The role of HIV-1 transmitted/founder virus characteristics in driving pathogenesis

HIV-1 transmission is associated with a severe bottleneck in which a limited number of variants from genetically diverse quasispecies establish infection. The IAVI protocol C cohort of discordant couples, female sex workers, other heterosexuals and men who have sex with men (MSM) present varying risks of HIV infection, diverse HIV-1 subtypes and present a unique opportunity to characterize transmitted/founder viruses (TFv) where disease outcome is known. To identify the TFv, the HIV-1 repertoire of 38 MSM was sequenced close to transmission (median 21dpi) and assessment of multivariant infection, subtype and genetic polymorphisms done. Patient derived gag genes were cloned into a NL4.3 provirus to generate chimeric viruses which were characterised for replicative capacity (RC) and mechanism of spread between cells. Finally, an evaluation of how the virus characteristics that were predictors of disease progression modified the immune response at both acute and chronic HIV-1 infection was done. There was higher incidence of multivariant infection compared with previously described heterosexual cohorts. TFv predictors of CD4 T-cell decline and set-point viral load included multivariant infection, subtype, drug resistance mutations and RC. A link was identified between these characteristics and both chronic immune activation and rapid CD4+ T cell decline except in multivariant infection where perturbations were restored after control of viremia. The cell entry and CD4+ T cell depletion mechanisms by high RC TFv overlapped with those involved in cell-cell transmission but not cell free spread and involved increased expression of RNA that encodes proteins involved in apoptosis, autophagy and necrosis. Strategies aimed at mitigating persistent immune activation could contribute toward improving HIV-1 prognosis and research presented in this thesis suggests that this may involve strategies that sieve out high RC TFv and tighten the stringency of the transmission bottleneck. Furthermore, the sequences and chimeric viruses provide a useful resource in the field of immunogen design, for their utility in designing TFv peptide sets and for use in functional assays to probe effective immune responses against TFv.Open Acces

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response

Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individual's CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design as a supplement to vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.Fil: McGowan, Ed. Imperial College London; Reino UnidoFil: Rosenthal, Rachel. Francis Crick Institute; Reino UnidoFil: Fiore Gartland, Andrew. Fred Hutchinson Cancer Research Cente; Estados UnidosFil: Macharia, Gladys. Imperial College London; Reino UnidoFil: Balinda, Sheila. Uganda Virus Research Institute; UgandaFil: Kapaata, Anne. Uganda Virus Research Institute; UgandaFil: Umviligihozo, Gisele. Center for Family Health Research; RuandaFil: Muok, Erick. Center for Family Health Research; RuandaFil: Dalel, Jama. Imperial College London; Reino UnidoFil: Streatfield, Claire L.. Imperial College London; Reino UnidoFil: Coutinho, Helen. Imperial College London; Reino UnidoFil: Dilernia, Dario. University of Emory; Estados UnidosFil: Monaco, Daniela C.. University of Emory; Estados UnidosFil: Morrison, David. South Walsham; Reino UnidoFil: Yue, Ling. University of Emory; Estados UnidosFil: Hunter, Eric. University of Emory; Estados UnidosFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gilmour, Jill. Imperial College London; Reino UnidoFil: Hare, Jonathan. International Aids Vaccine Initiative; Estados Unido

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

An overview of interventions to improve compliance with appointment keeping for medical services

