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Performance evaluation of a laboratory developed PCR test for quantitation of HIV-2 viral RNA

Citation

Jagodzinski, Linda et al. (2020), Performance evaluation of a laboratory developed PCR test for quantitation of HIV-2 viral RNA, Dryad, Dataset, https://doi.org/10.5061/dryad.95x69p8fx

Abstract

Management of Human Immunodeficiency Virus Type 2 (HIV-2) infections present unique challenges due to low viral titers, slow disease progression, and poor response to standard antiviral therapies.  The need for a nucleic acid assay to detect and quantify HIV-2 virus has led to the development of a number of molecular-based assays for detection and/or quantification of HIV-2 viral RNA in plasma in order to provide laboratory evidence of HIV-2 infection and viral loads for use in treatment decisions.  As HIV-2 is less pathogenic and transmissible than HIV-1 and has resistance to several of the antiretroviral drugs, delay of treatment is common. Cross sero-reactivity between HIV-1 and HIV-2 makes it difficult to distinguish between the two viruses based upon serological tests.  As such we developed a quantitative reverse transcription PCR (qRT-PCR) assay targeting the 5’ long terminal repeat of HIV-2 for detection and quantification of HIV-2 viral RNA in plasma to identify HIV-2 infection and for use in viral load monitoring.  Serial dilutions of cultured HIV-2 virus demonstrated a wide dynamic range (10 to 100,000 copies/ml) with excellent reproducibility (standard deviation from 0.12 - 0.19), linearity (R2 = 0.9994), and a lower limit of detection at 79 copies/ml (NIH-Z).  The assay is highly specific for HIV-2 Groups A and B and exhibits no cross reactivity to HIV-1, HBV or HCV.  Precision of the assay was demonstrated for the High (Mean = 6.41; SD = 0.12) and Medium (Mean = 4.46; SD = 0.13) HIV-2 positive controls.  Replicate testing of clinical specimens showed good reproducibility above 1,000 copies/ml, with higher variability under 1,000 copies/ml.  Analysis of 220 plasma samples from HIV-2 infected West African individuals demonstrated significantly lower viral loads than those observed in HIV-1 infections,  consistent with results of previous studies.  Slightly more than seven percent of clinical samples (7.3%) demonstrated viral loads above 100,000 copies/ml, while 37.3%  of samples were undetectable.  The high sensitivity, specificity, precision, and linearity of the WRAIR qRT-PCR assay makes it well suited for detection and monitoring of HIV-2 RNA levels in plasma of infected individuals.

Methods

Real-time quantiative RT-PCR results from 7500 Fast DX. Data converted to copies/ml or log10-transformed for analysis. Data analysis completed and included in PLOS ONE publication as Figures 1 - 6.

Usage Notes

One data point is missing in Figure 1 data.

Otherwise data is complete for Figures in PLOS ONE publication.

Funding

Medical Research and Materiel Command, Award: W81-XWH-11-2-0-0174