SARS-CoV-2 whole-genome sequencing for informed public health decision making and outbreak tracking and tracing in the Netherlands
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SUBMITTER: Bas Oude Munnink
PROVIDER: S-BSST662 | biostudies-other |
SECONDARY ACCESSION(S): PRJEB38388
REPOSITORIES: biostudies-other
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Project description:BackgroundPublic health professionals are increasingly expected to engage in evidence-informed decision making to inform practice and policy decisions. Evidence-informed decision making involves the use of research evidence along with expertise, existing public health resources, knowledge about community health issues, the local context and community, and the political climate. The National Collaborating Centre for Methods and Tools has identified a seven step process for evidence-informed decision making. Tools have been developed to support public health professionals as they work through each of these steps. This paper provides an overview of tools used in three Canadian public health departments involved in a study to develop capacity for evidence-informed decision making.MethodsAs part of a knowledge translation and exchange intervention, a Knowledge Broker worked with public health professionals to identify and apply tools for use with each of the steps of evidence-informed decision making. The Knowledge Broker maintained a reflective journal and interviews were conducted with a purposive sample of decision makers and public health professionals. This paper presents qualitative analysis of the perceived usefulness and usability of the tools.ResultsTools were used in the health departments to assist in: question identification and clarification; searching for the best available research evidence; assessing the research evidence for quality through critical appraisal; deciphering the 'actionable message(s)' from the research evidence; tailoring messages to the local context to ensure their relevance and suitability; deciding whether and planning how to implement research evidence in the local context; and evaluating the effectiveness of implementation efforts. Decision makers provided descriptions of how the tools were used within the health departments and made suggestions for improvement. Overall, the tools were perceived as valuable for advancing and sustaining evidence-informed decision making.ConclusionTools are available to support the process of evidence-informed decision making among public health professionals. The usability and usefulness of these tools for advancing and sustaining evidence-informed decision making are discussed, including recommendations for the tools' application in other public health settings beyond this study. Knowledge and awareness of these tools may assist other health professionals in their efforts to implement evidence-informed practice.
| S-EPMC4223550 | biostudies-literature
Project description:IntroductionThe unprecedented COVID-19 pandemic unveiled a strong need for advanced and informative surveillance tools. The Centre for Health Informatics (CHI) at the University of Calgary took action to develop a surveillance dashboard, which would facilitate the education of the public, and answer critical questions posed by local and national government.ObjectivesThe objective of this study was to create an interactive method of surveillance, or a "COVID-19 Tracker" for Canadian use. The Tracker offers user-friendly graphics characterizing various aspects of the current pandemic (e.g. case count, testing, hospitalizations, and policy interventions).MethodsSix publicly available data sources were used, and were selected based on the frequency of updates, accuracy and types of data, and data presentation. The datasets have different levels of granularity for different provinces, which limits the information that we are able to show. Additionally, some datasets have missing entries, for which the "last observation carried forward" method was used. The website was created and hosted online, with a backend server, which is updated on a daily basis. The Tracker development followed an iterative process, as new figures were added to meet the changing needs of policy-makers.ResultsThe resulting Tracker is a dashboard that visualizes real-time data, along with policy interventions from various countries, via user-friendly graphs with a hover option that reveals detailed information. The interactive features allow the user to customize the figures by jurisdiction, country/region, and the type of data shown. Data is displayed at the national and provincial level, as well as by health regions.ConclusionThe COVID-19 Tracker offers real-time, detailed, and interactive visualizations that have the potential to shape crucial decision-making and inform Albertans and Canadians of the current pandemic.
