SARS-CoV-2 whole-genome sequencing for informed public health decision making and outbreak tracking and tracing in the Netherlands
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ABSTRACT:
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:The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 13 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.
| S-EPMC10021969 | 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: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: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:The SARS-CoV-2 is still undergoing rapid evolution, resulting in the emergence of several variants of concern, especially the Omicron variants (B.1.1.529), which are surging worldwide. In this study, we tracked Omicron subvariant BA.5.1.3 as the causative agent in the Hainan Province wave in China, which started on 1 August 2022. This was China's first case of Omicron subvariant BA.5.1.3 and led to an indefinite total lockdown in Hainan with more than 8,500 confirmed cases. We obtained 391 whole genomes from positive nasopharyngeal swab samples in the city of Sanya in Hainan Province, which was the center of this outbreak. More than half of the infected cases were female (58%, 227/391) with a median age of 37.0 years (IQR 23.0-53.0). Median Ct values were 24.9 (IQR 22.6-27.3) and 25.2 (IQR 22.9-27.6) for ORF1ab and N genes, respectively. The total single-nucleotide polymorphism (SNP) numbers of Omicron BA.5.1.3 sampled in Sanya (median 69.0, IQR = 69.0-70.0) compared to those worldwide (median 63.0, IQR = 61.0-64.0) showed a significant difference (p < 0.05). Unique core mutations, including three non-synonymous mutations in ORF1ab (Y1064N, S2844G, and R3574K) and one synonymous mutation in ORF3a (S74S), were found. Phylogenetic analysis showed that virus from Sanya formed an independent sub-clade within the BA.5.1.3 subvariant, and could be divided into 15 haplotypes based on the S gene. The most recent common ancestor for the virus from Sanya was estimated as appearing on 5 July 2022, with 95% HPD ranging from 15 May to 20 September 2022. Thanks to our results, we were also able to delineate the mutational profile of this outbreak and highlight the importance of global genomic surveillance and data sharing.
| S-EPMC10232789 | 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:The focus on treatment of COVID19 patients during the Sars-CoV-2 outbreak has most likely implications for the extent and quality of diagnosis and treatment of non-COVID19 patients. Medical care of cancer patients is a particularly sensitive area. To draw holistic conclusions, it is necessary to analyze the provision of healthcare as broadly as possible with regard to the dimensions of access, processes and outcome during the Sars-CoV-2 pandemic. This will be implemented exemplarily for the early detection, diagnosis and treatment of colorectal cancer (CRC) and pancreatic cancer (PaCa) in Saxony. Patients with diagnosis, treatment or early detection measures for type 2 diabetes (T2D), coronary heart disease (CHD) and multiple sclerosis (MS) serve as comparison groups.
| 2743388 | ecrin-mdr-crc