Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19.

Acute viral infections can have durable functional impacts on the immune system long after recovery, but how they affect homeostatic immune states and responses to future perturbations remain poorly understood1-4. Here we use systems immunology approaches, including longitudinal multimodal single-cell analysis (surface proteins, transcriptome and V(D)J sequences) to comparatively assess baseline immune statuses and responses to influenza vaccination in 33 healthy individuals after recovery from mild, non-hospitalized COVID-19 (mean, 151 days after diagnosis) and 40 age- and sex-matched control individuals who had never had COVID-19. At the baseline and independent of time after COVID-19, recoverees had elevated T cell activation signatures and lower expression of innate immune genes including Toll-like receptors in monocytes. Male individuals who had recovered from COVID-19 had coordinately higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared with healthy male individuals and female individuals who had recovered from COVID-19, in part because male recoverees had monocytes with higher IL-15 responses early after vaccination coupled with elevated prevaccination frequencies of 'virtual memory'-like CD8+ T cells poised to produce more IFNγ after IL-15 stimulation. Moreover, the expression of the repressed innate immune genes in monocytes increased by day 1 to day 28 after vaccination in recoverees, therefore moving towards the prevaccination baseline of the healthy control individuals. By contrast, these genes decreased on day 1 and returned to the baseline by day 28 in the control individuals. Our study reveals sex-dimorphic effects of previous mild COVID-19 and suggests that viral infections in humans can establish new immunological set-points that affect future immune responses in an antigen-agnostic manner.

Cohort profile update: the Johns Hopkins HIV clinical cohort, 1989-2023.

The Johns Hopkins HIV Clinical Cohort, established in 1989, links comprehensive, longitudinal clinical data for adults with HIV receiving care in the Johns Hopkins John G. Bartlett Specialty Practice in Baltimore, Maryland, USA, to aid in understanding HIV care and treatment outcomes. Data include demographics, laboratory results, inpatient and outpatient visit information and clinical diagnoses, and prescribed and dispensed medications abstracted from medical records. A subset of patients separately consents to self-report patient-centric outcomes on standardized instruments approximately every 6 months, and another subset separately consents to contribute plasma and peripheral blood mononuclear cells to a linked specimen repository approximately annually. The cohort has cumulatively enrolled over 8000 people, with just under 2000 on average attending ≥ 1 HIV primary care visit in any given year. The cohort reflects the HIV epidemic in Baltimore: in 2021, median age was 57, 64% of participants were male, 77% were non-Hispanic Black, and 37% acquired HIV through injection drug use. This update to the cohort profile of the Johns Hopkins HIV Clinical Cohort illustrates both how the population of people with HIV in Baltimore, Maryland, USA has changed over three decades, and we have adapted data collection procedures over three decades to ensure this long-running cohort remains responsive to patient characteristics and research gaps in the provision of care to people with HIV and substance use.

The anxiety care continuum and its association with viral suppression among persons with HIV.

OBJECTIVE: It is unclear how often anxiety is diagnosed and treated and whether anxiety treatment is associated with improved viral suppression in persons with HIV. In this study, we characterized the anxiety care continuum and its association with viral suppression in a large urban HIV clinic in the United States. DESIGN: Observational cohort study. METHODS: We described the anxiety care continuum by combining data on self-reported anxiety symptoms, engagement in mental health care, clinical diagnoses and prescriptions from 1,967 persons receiving HIV care and treatment in Baltimore, Maryland, from 2014-23. We examined cross-sectional associations with viral suppression. All analyses were stratified by sex and race/ethnicity; a secondary analysis adjusted for age, years in care, and depressive symptoms. RESULTS: Nearly 1 in 5 patients reported mild-severe symptoms of anxiety but were not currently receiving mental health care or pharmacologic treatment for anxiety; 6% of patients reported anxiety symptoms but were receiving treatment, and 7% had been treated for anxiety that was currently in remission. The prevalence of viral suppression ranged from 87-89% across the anxiety care continuum except among patients with untreated moderate-severe anxiety, only 81% of whom were virally suppressed (95% CI: 80, 83). In adjusted models, untreated moderate-severe anxiety remained associated with viral non-suppression across demographic groups. CONCLUSION: We observed a robust association between untreated anxiety and viral non-suppression in a large urban cohort of persons with HIV. Screening for anxiety may identify patients with unmet mental health care needs who face barriers to maintaining viral suppression.

