A national prospective cohort study of SARS/COV2 pandemic outcomes in the U.S.: The CHASING COVID Cohort

Introduction: The Chasing COVID Cohort (C 3 ) study is a US-based, geographically and socio-demographically diverse sample of adults (18 and older) enrolled into a prospective cohort study during the upswing of the U.S. COVID-19 pandemic. Methods: We used internet-based strategies to enroll C 3 participants beginning March 28th, 2020. Following baseline questionnaire completion, study participants will be contacted monthly (for 6 months) to complete assessments of engagement in non-pharmaceutical interventions (e.g., use of cloth masks, avoiding large gatherings); COVID-19 symptoms; SARS/COV2 testing and diagnosis; hospitalizations; healthcare access; and uptake of health messaging. Dried blood spot (DBS) specimens will be collected at the first follow-up assessment (last week of April 2020) and at month 3 (last week of June 2020) and stored until a validated serologic test is available. Results: As of April 20, 2020, the number of people that completed the baseline survey and provided contact information for follow-up was 7,070. Participants resided in all 50 US states, the District of Columbia, Puerto Rico, and Guam. At least 24% of participants were frontline workers (healthcare and other essential workers). Twenty-three percent (23%) were 60+ years, 24% were Black or Hispanic, 52% were men, and 52% were currently employed. Nearly 20% reported recent COVID-like symptoms (cough, fever or shortness of breath) and a high proportion reported engaging in non-pharmaceutical interventions that reduce SARS/COV2 spread (93% avoided groups \u3e20, 58% wore masks; 73% quarantined). More than half (54%) had higher risk for severe COVID-19 illness should they become infected with SARS/COV2 based on age, underlying health conditions (e.g., chronic lung disease), or daily smoking. Discussion: A geographically and socio-demographically diverse group of participants was rapidly enrolled in the C3 during the upswing of the SARS/COV2 pandemic. Strengths of the C3 include the potential for direct observation of, and risk factors for, seroconversion and incident COVID disease (among those with or without antibodies to SARS/COV2) in areas of active transmission

Food Insecurity During the First Year of COVID-19: Employment and Sociodemographic Factors Among Participants in the CHASING COVID Cohort Study

Objective: While much has been reported about the impact of the COVID-19 pandemic on food insecurity, longitudinal data and the variability experienced by people working in various industries are limited. This study aims to further characterize people experiencing food insecurity during the pandemic in terms of employment, sociodemographic characteristics, and degree of food insecurity. Methods: The study sample consisted of people enrolled in the Communities, Households and SARS-CoV-2 Epidemiology (CHASING) COVID Cohort Study from visit 1 (April–July 2020) through visit 7 (May–June 2021). We created weights to account for participants with incomplete or missing data. We used descriptive statistics and logistic regression models to determine employment and sociodemographic correlates of food insecurity. We also examined patterns of food insecurity and use of food support programs. Results: Of 6740 participants, 39.6% (n = 2670) were food insecure. Non-Hispanic Black and Hispanic (vs non-Hispanic White) participants, participants in households with children (vs no children), and participants with lower (vs higher) income and education levels had higher odds of food insecurity. By industry, people employed in construction, leisure and hospitality, and trade, transportation, and utilities industries had the highest prevalence of both food insecurity and income loss. Among participants reporting food insecurity, 42.0% (1122 of 2670) were persistently food insecure (≥4 consecutive visits) and 43.9% (1172 of 2670) did not use any food support programs. Conclusions: The pandemic resulted in widespread food insecurity in our cohort, much of which was persistent. In addition to addressing sociodemographic disparities, future policies should focus on the needs of those working in industries vulnerable to economic disruption and ensure those experiencing food insecurity can access food support programs for which they are eligible

Household factors and the risk of severe COVID-like illness early in the U.S. pandemic

