G-formula for observational studies under stratified interference, with application to bed net use on malaria

Assessing population-level effects of vaccines and other infectious disease prevention measures is important to the field of public health. In infectious disease studies, one person's treatment may affect another individual's outcome, that is, there may be interference between units. For example, the use of bed nets to prevent malaria by one individual may have an indirect effect on other individuals living in close proximity. In some settings, individuals may form groups or clusters where interference only occurs within groups, that is, there is partial interference. Inverse probability weighted estimators have previously been developed for observational studies with partial interference. Unfortunately, these estimators are not well suited for studies with large clusters. Therefore, in this paper, the parametric g-formula is extended to allow for partial interference. G-formula estimators are proposed for overall effects, effects when treated, and effects when untreated. The proposed estimators can accommodate large clusters and do not suffer from the g-null paradox that may occur in the absence of interference. The large sample properties of the proposed estimators are derived assuming no unmeasured confounders and that the partial interference takes a particular form (referred to as 'weak stratified interference'). Simulation studies are presented demonstrating the finite-sample performance of the proposed estimators. The Demographic and Health Survey from the Democratic Republic of the Congo is then analyzed using the proposed g-formula estimators to assess the effects of bed net use on malaria.

Barriers to Cervical Cancer Screening by Sexual Orientation Among Low-Income Women in North Carolina

We sought to examine cervical cancer screening barriers by sexual orientation among low-income women in North Carolina. The MyBodyMyTest-3 Trial recruited low-income women (< 250% of federal poverty level) aged 25-64 years who were 1+ year overdue for cervical cancer screening. We compared perceptions of cervical cancer screening among those who self-identified as lesbian, gay, bisexual, or queer (LGBQ; n = 70) to straight/heterosexual women (n = 683). For both LGBQ and straight respondents, the greatest barriers to screening were lack of health insurance (63% and 66%) and cost (49% and 50%). LGBQ respondents were more likely than straight respondents to report forgetting to screen (16% vs. 8%, p = .05), transportation barriers (10% vs. 2%, p = .001), and competing mental or physical health problems (39% vs. 27%, p = .10). Addressing access remains important for improving cervical cancer screening among those under-screened. For LGBQ women, additional attention may be needed for reminders, co-occurring health needs, and transportation barriers.

An HIV-1 risk assessment tool for women aged 15-49 in African countries: A pooled analysis across 15 nationally representative surveys

BACKGROUND

Women in Africa disproportionately acquire HIV-1. Understanding which women are most likely to acquire HIV-1 can guide focused prevention with pre-exposure prophylaxis (PrEP). Our objective is to identify women at highest risk of HIV-1 and estimate PrEP efficiency at different sensitivity levels.

METHODS

Nationally representative data were collected from 2015-2019 from 15 population-based household surveys. This analysis included women aged 15-49 who tested HIV-1 sero-negative or had recent HIV-1. Least absolute shrinkage and selection operator regression models were fit with 28 variables to predict recent HIV-1. Models were trained on the full population and internally cross-validated. Performance was evaluated using area under the receiver-operating-characteristic curve (AUC), sensitivity, and number needed to treat (NNT) with PrEP to avert one infection.

RESULTS

Among 209,012 participants 248 had recent HIV-1 infection, representing 118 million women and 402,000 (95% CI: 309,000-495,000) new annual infections. Two variables were retained in the model: living in a subnational area with high HIV-1 viremia and having a sexual partner living outside the home. Full-population AUC was 0.80 (95% CI: 0.76-0.84); cross-validated AUC was 0.79 (95% CI: 0.75-0.84). At a sensitivity of 33%, up to 130,000 cases could be averted if 7.9 million women were perfectly adherent to PrEP; NNT would be 61. At a sensitivity of 67%, up to 260,000 cases could be averted if 25.1 million women were perfectly adherent to PrEP; the NNT would be 96.

CONCLUSIONS

This risk assessment tool was generalizable, predictive, and parsimonious with tradeoffs between reach and efficiency.

Fusing trial data for treatment comparisons: Single vs multi-span bridging

While randomized controlled trials (RCTs) are critical for establishing the efficacy of new therapies, there are limitations regarding what comparisons can be made directly from trial data. RCTs are limited to a small number of comparator arms and often compare a new therapeutic to a standard of care which has already proven efficacious. It is sometimes of interest to estimate the efficacy of the new therapy relative to a treatment that was not evaluated in the same trial, such as a placebo or an alternative therapy that was evaluated in a different trial. Such dual-study comparisons are challenging because of potential differences between trial populations that can affect the outcome. In this article, two bridging estimators are considered that allow for comparisons of treatments evaluated in different trials, accounting for measured differences in trial populations. A "multi-span" estimator leverages a shared arm between two trials, while a "single-span" estimator does not require a shared arm. A diagnostic statistic that compares the outcome in the standardized shared arms is provided. The two estimators are compared in simulations, where both estimators demonstrate minimal empirical bias and nominal confidence interval coverage when the identification assumptions are met. The estimators are applied to data from the AIDS Clinical Trials Group 320 and 388 to compare the efficacy of two-drug vs four-drug antiretroviral therapy on CD4 cell counts among persons with advanced HIV. The single-span approach requires weaker identification assumptions and was more efficient in simulations and the application.

CD3 downregulation identifies high-avidity human CD8 T cells

CD8 T cells recognize infected and cancerous cells via their T-cell receptor (TCR), which binds peptide-MHC complexes on the target cell. The affinity of the interaction between the TCR and peptide-MHC contributes to the antigen sensitivity, or functional avidity, of the CD8 T cell. In response to peptide-MHC stimulation, the TCR-CD3 complex and CD8 co-receptor are downmodulated. We quantified CD3 and CD8 downmodulation following stimulation of human CD8 T cells with CMV, EBV, and HIV peptides spanning eight MHC restrictions, observing a strong correlation between the levels of CD3 and CD8 downmodulation and functional avidity, regardless of peptide viral origin. In TCR-transduced T cells targeting a tumor-associated antigen, changes in TCR-peptide affinity were sufficient to modify CD3 and CD8 downmodulation. Correlation analysis and generalized linear modeling indicated that CD3 downmodulation was the stronger correlate of avidity. CD3 downmodulation, simply measured using flow cytometry, can be used to identify high-avidity CD8 T cells in a clinical context.

Quantifying the HIV reservoir with dilution assays and deep viral sequencing

People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but "latent" HIV still persists in viral reservoirs. Eliminating these reservoirs is the goal of HIV cure research. The quantitative viral outgrowth assay (QVOA) is commonly used to estimate the reservoir size, that is, the infectious units per million (IUPM) of HIV-persistent resting CD4+ T cells. A new variation of the QVOA, the ultra deep sequencing assay of the outgrowth virus (UDSA), was recently developed that further quantifies the number of viral lineages within a subset of infected wells. Performing the UDSA on a subset of wells provides additional information that can improve IUPM estimation. This paper considers statistical inference about the IUPM from combined dilution assay (QVOA) and deep viral sequencing (UDSA) data, even when some deep sequencing data are missing. Methods are proposed to accommodate assays with wells sequenced at multiple dilution levels and with imperfect sensitivity and specificity, and a novel bias-corrected estimator is included for small samples. The proposed methods are evaluated in a simulation study, applied to data from the University of North Carolina HIV Cure Center, and implemented in the open-source R package SLDeepAssay.

Higher-order evidence

Higher-order evidence is evidence about evidence. Epidemiologic examples of higher-order evidence include the settings where the study data constitute first-order evidence and estimates of misclassification comprise the second-order evidence (e.g., sensitivity, specificity) of a binary exposure or outcome collected in the main study. While sampling variability in higher-order evidence is typically acknowledged, higher-order evidence is often assumed to be free of measurement error (e.g., gold standard measures). Here we provide two examples, each with multiple scenarios where second-order evidence is imperfectly measured, and this measurement error can either amplify or attenuate standard corrections to first-order evidence. We propose a way to account for such imperfections that requires third-order evidence. Further illustrations and exploration of how higher-order evidence impacts results of epidemiologic studies is warranted.

