Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework

Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, Rt, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and Rt. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of Rt are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and Rt that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.

Simulated Fishing to Untangle Catchability and Availability in Fish Abundance Monitoring

In fisheries monitoring, catch is assumed to be a product of fishing intensity, catchability, and availability, where availability is defined as the number or biomass of fish present and catchability refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear used in sampling, which is not necessarily the entire population. Programs often deal with this problem by assuming that catchability is constant, but if catchability is not constant, it is not possible to separate the effects of catchability and population size using monitoring data alone. This study uses individual-based simulation to separate the effects of changing environmental conditions on catchability and availability in environmental monitoring data. The simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies. Results of this study indicate that given constraints on Delta Smelt swimming ability, it is unlikely that the apparent declines in Delta Smelt abundance are the result of changing water clarity affecting catchability.

Duration of SARS-CoV-2 sero-positivity in a large longitudinal sero-surveillance cohort: the COVID-19 Community Research Partnership

Background Estimating population prevalence and incidence of prior SARS-CoV-2 infection is essential to formulate public health recommendations concerning the COVID-19 pandemic. However, interpreting estimates based on sero-surveillance requires an understanding of the duration of elevated antibodies following SARS-CoV-2 infection, especially in the large number of people with pauci-symptomatic or asymptomatic disease. Methods We examined > 30,000 serology assays for SARS-CoV-2 specific IgG and IgM assays acquired longitudinally in 11,468 adults between April and November 2020 in the COVID-19 Community Research Partnership. Results Among participants with serologic evidence for infection but few or no symptoms or clinical disease, roughly 50% sero-reverted in 30 days of their initial positive test. Sero-reversion occurred more quickly for IgM than IgG and for antibodies targeting nucleocapsid protein compared with spike proteins, but was not associated with age, sex, race/ethnicity, or healthcare worker status. Conclusions The short duration of antibody response suggests that the true population prevalence of prior SARS-CoV-2 infection may be significantly higher than presumed based on earlier sero-surveillance studies. The impact of the large number of minimally symptomatic COVID-19 cases with only a brief antibody response on population immunity remains to be determined.

Simulated Fishing to Untangle Catchability and Availability in Fish Abundance Monitoring

In fisheries monitoring, catch is assumed to be a product of fishing intensity, catchability, and availability, where availability is defined as the number or biomass of fish present and catchability refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear that is used in sampling, which is not necessarily the entire population. Programs often deal with this problem by assuming that catchability is constant, but if catchability is not constant, it is not possible to separate the effects of catchability and population size using monitoring data alone. This study uses individual-based simulation to separate the effects of changing environmental conditions on catchability and availability in environmental monitoring data. The simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well-monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies. Results of this study indicate that given constraints on Delta Smelt swimming ability, it is unlikely that the apparent declines in Delta Smelt abundance are due to an effect of changing water clarity on catchability.

Trends in Thoracic Impedance and Arrhythmia Burden Among Patients with Implanted Cardiac Defibrillators During the COVID-19 Pandemic

ABSTRACTHospitalizations for acute cardiac conditions have markedly declined during the coronavirus disease 2019 (COVID-19) pandemic, yet the cause of this decline is not clear. Using remote monitoring data of 4,029 patients with implantable cardiac defibrillators (ICDs) living in New York City and Minneapolis/Saint Paul, we assessed changes in markers of cardiac status among these patients and compared thoracic impedance and arrhythmia burden in 2019 and 2020 from January through August. We found no change in several key disease decompensation markers among patients with implanted ICD devices during the first phase of COVID-19 pandemic, suggesting that the decrease in cardiovascular hospitalizations in this period is not reflective of a true population-level improvement in cardiovascular health.

Duration of SARS-CoV-2 Sero-Positivity in a Large Longitudinal Sero-Surveillance Cohort: The COVID-19 Community Research Partnership

Background: Estimating population prevalence and incidence of prior SARS-CoV-2 infection is essential to formulate public health recommendations concerning the COVID-19 pandemic. However, interpreting estimates based on sero-surveillance requires an understanding of the duration of elevated antibodies following SARS-CoV-2 infection, especially in the large number of people with pauci-symptomatic or asymptomatic disease. Methods: We examined >30,000 serology assays for SARS-CoV-2 specific IgG and IgM assays acquired longitudinally in 11,468 adults between April and November 2020 in the COVID-19 Community Research Partnership. Findings: Among participants with serologic evidence for infection but few or no symptoms or clinical disease, roughly 50% sero-reverted in 30 days of their initial positive test. Sero-reversion occurred more quickly for IgM than IgG and for antibodies targeting nucleocapsid protein compared with spike proteins, but was not associated with age, sex, race/ethnicity, or healthcare worker status. Interpretation: The short duration of antibody response suggests that the true population prevalence of prior SARS-CoV-2 infection may be significantly higher than presumed based on earlier sero-surveillance studies. The impact of the large number of minimally symptomatic COVID-19 cases with only a brief antibody response on population immunity remains to be determined.

