More Like this

1. The Arbovirus Mapping and Prediction (ArboMAP) system for West Nile virus forecasting

   https://doi.org/10.1093/jamiaopen/ooad110  

   Nekorchuk, Dawn M ; Bharadwaja, Anita ; Simonson, Sean ; Ortega, Emma ; França, Caio_M B ; Dinh, Emily ; Reik, Rebecca ; Burkholder, Rachel ; Wimberly, Michael C ( January 2024 , JAMIA Open)

   West Nile virus (WNV) is the most common mosquito-borne disease in the United States. Predicting the location and timing of outbreaks would allow targeting of disease prevention and mosquito control activities. Our objective was to develop software (ArboMAP) for routine WNV forecasting using public health surveillance data and meteorological observations.

   ArboMAP was implemented using an R markdown script for data processing, modeling, and report generation. A Google Earth Engine application was developed to summarize and download weather data. Generalized additive models were used to make county-level predictions of WNV cases.

   ArboMAP minimized the number of manual steps required to make weekly forecasts, generated information that was useful for decision-makers, and has been tested and implemented in multiple public health institutions.

   Routine prediction of mosquito-borne disease risk is feasible and can be implemented by public health departments using ArboMAP.

    

   more » « less
2. Nextstrain: real-time tracking of pathogen evolution

   https://doi.org/10.1093/bioinformatics/bty407  

   Hadfield, James ; Megill, Colin ; Bell, Sidney M. ; Huddleston, John ; Potter, Barney ; Callender, Charlton ; Sagulenko, Pavel ; Bedford, Trevor ; Neher, Richard A. ; Kelso, ed., Janet ( May 2018 , Bioinformatics)

   Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike.

   All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

    

   more » « less
3. Participatory COVID-19 Surveillance Tool in Rural Appalachia: Real-Time Disease Monitoring and Regional Response

   https://doi.org/10.1177/0033354921990372  

   Runkle, Jennifer_D ; Sugg, Maggie_M ; Graham, Garrett ; Hodge, Bryan ; March, Terri ; Mullendore, Jennifer ; Tove, Fletcher ; Salyers, Martha ; Valeika, Steve ; Vaughan, Ellis ( February 2021 , Public Health Reports®)

   Few US studies have examined the usefulness of participatory surveillance during the coronavirus disease 2019 (COVID-19) pandemic for enhancing local health response efforts, particularly in rural settings. We report on the development and implementation of an internet-based COVID-19 participatory surveillance tool in rural Appalachia.

   A regional collaboration among public health partners culminated in the design and implementation of the COVID-19 Self-Checker, a local online symptom tracker. The tool collected data on participant demographic characteristics and health history. County residents were then invited to take part in an automated daily electronic follow-up to monitor symptom progression, assess barriers to care and testing, and collect data on COVID-19 test results and symptom resolution.

   Nearly 6500 county residents visited and 1755 residents completed the COVID-19 Self-Checker from April 30 through June 9, 2020. Of the 579 residents who reported severe or mild COVID-19 symptoms, COVID-19 symptoms were primarily reported among women (n = 408, 70.5%), adults with preexisting health conditions (n = 246, 70.5%), adults aged 18-44 (n = 301, 52.0%), and users who reported not having a health care provider (n = 131, 22.6%). Initial findings showed underrepresentation of some racial/ethnic and non–English-speaking groups.

   This low-cost internet-based platform provided a flexible means to collect participatory surveillance data on local changes in COVID-19 symptoms and adapt to guidance. Data from this tool can be used to monitor the efficacy of public health response measures at the local level in rural Appalachia.

    

   more » « less
4. Wastewater surveillance for bacterial targets: current challenges and future goals

   https://doi.org/10.1128/aem.01428-23  

   Philo, Sarah E ; De_León, Kara B ; Noble, Rachel T ; Zhou, Nicolette A ; Alghafri, Rashed ; Bar-Or, Itay ; Darling, Amanda ; D'Souza, Nishita ; Hachimi, Oumaima ; Kaya, Devrim ; et al ( January 2024 , Applied and Environmental Microbiology)

   Elkins, Christopher A (Ed.)

