Design and methods of the Apple Women's Health Study: a digital longitudinal cohort study.

http://www.ajog.org/article/S0002937821010929/pdf

Design and methods of the Apple Women’s Health Study: a digital longitudinal cohort study

Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW™ COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from RT-PCR-based assays utilizing a swab in viral transport media. 

/pdf/sequencing-sars-cov-2-from-antigen-tests-2fru2tnd.pdf

Sequencing SARS-CoV-2 from antigen tests

During the first wave of the COVID-19 pandemic, a lockdown was imposed on the Danish society. Reports from other countries that were hit by the COVID-19 pandemic before Denmark instilled fear of flooding of the emergency departments. To mitigate this flooding, increased competencies were conveyed to the paramedics in the ambulances aiming to allow for a release of a higher number of patients prehospitally. The increased competencies in the prehospital personnel were expected to increase the on-scene time and thus the total workload of the ambulances potentially resulting in delays in the acute care. We sought to elucidate the effects of the pandemic on the workload of the prehospital system during the first wave.This was a retrospective study using operational data from the regional emergency medical dispatch centre in the Region of Southern Denmark. We collected the number of ambulance runs, the response times, the on-scene times, and the mission outcome of all ambulance runs with lights and sirens in the Region of Southern Denmark during the first wave of the pandemic. We compared the numbers with a similar period in the year before.Compared with the year before the pandemic we observed a 10.3% reduction in call volume and a corresponding reduction in the total number of missions with lights and sirens. We found an increase in on-scene times in both missions with patients conveyed to hospital (20.6 min vs. 18.7 min) and missions with non-conveyed patients (37.4 min versus 30.7 min). The response times were unaffected.The increased on-scene times of the ambulances may largely be attributed to time utilised to exert the increased competencies concerning treat-and-release of patients.. Despite an increased on-scene time of the ambulances, we believe that the combination of a reduction in the number of total missions and the existing capacity in the ambulance service in the Region of Southern Denmark nullified the prolongation of ambulance response times that was seen in other countries during the pandemic. This capacity allowed for time spent performing in-depth examinations of patients with the potential to be released at the scene. 

/pdf/increased-ambulance-on-scene-times-but-unaffected-response-rfgpfwrh.pdf

Increased ambulance on-scene times but unaffected response times during the first wave of the COVID-19 pandemic in Southern Denmark

This study compares the effectiveness of COVID-19 control policies on the virus’s spread and on the change of the infection dynamics in China, Germany, Austria, and the USA relying on a regression discontinuity in time and ‘earlyR’ epidemic models. The effectiveness of policies is measured by real-time reproduction number and cases counts. Comparison between the two lockdowns within each country showed the importance of people's risk perception for the effectiveness of the measures. Results suggest that restrictions applied for a long period or reintroduced later may cause at-tenuated effect on the circulation of the virus and the number of casualties.

Analyzing the Effectiveness of COVID-19 Lockdown Policies Using the Time-Dependent Reproduction Number and the Regression Discontinuity Framework: Comparison between Countries

Objectives The COVID-19 pandemic caused by the novel SARS-CoV-2 coronavirus has drastically altered the global realities. Harnessing national scale data from the COVID-19 pandemic may better inform policy makers in decision making surrounding the reopening of society. We examined country-level, daily-confirmed, COVID-19 case data from the World Health Organization (WHO) to better understand the comparative dynamics associated with the ongoing global pandemic at a national scale. Study design Observational study. Methods We included data from 20 countries in Europe, the Americas, Africa, Eastern Mediterranean and West Pacific regions, and obtained the aggregated daily new case data for the European Union including 27 countries. We utilized an innovative analytic approach by applying statistical change point models, which have been previously employed to model volatility in stock markets, changes in genomic data, and data dynamics in other scientific disciplines, to segment the transformed case data. This allowed us to identify possible change or turning points as indicated by the dynamics of daily COVID-19 incidences. We also employed B-spline regression models to express the estimated (predicted) trend of daily new incidences for each country’s COVID-19 disease burden with the identified key change points in the model. Results We identified subtle, yet different change points (translated to actual calendar days) by either the mean and variance change point model with small p-values or by a Bayesian online change point algorithm with large posterior probability in the trend of COVID-19 incidences for different countries. We correlated these statistically identified change points with evidence from the literature surrounding these countries’ policies regarding opening and closing of their societies in an effort to slow the spread of COVID-19. The days when change points were detected were ahead of the actual policy implementation days, and in most of the countries included in this study the decision lagged the change point days too long to prevent potential widespread extension of the pandemic. Conclusions Our models describe the behavior of COVID-19 prevalence at a national scale and identify changes in national disease burden as relating to chronological changes in restrictive societal activity. Globally, social distancing measures may have been most effective in smaller countries with single governmental and public health organizational structures. Further research examining the impact of heterogeneous governmental responses to pandemic management appears warranted.

Early detection of change patterns in COVID-19 incidence and the implementation of public health policies: a multi-national study

Background Many cancer survivors face financial difficulties that prevent them from receiving appropriate health care. Racial/ethnic disparities in receipt of health care have been reported among cancer survivors, but recent data for important racial/ethnic subgroups of the US population are lacking. Methods To learn more about barriers to healthcare access faced by cancer survivors, we analyzed data from the NIH "All of Us" Research Program. Data were analyzed about demographic factors and other personal characteristics, personal medical history of cancer, healthcare utilization, and access to care. Results As of November 2020, a total of 5426 participants had a history of cancer (excluding skin cancer). About 88.2% were non-Hispanic White; 3.9% were Black, African American, or African; 1.3% were Asian; 4.1% were Hispanic, Latino, or Spanish; and 1.2% reported more than one race. Just over one-half had an annual income of $75,000 or greater. The majority of the participants (71.7%) were college graduates or had an advanced degree. About 47.0%% had private health insurance, 41.0% had Medicare, 6.0% had Medicaid, and the remainder had military, Veterans Affairs, other insurance, or no health insurance. Frequently cited reasons for delayed care in the past 12 months were "had to pay out of pocket for some or all of the procedures," "deductible was too high/or could not afford the deductible," "couldn't afford the copay," "couldn't get time off work," and "were nervous about seeing a health care provider." Discussion A minority of cancer survivors who participated in the NIH "All of Us" Program had difficulty paying for health care in the past 12 months. Of particular concern are minorities such as African American and Hispanic cancer survivors along with those who are low income.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/cam4.3924

Jie Chen

Papers

Early detection of change patterns in COVID-19 incidence and the implementation of public health policies: a multi-national study

Health care access and utilization among adult cancer survivors: Results from the National Institutes of Health “All of Us” Research Program

onlineBcp: An R package for online change point detection using a Bayesian approach