Testing and vaccination to reduce the impact of COVID-19 in nursing homes: an agent-based approach.

BACKGROUND: Efforts to protect residents in nursing homes involve non-pharmaceutical interventions, testing, and vaccine. We sought to quantify the effect of testing and vaccine strategies on the attack rate, length of the epidemic, and hospitalization. METHODS: We developed an agent-based model to simulate the dynamics of SARS-CoV-2 transmission among resident and staff agents in a nursing home. Interactions between 172 residents and 170 staff based on data from a nursing home in Los Angeles, CA. Scenarios were simulated assuming different levels of non-pharmaceutical interventions, testing frequencies, and vaccine efficacy to reduce transmission. RESULTS: Under the hypothetical scenario of widespread SARS-CoV-2 in the community, 3-day testing frequency minimized the attack rate and the time to eradicate an outbreak. Prioritization of vaccine among staff or staff and residents minimized the cumulative number of infections and hospitalization, particularly in the scenario of high probability of an introduction. Reducing the probability of a viral introduction eased the demand on testing and vaccination rate to decrease infections and hospitalizations. CONCLUSIONS: Improving frequency of testing from 7-days to 3-days minimized the number of infections and hospitalizations, despite widespread community transmission. Vaccine prioritization of staff provides the best protection strategy when the risk of viral introduction is high.

COVID-19 hospitalizations in five California hospitals: a retrospective cohort study.

BACKGROUND: The novel coronavirus pandemic has had a differential impact on communities of color across the US. The University of California hospital system serves a large population of people who are often underrepresented elsewhere. Data from hospital stays can provide much-needed localized information on risk factors for severe cases and/or death. METHODS: Patient-level retrospective case series of laboratory-confirmed COVID-19 hospital admissions at five UC hospitals (N = 4730). Odds ratios of ICU admission, death, and a composite of both outcomes were calculated with univariate and multivariate logistic regression based on patient characteristics, including sex, race/ethnicity, and select comorbidities. Associations between comorbidities were quantified and visualized with a correlation network. RESULTS: Overall mortality rate was 7.0% (329/4,730). ICU mortality rate was 18.8% (225/1,194). The rate of the composite outcome (ICU admission and/or death) was 27.4% (1298/4730). Comorbidity-controlled odds of a composite outcome were increased for age 75-84 (OR 1.47, 95% CI 1.11-1.93) and 85-59 (OR 1.39, 95% CI 1.04-1.87) compared to 18-34 year-olds, males (OR 1.39, 95% CI 1.21-1.59) vs. females, and patients identifying as Hispanic/Latino (OR 1.35, 95% CI 1.14-1.61) or Asian (OR 1.43, 95% CI 1.23-1.82) compared to White. Patients with 5 or more comorbidities were exceedingly likely to experience a composite outcome (OR 2.74, 95% CI 2.32-3.25). CONCLUSIONS: Males, older patients, those with multiple pre-existing comorbidities, and those identifying as Hispanic/Latino or Asian experienced an increased risk of ICU admission and/or death. These results are consistent with reported risks among the Hispanic/Latino population elsewhere in the United States, and confirm multiple concerns about heightened risk among the Asian population in California.

Assessing SARS-CoV-2 Testing Adherence in a University Town: Recurrent Event Modeling Analysis.

