Rocky Mountain West COVID-19 Modeling: A Descriptive Assessment of Public Health Needs During the COVID-19 Pandemic to Endemic Transition in Summer 2022.

Objectives: Although federal funding for COVID-19 pandemic response measures has ended, opportunities remain to understand the needs of public health departments and the potential use of infectious disease models in the postacute pandemic response. We conducted semistructured interviews with public health representatives representing state, local, and regional/tribal public health departments in the Rocky Mountain West in summer 2022 to understand their COVID-19 priorities, decision-making needs, and data resources.

Methods: We interviewed representatives from 6 organizations representing 3 state, local, and regional/tribal public health departments in the Rocky Mountain West.

Identifying real time surveillance indicators to estimate COVID-19 hospital admissions in Colorado during and after the public health emergency.

Questions remain about how best to focus surveillance efforts for COVID-19 and other emerging respiratory diseases. We used an archive of COVID-19 data in Colorado from October 2020 to March 2024 to reconstruct seven real-time surveillance indicators. We assessed how well the indicators predicted 7-day average COVID-19 hospital admissions, a key indicator of outbreak severity, using machine learning and regression models, and used cross-correlation analysis to identify leading indicators.

Heat exposure, heat strain, and off-work recovery of Guatemalan sugarcane workers.

Agricultural workers are at high risk for heat-related illnesses when performing heavy labor in hot conditions. Occupational heat strain, the physiological response to heat stress, is hypothesized to be common in this worker population but has rarely been measured objectively through core body temperature (T). The objective of this study was twofold: ) evaluate workday heat strain and ) examine the trajectory of heat exposure and T from the workday through the off-work hours to advance understanding of the recovery process and conditions of heat-exposed agricultural workers.

Healthcare utilization patterns before and after a long COVID diagnosis: a case-control study.

Background: Documenting Long COVID cases has been challenging partly due to the lack of population-level data and uncertain diagnostic criteria, hindering the ability to ascertain healthcare utilization patterns over time. The objective of this study is to examine the characteristics and healthcare utilization patterns of Long COVID patients in Colorado pre- and post-diagnosis compared to controls.

Methods: Retrospective, longitudinal case-control study using a 100% sample of Colorado's All-Payer Claims Database.

Does behavior mediate the effect of weather on SARS-CoV-2 transmission? evidence from cell-phone data.

There is growing evidence that weather alters SARS-CoV-2 transmission, but it remains unclear what drives the phenomenon. One prevailing hypothesis is that people spend more time indoors in cooler weather, leading to increased spread of SARS-CoV-2 related to time spent in confined spaces and close contact with others. However, the evidence in support of that hypothesis is limited and, at times, conflicting.

Investigating the relationship between extreme weather and cryptosporidiosis and giardiasis in Colorado: A multi-decade study using distributed-lag nonlinear models.

Environmentally-mediated protozoan diseases like cryptosporidiosis and giardiasis are likely to be highly impacted by extreme weather, as climate-related conditions like temperature and precipitation have been linked to their survival, distribution, and overall transmission success. Our aim was to investigate the relationship between extreme temperature and precipitation and cryptosporidiosis and giardiasis infection using monthly weather data and case reports from Colorado counties over a twenty-one year period. Data on reportable diseases and weather among Colorado counties were collected using the Colorado Electronic Disease Reporting System (CEDRS) and the Daily Surface Weather and Climatological Summaries (Daymet) Version 3 dataset, respectively.

Did COVID-19 ICU patient mortality risk increase as Colorado hospitals filled? A retrospective cohort study.

Objectives: To assess whether increasing levels of hospital stress-measured by intensive care unit (ICU) bed occupancy (primary), ventilators in use and emergency department (ED) overflow-were associated with decreasing COVID-19 ICU patient survival in Colorado ICUs during the pre-Delta, Delta and Omicron variant eras.

Design: A retrospective cohort study using discrete-time survival models, fit with generalised estimating equations.

Setting: 34 hospital systems in Colorado, USA, with the highest patient volume ICUs during the COVID-19 pandemic.

Does behavior mediate the effect of weather on SARS-CoV-2 transmission? Evidence from cell-phone data.

Background: There is growing evidence that weather alters SARS-CoV-2 transmission, but it remains unclear what drives the phenomenon. One prevailing hypothesis is that people spend more time indoors in cooler weather, leading to increased spread of SARS-CoV-2 related to time spent in confined spaces and close contact with others. However, the evidence in support of that hypothesis is limited and, at times, conflicting.

Open-source environmental data as an alternative to snail surveys to assess schistosomiasis risk in areas approaching elimination.

Background: Although the presence of intermediate snails is a necessary condition for local schistosomiasis transmission to occur, using them as surveillance targets in areas approaching elimination is challenging because the patchy and dynamic quality of snail host habitats makes collecting and testing snails labor-intensive. Meanwhile, geospatial analyses that rely on remotely sensed data are becoming popular tools for identifying environmental conditions that contribute to pathogen emergence and persistence.

Methods: In this study, we assessed whether open-source environmental data can be used to predict the presence of human Schistosoma japonicum infections among households with a similar or improved degree of accuracy compared to prediction models developed using data from comprehensive snail surveys.