Association between switching to integrase strand transfer inhibitors and incident diabetes in people with HIV.

OBJECTIVE: Integrase strand transfer inhibitors (INSTI) are associated with weight gain in people with HIV (PWH), but their impact on diabetes is unclear. We evaluated the association between switching from nonnucleoside reverse-transcriptase inhibitors (NNRTI) or protease inhibitors (PI) to INSTI and incident diabetes. DESIGN: Longitudinal cohort study. METHODS: We included PWH aged ≥18 years from the Johns Hopkins HIV Clinical Cohort (2007-2023) without history of diabetes who had used NNRTI or PI for ≥180 days. We followed participants up to 10 years from HIV primary care visits where they switched to INSTI or continued NNRTI or PI. We estimated the hazard of incident diabetes associated with switching to INSTI using weighted Cox regression with robust variance estimator. RESULTS: We included 2075 PWH who attended 22 116 visits where they continued NNRTI or PI and 631 visits where they switched to INSTI. Switching to INSTI was associated with a weighted hazard ratio (wHR) of 1.11 [95% confidence interval (CI), 0.77-1.59] for incident diabetes. The association if no weight gain occurred during the first two years was not qualitatively different (wHR 1.22; 95% CI, 0.82-1.80). In a posthoc analysis, switching to INSTI conferred a significant wHR of 1.79 (95% CI, 1.13-2.84) for diabetes within the first two years but not after. CONCLUSIONS: Switching from NNRTI or PI to INSTI did not significantly increase overall diabetes incidence in PWH, although there may be elevated risk in the first two years. These findings can inform considerations when switching to INSTI-based regimens.

The association of changes in depression severity after the onset of the COVID-19 pandemic and viral nonsuppression among people with HIV.

OBJECTIVE: This study sought to characterize changes in depressive symptom severity during the COVID-19 pandemic and the association of these changes with HIV viral nonsuppression among people with HIV (PWH). DESIGN: A clinical cohort study. METHODS: We included PWH in the Johns Hopkins HIV Clinical Cohort who completed the Patient Health Questionnaire 8 (PHQ-8) prepandemic (1 March 2018 to 28 February 2020) and during the COVID-era (1 September 2020 to 28 February 2022). PWH were classified according to depression severity categories prepandemic and during the COVID-era as: consistently depressed (prepandemic PHQ-8 >4 and no change in severity category); consistently nondepressed (prepandemic PHQ-8 ≤4 and no change in severity category); worsened (changed to a higher severity category) and; improved (change to a lower severity category). The association between changes in depressive symptom severity and viral nonsuppression (HIV RNA >200 copies/ml on the earliest viral load measured 7 days before to 12 months after the COVID-era PHQ-8 survey) was assessed using multivariable logistic regression. RESULTS: Of 793 PWH, mean age was 56 (SD 10) years, 60% were male individuals and 88% were Black. After the onset of the pandemic, 60% were consistently nondepressed, 9% were consistently depressed, 15% worsened and 16% improved. PWH who worsened had 2.47 times the odds of viral nonsuppression (95% CI: 1.09-5.55) compared with the nondepressed group. Associations among other groups were not statistically significant. CONCLUSION: Worsening depression during the COVID-era was associated with HIV viral nonsuppression. Strategies to monitor and address depression among PWH may contribute to reduced risk of viral nonsuppression.

Measuring time in buprenorphine treatment stages among people with HIV and opioid use disorder by retention definition and its association with cocaine and hazardous alcohol use.