Objective: To determine, by a quantitative meta-analysis of randomized trials, the effectiveness of strategies to improve patient compliance with screening, referral, and clinic appointments for health services that are provided at the time of the visit. Data Sources: Computerized searches of MEDLINE (1966 through 1990) were done using two search strategies: (1) (Patient Compliance OR Adhere OR Dropout) AND (Appointment) AND (Screen OR Follow OR Refer ); and (2) (Patient Compliance OR*Adhere OR Dropout ) AND (Attend OR Screen ) OR (Appointment*). A computerized search of PSYCHLIT was done with the terms Compliance AND Appointment*. In addition, the reference list of each retrieved article was reviewed and relevant citations retrieved. Study Selection: Only randomized trials with quantitative data concerning the effect of interventions to improve attendance at appointments for supervised administration of care were considered for detailed review. Studies of appointment keeping for self-administered treatments or tests were excluded. Two independent reviewers assessed each article for inclusion (κ, for agreement, 0.66 for MEDLINE; 0.95 for PSYCHLIT) and validity (κ, 0.62) using a priori criteria. Twenty-three (26%) of 88 relevant articles met all criteria. Data Extraction: Data on study populations, interventions, and outcomes were extracted and analyzed using pooled odds ratios (ORs). Data Synthesis: The average rate of compliance with appointments was 58%. Mailed reminders and telephone prompts were consistently useful in reducing broken appointments (OR, 2.2; 95% confidence interval [Cl], 1.7 to 2.9; and OR, 2.9, Cl, 1.9 to 4.3, respectively). An orientation statement (OR, 2.9; Cl, 1.5 to 5.6), contracting with patients (OR, 1.9; Cl, 1.04 to 3.5), and prompts from physicians (OR, 1.6; Cl, 1.4 to 2.0) showed positive effects as well. Conclusions: In clinic settings where kept appointments can be an accurate measure of patient compliance with health care interventions, broken appointments can be reduced by mail, telephone, or physician reminders; orienting patients to the clinic; or contracting with patients

An overview of interventions to improve compliance with appointment keeping for medical services

Objective: To determine, by a quantitative meta-analysis of randomized trials, the effectiveness of strategies to improve patient compliance with screening, referral, and clinic appointments for health services that are provided at the time of the visit. Data Sources: Computerized searches of MEDLINE (1966 through 1990) were done using two search strategies: (1) (Patient Compliance OR Adhere OR Dropout) AND (Appointment) AND (Screen OR Follow OR Refer ); and (2) (Patient Compliance OR*Adhere OR Dropout ) AND (Attend OR Screen ) OR (Appointment*). A computerized search of PSYCHLIT was done with the terms Compliance AND Appointment*. In addition, the reference list of each retrieved article was reviewed and relevant citations retrieved. Study Selection: Only randomized trials with quantitative data concerning the effect of interventions to improve attendance at appointments for supervised administration of care were considered for detailed review. Studies of appointment keeping for self-administered treatments or tests were excluded. Two independent reviewers assessed each article for inclusion (κ, for agreement, 0.66 for MEDLINE; 0.95 for PSYCHLIT) and validity (κ, 0.62) using a priori criteria. Twenty-three (26%) of 88 relevant articles met all criteria. Data Extraction: Data on study populations, interventions, and outcomes were extracted and analyzed using pooled odds ratios (ORs). Data Synthesis: The average rate of compliance with appointments was 58%. Mailed reminders and telephone prompts were consistently useful in reducing broken appointments (OR, 2.2; 95% confidence interval [Cl], 1.7 to 2.9; and OR, 2.9, Cl, 1.9 to 4.3, respectively). An orientation statement (OR, 2.9; Cl, 1.5 to 5.6), contracting with patients (OR, 1.9; Cl, 1.04 to 3.5), and prompts from physicians (OR, 1.6; Cl, 1.4 to 2.0) showed positive effects as well. Conclusions: In clinic settings where kept appointments can be an accurate measure of patient compliance with health care interventions, broken appointments can be reduced by mail, telephone, or physician reminders; orienting patients to the clinic; or contracting with patients

Is this patient taking the treatment as prescribed?

CLINICAL SCENARIOS Case 1 A 28-year-old woman presents to the emergency department in acute distress with a 3-day history of worsening asthma. Her prescribed medications include an inhaled β2-agonist and an inhaled steroid. When questioned, she breathlessly admits to occasionally missing her medications but indicates that this is maybe only once or twice. Case 2 A 55-year-old man with posttraumatic seizure disorder has been taking phenytoin since his injury. His seizures were initially adequately controlled but he recently has been having weekly seizures. In an office visit he resentfully denies missing any of his medication. THE IMPORTANCE OF CLINICAL EXAMINATION Physicians should measure compliance for patients prescribed a self-administered treatment because noncompliance is common and physicians can help patients to improve their compliance1,2 and increase the benefit they derive from therapy. Compliance with long-term self-administered medication therapy is approximately 50% for those who remain in care.