BACKGROUND: Healthy Davis Together was a program launched in September 2020 in the city of Davis, California, to mitigate the spread of COVID-19 and facilitate the return to normalcy. The program involved multiple interventions, including free saliva-based asymptomatic testing, targeted communication campaigns, education efforts, and distribution of personal protective equipment, community partnerships, and investments in the local economy. OBJECTIVE: This study identified demographic characteristics of individuals that underwent testing and assessed adherence to testing over time in a community pandemic-response program launched in a college town in California, United States. METHODS: This study outlines overall testing engagement, identifies demographic characteristics of participants, and evaluates testing participation changes over 4 periods of the COVID-19 pandemic, distinguished by the dominant variants Delta and Omicron. Additionally, a recurrent model is employed to explore testing patterns based on the participants' frequency, timing, and demographic characteristics. RESULTS: A total of 770,165 tests were performed between November 18, 2020, and June 30, 2022, among 89,924 (41.1% of total population) residents of Yolo County, with significant participation from racially or ethnically diverse participants and across age groups. Most positive cases (6351 of total) and highest daily participation (895 per 100,000 population) were during the Omicron period. There were some gender and age-related differences in the pattern of recurrent COVID-19 testing. Men were slightly less likely (hazard ratio [HR] 0.969, 95% CI 0.943-0.996) to be retested and more likely (HR 1.104, 95% CI 1.075-1.134) to stop testing altogether than women. People aged between 20 and 34 years were less likely to be retested (HR 0.861, 95% CI 0.828-0.895) and more likely to stop testing altogether (HR 2.617, 95% CI 2.538-2.699). However, older age groups were less likely to stop testing, especially those aged between 65-74 years and 75-84 years, than those aged between 0 and 19 years. The likelihood of stopping testing was lower (HR 0.93, 95% CI 0.889-0.976) for the Asian group and higher for the Hispanic or Latino (HR 1.185, 95% CI 1.148-1.223) and Black or African American (HR 1.198, 95% CI 1.054-1.350) groups than the White group. CONCLUSIONS: The unique features of a pandemic response program that supported community-wide access to free asymptomatic testing provide a unique opportunity to evaluate adherence to testing recommendations and testing trends over time. Identification of individual and group-level factors associated with testing behaviors can provide insights for identifying potential areas of improvement in future testing initiatives.

Model training periods impact estimation of COVID-19 incidence from wastewater viral loads.

Wastewater-based epidemiology (WBE) has been deployed broadly as an early warning tool for emerging COVID-19 outbreaks. WBE can inform targeted interventions and identify communities with high transmission, enabling quick and effective responses. As the wastewater (WW) becomes an increasingly important indicator for COVID-19 transmission, more robust methods and metrics are needed to guide public health decision-making. This research aimed to develop and implement a mathematical framework to infer incident cases of COVID-19 from SARS-CoV-2 levels measured in WW. We propose a classification scheme to assess the adequacy of model training periods based on clinical testing rates and assess the sensitivity of model predictions to training periods. A testing period is classified as adequate when the rate of change in testing is greater than the rate of change in cases. We present a Bayesian deconvolution and linear regression model to estimate COVID-19 cases from WW data. The effective reproductive number is estimated from reconstructed cases using WW. The proposed modeling framework was applied to three Northern California communities served by distinct WW treatment plants. The results showed that training periods with adequate testing are essential to provide accurate projections of COVID-19 incidence.

Using Non-Pharmaceutical Interventions and High Isolation of Asymptomatic Carriers to Contain the Spread of SARS-CoV-2 in Nursing Homes.

More than 40% of the deaths recorded in the first wave of the SARS-CoV-2 pandemic were linked to nursing homes. Not only are the residents of long-term care facilities (LTCFs) typically older and more susceptible to endemic infections, the facilities' high degree of connection to wider communities makes them especially vulnerable to local COVID-19 outbreaks. In 2008, in the wake of the SARS-CoV-1 and MERS epidemics and anticipating an influenza pandemic, we created a stochastic compartmental model to evaluate the deployment of non-pharmaceutical interventions (NPIs) in LTCFs during influenza epidemics. In that model, the most effective NPI by far was a staff schedule consisting of 5-day duty periods with onsite residence, followed by an 4-to-5 day off-duty period with a 3-day quarantine period just prior to the return to work. Unlike influenza, COVID-19 appears to have significant rates of pre-symptomatic transmission. In this study, we modified our prior modeling framework to include new parameters and a set of NPIs to identify and control the degree of pre-symptomatic transmission. We found that infections, deaths, hospitalizations, and ICU utilization were projected to be high and largely irreducible, even with rigorous application of all defined NPIs, unless pre-symptomatic carriers can be identified and isolated at high rates. We found that increasingly rigorous application of NPIs is likely to significantly decrease the peak of infections; but even with complete isolation of symptomatic persons, and a 50% reduction in silent transmission, the attack rate is projected to be nearly 95%.

The impact of COVID-19 vaccination on California's return to normalcy.