Identifying and estimating effects of sustained interventions under parallel trends assumptions

Many research questions in public health and medicine concern sustained interventions in populations defined by substantive priorities. Existing methods to answer such questions typically require a measured covariate set sufficient to control confounding, which can be questionable in observational studies. Differences-in-differences rely instead on the parallel trends assumption, allowing for some types of time-invariant unmeasured confounding. However, most existing difference-in-differences implementations are limited to point treatments in restricted subpopulations. We derive identification results for population effects of sustained treatments under parallel trends assumptions. In particular, in settings where all individuals begin follow-up with exposure status consistent with the treatment plan of interest but may deviate at later times, a version of Robins' g-formula identifies the intervention-specific mean under stable unit treatment value assumption, positivity, and parallel trends. We develop consistent asymptotically normal estimators based on inverse-probability weighting, outcome regression, and a double robust estimator based on targeted maximum likelihood. Simulation studies confirm theoretical results and support the use of the proposed estimators at realistic sample sizes. As an example, the methods are used to estimate the effect of a hypothetical federal stay-at-home order on all-cause mortality during the COVID-19 pandemic in spring 2020 in the United States.

Dominant CD4+ T cell receptors remain stable throughout antiretroviral therapy-mediated immune restoration in people with HIV

In people with HIV (PWH), the post-antiretroviral therapy (ART) window is critical for immune restoration and HIV reservoir stabilization. We employ deep immune profiling and T cell receptor (TCR) sequencing and examine proliferation to assess how ART impacts T cell homeostasis. In PWH on long-term ART, lymphocyte frequencies and phenotypes are mostly stable. By contrast, broad phenotypic changes in natural killer (NK) cells, γδ T cells, B cells, and CD4+ and CD8+ T cells are observed in the post-ART window. Whereas CD8+ T cells mostly restore, memory CD4+ T subsets and cytolytic NK cells show incomplete restoration 1.4 years post ART. Surprisingly, the hierarchies and frequencies of dominant CD4 TCR clonotypes (0.1%-11% of all CD4+ T cells) remain stable post ART, suggesting that clonal homeostasis can be independent of homeostatic processes regulating CD4+ T cell absolute number, phenotypes, and function. The slow restoration of host immunity post ART also has implications for the design of ART interruption studies.

Germline-targeting SOSIP trimer immunization elicits precursor CD4 binding-site targeting broadly neutralizing antibodies in infant macaques

A vaccine that can achieve protective immunity prior to sexual debut is critical to prevent the estimated 410,000 new HIV infections that occur yearly in adolescents. As children living with HIV can make broadly neutralizing antibody (bnAb) responses in plasma at a faster rate than adults, early childhood is an opportune window for implementation of a multi-dose HIV immunization strategy to elicit protective immunity prior to adolescence. Therefore, the goal of our study was to assess the ability of a B cell lineage-designed HIV envelope SOSIP to induce bnAbs in early life. Infant rhesus macaques (RMs) received either BG505 SOSIP or the germline-targeting BG505 GT1.1 SOSIP (n=5/group) with the 3M-052-SE adjuvant at 0, 6, and 12 weeks of age. All infant RMs were then boosted with the BG505 SOSIP at weeks 26, 52 and 78, mimicking a pediatric immunization schedule of multiple vaccine boosts within the first two years of life. Both immunization strategies induced durable, high magnitude binding antibodies and plasma autologous virus neutralization that primarily targeted the CD4-binding site (CD4bs) or C3/465 epitope. Notably, three BG505 GT1.1-immunized infants exhibited a plasma HIV neutralization signature reflective of VRC01-like CD4bs bnAb precursor development and heterologous virus neutralization. Finally, infant RMs developed precursor bnAb responses at a similar frequency to that of adult RMs receiving a similar immunization strategy. Thus, a multi-dose immunization regimen with bnAb lineage designed SOSIPs is a promising strategy for inducing protective HIV bnAb responses in childhood prior to adolescence when sexual HIV exposure risk begins.

Estimating SARS-CoV-2 seroprevalence

Governments and public health authorities use seroprevalence studies to guide responses to the COVID-19 pandemic. Seroprevalence surveys estimate the proportion of individuals who have detectable SARS-CoV-2 antibodies. However, serologic assays are prone to misclassification error, and non-probability sampling may induce selection bias. In this paper, non-parametric and parametric seroprevalence estimators are considered that address both challenges by leveraging validation data and assuming equal probabilities of sample inclusion within covariate-defined strata. Both estimators are shown to be consistent and asymptotically normal, and consistent variance estimators are derived. Simulation studies are presented comparing the estimators over a range of scenarios. The methods are used to estimate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence in New York City, Belgium, and North Carolina.

Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1

Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.

Utilization of Treat-to-Target Monitoring Colonoscopy After Treatment Initiation in the US-Based Study of a Prospective Adult Research Cohort With Inflammatory Bowel Disease

INTRODUCTION

Endoscopic healing has been associated with improved long-term clinical outcomes in inflammatory bowel disease (IBD) and is a recommended target for treatment. Evidence is limited regarding real-world uptake and patterns of treat-to-target monitoring to assess endoscopic healing after treatment initiation. We aimed to estimate the proportion of patients in the Study of a Prospective Adult Research Cohort with IBD (SPARC IBD) who received colonoscopy in the 3-15 months after starting a new IBD treatment.

METHODS

We identified SPARC IBD patients who initiated a new biologic (infliximab, adalimumab, certolizumab pegol, golimumab, vedolizumab, and ustekinumab) or tofacitinib. We estimated the proportion of patients who received colonoscopies in the 3-15 months after IBD treatment initiation and described use by patient subgroups.

RESULTS

Among 1,708 eligible initiations from 2017 to 2022, the most common medications were ustekinumab (32%), infliximab (22%), vedolizumab (20%), and adalimumab (16%). The median patient age was 38 years, with 66% Crohn's disease; 55% were female, and 12% were non-White. In the 3-15 months after medication initiation, 49.3% (95% confidence interval 46.2%-52.5%) of initiations were followed by a colonoscopy. Colonoscopy use was similar between ulcerative colitis and Crohn's disease, but was higher among male patients, those older than 40 years, and those who received colonoscopy within 3 months of initiation. Colonoscopy use varied between study sites, from 26.6% (15.0%-38.3%) to 63.2% (54.5%-72.0%).

DISCUSSION

Approximately half of SPARC IBD patients received colonoscopy in the 3-15 months after initiation to a new IBD treatment, suggesting a low uptake of treat-to-target colonoscopy for the assessment of mucosal healing in real-world clinical practice. The variation in colonoscopy use between study sites suggests a lack of consensus and a need for more robust evidence around whether or not the practice of routine monitoring colonoscopy is associated with improved patient outcomes.

Sensitivity Analyses for Means or Proportions with Missing Outcome Data

We describe an approach to sensitivity analysis introduced by Robins et al (1999), for the setting where the outcome is missing for some observations. This flexible approach focuses on the relationship between the outcomes and missingness, where data can be missing completely at random, missing at random given observed data, or missing not at random. We provide examples from HIV that include the sensitivity of the estimation of a mean and proportion under different missingness mechanisms. The approach illustrated provides a method for examining how the results of epidemiologic studies might shift as a function of bias due to missing data.