| S-EPMC8111700 | biostudies-literature
Project description:Background: The ongoing COVID-19 pandemic is a global health crisis caused by the spread of SARS-CoV-2. Establishing links between known cases is crucial for the containment of COVID-19. In the healthcare setting, the ability to rapidly identify potential healthcare-associated COVID-19 clusters is critical for healthcare worker and patient safety. Increasing sequencing technology accessibility has allowed routine clinical diagnostic laboratories to sequence SARS-CoV-2 in clinical samples. However, these laboratories often lack specialized informatics skills required for sequence analysis. Therefore, an on-site, intuitive sequence analysis tool that enables clinical laboratory users to analyze multiple genomes and derive clinically relevant information within an actionable timeframe is needed. Results: We propose CalmBelt, an integrated framework for on-site whole genome characterization and outbreak tracking. Nanopore sequencing technology enables on-site sequencing and construction of draft genomes for multiple SARS-CoV-2 samples within 12 h. CalmBelt's interactive interface allows users to analyse multiple SARS-CoV-2 genomes by utilizing whole genome information, collection date, and additional information such as predefined potential clusters from epidemiological investigations. CalmBelt also integrates established SARS-CoV-2 nomenclature assignments, GISAID clades and PANGO lineages, allowing users to visualize relatedness between samples together with the nomenclatures. We demonstrated multiple use cases including investigation of potential hospital transmission, mining transmission patterns in a large outbreak, and monitoring possible diagnostic-escape. Conclusions: This paper presents an on-site rapid framework for SARS-CoV-2 whole genome characterization. CalmBelt interactive web application allows non-technical users, such as routine clinical laboratory users in hospitals to determine SARS-CoV-2 variants of concern, as well as investigate the presence of potential transmission clusters. The framework is designed to be compatible with routine usage in clinical laboratories as it only requires readily available sample data, and generates information that impacts immediate infection control mitigations.
| S-EPMC8712659 | biostudies-literature
Project description:Core competencies for public health in Canada require proficiency in evidence informed decision making (EIDM). However, decision makers often lack access to information, many workers lack knowledge and skills to conduct systematic literature reviews, and public health settings typically lack infrastructure to support EIDM activities. This research was conducted to explore and describe critical factors and dynamics in the early implementation of one public health unit's strategic initiative to develop capacity to make EIDM standard practice.This qualitative case study was conducted in one public health unit in Ontario, Canada between 2008 and 2010. In-depth information was gathered from two sets of semi-structured interviews and focus groups (n = 27) with 70 members of the health unit, and through a review of 137 documents. Thematic analysis was used to code the key informant and document data.The critical factors and dynamics for building EIDM capacity at an organizational level included: clear vision and strong leadership, workforce and skills development, ability to access research (library services), fiscal investments, acquisition and development of technological resources, a knowledge management strategy, effective communication, a receptive organizational culture, and a focus on change management.With leadership, planning, commitment and substantial investments, a public health department has made significant progress, within the first two years of a 10-year initiative, towards achieving its goal of becoming an evidence informed decision making organization.
| S-EPMC3305606 | biostudies-literature
Project description:BackgroundKnowledge exchange portals are emerging as web tools that can help facilitate knowledge management in public health. We conducted a review to better understand the nature of these portals and their contribution to knowledge management in public health, with the aim of informing future development of portals in this field.MethodsA systematic literature search was conducted of the peer-reviewed and grey literature to identify articles that described the design, development or evaluation of Knowledge Exchange Portals KEPs in the public health field. The content of the articles was analysed, interpreted and synthesised in light of the objectives of the review.ResultsThe systematic search yielded 2223 articles, of which fifteen were deemed eligible for review, including eight case studies, six evaluation studies and one commentary article. Knowledge exchange portals mainly included design features to support knowledge access and creation, but formative evaluation studies examining user needs suggested collaborative features supporting knowledge exchange would also be useful. Overall web usage statistics revealed increasing use of some of these portals over time; however difficulties remain in retaining users. There is some evidence to suggest that the use of a knowledge exchange portal in combination with tailored and targeted messaging can increase the use of evidence in policy and program decision making at the organisational level.ConclusionsKnowledge exchange portals can be a platform for providing integrated access to relevant content and resources in one location, for sharing and distributing information and for bringing people together for knowledge exchange. However more performance evaluation studies are needed to determine how they can best support evidence-informed decision making in public health.