Utilizing citizen science to model the distribution of in West Africa.

In the rapidly urbanizing region of West Africa, mosquitoes pose an emerging threat of infectious disease that is compounded by limited vector surveillance. Citizen science has been proposed as a way to fill surveillance gaps by training local residents to collect and share information on disease vectors. Understanding the distribution of arbovirus vectors in West Africa can inform researchers and public health officials on where to conduct disease surveillance and focus public health interventions.

The Association Between Rainfall, Temperature, and Reported Drinking Water Source: A Multi-Country Analysis.

Climate change may alter access to safe drinking water, with important implications for health. We assessed the relationship between temperature and rainfall and utilization of basic drinking water (BDW) in The Gambia, Mozambique, Pakistan, and Kenya. The outcomes of interest were (a) whether the reported drinking water source used in the past 2 weeks met the World Health Organization definition of BDW and (b) use of a BDW source that was always available.

Prospects for genomic surveillance for selection in schistosome parasites.

Schistosomiasis is a neglected tropical disease caused by multiple parasitic species, and which impacts over 200 million people globally, mainly in low- and middle-income countries. Genomic surveillance to detect evidence for natural selection in schistosome populations represents an emerging and promising approach to identify and interpret schistosome responses to ongoing control efforts or other environmental factors. Here we review how genomic variation is used to detect selection, how these approaches have been applied to schistosomes, and how future studies to detect selection may be improved.

Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination.

The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes.

Predictors of bovine Schistosoma japonicum infection in rural Sichuan, China.

In China, bovines are believed to be the most common animal source of human schistosomiasis infections, though little is known about what factors promote bovine infections. The current body of literature features inconsistent, and sometimes contradictory results, and to date, few studies have looked beyond physical characteristics to identify the broader environmental conditions that predict bovine schistosomiasis. Because schistosomiasis is a sanitation-related, water-borne disease transmitted by many animals, we hypothesised that several environmental factors - such as the lack of improved sanitation systems, or participation in agricultural production that is water-intensive - could promote schistosomiasis infection in bovines.

A genomic can of worms for schistosome host-specificity.

Understanding the genetic underpinnings of schistosome host preferences is critical. Luo et al. recently identified genes associated with intermediate and definitive host-switching based on a new chromosome-level genome for Schistosoma japonicum, population genetic comparisons, and follow-up experiments.

Novel use of online optimization in a mathematical model of COVID-19 to guide the relaxation of pandemic mitigation measures.

Since early 2020, non-pharmaceutical interventions (NPIs)-implemented at varying levels of severity and based on widely-divergent perspectives of risk tolerance-have been the primary means to control SARS-CoV-2 transmission. This paper aims to identify how risk tolerance and vaccination rates impact the rate at which a population can return to pre-pandemic contact behavior. To this end, we developed a novel mathematical model and we used techniques from feedback control to inform data-driven decision-making.

Environmental Factors Influencing COVID-19 Incidence and Severity.

Emerging evidence supports a link between environmental factors-including air pollution and chemical exposures, climate, and the built environment-and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and coronavirus disease 2019 (COVID-19) susceptibility and severity. Climate, air pollution, and the built environment have long been recognized to influence viral respiratory infections, and studies have established similar associations with COVID-19 outcomes. More limited evidence links chemical exposures to COVID-19.

Early Adoption of Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care Facilities: Prevalence, Virologic and Sequence Analysis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 has been notable due to its impacts on residents in long-term care facilities (LTCFs). LTCF residents tend to possess several risk factors for severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of comorbidities.

Estimating the Impact of Statewide Policies to Reduce Spread of Severe Acute Respiratory Syndrome Coronavirus 2 in Real Time, Colorado, USA.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic necessitated rapid local public health response, but studies examining the impact of social distancing policies on SARS-CoV-2 transmission have struggled to capture regional-level dynamics. We developed a susceptible-exposed-infected-recovered transmission model, parameterized to Colorado, USA‒specific data, to estimate the impact of coronavirus disease‒related policy measures on mobility and SARS-CoV-2 transmission in real time. During March‒June 2020, we estimated unknown parameter values and generated scenario-based projections of future clinical care needs.

Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts.

Schistosomiasis persists in Asian regions despite aggressive elimination measures. To identify factors enabling continued parasite transmission, we performed reduced representation genome sequencing on Schistosoma japonicum miracidia collected across multiple years from transmission hotspots in Sichuan, China. We discovered strong geographic structure, suggesting that local, rather than imported, reservoirs are key sources of persistent infections in the region.

Human Mobility Associated With Risk of Schistosoma japonicum Infection in Sichuan, China.

Urbanization increases human mobility in ways that can alter the transmission of classically rural, vector-borne diseases like schistosomiasis. The impact of human mobility on individual-level Schistosoma risk is poorly characterized. Travel outside endemic areas may protect against infection by reducing exposure opportunities, whereas travel to other endemic regions may increase risk.

Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum).

Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia.

Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2.

Due to the scope and impact of the COVID-19 pandemic there exists a strong desire to understand where the SARS-CoV-2 virus came from and how it jumped species boundaries to humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness and divergence times of viruses and identifying past selective pressures. However, we must uphold rigorous standards of inference and interpretation on this topic because of the ramifications of being wrong.