Cervical Cancer Screening Knowledge, Perceptions, and Behaviors in a Multiracial Cohort of Low-Income, Underscreened Women in North Carolina

Background: Underscreened, low-income, and uninsured or publicly insured women in the United States bear a greater burden of cervical cancer morbidity and mortality and may face unique barriers that preclude screening adherence. Methods: Participants were 710 My Body My Test-3 clinical trial participants who were publicly insured or uninsured with incomes ≤250% of the U.S. Federal Poverty Level, aged 25-64 years, and not up to date on cervical cancer screening as per national guidelines. Using Health Belief Model constructs, we assessed screening-related knowledge, perceptions, and behaviors-overall and stratified by race and ethnicity-and estimated associations with past-year attempted screening using multivariable regression models. Results: Overall, knowledge was low about the human papillomavirus, purpose of a Pap test, and recommended screening interval. Perceived severity of cervical cancer was high (3.63 on a 4-point scale). Black and Latina/Hispanic women were more likely to perceive screening as lowering their risk of cervical cancer than White women. Black women reported lower perceived risk of cervical cancer compared with White women (p = 0.03), but Black women were more likely to have sought screening in the past year (p = 0.01). Having at least three doctor visits in the past year was associated with a screening attempt. Greater perceived risk of cervical cancer, more positive perceptions of screening, and feeling more nervousness about screening were also associated with a screening attempt (all p < 0.05). Conclusions: Addressing knowledge gaps and misconceptions about cervical cancer screening and leveraging positive perceptions of screening may improve screening uptake and adherence among diverse underscreened U.S. women. Clinical Trial Registration Number: NCT02651883.

A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection

Germ-free (GF) mice, which are depleted of their resident microbiota, are the gold standard for exploring the role of the microbiome in health and disease; however, they are of limited value in the study of human-specific pathogens because they do not support their replication. Here, we develop GF mice systemically reconstituted with human immune cells and use them to evaluate the role of the resident microbiome in the acquisition, replication and pathogenesis of two human-specific pathogens, Epstein-Barr virus (EBV) and human immunodeficiency virus (HIV). Comparison with conventional (CV) humanized mice showed that resident microbiota enhance the establishment of EBV infection and EBV-induced tumorigenesis and increase mucosal HIV acquisition and replication. HIV RNA levels were higher in plasma and tissues of CV humanized mice compared with GF humanized mice. The frequency of CCR5+ CD4+ T cells throughout the intestine was also higher in CV humanized mice, indicating that resident microbiota govern levels of HIV target cells. Thus, resident microbiota promote the acquisition and pathogenesis of two clinically relevant human-specific pathogens.

Optimizing Treatment for Human Immunodeficiency Virus to Improve Clinical Outcomes Using Precision Medicine

In first-line antiretroviral therapy (ART) for human immunodeficiency virus (HIV) treatment, some subgroups of patients may respond better to an efavirenz-based regimen than an integrase strand transfer inhibitor (InSTI)-based regimen, or vice versa, due to patient characteristics modifying treatment effects. Using data based on nearly 16,000 patients from the North American AIDS Cohort Collaboration on Research and Design from 2009-2016, statistical methods for precision medicine were employed to estimate an optimal treatment rule that minimizes the 5-year risk of the composite outcome of acquired immune deficiency syndrome (AIDS)-defining illnesses, serious non-AIDS events, and all-cause mortality. The treatment rules considered were functions that recommend either an efavirenz- or InSTI-based regimen conditional on baseline patient characteristics such as demographic information, laboratory results, and health history. The estimated 5-year risk under the estimated optimal treatment rule was 10.0% (95% confidence interval (CI): 8.6, 11.3), corresponding to an absolute risk reduction of 2.3% (95% CI: 0.9, 3.8) when compared with recommending an efavirenz-based regimen for all patients and 2.6% (95% CI: 1.0, 4.2) when compared with recommending an InSTI-based regimen for all. Tailoring ART to individual patient characteristics may reduce 5-year risk of the composite outcome compared with assigning all patients the same drug regimen.

Cost-effectiveness of Human Papillomavirus Self-collection Intervention on Cervical Cancer Screening Uptake among Underscreened U.S. Persons with a Cervix

BACKGROUND

We evaluate the cost-effectiveness of human papillomavirus (HPV) self-collection (followed by scheduling assistance for those who were HPV+ or inconclusive) compared with scheduling assistance only and usual care among underscreened persons with a cervix (PWAC).

METHODS

A decision tree analysis was used to estimate the incremental cost-effectiveness ratios (ICER), or the cost per additional PWAC screened, from the Medicaid/state and clinic perspectives. A hypothetical cohort represented 90,807 low-income, underscreened individuals. Costs and health outcomes were derived from the MyBodyMyTest-3 randomized trial except the usual care health outcomes were derived from literature. We performed probabilistic sensitivity analyses (PSA) to evaluate model uncertainty.

RESULTS

Screening uptake was highest in the self-collection alternative (n = 65,721), followed by the scheduling assistance alternative (n = 34,003) and usual care (n = 18,161). The self-collection alternative costs less and was more effective than the scheduling assistance alternative from the Medicaid/state perspective. Comparing the self-collection alternative with usual care, the ICERs were $284 per additional PWAC screened from the Medicaid/state perspective and $298 per additional PWAC screened from the clinic perspective. PSAs demonstrated that the self-collection alternative was cost-effective compared with usual care at a willingness-to-pay threshold of $300 per additional PWAC screened in 66% of simulations from the Medicaid/state perspective and 58% of simulations from the clinic perspective.

CONCLUSIONS

Compared with usual care and scheduling assistance, mailing HPV self-collection kits to underscreened individuals appears to be cost-effective in increasing screening uptake.

IMPACT

This is the first analysis to demonstrate the cost-effectiveness of mailed self-collection in the United States.

Reducing Bias in Estimates of Per Protocol Treatment Effects: A Secondary Analysis of a Randomized Clinical Trial

This secondary analysis of a randomized clinical trial evaluates ways of reducing bias in estimates of per protocol treatment effects.

Assessing intervention effects in a randomized trial within a social network

Studies of social networks provide unique opportunities to assess the causal effects of interventions that may impact more of the population than just those intervened on directly. Such effects are sometimes called peer or spillover effects, and may exist in the presence of interference, that is, when one individual's treatment affects another individual's outcome. Randomization-based inference (RI) methods provide a theoretical basis for causal inference in randomized studies, even in the presence of interference. In this article, we consider RI of the intervention effect in the eX-FLU trial, a randomized study designed to assess the effect of a social distancing intervention on influenza-like-illness transmission in a connected network of college students. The approach considered enables inference about the effect of the social distancing intervention on the per-contact probability of influenza-like-illness transmission in the observed network. The methods allow for interference between connected individuals and for heterogeneous treatment effects. The proposed methods are evaluated empirically via simulation studies, and then applied to data from the eX-FLU trial.

Effect of HPV self-collection kits on cervical cancer screening uptake among under-screened women from low-income US backgrounds (MBMT-3): a phase 3, open-label, randomised controlled trial

BACKGROUND

Most cervical cancer in the USA occurs in under-screened women. The My Body, My Test-3 (MBMT-3) trial sought to assess the efficacy of mailed human papillomavirus (HPV) self-collection kits with appointment-scheduling assistance to increase uptake of cervical cancer screening among under-screened women from low-income backgrounds compared with scheduling assistance alone.