| S-EPMC4046147 | biostudies-literature
Project description:Abstract The depths of the impact of COVID‐19 on nearly every aspect of our personal and professional lives was becoming painfully clear in May and June of 2020. While institutions of higher education had implemented crisis/emergency plans in the immediate onset of the pandemic, and largely extended those efforts into summer terms, the fall 2020 term loomed large. Institutional researchers were asked for myriad kinds of data and reports, ostensibly to inform executive leaders’ decision‐making regarding how to operate for the fall term. On its face, this fits with the current conceptualization of IR's work largely as decision support. Despite these requests, however, the question remains as to what was really driving decision‐making about the fall. This research examined a random, representative sample of public statements regarding fall operations, often released in the name of a president or chancellor, to determine what factors these leaders espoused publicly as informing their fall plans.
| S-EPMC8652806 | biostudies-literature
Project description:There are professional expectations for public health nurses to develop competencies in evidence-informed decision-making (EIDM) due to its potential for improved client outcomes. Robust tools to assess EIDM competence can encourage increased EIDM engagement and uptake. This study aimed to develop and validate the content of a measure to assess EIDM competence among public health nurses. A four-stage process, based on measure development principles and the Standards for Educational and Psychological Testing, was used to develop and refine items for a new EIDM competence measure: a) content coverage assessment of existing measures; b) identification of existing measures for use and development of items; c) validity assessment based on content; d) validity assessment based on response process. An EIDM competence measurement tool consisting of EIDM knowledge, skills, attitudes/beliefs, and behaviour items was developed using conceptual literature and existing measures (Evidence-Based Practice Competency Tool and Evidence-Based Practice Beliefs Scale) to address limitations of existing EIDM tools identified from the content coverage assessment. Item content validity index ratings ranged from 0.64-1.00. Qualitative themes from validity assessment based on content and response process included word changes to improve clarity, reducing item redundancy, separating multi-component items, and ensuring items reflect nursing role expectations. Upon determining its reliability and validity, there is potential for the EIDM competence measure to be used in: public health nursing practice to identify competence gaps and strengths to facilitate professional development activities; in research to support development of strategies to build EIDM capacity; and for curriculum planning and development across nursing education programs.
| S-EPMC7946311 | biostudies-literature
Project description:BackgroundHealth insurance enrollment is a difficult financial decision with large health impacts. Challenges such as low health insurance literacy and lack of knowledge about choosing a plan further complicate this decision-making process. Therefore, to support consumers in their choice of a health insurance plan, it is essential to understand how individuals go about making this decision.ObjectiveThis study aims to understand the sources of information used by individuals to support their employer-provided health insurance enrollment decisions. It seeks to describe how individual descriptive factors lead to choosing a particular type of information source.MethodsAn introduction was presented on health insurance plan selection and the sources of information used to support these decisions from the 1980s to the present. Subsequently, an electronic survey of 151 full-time faculty and staff members was conducted. The survey consisted of four sections: demographics, sources of information, health insurance literacy, and technology acceptance. Descriptive statistics were used to show the demographic characteristics of the 126 eligible respondents and to study the response behaviors in the remaining survey sections. Proportion data analysis was performed using the Cochran-Armitage trend test to understand the strength of the association between our variables and the types of sources used by the respondents.ResultsIn terms of demographics, most of the respondents were women (103/126, 81.7%), represented a small household (1-2 persons; 87/126, 69%), and used their insurance 3-12 times a year (52/126, 41.3%). They assessed themselves as having moderate to high health insurance literacy and high acceptance of technology. The most selected and top-ranked sources were Official employer or state websites and Official Human Resources Virtual Benefits Counselor Alex. From our data analysis, we found that the use of official primary sources was constant across age groups and health insurance use groups. Meanwhile, the use of friends or family as a primary source slightly decreased as age and use increased.ConclusionsIn this exploratory study, we identified the main sources of health insurance information among full-time employees from a large state university and found that most of the respondents needed 2-3 sources to gather all the information that they desired. We also studied and identified the relationships between individual factors (such as age, gender, and literacy) and 2 dependent variables on the types of primary sources of information. We encountered several limitations, which will be addressed in future studies.
