Semiparametric g-computation for survival outcomes with time-fixed exposures: An illustration.

PURPOSE: Generalized (g-) computation is a useful tool for causal inference in epidemiology. However, in settings when the outcome is a survival time subject to right censoring, the standard pooled logistic regression approach to g-computation requires arbitrary discretization of time, parametric modeling of the baseline hazard function, and the need to expand one's dataset. We illustrate a semiparametric Breslow estimator for g-computation with time-fixed treatments and survival outcomes that is not subject to these limitations. METHODS: We compare performance of the Breslow g-computation estimator to the pooled logistic g-computation estimator in simulations and illustrate both approaches to estimate the effect of a 3-drug vs 2-drug antiretroviral therapy regimen among people with HIV. RESULTS: In simulations, both approaches performed well at the end of follow-up. The pooled logistic approach was biased at times between the endpoints of the discrete time intervals used, while the Breslow approach was not. In the example, both approaches estimated a 1-year risk difference of about 6 % in favor of the 3-drug regimen, but the shape of the survival curves differed. CONCLUSIONS: The Breslow g-computation estimator of counterfactual risk functions does not rely on strong parametric assumptions about the time-to-event distribution or onerous dataset expansions.

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.

Combined oral contraceptive utilization and uterine fibroid incidence: A prospective study in a cohort of African-American women.

Published associations between combined oral contraceptive use and uterine fibroid development have lacked prospective imaging with ultrasound to distinguish between incident and prevalent fibroids. The Study of Environment, Lifestyle, and Fibroids prospectively followed fibroid-free, African-American women (the group with the highest disease burden in the U.S.) to identify incident cases. We examined associations between combined oral contraceptive use and the 40-month cumulative risk of fibroids. History of hormonal contraceptive use was collected via telephone interview at enrollment. Fibroid identification was performed using transvaginal ultrasonography at enrollment, and at 20 and 40-months of follow-up. Inverse probability weights for exposures and censoring were used to construct weighted risk ratios (wRR) and weighted risk different (wRD) estimators which control for differences in fibroid risk factors between exposure groups. In addition, unweighted fully adjusted log-binomial regression models (aRR) were run for comparison. Of the 1,308 participants in the analysis sample, 70% had used combined oral contraceptives and 17% developed fibroids by 40 months. We observed an inverse association between ever use of combined oral contraceptives and cumulative fibroid incidence (wRR: 0.78; 95% Confidence Interval (CI): 0.60, 1.00; wRD: -0.05, 95% CI: -0.11, 0; aRR: 0.76, 95% CI: 0.60, 0.98). Fibroid incidence was greater in participants who started using combined oral contraceptives after age 17 years than among younger initiators, though the restriction to ever-users made this estimate less precise (wRR: 1.25; 95% CI: 0.89, 1.76; wRD: 0.04, 95% CI: -0.02, 0.10). No consistent patterns of fibroid incidence were seen among ever-users for duration of, or years since, last combined oral contraceptives use.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.