METHODS

MBMT-3 is a phase 3, open-label, two-arm, randomised controlled trial. Participants were recruited from 22 counties in North Carolina state, USA, and we partnered with 21 clinics across these counties. Participants were eligible for inclusion if they were aged 25-64 years, had an intact cervix, were uninsured or enrolled in Medicaid or Medicare, had an income of 250% or less of the US Federal Poverty Level, were living within the catchment area of a trial-associated clinic, and were overdue for screening (ie, Papanicolaou test ≥4 years ago or high-risk HPV test ≥6 years ago). Participants were randomly assigned (2:1) to receive a mailed HPV self-collection kit and assistance for scheduling a free screening appointment (intervention group) or to receive scheduling assistance alone (control group). Randomisation was conducted by county using permuted blocks of nine patients and assignment to group was not masked. Participants in the intervention group were mailed HPV self-collection kits to collect a cervical-vaginal sample and return it by mail for testing. Samples were tested with the Aptima HPV assay (Hologic, San Diego, CA, USA), and participants were informed of high-risk HPV results by telephone call. Trial staff made up to three telephone call attempts to provide scheduling assistance for in-clinic screening for all participants. The primary outcome was cervical cancer screening uptake (ie, attending an in-clinic screening appointment or testing negative for high-risk HPV with a returned self-collected sample) within 6 months of enrolment in the intention-to-treat population. This trial is registered with ClinicalTrials.gov, NCT02651883, and has been completed.

FINDINGS

Recruitment occurred between April 11, 2016, and Dec 16, 2019. 4256 women contacted the trial to participate, of whom 899 (21%) were eligible for inclusion and 697 (78%) returned consent forms. Of those who consented, 461 (66%) women were randomly assigned to the intervention group and 236 (34%) women were randomly assigned to the control group. We excluded 32 ineligible women post-randomisation, leaving 665 for primary analysis. Screening uptake was higher in the intervention group (317 [72%] of 438) than control group (85 [37%] of 227; risk ratio 1·93, 95% CI 1·62-2·31). Among intervention participants, 341 (78%) of 438 returned a self-collection kit. Three participants reported hurt or injury when using the self-collection kit; no participants withdrew due to adverse effects.

INTERPRETATION

Among under-screened women from low-income backgrounds, mailed HPV self-collection kits with scheduling assistance led to greater uptake of cervical cancer screening than scheduling assistance alone. At-home HPV self-collection testing has the potential to increase screening uptake among under-screened women.

FUNDING

National Cancer Institute.

Nonparametric estimation of marked survival data in the presence of dependent censoring

We consider nonparametrically estimating the joint distribution of a survival time and mark variable, where the survival time is subject to right censoring and the mark variable is only observed when the survival time is not censored. The possibility of dependent censoring is allowed for using inverse probability of censoring weights. The proposed estimator is shown to be consistent and asymptotically normal. Finite sample behavior of the proposed methods are investigated via simulation study. Finally, we illustrate the nonparametric estimator from a recent HIV vaccine efficacy trial.

Adolescents Living With or at Risk for HIV: A Pooled Descriptive Analysis of Studies From the Adolescent Medicine Trials Network for HIV/AIDS Interventions

PURPOSE

This study aims to describe the cohort of Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN) research program participants and evaluate whether the ATN's recently completed 5-year cycle recruited study participants who parallel the populations most impacted by HIV in the United States.

METHODS

Harmonized measures across ATN studies collected at baseline were aggregated for participants aged 13-24 years. Pooled means and proportions stratified by HIV status (at risk for or living with HIV) were calculated using unweighted averages of study-specific aggregate data. Medians were estimated using a weighted median of medians method. Public use 2019 Centers for Disease Control and Prevention surveillance data for state-level new HIV diagnoses and HIV prevalence among US youth aged 13-24 years were obtained for use as reference populations for ATN at-risk youth and youth living with HIV (YLWH), respectively.

RESULTS

Data from 3,185 youth at-risk for HIV and 542 YLWH were pooled from 21 ATN study phases conducted across the United States. Among ATN studies tailored to at-risk youth, a higher proportion of participants were White and a lower proportion were Black/African American and Hispanic/Latinx compared to youth newly diagnosed with HIV in the United States in 2019. Participants in ATN studies tailored to YLWH were demographically similar to YLWH in the United States.

DISCUSSION

The development of data harmonization guidelines for ATN research activities facilitated this cross-network pooled analysis. These findings suggest the ATN's YLWH are representative, but that future studies of at-risk youth should prioritize recruitment strategies to enroll more participants from African American and Hispanic/Latinx populations.

Infant rhesus macaques immunized against SARS-CoV-2 are protected against heterologous virus challenge 1 year later

The U.S. Food and Drug Administration only gave emergency use authorization of the BNT162b2 and mRNA-1273 SARS-CoV-2 vaccines for infants 6 months and older in June 2022. Yet questions regarding the durability of vaccine efficacy, especially against emerging variants, in this age group remain. We demonstrated previously that a two-dose regimen of stabilized prefusion Washington SARS-CoV-2 S-2P spike (S) protein encoded by mRNA encapsulated in lipid nanoparticles (mRNA-LNP) or purified S-2P mixed with 3M-052, a synthetic Toll-like receptor (TLR) 7/8 agonist, in a squalene emulsion (Protein+3M-052-SE) was safe and immunogenic in infant rhesus macaques. Here, we demonstrate that broadly neutralizing and spike-binding antibodies against variants of concern (VOCs), as well as T cell responses, persisted for 12 months. At 1 year, corresponding to human toddler age, we challenged vaccinated rhesus macaques and age-matched nonvaccinated controls intranasally and intratracheally with a high dose of heterologous SARS-CoV-2 B.1.617.2 (Delta). Seven of eight control rhesus macaques exhibited severe interstitial pneumonia and high virus replication in the upper and lower respiratory tract. In contrast, vaccinated rhesus macaques had faster viral clearance with mild to no pneumonia. Neutralizing and binding antibody responses to the B.1.617.2 variant at the day of challenge correlated with lung pathology and reduced virus replication. Overall, the Protein+3M-052-SE vaccine provided superior protection to the mRNA-LNP vaccine, emphasizing opportunities for optimization of current vaccine platforms. The observed efficacy of both vaccines 1 year after vaccination supports the implementation of an early-life SARS-CoV-2 vaccine.

Adult HIV-1 incidence across 15 high-burden countries in sub-Saharan Africa from 2015 to 2019: a pooled analysis of nationally representative data

BACKGROUND

Harmonised population-based surveys with recent HIV-1 infection testing algorithms permit pooled cross-sectional estimation of HIV incidence across multiple countries. We aimed to estimate adult HIV-1 incidence rates and number of new infections by sex, age, and subregion in sub-Saharan Africa.

METHODS

We analysed data from 13 Population-Based HIV Impact Assessment (PHIA) surveys and two additional population-based surveys done between 2015 and 2019 in 15 sub-Saharan African countries. HIV-seropositive samples from adults aged 15-59 years were tested for recent HIV-1 infection by use of an algorithm consisting of the HIV-1 limiting antigen avidity enzyme immunoassay, HIV-1 viral load, and qualitative detection of antiretroviral agents. Data were pooled across countries; sampling weights were incorporated to represent all adults in the 15 national populations. Analyses accounted for the complex sample designs. HIV incidence rates, incidence rate differences, and number of new annual infections were estimated.

FINDINGS

Among 445 979 adults sampled, 382 had recent HIV-1 infection. The estimated HIV-1 incidence rate was 3·3 per 1000 person-years (95% CI 2·6-4·0) among women and 2·0 per 1000 person-years (1·2-2·7) among men (incidence rate difference 1·3 per 1000 person-years, 95% CI 0·3-2·3). Among adults aged 15-24 years, the incidence rate was higher for women (3·5 per 1000 person-years) than men (1·2 per 1000 person-years; difference 2·3, 95% CI 0·8-3·8), but infection rates were similar between sexes in all other age groups. The HIV-1 incidence rate was 7·4 per 1000 person-years (95% CI 5·0-9·7) in southern sub-Saharan Africa, 2·3 per 1000 person-years (1·7-2·9) in the eastern subregion, and 0·9 per 1000 person-years (0·6-1·2) in the western and central subregion. 689 000 (95% CI 546 000-833 000) new HIV cases were estimated annually among the 265 million susceptible adults (61·6% in women).

