increasingly used prior to the initiation of CCR5 antagonist therapy in HIV-infected individuals. Normally performed on plasma-derived virus, the test is challenging when performed in patients with suppressed viraemia. We aimed to evaluate the performance of cell-associated proviral DNA against plasma-derived viral RNA as the genetic material for GTT in an Indian clinical setting. Methods: From 52 HIV-1-infected individuals, the env V3 region was successfully amplified and sequenced from both proviral DNA and plasma RNA paired samples having a viral load.2500 copies/mL (n 1/4 42) and from proviral DNA only in 10 antiretroviral therapy (ART)-experienced patients with a viral load, 500 copies/mL. GTT was performed using the Geno2Pheno algorithm with the interpretative false positive rate (FPR) cut-offof 10%. Results: Among paired samples, 40 of 42 patients harboured subtype C strains. Plasma RNA tropism prediction revealed X4 tropism in 4 of 42 (9.5%). A high concordance of 97.6% in tropism prediction was noted in simultaneous RNA/DNA samples (38 R5 and 3 X4). Discordance was observed in one sample showing R5 tropism in proviral DNA and X4 tropism in plasma RNA. Comparison of Geno2Pheno FPRs in both the plasma and proviral compartments showed good correlation (overall, r 1/4 0.87; ART-naive patients, r 1/4 0.79; ART-failing patients, r 1/4 0.97). GTT was successfully performed in all 10 whole blood DNA samples having a viral load, 500 copies/mL, all showing R5 tropism. Conclusions: High concordance in tropism prediction from proviral DNA and plasma-viral RNA suggests that prediction of viral tropism using proviral DNA is accurate and feasible in resource-limited clinical settings, particularly in patients with low or suppressed viraemia.

Original languageEnglish (US)
Article numberdkt138
Pages (from-to)2003-2006
Number of pages4
JournalJournal of Antimicrobial Chemotherapy
Volume68
Issue number9
DOIs
StatePublished - Sep 2013
Externally publishedYes

Fingerprint

Tropism
Viral RNA
HIV-1
DNA
RNA
Viremia
Viral Load
Viral Tropism
HIV
Therapeutics
Viruses

Keywords

  • Geno2Pheno
  • Genotypic tropism testing
  • HIV

ASJC Scopus subject areas

  • Pharmacology
  • Pharmacology (medical)
  • Infectious Diseases

Cite this

High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C : Implications for use of whole blood DNA in resource-limited settings. / Gupta, Soham; Neogi, Ujjwal; Srinivasa, Hiresave; Shet, Anita.

In: Journal of Antimicrobial Chemotherapy, Vol. 68, No. 9, dkt138, 09.2013, p. 2003-2006.

Research output: Contribution to journalArticle

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abstract = "Objectives: Genotypic tropism testing (GTT) of HIV is increasingly used prior to the initiation of CCR5 antagonist therapy in HIV-infected individuals. Normally performed on plasma-derived virus, the test is challenging when performed in patients with suppressed viraemia. We aimed to evaluate the performance of cell-associated proviral DNA against plasma-derived viral RNA as the genetic material for GTT in an Indian clinical setting. Methods: From 52 HIV-1-infected individuals, the env V3 region was successfully amplified and sequenced from both proviral DNA and plasma RNA paired samples having a viral load.2500 copies/mL (n 1/4 42) and from proviral DNA only in 10 antiretroviral therapy (ART)-experienced patients with a viral load, 500 copies/mL. GTT was performed using the Geno2Pheno algorithm with the interpretative false positive rate (FPR) cut-offof 10{\%}. Results: Among paired samples, 40 of 42 patients harboured subtype C strains. Plasma RNA tropism prediction revealed X4 tropism in 4 of 42 (9.5{\%}). A high concordance of 97.6{\%} in tropism prediction was noted in simultaneous RNA/DNA samples (38 R5 and 3 X4). Discordance was observed in one sample showing R5 tropism in proviral DNA and X4 tropism in plasma RNA. Comparison of Geno2Pheno FPRs in both the plasma and proviral compartments showed good correlation (overall, r 1/4 0.87; ART-naive patients, r 1/4 0.79; ART-failing patients, r 1/4 0.97). GTT was successfully performed in all 10 whole blood DNA samples having a viral load, 500 copies/mL, all showing R5 tropism. Conclusions: High concordance in tropism prediction from proviral DNA and plasma-viral RNA suggests that prediction of viral tropism using proviral DNA is accurate and feasible in resource-limited clinical settings, particularly in patients with low or suppressed viraemia.",
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