   Wastewater-based epidemiology (WBE) expanded rapidly in response to the COVID-19 pandemic. As the public health emergency has ended, researchers and practitioners are looking to shift the focus of existing wastewater surveillance programs to other targets, including bacteria. Bacterial targets may pose some unique challenges for WBE applications. To explore the current state of the field, the National Science Foundation-funded Research Coordination Network (RCN) on Wastewater Based Epidemiology for SARS-CoV-2 and Emerging Public Health Threats held a workshop in April 2023 to discuss the challenges and needs for wastewater bacterial surveillance. The targets and methods used in existing programs were diverse, with twelve different targets and nine different methods listed. Discussions during the workshop highlighted the challenges in adapting existing programs and identified research gaps in four key areas: choosing new targets, relating bacterial wastewater data to human disease incidence and prevalence, developing methods, and normalizing results. To help with these challenges and research gaps, the authors identified steps the larger community can take to improve bacteria wastewater surveillance. This includes developing data reporting standards and method optimization and validation for bacterial programs. Additionally, more work is needed to understand shedding patterns for potential bacterial targets to better relate wastewater data to human infections. Wastewater surveillance for bacteria can help provide insight into the underlying prevalence in communities, but much work is needed to establish these methods.

   Wastewater surveillance was a useful tool to elucidate the burden and spread of SARS-CoV-2 during the pandemic. Public health officials and researchers are interested in expanding these surveillance programs to include bacterial targets, but many questions remain. The NSF-funded Research Coordination Network for Wastewater Surveillance of SARS-CoV-2 and Emerging Public Health Threats held a workshop to identify barriers and research gaps to implementing bacterial wastewater surveillance programs.

    

   more » « less
5. Assessing the value and knowledge gains from an online tick identification and tick-borne disease management course for the Southeastern United States

   https://doi.org/10.1186/s12889-024-19307-x  

   Lippi, Catherine_A ; Gaff, Holly_D ; White, Alexis_L ; Ryan, Sadie_J ( July 2024 , BMC Public Health)

   Tick-borne diseases are a growing public health threat in the United States. Despite the prevalence and rising burden of tick-borne diseases, there are major gaps in baseline knowledge and surveillance efforts for tick vectors, even among vector control districts and public health agencies. To address this issue, an online tick training course (OTTC) was developed through the Southeastern Center of Excellence in Vector-Borne Diseases (SECOEVBD) to provide a comprehensive knowledge base on ticks, tick-borne diseases, and their management.

   The OTTC consisted of training modules covering topics including tick biology, tick identification, tick-borne diseases, and public health, personal tick safety, and tick surveillance. The course was largely promoted to vector control specialists and public health employees throughout the Southeastern US. We collected assessment and survey data on participants to gauge learning outcomes, perceptions of the utility of knowledge gained, and barriers and facilitators to applying the knowledge in the field.

   The OTTC was successful in increasing participants’ baseline knowledge across all course subject areas, with the average score on assessment increasing from 62.6% (pre-course) to 86.7% (post-course). More than half of participants (63.6%) indicated that they would definitely use information from the course in their work. Barriers to using information identified in the delayed assessment included lack of opportunities to apply skills (18.5%) and the need for additional specialized training beyond what the OTTC currently offers (18.5%), while the main facilitator (70.4%) for applying knowledge was having opportunities at work, such as an existing tick surveillance program.

   Overall, this OTTC demonstrated capacity to improve knowledge in a necessary and underserved public health field, and more than half of participants use or plan to use the information in their work. The geographic reach of this online resource was much larger than simply for the Southeastern region for which it was designed, suggesting a much broader need for this resource. Understanding the utility and penetrance of training programs such as these is important for refining materials and assessing optimal targets for training.

    

   more » « less