SARS-CoV-2 has infected nearly 3.7 million and killed 61,722 Californians, as of May 22, 2021. Non-pharmaceutical interventions have been instrumental in mitigating the spread of the coronavirus. However, as we ease restrictions, widespread implementation of COVID-19 vaccines is essential to prevent its resurgence. In this work, we addressed the adequacy and deficiency of vaccine uptake within California and the possibility and severity of resurgence of COVID-19 as restrictions are lifted given the current vaccination rates. We implemented a real-time Bayesian data assimilation approach to provide projections of incident cases and deaths in California following the reopening of its economy on June 15, 2021. We implemented scenarios that vary vaccine uptake prior to reopening, and transmission rates and effective population sizes following the reopening. For comparison purposes, we adopted a baseline scenario using the current vaccination rates, which projects a total 11,429 cases and 429 deaths in a 15-day period after reopening. We used posterior estimates based on CA historical data to provide realistic model parameters after reopening. When the transmission rate is increased after reopening, we projected an increase in cases by 21.8% and deaths by 4.4% above the baseline after reopening. When the effective population is increased after reopening, we observed an increase in cases by 51.8% and deaths by 12.3% above baseline. A 30% reduction in vaccine uptake alone has the potential to increase cases and deaths by 35% and 21.6%, respectively. Conversely, increasing vaccine uptake by 30% could decrease cases and deaths by 26.1% and 17.9%, respectively. As California unfolds its plan to reopen its economy on June 15, 2021, it is critical that social distancing and public behavior changes continue to be promoted, particularly in communities with low vaccine uptake. The Centers for Disease Control and Prevention (CDC) recommendation to ease mask-wearing for fully vaccinated individuals despite major inequities in vaccine uptake in counties across the state highlights some of the logistical challenges that society faces as we enthusiastically phase out of this pandemic.

The Role of SARS-CoV-2 Testing on Hospitalizations in California.

The rapid spread of the new SARS-CoV-2 virus triggered a global health crisis, disproportionately impacting people with pre-existing health conditions and particular demographic and socioeconomic characteristics. One of the main concerns of governments has been to avoid health systems becoming overwhelmed. For this reason, they have implemented a series of non-pharmaceutical measures to control the spread of the virus, with mass tests being one of the most effective controls. To date, public health officials continue to promote some of these measures, mainly due to delays in mass vaccination and the emergence of new virus strains. In this research, we studied the association between COVID-19 positivity rate and hospitalization rates at the county level in California using a mixed linear model. The analysis was performed in the three waves of confirmed COVID-19 cases registered in the state to September 2021. Our findings suggest that test positivity rate is consistently associated with hospitalization rates at the county level for all study waves. Demographic factors that seem to be related to higher hospitalization rates changed over time, as the profile of the pandemic impacted different fractions of the population in counties across California.

Differences in Incidence and Case Fatality of Abusive Head Trauma.

BACKGROUND: Abusive head trauma (AHT) in children older than 1 and younger than 5 years old is thought uncommon and rarely studied. OBJECTIVE: This study estimates national incidence and case fatality rate of abusive head trauma (AHT), and evaluates differences by age, sex, race, and region, with a focus on children of 2-4 years. PARTICIPANTS AND SETTING: Hospital discharges were extracted from The Healthcare Cost and Utilization Project's Kids' Inpatient Database from 2000, 2003, 2006, 2009, and 2012 using the CDC's narrow definition of AHT. METHODS: Survey-weighted chi-square tests were used to assess differences in incidence and case fatality rates. RESULTS: The average annual incidence per 100,000 children was highest in <1 year-olds (27), followed by age 1 (4), age 2 (3), and age 3-4 (1). Average annual incidence varied significantly by sex (p = 0.0001), race (p < 0.0001), and region (p = 0.0002) within each age category. The average annual case fatality rate increased significantly with age, with a rate of 0.10 among children age <1 year, 0.15 for age 1, 0.23 for age 2, and 0.20 for age 3-4 years. The average annual case fatality rate was higher in the South (0.12) than West (0.10), Midwest (0.09), and Northeast (0.08) among children <1 year of age. CONCLUSIONS: Black and Hispanic children and hospitals in the Midwest experienced higher incidence of AHT than White children and Northeast hospitals, respectively, especially in cases <1 year of age. Case fatality rates increased significantly with age, and the South experienced the highest rates for infants <1 year.