BACKGROUND: We use a novel, longitudinal approach to describe average time spent in opioid use disorder (OUD) cascade of care stages for people with HIV (PWH) and with OUD, incorporating four definitions of treatment retention. Using this approach, we describe the impact of cocaine or hazardous alcohol use on time spent retained on buprenorphine. METHODS: We followed PWH with OUD enrolled in the Johns Hopkins HIV Clinical Cohort from their first buprenorphine treatment episode between 2013 and 2020. We estimated 4-year restricted mean time spent on buprenorphine below buprenorphine retention threshold, on buprenorphine above retention threshold, off buprenorphine and in HIV care, loss to follow-up, and death. Retention definitions were based on retention threshold (180 vs 90 days) and allowable treatment gap (7 vs 30 days). Differences in 2-year restricted mean time spent retained on buprenorphine were estimated for patients with and without cocaine or hazardous alcohol use. RESULTS: The study sample (N = 179) was 63% male, 82% non-Hispanic Black, and mean age was 53 (SD 8) years. Patients spent on average 13.9 months (95% CI 11.4, 16.4) on buprenorphine over 4 years. There were differences in time spent retained on buprenorphine based on the retention definition, ranging from 6.5 months (95% CI 4.6, 8.5) to 9.6 months (95% CI 7.4, 11.8). Patients with cocaine use spent fewer months retained on buprenorphine. There were no differences for patients with hazardous alcohol use. CONCLUSIONS: PWH with OUD spend relatively little time receiving buprenorphine in their HIV primary care clinic. Concurrent cocaine use at buprenorphine initiation negatively impact time on buprenorphine.

Influenza vaccination and single cell multiomics reveal sex dimorphic immune imprints of prior mild COVID-19.

Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination. Identification of both sex-specific and -independent temporally stable changes, including signatures of T-cell activation and repression of innate defense/immune receptor genes (e.g., Toll-like receptors) in monocytes, suggest that mild COVID-19 can establish new post-recovery immunological set-points. COVID-19-recovered males had higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy males and COVID-19-recovered females, partly attributable to elevated pre-vaccination frequencies of a GPR56 expressing CD8+ T-cell subset in male recoverees that are "poised" to produce higher levels of IFNγ upon inflammatory stimulation. Intriguingly, by day 1 post-vaccination in COVID-19-recovered subjects, the expression of the repressed genes in monocytes increased and moved towards the pre-vaccination baseline of healthy controls, suggesting that the acute inflammation induced by vaccination could partly reset the immune states established by mild COVID-19. Our study reveals sex-dimorphic immune imprints and in vivo functional impacts of mild COVID-19 in humans, suggesting that prior COVID-19, and possibly respiratory viral infections in general, could change future responses to vaccination and in turn, vaccines could help reset the immune system after COVID-19, both in an antigen-agnostic manner.

Lymphocyte-driven regional immunopathology in pneumonitis caused by impaired central immune tolerance.

Autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), a monogenic disorder caused by AIRE mutations, presents with several autoimmune diseases. Among these, endocrine organ failure is widely recognized, but the prevalence, immunopathogenesis, and treatment of non-endocrine manifestations such as pneumonitis remain poorly characterized. We enrolled 50 patients with APECED in a prospective observational study and comprehensively examined their clinical and radiographic findings, performed pulmonary function tests, and analyzed immunological characteristics in blood, bronchoalveolar lavage fluid, and endobronchial and lung biopsies. Pneumonitis was found in >40% of our patients, presented early in life, was misdiagnosed despite chronic respiratory symptoms and accompanying radiographic and pulmonary function abnormalities, and caused hypoxemic respiratory failure and death. Autoantibodies against BPIFB1 and KCNRG and the homozygous c.967_979del13 AIRE mutation are associated with pneumonitis development. APECED pneumonitis features compartmentalized immunopathology, with accumulation of activated neutrophils in the airways and lymphocytic infiltration in intraepithelial, submucosal, peribronchiolar, and interstitial areas. Beyond APECED, we extend these observations to lung disease seen in other conditions with secondary AIRE deficiency (thymoma and RAG deficiency). Aire-deficient mice had similar compartmentalized cellular immune responses in the airways and lung tissue, which was ameliorated by deficiency of T and B lymphocytes. Accordingly, T and B lymphocyte-directed immunomodulation controlled symptoms and radiographic abnormalities and improved pulmonary function in patients with APECED pneumonitis. Collectively, our findings unveil lung autoimmunity as a common, early, and unrecognized manifestation of APECED and provide insights into the immunopathogenesis and treatment of pulmonary autoimmunity associated with impaired central immune tolerance.