Browsing by Author "Michael, Nelson L."

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    Elevated Natural Killer Cell Activity Despite Altered Functional and Phenotypic Profile in Ugandans With HIV-1 Clade A or Clade D Infection
    (JAIDS Journal of Acquired Immune Deficiency Syndromes, 2009) Eller, Michael A.; Eller, Leigh Anne; Ouma, Benson J.; Thelian, Doris; Gonzalez, Veronica D.; Guwatudde, David; McCutchan, Francine E.; Marovich, Mary A.; Michael, Nelson L.; Souza, Mark S. de; Wabwire-Mangen, Fred; Robb, Merlin L.; Currier, Jeffrey R.; Sandberg, Johan K.
    Natural killer (NK) cells most likely contribute toward limiting HIV-1 replication, and investigation into their function throughout the course of infection is therefore important. We here aimed to determine the state of the NK cell compartment in Ugandans with untreated HIV-1 clade A or D infection in comparison with matched uninfected controls. Methods and Results: The function and phenotype of NK cells were investigated using 10-color flow cytometry. Surprisingly, NK cells displayed elevated production of interferon-g and macrophage inflammatory protein 1b, as well as CD107a degranulation in infected subjects. This included unexpected levels of degranulation in the CD56bright subset of NK cells and high levels of macrophage inflammatory protein 1b in CD56negative NK cells. HIV-1 infection was associated with reduced expression of KIR2DL1, NKG2A, CD161, and NKp30 in CD56dim and CD56negative NK cells, whereas lowered CD161 expression was the only alteration in the CD56bright subset. Interestingly, low CD4 counts were associated with increased levels of interferon-g and degranulation in CD56bright NK cells, as well as increased NKp44 expression in the CD56dim cells. NK cells in HIV-1–infected Ugandans display elevated activity, despite an altered functional and phenotypic profile. Furthermore, specific alterations in the CD56bright and CD56dim subsets occur in patients with severe CD4 loss.
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    Factors influencing estimates of HIV-1 infection timing using BEAST
    (PLOS Computational Biology, 2021) Dearlove, Bethany; Tovanabutra, Sodsai; Owen, Christopher L.; Kibuuka, Hannah; Maganga, Lucas; Michael, Nelson L.; Robb, Merlin L.; Rolland, Morgane
    While large datasets of HIV-1 sequences are increasingly being generated, many studies rely on a single gene or fragment of the genome and few comparative studies across genes have been done. We performed genome-based and gene-specific Bayesian phylogenetic analyses to investigate how certain factors impact estimates of the infection dates in an acute HIV-1 infection cohort, RV217. In this cohort, HIV-1 diagnosis corresponded to the first RNA positive test and occurred a median of four days after the last negative test, allowing us to compare timing estimates using BEAST to a narrow window of infection. We analyzed HIV-1 sequences sampled one week, one month and six months after HIV-1 diagnosis in 39 individuals. We found that shared diversity and temporal signal was limited in acute infection, and insufficient to allow timing inferences in the shortest HIV-1 genes, thus dated phylogenies were primarily analyzed for env, gag, pol and near full-length genomes. There was no one best-fitting model across participants and genes, though relaxed molecular clocks (73% of best-fitting models) and the Bayesian skyline (49%) tended to be favored. For infections with single founders, the infection date was estimated to be around one week pre-diagnosis for env (IQR: 3–9 days) and gag (IQR: 5–9 days), whilst the genome placed it at a median of 10 days (IQR: 4–19). Multiply-founded infections proved problematic to date. Our ability to compare timing inferences to precise estimates of HIV-1 infection (within a week) highlights that molecular dating methods can be applied to withinhost datasets from early infection. Nonetheless, our results also suggest caution when using uniform clock and population models or short genes with limited information content.
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    Human Immunodeficiency Virus Type 1 Infection Is Associated with Increased NK Cell Polyfunctionality and Higher Levels of KIR3DL1+ NK Cells in Ugandans Carrying the HLA-B Bw4 Motif
    (The Journal of infectious diseases, 2000) Eller, Michael A.; Koehler, Rebecca N.; Kijak, Gustavo H.; Anne Eller, Leigh; Guwatudde, David; Marovich, Mary A.; Michael, Nelson L.; de Souza, Mark S.; Wabwire-Mangen, Fred; Robb, Merlin L.; Currier, Jeffrey R.; Sandberg, Johan K.
