PubMed · 1607291
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P Carr. Buying time.. https://doi.org/10.1097/00004045-199205000-00011
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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.
OBJECTIVES: To determine how representative the genotype of HIV-1 circulating in plasma is of the genotype of the virus present in lymphoid tissue. METHODS: Paired plasma and tonsillar tissue samples were prospectively obtained from patients with various levels of plasma HIV-1 RNA who were receiving combination antiretroviral therapy. HIV-1 reverse transcriptase and protease sequences were amplified from plasma and lymphoid tissue specimens by nested polymerase chain reaction and analyzed using an automated sequencing system. Results were compared with consensus HIV-1 sequences to determine whether drug-resistance mutations were present in the regions analyzed. RESULTS: HIV-1 protease sequences were compared in 11 plasma/tissue pairs obtained from eight patients; HIV reverse transcriptase sequences were compared in 12 plasma/tissue pairs obtained from nine patients. Sequence homology between plasma and tissue RNA, tissue RNA and DNA, and plasma and tissue DNA ranged from 97% to 100%. Few discrepancies were found when the percentage of mutant sequences at resistance codons was compared among paired samples. In most instances, tissue RNA or plasma contained a higher percentage of mutant sequences than did tissue DNA. CONCLUSION: The genotype of plasma HIV-1 is similar to the genotype of the virus in lymphoid tissue. Resistance studies using plasma samples should provide accurate information regarding the genotype of HIV-1 in lymphoid tissues.
T-lymphocytes expressing the gamma delta T-cell receptor (TCR) comprise a small proportion (1-5%) of circulating CD3(+) T-lymphocytes. While T-cells expressing a V delta 2V gamma 9-encoded TCR dominate among peripheral blood gamma delta T-lymphocytes in healthy individuals, significant alterations in the gamma delta TCR repertoire are observed in HIV-infected persons. These changes are due to the selective preservation (and frequently moderate expansion) of V delta 1-expressing cells and the simultaneous depletion of V delta 2-expressing cells. In this brief review, we discuss the alterations in the gamma delta T-lymphocyte compartment in HIV infection, with special emphasis on the potential role of gamma delta T-cell in the immune defense against HIV.