PubMed · 7603070
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J B Thomison. 1995. Rolling the dice.. https://pubmed.ncbi.nlm.nih.gov/7603070/
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BACKGROUND: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention. RESULTS: We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9 years, with a mean absolute error of less than 12 months overall and less than 5 months for infections with a TSI of up to a year. It performs equally well for all major HIV subtypes based on data from African and European cohorts. CONCLUSIONS: We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.
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HIV-1 viremia is a marker of choice for staging, prognosis, and monitoring treatment efficiency in HIV infection. Among the commercial assays, the Amplicor HIV Monitor (Roche, Basel, Switzerland) test has the highest sensitivity for HIV-1 RNA quantitation in plasma with a detection limit of 200 copies per milliliter. To measure HIV-1 viremia below this threshold, boosted versions of the Amplicor assay were developed by adding a centrifugation step prior to RNA extraction and by decreasing dilution factors. In the boosted version, the increase in analytical sensitivity for HIV-1 RNA detection directly correlates with the input of plasma. For 1,500 microl of plasma, the sensitivity of the assay increases by a factor of 30. For routine clinical analysis, we use a boosted assay format with an input plasma volume of 500 microl and a lower detection limit of 20 copies/milliliter. Coefficients of intra- and interassay variation are similar to those reported for the standard assay (approximately 30%). Thirteen (45%) of 29 plasma samples of HIV-infected individuals with undetectable viremia in the standard assay had detectable viremia between 20 and 200 copies/milliliter.