Simulated Fishing to Untangle Catchability and Availability in Fish Abundance Monitoring

In fisheries monitoring, catch is assumed to be a product of fishing intensity, catchability, and availability, where availability is defined as the number or biomass of fish present and catchability refers to the relationship between catch rate and the true population. Ecological monitoring programs use catch per unit of effort (CPUE) to standardize catch and monitor changes in fish populations; however, CPUE is proportional to the portion of the population that is vulnerable to the type of gear that is used in sampling, which is not necessarily the entire population. Programs often deal with this problem by assuming that catchability is constant, but if catchability is not constant, it is not possible to separate the effects of catchability and population size using monitoring data alone. This study uses individual-based simulation to separate the effects of changing environmental conditions on catchability and availability in environmental monitoring data. The simulation combines a module for sampling conditions with a module for individual fish behavior to estimate the proportion of available fish that would escape from the sample. The method is applied to the case study of the well-monitored fish species Delta Smelt (Hypomesus transpacificus) in the San Francisco Estuary, where it has been hypothesized that changing water clarity may affect catchability for long-term monitoring studies. Results of this study indicate that given constraints on Delta Smelt swimming ability, it is unlikely that the apparent declines in Delta Smelt abundance are due to an effect of changing water clarity on catchability.

Estimation Under Mode Effects and Proxy Surveys, Accounting for Non-ignorable Nonresponse

We propose a new, model-based methodology to address two major problems in survey sampling: The first problem is known as mode effects, under which responses of sampled units possibly depend on the mode of response, whether by internet, telephone, personal interview, etc. The second problem is of proxy surveys, whereby sampled units respond not only about themselves but also for other sampled. For example, in many familiar household surveys, one member of the household provides information for all other members, possibly with measurement errors. Ignoring the existence of mode effects and/or possible measurement errors in proxy surveys could result in possible bias in point estimators and subsequent inference. Our approach accounts also for nonignorable nonresponse. We illustrate the proposed methodology by use of simulation experiments and real sample data, with known true population values.

The Population Health Model: A Timely Approach for Mission Hospitals

Mission hospitals have long provided a source of care along with spiritual support for populations around the world, often serving the disadvantaged not served by other facilities. For a variety of reasons, the future of mission hospitals has been thrown into doubt, and options for repurposing these institutions are being explored. Because of the mission of mission hospitals, there approach has historically differed from those of other health system (including many faith-based facilities). The multi-purpose attribute of mission hospitals makes them excellent candidates for adopting a population health approach. The population health model as now being developed in the United States represents a radical departure from traditional clinical practice and, in fact, reduces the significance of medical care as a means to improving community health. The model emphasizes treatment of populations rather than individuals, takes a holistic approach to the provision of care (to the point of addressing social determinants of health), and enlists the community in collaborative arrangements for collective impact. Mainstream hospitals have had difficulty in implementing a true population health approach for a variety of reasons, and mission hospitals appear to represent an effective vehicle for putting the model into practice.

Estimation of Forest Disturbance from Retrospective Observations in a Broad-Scale Inventory

Understanding the extent and timing of forest disturbances and their impacts is critical to formulating effective management and policy responses. Broad-scale inventory programs provide key estimates of forest parameters that indicate the extent and severity of disturbance impacts. Here, we review the use of a post-stratified estimator in a panelized design, in the context of disturbance observations that are collected retrospectively. We further develop a sample weight adjustment that is requisite for proper estimation of the extent and timing of disturbances. Using populations from areas of Arkansas, California, and Maine in the US, the weight adjustment technique was tested in a Monte Carlo simulation. We found that the estimated area of disturbance using the weight adjustment technique had satisfactory agreement with the true population values and performed considerably better than the conventional post-stratified estimation approach. The proliferation of panelized forest inventory designs globally suggests that accurate estimates of areal extent and timing of disturbances will often require that weighting adjustment techniques be employed in the estimation process.