    Natural killer (NK) cells are important innate effector cells controlled by an array of activating and inhibitory receptors. Some alleles of the inhibitory killer-cell immunoglobulin-like receptor KIR3DL1 in combination with its HLA class I ligand Bw4 have been genetically associated with slower HIV-1 disease progression. Here, we observed that the presence of HLA-B Bw4 was associated with elevated frequencies of KIR3DL1 CD56dim NK cells in chronically HIV-1-infected individuals from the rural district of Kayunga, Uganda. In contrast, levels of KIR2DL1 CD56dim NK cells were decreased, and levels of KIR2DL3 CD56dim NK cells were unchanged in infected subjects carrying their respective HLA-C ligands. Furthermore, the size of the KIR3DL1 NK cell subset correlated directly with viral load, and this effect occurred only in HLA-B Bw4 patients, suggesting that these cells expand in response to viral replication but may have relatively poor antiviral capacity. In contrast, no association with viral load was present for KIR2DL1 and KIR2DL3 NK cells. Interestingly, chronic HIV-1 infection was associated with an increased polyfunctional response in the NK cell compartment, and, upon further investigation, KIR3DL1 CD56dim NK cells exhibited a significantly increased functional response in the patients carrying HLA-B Bw4. These results indicate that chronic HIV-1 infection is associated with increased NK cell polyfunctionality and elevated levels of KIR3DL1 NK cells in Ugandans carrying the HLA-B Bw4 motif.
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    Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
    (PLoS Pathog, 2020) Rolland, Morgane; Tovanabutra, Sodsai; Dearlove, Bethany; Li, Yifan; Kibuuka, Hannah; Maganga, Lucas; Michael, Nelson L.; Robb, Merlin L.
    Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is crucial information for studies that document transmission networks or drug levels at infection. To improve infection timing, we used the prospective RV217 cohort where the window when plasma viremia becomes detectable is narrow: the last negative visit occurred a median of four days before the first detectable HIV-1 viremia with an RNA test, referred below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequencebased methods and a viral load regression method. Bayesian coalescent and viral load regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR: 9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of hamming distances among sequences, estimated a median of 7 days prior to diagnosis (IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield plausible results using sequences sampled at 32 days. Fourteen participants reported a high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior). These different methods concurred that HIV-1 infection occurred about a week before detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load.
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    Single-Cell Level Response of HIV-Specific and Cytomegalovirus-Specific CD4 T Cells Correlate With Viral Control in Chronic HIV-1 Subtype A Infection
    (JAIDS Journal of Acquired Immune Deficiency Syndromes, 2012) Eller, Michael A.; Eller, Leigh Anne; Ratto-Kim, Silvia; Ouma, Benson J.; Lo, Vicky; Souza, Mark de; Guwatudde, David; Nails, Barbara; Michael, Nelson L.; Wabwire-Mangen, Fred; Robb, Merlin L.; Marovich, Mary A.; Sandberg, Johan K.; Currier, Jeffrey R.
    HIV-1 subtype A is the second most prevalent subtype globally and is associated with reduced viral load, higher CD4 absolute counts, and slower disease progression. To study the possible role of T cells associated with better outcome, we examined CD4 and CD8 T-cell responses against HIV-1 and cytomegalovirus (CMV) in Ugandans infected with subtype A HIV-1. Methods: T-cell responses were investigated using flow cytometry and novel subtype A variant inclusive peptide (VIP) sets designed for this evaluation. CD4 T-cell responses focused primarily on Gag, whereas CD8 T-cell responses were broadly directed against Gag, gp41, and Nef VIP sets. CD4 T cells primarily responded with interferon (IFN)-g, whereas CD8 cells were more diverse with degranulation (CD107a), IFN-g, and macrophage inflammatory protein (MIP)-1b production. Results: No relationship was observed between CD8 T-cell responses and the HIV-1 load. Similarly, the frequency of CD4 T cells responding to these antigens did not associate with viral control. However, in CD4 T cells responding against Gag or CMV, the IFN-g intensity, indicative of the production at the singlecell level, was inversely proportional to viral load. No significant relationship was found between T-cell effector/memory phenotype and viral control. Conclusions: The per cell production of IFN-g in CD4 T cells responding to HIV-1 or CMV correlated with viral control in chronic HIV-1 subtype A infection. These data suggest that quantitative aspects at the single-cell level may be more important than the frequency of antigen-specific CD4 T cells in HIV-1 subtype A infection control.