Control of Viremia Enables Acquisition of Resting Memory B Cells with Age and Normalization of Activated B Cell Phenotypes in HIV-Infected Children.

HIV affects the function of all lymphocyte populations, including B cells. Phenotypic and functional defects of B cells in HIV-infected adults have been well characterized, but defects in children have not been studied to the same extent. We determined the proportion of B cell subsets and frequencies of Ag-specific memory B cells in peripheral blood from HIV-infected children and healthy controls, using flow cytometry and B cell ELISPOT, respectively. In addition, we measured the quantities and avidities of plasma Abs against various Ags by ELISA. We also determined plasma levels of BAFF and expression of BAFF receptors on B cells. Children with high HIV viremia had increased proportions of activated mature B cells, tissue-like memory B cells and plasmablasts, and low proportions of naive B cells when compared with community controls and children with low HIV viremia, similar to adults infected with HIV. HIV-infected groups had lower proportions of resting memory B cells than did community controls. Notably, high HIV viremia prevented the age-dependent accumulation of class-switched resting memory B cells. HIV-infected children, regardless of the level of viremia, showed lower quantities and avidities of IgG and lower frequencies of memory B cells against Expanded Program on Immunization vaccines. The HIV-infected children had an altered BAFF profile that could have affected their B cell compartment. Therefore, B cell defects in HIV-infected children are similar to those seen in HIV-infected adults. However, control of HIV viremia is associated with normalization of activated B cell subsets and allows age-dependent accumulation of resting memory B cells

Infection with HIV-1 subtype D among acutely infected Ugandans is associated with higher median concentration of cytokines compared to subtype A.

OBJECTIVE: The observation that HIV-1 subtype D progresses faster to disease than subtype A prompted us to examine cytokine levels early after infection within the predominant viral subtypes that circulate in Uganda and address the following research questions: (1) Do cytokine levels vary between subtypes A1 and D? (2) Do cytokine profiles correlate with disease outcomes? METHODS: To address these questions, HIV-1 subtypes were determined by population sequencing of the HIV-1 pol gene and 37 plasma cytokine concentrations were evaluated using V-Plex kits on Meso Scale Discovery platform in 65 recent sero-converters. RESULTS: HIV-1 subtype D (pol) infections exhibited significantly higher median plasma concentrations of IL-5, IL-16, IL-1α, IL-7, IL-17A, CCL11 (Eotaxin-1), CXCL10 (IP-10), CCL13 (MCP-4) and VEGF-D compared to subtype A1 (pol) infections. We also found that IL-12/23p40 and IL-1α were associated with faster CD4+T cell count decline, while bFGF was associated with maintenance of CD4+ counts above 350 cells/microliter. CONCLUSION: Our results suggest that increased production of cytokines in early HIV infection may trigger a disruption of the immune environment and contribute to pathogenic mechanisms underlying the accelerated disease progression seen in individuals infected with HIV-1 subtype D in Uganda

In the HIV-infected cohort, proportions of total follicular-homing CD4 T cells are directly correlated with CD4 percentages.

<p>Correlation analyses between CD4 T cells (as percentage of total lymphocytes) and: (A) total follicular-homing CD4 T cells (CXCR5⁺CD4⁺), (B) memory follicular-homing CD4 T cells (CXCR5⁺CD45RO⁺CD4⁺), (C) memory T_FH cells (CXCR5⁺CD45RO⁺PD1⁺CD4⁺), (D) central memory follicular-homing CD4 T cells (CXCR5⁺CD45RO⁺CCR7⁺CD4⁺), (E) effector memory follicular-homing CD4 T cells (CXCR5⁺CD45RO⁺CCR7^-CD4⁺), (F) central memory T_FH cells (CXCR5⁺CD45RO⁺PD1⁺CCR7⁺CD4⁺) and (G) effector memory T_FH cells (CXCR5⁺CD45RO⁺PD1⁺CCR7^-CD4⁺). Circles represent highly viremic children and squares represent lowly viremic children. Red symbols represent HAART-naïve children and blue symbols represent HAART-treated children. Statistical test: Spearman’s rank-order correlation.</p