Objective To investigate the role of children in the home and household crowding as risk factors for severe COVID-19 disease. Methods We used interview data from 6,831 U.S. adults screened for the Communities, Households and SARS/CoV-2 Epidemiology (CHASING) COVID Cohort Study in April 2020. Results In logistic regression models, the adjusted odds ratio [aOR] of hospitalization due to COVID-19 for having (versus not having) children in the home was 10.5 (95% CI:5.7–19.1) among study participants living in multi-unit dwellings and 2.2 (95% CI:1.2–6.5) among those living in single unit dwellings. Among participants living in multi-unit dwellings, the aOR for COVID-19 hospitalization among participants with more than 4 persons in their household (versus 1 person) was 2.5 (95% CI:1.0–6.1), and 0.8 (95% CI:0.15–4.1) among those living in single unit dwellings. Conclusion Early in the US SARS-CoV-2 pandemic, certain household exposures likely increased the risk of both SARS-CoV-2 acquisition and the risk of severe COVID-19 disease

Strengthening The Organization and Reporting of Microbiome Studies (STORMS): A Reporting Checklist for Human Microbiome Research

Background Human microbiome research is a growing field with the potential for improving our understanding and treatment of diseases and other conditions. The field is interdisciplinary, making concise organization and reporting of results across different styles of epidemiology, biology, bioinformatics, translational medicine, and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Methods A multidisciplinary group of microbiome epidemiology researchers reviewed elements of available reporting guidelines for observational and genetic studies and adapted these for application to culture-independent human microbiome studies. New reporting elements were developed for laboratory, bioinformatic, and statistical analyses tailored to microbiome studies, and other parts of these checklists were streamlined to keep reporting manageable. Results STORMS is a 17-item checklist for reporting on human microbiome studies, organized into six sections covering typical sections of a scientific publication, presented as a table with space for author-provided details and intended for inclusion in supplementary materials. Conclusions STORMS provides guidance for authors and standardization for interdisciplinary microbiome studies, facilitating complete and concise reporting and augments information extraction for downstream applications. Availability The STORMS checklist is available as a versioned spreadsheet from https://www.stormsmicrobiome.org/

Improving Microbiome Research Through Enhanced Reporting and Modeling the Effects of Antibiotic Usage

I consider two key areas in the growing field of human microbiome research: improving the quality of study reporting and the impact of antibiotics on participants in human gut microbiome research studies. In the first chapter, a team of evaluators used the Strengthening the Organization and Reporting of Microbiome Studies (STORMS) checklist to assess recently published microbiome literature. I found moderate agreement and reliability between evaluators, identified several items in STORMS that could be improved, and confirmed that the STORMS checklist can serve as a tool for assessing the reporting quality of published microbiome study. The next chapter considers pre-exposure gut microbiome composition as a potential effect modifier of the relationship between antibiotics and post-exposure microbiome. In a cohort study of infants, I find that it does modify this relationship for several important bacterial taxa linked to infant development. The fourth chapter looks at four datasets comparing stool microbiome measurements recently following antibiotics exposure to unexposed controls and fits predictive models for recent antibiotics exposure in each dataset. The results are mixed with smaller, more controlled studies having excellent model results while models becoming worse in less controlled conditions. The implications of this dissertation for improving the rigor of human microbiome research are discussed

Demographic, clinical guideline criteria, Medicaid expansion and state of residency: A multilevel analysis of PrEP use on a large US sample

Objective To explore the association of clinical guideline-related variables, demographics and Medicaid expansion on pre-exposure prophylaxis (PrEP) uptake in one of the largest US sample of men who have sex with men(MSM) and transgender and gender non-binary (TGNB) people ever analysed. Methods We cross-sectionally analysed predictors of current PrEP use using demographic and HIV risk-related variables (level-1), as well as state-level variables (level-2) (ie, Medicaid expansion status). We further explored the role state of residence plays in PrEP uptake disparities across the USA. Results We found that the odds of PrEP use were significantly greater in older age, white, cisgender men. Moreover, individuals who reported recent post-exposure prophylaxis use, a recent sexually transmitted infection diagnosis and recent drug use were significantly more likely to report PrEP use. Finally, we found that the median odds of PrEP use between similar individuals from different states were 1.40 for the ones living in the Medicaid expansion states, compared with those not living in Medicaid expansion states. State of residence did not play a significant role in explaining PrEP disparities overall. Conclusion Our analysis showed that PrEP use is less common in communities standing to benefit the most from it - young MSM and TGNB of colour. However, individuals meeting federal guidelines for PrEP were significantly more likely to use PrEP. Though we found a positive association between living in Medicaid expansion states and PrEP use; that variable, as well as one\u27s state of residency, were not suitable to explain variations in PrEP use in the US