INTERPRETATION

HIV-1 incidence and number of new infections differed by age, sex, and subregion. Approaches for risk stratification are needed to guide comprehensive HIV-1 prevention.

FUNDING

National Institutes of Health.

Illustration of 2 Fusion Designs and Estimators

"Fusion" study designs combine data from different sources to answer questions that could not be answered (as well) by subsets of the data. Studies that augment main study data with validation data, as in measurement-error correction studies or generalizability studies, are examples of fusion designs. Fusion estimators, here solutions to stacked estimating functions, produce consistent answers to identified research questions using data from fusion designs. In this paper, we describe a pair of examples of fusion designs and estimators, one where we generalize a proportion to a target population and one where we correct measurement error in a proportion. For each case, we present an example motivated by human immunodeficiency virus research and summarize results from simulation studies. Simulations demonstrate that the fusion estimators provide approximately unbiased results with appropriate 95% confidence interval coverage. Fusion estimators can be used to appropriately combine data in answering important questions that benefit from multiple sources of information.

Aminobisphosphonates reactivate the latent reservoir in people living with HIV-1

Antiretroviral therapy (ART) is not curative due to the existence of cellular reservoirs of latent HIV-1 that persist during therapy. Current research efforts to cure HIV-1 infection include "shock and kill" strategies to disrupt latency using small molecules or latency-reversing agents (LRAs) to induce expression of HIV-1 enabling cytotoxic immune cells to eliminate infected cells. The modest success of current LRAs urges the field to identify novel drugs with increased clinical efficacy. Aminobisphosphonates (N-BPs) that include pamidronate, zoledronate, or alendronate, are the first-line treatment of bone-related diseases including osteoporosis and bone malignancies. Here, we show the use of N-BPs as a novel class of LRA: we found in ex vivo assays using primary cells from ART-suppressed people living with HIV-1 that N-BPs induce HIV-1 from latency to levels that are comparable to the T cell activator phytohemagglutinin (PHA). RNA sequencing and mechanistic data suggested that reactivation may occur through activation of the activator protein 1 signaling pathway. Stored samples from a prior clinical trial aimed at analyzing the effect of alendronate on bone mineral density, provided further evidence of alendronate-mediated latency reversal and activation of immune effector cells. Decay of the reservoir measured by IPDA was however not detected. Our results demonstrate the novel use of N-BPs to reverse HIV-1 latency while inducing immune effector functions. This preliminary evidence merits further investigation in a controlled clinical setting possibly in combination with therapeutic vaccination.

Corrigendum: Reliable estimation of CD8 T cell inhibition of in vitro HIV-1 replication

[This corrects the article DOI: 10.3389/fimmu.2021.666991.].

Propensity Score in the Face of Interference: Discussion of

Rosenbaum and Rubin's (1983) propensity score revolutionized the field of causal inference and has emerged as a standard tool when researchers reason about cause-and-effect relationship across many disciplines. This discussion centers around the key "no interference" assumption in Rosenbaum and Rubin's original development of the propensity score and reviews some recent advances in extending the propensity score to studies involving dependent happenings.

Unique Molecular Identifiers and Multiplexing Amplicons Maximize the Utility of Deep Sequencing To Critically Assess Population Diversity in RNA Viruses

Next generation sequencing (NGS)/deep sequencing has become an important tool in the study of viruses. The use of unique molecular identifiers (UMI) can overcome the limitations of PCR errors and PCR-mediated recombination and reveal the true sampling depth of a viral population being sequenced in an NGS experiment. This approach of enhanced sequence data represents an ideal tool to study both high and low abundance drug resistance mutations and more generally to explore the genetic structure of viral populations. Central to the use of the UMI/Primer ID approach is the creation of a template consensus sequence (TCS) for each genome sequenced. Here we describe a series of experiments to validate several aspects of the Multiplexed Primer ID (MPID) sequencing approach using the MiSeq platform. We have evaluated how multiplexing of cDNA synthesis and amplicons affects the sampling depth of the viral population for each individual cDNA and amplicon to understand the relationship between broader genome coverage versus maximal sequencing depth. We have validated reproducibility of the MPID assay in the detection of minority mutations in viral genomes. We have also examined the determinants that allow sequencing reads of PCR recombinants to contaminate the final TCS data set and show how such contamination can be limited. Finally, we provide several examples where we have applied MPID to analyze features of minority variants and describe limits on their detection in viral populations of HIV-1 and SARS-CoV-2 to demonstrate the generalizable utility of this approach with any RNA virus.

Estimating the Number of Persons with HIV in Jails via Web Scraping and Record Linkage

This paper presents methods to estimate the number of persons with HIV in North Carolina jails by applying finite population inferential approaches to data collected using web scraping and record linkage techniques. Administrative data are linked with web-scraped rosters of incarcerated persons in a nonrandom subset of counties. Outcome regression and calibration weighting are adapted for state-level estimation. Methods are compared in simulations and are applied to data from the US state of North Carolina. Outcome regression yielded more precise inference and allowed for county-level estimates, an important study objective, while calibration weighting exhibited double robustness under misspecification of the outcome or weight model.

Paired serial limiting dilution assays

Serial limiting dilution (SLD) assays are a widely used tool in many areas of public health research to measure the concentration of target entities. This concentration can be estimated via maximum likelihood. Asymptotic as well as exact inference methods have been proposed for hypothesis testing and confidence interval construction in this one-sample problem. However, in many scientific applications, it may be of interest to compare the concentration of target entities between a pair of samples and construct valid confidence intervals for the difference in concentrations. In this paper, an exact, computationally efficient inferential procedure is proposed for hypothesis testing and confidence interval construction in the two-sample SLD assay problem. The proposed exact method is compared to an approach based on asymptotic approximations in simulation studies. The methods are illustrated using data from the University of North Carolina HIV Cure Center.

Targeted maximum likelihood estimation of causal effects with interference: A simulation study

Interference, the dependency of an individual's potential outcome on the exposure of other individuals, is a common occurrence in medicine and public health. Recently, targeted maximum likelihood estimation (TMLE) has been extended to settings of interference, including in the context of estimation of the mean of an outcome under a specified distribution of exposure, referred to as a policy. This paper summarizes how TMLE for independent data is extended to general interference (network-TMLE). An extensive simulation study is presented of network-TMLE, consisting of four data generating mechanisms (unit-treatment effect only, spillover effects only, unit-treatment and spillover effects, infection transmission) in networks of varying structures. Simulations show that network-TMLE performs well across scenarios with interference, but issues manifest when policies are not well-supported by the observed data, potentially leading to poor confidence interval coverage. Guidance for practical application, freely available software, and areas of future work are provided.

Reservoir-Style Polymeric Drug Delivery Systems: Empirical and Predictive Models for Implant Design

Controlled drug delivery systems can provide sustained release profiles, favorable pharmacokinetics, and improved patient adherence. Here, a reservoir-style implant comprising a biodegradable polymer, poly(ε-caprolactone) (PCL), was developed to deliver drugs subcutaneously. This work addresses a key challenge when designing these implantable drug delivery systems, namely the accurate prediction of drug release profiles when using different formulations or form factors of the implant. The ability to model and predict the release behavior of drugs from an implant based on their physicochemical properties enables rational design and optimization without extensive and laborious in vitro testing. By leveraging experimental observations, we propose a mathematical model that predicts the empirical parameters describing the drug diffusion and partitioning processes based on the physicochemical properties of the drug. We demonstrate that the model enables an adequate fit predicting empirical parameters close to experimental values for various drugs. The model was further used to predict the release performance of new drug formulations from the implant, which aligned with experimental results for implants exhibiting zero-order release kinetics. Thus, the proposed empirical models provide useful tools to inform the implant design to achieve a target release profile.