| S-EPMC8391737 | biostudies-literature
Project description:BackgroundCareful patient-clinician shared decision-making about dialysis initiation has been promoted, but few studies have addressed patient perspectives on the extent of information provided and how decisions to start dialysis are made.MethodsNinety-nine maintenance dialysis patients recruited from 15 outpatient dialysis centers in North Carolina completed semistructured interviews on information provision and communication about the initiation of dialysis. These data were examined with content analysis. In addition, informed decision-making (IDM) scores were created by summing patient responses (yes/no) to 10 questions about the decision-making.ResultsThe mean IDM score was 4.4 (of 10; SD = 2.0); 67% scored 5 or lower. Age at the time of decision-making (r = -0.27, P = 0.006), years of education (r = 0.24, P = 0.02) and presence of a warning about progressing to end-stage kidney disease (t = 2.9, P = 0.005) were significantly associated with IDM scores. Nearly 70% said that the risks and burdens of dialysis were not mentioned at all, and only one patient recalled that the doctor offered the option of not starting dialysis. While a majority (67%) said that they felt they had no choice about starting dialysis (because the alternative would be death) or about dialysis modality, only 21.2% said that they had felt rushed to make a decision. About one-third of the patients perceived that the decision to start dialysis and modality was already made by the doctor.ConclusionsA majority of patients felt unprepared and ill-informed about the initiation of dialysis. Improving the extent of IDM about dialysis may optimize patient preparation prior to starting treatment and their perceptions about the decision-making process.
| S-EPMC3811056 | biostudies-literature
Project description:Given the widespread concern but general lack of information over the possibility of SARS-CoV-2 infection in public transport, key issues such as passenger personal hygiene, efficient air circulation systems, and the effective disinfection of frequently touched surfaces need to be evaluated to educate the public and diminish the risk of viral transmission as we learn to live with the ongoing pandemic. In this context we report on a study involving the collection of 99 samples taken from inside Barcelona buses and subway trains in May to July 2020. From this sample group 82 (58 surface swabs, 9 air conditioning (a/c) filters, 3 a/c dust, 12 ambient air) were selected to be analysed by RT-PCR for traces of the SARS-CoV-2 virus. Thirty of these selected samples showed evidence for one or more of 3 target RNA gene regions specific for this virus (IP2, IP4, E). Most (24) of these 30 samples showed positivity for only 1 of the 3 RNA targets, 4 samples yielded 2 targets, and 2 samples provided evidence for all 3 targets. RNA remnants were more common in surface swabs from support bars (23 out of 58) than in ambient air inside the vehicles (3 out of 12), with relatively higher concentrations of viral RNA fragments in buses rather than in trains. Whereas subway train a/c filters examined were all virus-free, 4 of the 9 bus a/c filter/dust samples yielded evidence for viral RNA. After nocturnal maintenance and cleaning most buses initially yielding positive results subsequently showed elimination of the RT-PCR signal, although signs of viral RNA remained in 4 of 13 initially positive samples. The presence of such remnant viral traces however does not demonstrate infectivity, which in the present study is considered unlikely given the fragmentary nature of the gene targets detected. Nevertheless, best practice demands that close attention to ventilation systems and regular vehicle disinfection in public transport worldwide need to be rigorously applied to be effective at eliminating traces of the virus throughout the vehicle, especially at times when COVID-19 cases are peaking. Additionally, infectivity tests should be implemented to evaluate the efficiency of disinfection procedures to complement the information resulting from RT-PCR analysis. Modelling the probability of infection whilst travelling in buses under different scenarios indicates that forced ventilation greatly reduces the risk.
| S-EPMC7723781 | biostudies-literature