Extended Human Papillomavirus Genotyping to Predict Progression to High-Grade Cervical Precancer: A Prospective Cohort Study in the Southeastern United States

BACKGROUND

High-risk human papillomavirus (hrHPV) testing is utilized in primary cervical cancer screening, generally along with cytology, to triage abnormalities to colposcopy. Most screening-based hrHPV testing involves pooled detection of any hrHPV or of HPV16/18. Cervical neoplasia progression risks based on extended hrHPV genotyping-particularly non-16/18 hrHPV types-are not well characterized. HPV genotype-specific incidence of high-grade cervical intraepithelial neoplasia or more severe (CIN2+) following an abnormal screening result was examined.

METHODS

We assessed a US-based prospective, multiracial, clinical cohort of 343 colposcopy patients with normal histology (n = 226) or CIN1 (n = 117). Baseline cervical samples underwent HPV DNA genotyping, and participants were followed up to 5 years. Genotype-specific CIN2+ incidence rates (IR) were estimated with accelerated failure time models. Five-year CIN2+ risks were estimated nonparametrically for hierarchical hrHPV risk groups (HPV16; else HPV18/45; else HPV31/33/35/52/58; else HPV39/51/56/59/68).

RESULTS

At enrollment, median participant age was 30.1 years; most (63%) were hrHPV-positive. Over follow-up, 24 participants progressed to CIN2+ (7.0%). CIN2+ IR among hrHPV-positive participants was 3.4/1,000 person-months. CIN2+ IRs were highest for HPV16 (8.3), HPV33 (7.8), and HPV58 (4.9). Five-year CIN2+ risk was higher for HPV16 (0.34) compared with HPV18/45 (0.12), HPV31/33/35/52/58 (0.12), and HPV39/51/56/59/68 (0.16) (P = 0.05).

CONCLUSIONS

Non-16/18 hrHPV types are associated with differential CIN2+ progression rates. HPV16, 33, and 58 exhibited the highest rates over 5 years. HPV risk groups warrant further investigation in diverse US populations.

IMPACT

These novel data assessing extended HPV genotyping in a diverse clinical cohort can inform future directions to improve screening practices in the general population.

Leveraging antigenic seniority for maternal vaccination to prevent mother-to-child transmission of HIV-1

The development of a maternal HIV vaccine to synergize with current antiretroviral drug prophylaxis can overcome implementation challenges and further reduce mother-to-child transmission (MTCT) of HIV. Both the epitope-specificity and autologous neutralization capacity of maternal HIV envelope (Env)-specific antibodies have been implicated in decreased risk of MTCT of HIV. Our goal was to determine if heterologous HIV Env immunization of SHIV.C.CH505-infected, ART-suppressed female rhesus macaques (RMs) could boost autologous Env-specific antibodies. SHIV.C.CH505-infected female RMs (n = 12), began a daily ART regimen at 12 weeks post-infection (wpi), which was continued for 12 weeks. Starting 2 weeks after ART initiation, RMs received 3 monthly immunizations with HIV b.63521/1086.C gp120 or placebo (n = 6/group) vaccine with adjuvant STR8S-C. Compared to the placebo-immunized animals, Env-vaccinated, SHIV-infected RMs exhibited enhanced IgG binding, avidity, and ADCC responses against the vaccine immunogens and the autologous SHIV.C.CH505 Env. Notably, the Env-specific memory B cells elicited by heterologous vaccination were dominated by cells that recognized the SHIV.C.CH505 Env, the antigen of primary exposure. Thus, vaccination of SHIV-infected, ART-suppressed RMs with heterologous HIV Envs can augment multiple components of the antibody response against the Env antigen of primary exposure, suggesting antigenic seniority. Our results suggest that a universal maternal HIV vaccination regimen can be developed to leverage antigenic seniority in targeting the maternal autologous virus pool.

Abstract 2230: Extended human papillomavirus genotyping to predict progression to high-grade cervical precancer: A prospective cohort study in the southeastern United States

Background: High-risk human papillomavirus (hrHPV) testing is recommended for primary cervical cancer screening and is used alongside cytology to triage screening abnormalities to colposcopy. Most screening-based hrHPV tests involve pooled detection of any hrHPV type or of HPV 16/18 only. Extended HPV genotyping, particularly of non-16/18 hrHPV types, may improve risk stratification for millions of cervical abnormalities detected each year, but HPV genotype-specific progression risks are not well characterized. HPV genotype-specific incidence of high-grade cervical intraepithelial neoplasia or more severe (CIN2+) was examined among individuals with normal or low-grade (CIN1) histology following an abnormal screening cytology result.

Methods: A US-based prospective, multiracial cohort of 343 colposcopy referral patients with normal (n=226) or CIN1 (n=117) histology was assessed. Baseline cervical samples underwent HPV DNA genotyping. Participants were followed for up to five years. Genotype-specific CIN2+ incidence rates (IR) were estimated with accelerated failure time models for interval-censored data. Cumulative CIN2+ risk over five years was estimated non-parametrically and compared for HPV risk groups (HPV 16/31/18, else HPV 33/58/52/45, else HPV 39/68/35/51/59/56/66) and age groups (ages 21-24, 25-29, 30+).

Results: At enrollment, median participant age was 30.1 years; 67.1% were hrHPV-positive. During follow-up (median 24.3 months), 24 participants progressed to CIN2+ (7.0%; 6.2% among normal histology and 8.6% among CIN1). CIN2+ IR among hrHPV-positive participants was 3.2/1,000 person-months. CIN2+ IRs were highest for HPV 16 (IR 8.3; 95% CI 4.1, 16.6), HPV 33 (IR 7.8; 95% CI 2.0, 31.3), and HPV 58 (IR 4.9; 95% CI 1.2, 19.6). IRs were highest for HPV 16, 68, and 33 among normal histology and for HPV 33, 31, 16, and 58 among CIN1. Five-year CIN2+ risks were 0.27 for HPV 16/31/18, 0.11 for HPV 33/58/52/45, and 0.13 for HPV 39/68/35/51/59/56/66 (p=0.04). CIN2+ risk did not differ by age group.

Conclusion: In addition to the established HPV type 16, HPV 33 and 58 were consistently predictive of progression to CIN2+ over a five-year period in this cohort. These findings also support the utility of HPV risk groups to stratify women with non-16/18 hrHPV positivity who exhibit differential risks of progression. Additionally, HPV risk groups appear to predict progression regardless of age; thus, although hrHPV testing is not recommended for initial screening of women under 30 years of age, it may be a risk-stratification tool for these younger women, once a cervical abnormality is found. In conclusion, extended genotyping of non-16/18 hrHPV may be useful to identify individuals with normal or low-grade histology results who are at increased risk of progression to CIN2+, thereby improving the efficacy of cervical cancer screening.

Citation Format: Alexandra Bukowski, Cathrine Hoyo, Michael G. Hudgens, Wendy R. Brewster, Fidel Valea, Rex C. Bentley, Adriana C. Vidal, Rachel L. Maguire, John W. Schmitt, Susan K. Murphy, Kari E. North, Jennifer S. Smith. Extended human papillomavirus genotyping to predict progression to high-grade cervical precancer: A prospective cohort study in the southeastern United States [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2230.

CD4 T cell memory restoration upon antiretroviral initiation in people living with HIV

HIV infection depletes CD4 T cells and dysregulates formation of long-lived memory CD4 T cells. Studies show that antiretroviral therapy (ART) in people with HIV (PWH) more effectively restores CD4 T cell memory phenotypes when initiated early (&lt; Fiebig V). We used a 31 marker mass cytometry panel to assess CD4 T cell phenotype in PWH treated in acute infection (AHI) (median 2.3 years post ART initiation) and chronic infection (CHI) (median 5.8 years post ART initiation) compared to healthy donors (HD) (n=10 per group). Markers of activation (HLA-DR, CD25), exhaustion (PD-1), survival (Bcl-2) and memory (CD127) were examined. CD4 T cell memory phenotypes of AHI clustered closely with HD whereas CHI had fewer central memory CD4 T cells. We also examined IL-7 signaling in CD4 T cells, measuring STAT5 phosphorylation (pSTAT5) in response to IL-7. CHI exhibited significantly lower pSTAT5 than HD in contrast to AHI who exhibited restored IL-7 signaling. This suggests ongoing and underappreciated functional defects in CD4 T cells in CHI. To examine this further, we are completing detailed analysis of CHI before and after ART initiation (pre-ART, day 2, 7, 10, 14, 28, month 5, 9 and 18). Data will be compared to our recent work showing that CD4 T cell memory subsets, activation and exhaustion markers are highly stable in durably suppressed CHI on ART over 19–27 months. New work is examining CD4 T cell function in immunological non-responders (INR) who fail to restore CD4 counts following ART. Altogether these studies will inform how HIV impacts formation of both CD4 memory and the HIV reservoir (which is largely harbored in long lived memory CD4 T cells) following ART initiation, potentially identifying novel therapeutic targets to accelerate HIV cure in CHI.

This work was made possible by the National Institute of Allergy and Infectious Diseases U01 AI131310, Collaboratory of AIDS Researchers for Eradication (UM1 AI164567) and UNC WIHS (U01 AI103390).

Conserved-region MVA vaccines can shift HIV T cell immunodominance in PWH on ART - the M&M Study

CD8+ T cell immunity is essential to the control of HIV viremia. We examined the safety and immunogenicity of MVA-vectored vaccines expressing highly conserved HIV regions in a first-in-man Phase I study in people living with HIV on ART. Participants received a single intramuscular dose of MVA.tHIVconsv3 (M3), MVA.tHIVconsv4 (M4), combined M3+M4 or saline in a 7:7:7:3 ratio. M3 and M4 span the same 6 HIV regions but differ by approximately 10% of amino acids; a design to increase vaccine coverage of circulating HIV variants. We employed ex vivo IFN-g ELISpot assays to measure changes in HIV-specific T cell magnitude and breadth to M3 and/or M4 immunogens following vaccination. We also examined whether M3, M4 or M3+M4 vaccination increased the ability of CD8+ T cells inhibit HIV in vitro replication.

The M&M study is fully enrolled but presently is blinded. Analysis of blinded data show that vaccination was safe and well tolerated. Vaccination induced strong increases in the T cell response to M3, M4 vaccine immunogens producing a 2- to 18-fold increase in magnitude in 16/20 participants tested to date. M3/M4-specific T cell breadth also increased across participants. Vaccine-associated T cell responses mostly remained elevated (&gt;2-fold increase) for at least 70 days post-vaccination visit. Vaccination was also associated with clear and sustained increases in in vitro virus inhibition. The percentage of the total HIV T cell response targeting conserved HIV regions in participants increased on average from 40 to 60% post-vaccination, suggesting M3/M4/M3+4 vaccination successfully produced a sustained shift in T cell immunodominance. Unblinded data will be presented at this meeting.

Supported by U01AI131310

CD8 T Cell Virus Inhibition Assay Protocol

The human immunodeficiency virus (HIV)-1 viral inhibition assay (VIA) measures CD8⁺ T cell-mediated inhibition of HIV replication in CD4⁺ T cells and is increasingly used for clinical testing of HIV vaccines and immunotherapies. Different VIAs that differ in length of CD8:CD4 T cell culture periods (6-13 days), purity of CD4 cultures [isolated CD4⁺ T cells or CD8⁺ depleted peripheral blood mononuclear cells (PBMCs)], HIV strains (laboratory strains, isolates, reporter viruses) and read-outs of virus inhibition (p24 ELISA, intracellular measurement of p24, luciferase reporter expression, and viral gag RNA) have been reported. Here, we describe multiple modifications to a 7-day VIA protocol, the most impactful being the introduction of independent replicate cultures for both HIV infected-CD4 (HIV-CD4) and HIV-CD4:CD8 T cell cultures. Virus inhibition was quantified using a ratio of weighted averages of p24⁺ cells in replicate cultures and the corresponding 95% confidence intervals. We identify methodological and analysis changes that could be incorporated into other protocols to improve assay reproducibility. We found that in people living with HIV (PLWH) on antiretroviral therapy (ART), CD8 T cell virus inhibition was largely stable over time, supporting the use of this assay and/or analysis methods to examine therapeutic interventions. Graphic abstract.

Rates of Sexually Transmitted Infection Diagnoses Among US Youth With Perinatally and Nonperinatally Acquired HIV

BACKGROUND

Of new sexually transmitted infections (STIs) in the United States, 50% occur among youth aged 15 to 24 years. Previous studies among youth with HIV (YHIV) do not distinguish STI trends among individuals with perinatally (YPHIV) and nonperinatally (YNPHIV) acquired HIV.

METHODS

Among 3 Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN) studies conducted between 2009 and 2015, we estimated incident diagnoses of trichomonal, bacterial, viral, and overall STIs stratified by sex assigned at birth, mode of HIV acquisition (perinatal [YPHIV] and nonperinatal [YNPHIV]), age (13-17 and 18-24 years), CD4 count (<200, 200-499, and ≥500/μL), and HIV viral load (VL) (<400 and ≥400 copies/mL).

RESULTS

Among 3131 YHIV, across the 3 studies, mean (SD) age was 20.6 (2.6) years, 888 (28%) were female, 2498 (80%) had nonperinatal HIV acquisition recorded, and 2298 (73%) were African American/Black. Mean follow-up was 0.9 (0.3) years. Compared with YPHIV, YNPHIV spent less person-time with VL <400 copies/mL (47% vs. 53%) and more time off antiretroviral therapy (49% vs. 15%), and had higher overall STI rates (males, 65.9 vs. 8.5/100 person-years [PY]; females, 54.7 vs. 17.2/100 PY). Among YPHIV, bacterial STIs were higher during person-time spent with VL ≥400 vs. <400 copies/mL (male YPHIV, 10.9 vs. 0.6/100 PY; female YPHIV, 11.2 vs. 2.9/100 PY); no difference was observed among YNPHIV, which may be due to concurrent acquisition of HIV and other STIs and limited follow-up.

CONCLUSIONS

Compared with YPHIV, YNPHIV spent less time on antiretroviral therapy and virologically suppressed; YNPHIV also had higher STI diagnosis rates. Very high STI diagnosis rates among YHIV, including among those without virologic suppression, highlight the importance of youth-focused efforts to support durable virologic suppression and identify and treat STIs.

Prevalence of High-Risk Human Papillomavirus by RNA Assay in Home Self-Collected Samples Among Underscreened People in North Carolina

BACKGROUND

Low-income and uninsured people with a cervix (PWC) are at the highest risk of being underscreened for cervical cancer. We evaluated the prevalence of high-risk human papillomavirus (hrHPV) on home self-collected samples, as well as rates of in-clinic follow-up and risk factors associated with hrHPV positivity in this at-risk population.

METHODS

My Body My Test 3 was conducted between 2016 and 2019 in North Carolina among individuals aged 25 to 64 years, overdue for cervical cancer screening, and with incomes of <250% of the US Federal Poverty Level. Our analytic sample included participants randomized to the self-collection arm who returned self-collected cervicovaginal brush samples for HPV testing (n = 329). Samples were tested for 14 hrHPV types by an HPV RNA assay and further genotyped for HPV-16 and HPV-18/45. We examined behavioral risk factors for hrHPV positivity using logistic regression and between-subject t tests.

RESULTS

High-risk HPV RNA prevalence was 16% (n = 52/329) in self-collected samples. Of the hrHPV-positive participants, 24 (46%) presented for in-clinic cervical cancer screening, compared with 56 (20%) of hrHPV-negative participants. Those with ≥2 sexual partners in the past year were twice as likely to be hrHPV positive in adjusted analyses (adjusted odds ratio, 2.00 [95% confidence interval, 1.03-3.88]). High-risk HPV-positive and HPV-negative participants had similar attitudes toward screening, with the exception of hrHPV-positive participants who reported a lower perceived risk of cervical cancer than those who were hrHPV negative (P < 0.05).

CONCLUSION

The hrHPV RNA prevalence was similar to findings in other underscreened PWC in the United States. Efforts to reach underscreened PWC are critical for cervical cancer prevention. Future studies aimed at home self-collection should address methods of increasing clinic attendance and completion of treatment among those with HPV-positive results.

Power and sample size for observational studies of point exposure effects

Inverse probability of treatment weights (IPTWs) are commonly used to control for confounding when estimating causal effects of point exposures from observational data. When planning a study that will be analyzed with IPTWs, determining the required sample size for a given level of statistical power is challenging because of the effect of weighting on the variance of the estimated causal means. This paper considers the utility of the design effect to quantify the effect of weighting on the precision of causal estimates. The design effect is defined as the ratio of the variance of the causal mean estimator divided by the variance of a naïve estimator if, counter to fact, no confounding had been present and weights were not needed. A simple, closed-form approximation of the design effect is derived that is outcome invariant and can be estimated during the study design phase. Once the design effect is approximated for each treatment group, sample size calculations are conducted as for a randomized trial, but with variances inflated by the design effects to account for weighting. Simulations demonstrate the accuracy of the design effect approximation, and practical considerations are discussed.

On Variance of the Treatment Effect in the Treated When Estimated by Inverse Probability Weighting

In the analysis of observational studies, inverse probability weighting (IPW) is commonly used to consistently estimate the average treatment effect (ATE) or the average treatment effect in the treated (ATT). The variance of the IPW ATE estimator is often estimated by assuming that the weights are known and then using the so-called "robust" (Huber-White) sandwich estimator, which results in conservative standard errors (SEs). Here we show that using such an approach when estimating the variance of the IPW ATT estimator does not necessarily result in conservative SE estimates. That is, assuming the weights are known, the robust sandwich estimator may be either conservative or anticonservative. Thus, confidence intervals for the ATT using the robust SE estimate will not be valid, in general. Instead, stacked estimating equations which account for the weight estimation can be used to compute a consistent, closed-form variance estimator for the IPW ATT estimator. The 2 variance estimators are compared via simulation studies and in a data analysis of the association between smoking and gene expression.

Virologic outcomes among adults with HIV using integrase inhibitor-based antiretroviral therapy

BACKGROUND

Integrase strand transfer inhibitor (InSTI)-based regimens have been recommended as first-line antiretroviral therapy (ART) for adults with HIV. But data on long-term effects of InSTI-based regimens on virologic outcomes remain limited. Here we examined whether InSTI improved long-term virologic outcomes compared with efavirenz (EFV).

METHODS

We included adults from the North American AIDS Cohort Collaboration on Research and Design who initiated their first ART regimen containing either InSTI or EFV between 2009 and 2016. We estimated differences in the proportion virologically suppressed up to 7 years of follow-up in observational intention-to-treat and per-protocol analyses.

RESULTS

Of 15 318 participants, 5519 (36%) initiated an InSTI-based regimen and 9799 (64%) initiated the EFV-based regimen. In observational intention-to-treat analysis, 81.3% of patients in the InSTI group and 67.3% in the EFV group experienced virologic suppression at 3 months after ART initiation, corresponding to a difference of 14.0% (95% CI 12.4-15.6). At 1 year after ART initiation, the proportion virologically suppressed was 89.5% in the InSTI group and 90.2% in the EFV group, corresponding to a difference of -0.7% (95% CI -2.1 to 0.8). At 7 years, the proportion virologically suppressed was 94.5% in the InSTI group and 92.5% in the EFV group, corresponding to a difference of 2.0% (95% CI -7.3 to 11.3). The observational per-protocol results were similar to intention-to-treat analyses.

CONCLUSIONS

Although InSTI-based initial ART regimens had more rapid virologic response than EFV-based regimens, the long-term virologic effect was similar. Our findings may inform guidelines regarding preferred initial regimens for HIV treatment.

Family Composition and Stability for Orphans: A Longitudinal Study of Well-Being in 5 Low- and Middle-Income Countries

Objectives: Many orphaned children in low- and middle-income countries live with family. Yet, their household composition and its stability are not well-characterized, nor is impact of stability on longer-term outcomes.

Methods: We used the longitudinal, multi-country Positive Outcomes for Orphans cohort to describe adult family living with orphans. Stability was measured by changes in presence of six familial relations over time, and related to three outcomes: 1) incident abuse, 2) cognitive functioning, 3) emotional difficulties. Associations were estimated using generalized linear models fit with generalized estimating equations. For abuse, Poisson regression estimated risk ratios. For continuous scores of cognitive functioning and emotional difficulties, linear models estimated mean differences (MDs) with 95% confidence intervals.

Results: Among 1,359 orphans, 53–61% reported living with their mother each year; 7–13% with father; nearly 60% reported ≥1 change in composition over follow-up. Compared to 0 changes, difficulties increased with 1 change [MD: 0.23 (−0.33, 0.79)], 2 changes [MD: 0.57 (0.00, 1.16)] and ≥3 changes [MD: 0.73 (0.18, 1.29)]. No associations were found with abuse or cognitive functioning.

Conclusion: Orphan well-being may be improved through supports stabilizing household composition or targeting emotional resilience.

Early Post-Vaccination Gene Signatures Correlate With the Magnitude and Function of Vaccine-Induced HIV Envelope-Specific Plasma Antibodies in Infant Rhesus Macaques

A better understanding of the impact of early innate immune responses after vaccine priming on vaccine-elicited adaptive immune responses could inform rational design for effective HIV vaccines. The current study compared the whole blood molecular immune signatures of a 3M-052-SE adjuvanted HIV Env protein vaccine to a regimen combining the adjuvanted Env protein with simultaneous administration of a modified Vaccinia Ankara vector expressing HIV Env in infant rhesus macaques at days 0, 1, and 3 post vaccine prime. Both vaccines induced a rapid innate response, evident by elevated inflammatory plasma cytokines and altered gene expression. We identified 25 differentially-expressed genes (DEG) on day 1 compared to day 0 in the HIV protein vaccine group. In contrast, in the group that received both the Env protein and the MVA-Env vaccine only two DEG were identified, implying that the MVA-Env modified the innate response to the adjuvanted protein vaccine. By day 3, only three DEG maintained altered expression, indicative of the transient nature of the innate response. The DEG represented immune pathways associated with complement activation, type I interferon and interleukin signaling, pathogen sensing, and induction of adaptive immunity. DEG expression on day 1 was correlated to Env-specific antibody responses, in particular antibody-dependent cytotoxicity responses at week 34, and Env-specific follicular T helper cells. Results from network analysis supported the interaction of DEG and their proteins in B cell activation. These results emphasize that vaccine-induced HIV-specific antibody responses can be optimized through the modulation of the innate response to the vaccine prime.

diproperm: An R Package for the DiProPerm Test

High-dimensional low sample size (HDLSS) data sets frequently emerge in many biomedical applications. The direction-projection-permutation (DiProPerm) test is a two-sample hypothesis test for comparing two high-dimensional distributions. The DiProPerm test is exact, i.e., the type I error is guaranteed to be controlled at the nominal level for any sample size, and thus is applicable in the HDLSS setting. This paper discusses the key components of the DiProPerm test, introduces the diproperm R package, and demonstrates the package on a real-world data set.