Introduction to the genomics of infectious diseases

2020 ◽  
pp. 175573802097213
Author(s):  
Imran Rafi ◽  
Judith Hayward ◽  
Peter English
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Global Scale ◽  
Whole Genome ◽  
Vaccine Research ◽  
Public Health Agencies ◽  
Health Agencies ◽  
The Uk ◽  
Pathogen Diagnosis ◽  
Significant Mortality

The COVID-19 Genomics UK (COG-UK) Consortium was created to deliver large-scale and rapid whole-genome virus sequencing. Its data will help Public Health Agencies to manage the COVID-19 pandemic in the UK and inform vaccine research efforts. From a wider perspective, data sharing around the genomics of viruses (and bacteria, protozoa parasites and fungi) offers researchers contrasting perspectives and new biological insights into the evolution of microbes and the development of new tools in managing infectious disease, which on a global scale causes significant mortality. Genomics has an evolving role in pathogen diagnosis and surveillance.

scholarly journals Ten Recommendations for Supporting Open Pathogen Genomic Analysis in Public Health Settings

2020 ◽  
Author(s):  
Allison Black ◽  
Duncan R. MacCannell ◽  
Thomas R. Sibley ◽  
Trevor Bedford
Keyword(s):  
Public Health ◽  
Population Dynamics ◽  
Large Scale ◽  
Genomic Analysis ◽  
Molecular Data ◽  
Whole Genome ◽  
Public Health Agencies ◽  
Health Agencies ◽  
Scale Population ◽  
Informatics Infrastructure

Public health agencies are increasingly using pathogen whole genome sequencing (WGS) to support surveillance and epidemiologic investigations. As access to WGS has grown, greater amounts of molecular data have helped improve our ability to detect outbreaks, investigate transmission chains, and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of WGS also poses challenges due to the amount of data generated and the need to transform raw data prior to analysis. This complexity means that public health agencies may need more advanced computational infrastructure, a broader technical workforce, and new approaches to data management and stewardship. As both a guide for how this development could occur, and a place to initiate discussion, we describe ten proposals for developing and supporting an informatics infrastructure for public health.

scholarly journals How many are at increased risk of severe COVID-19 disease? Rapid global, regional and national estimates for 2020

2020 ◽  
Author(s):  
Andrew Clark ◽  
Mark Jit ◽  
Charlotte Warren-Gash ◽  
Bruce Guthrie ◽  
Harry HX Wang ◽  
...  
Keyword(s):  
Public Health ◽  
Older Individuals ◽  
Prevalence Data ◽  
Underlying Condition ◽  
Public Health Agencies ◽  
Increased Risk ◽  
Health Agencies ◽  
High Prevalence ◽  
The Uk ◽  
Number Of Individuals

BackgroundThe risk of severe COVID-19 disease is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 illness, and how this varies between countries may inform the design of possible strategies to shield those at highest risk.MethodsWe estimated the number of individuals at increased risk of severe COVID-19 disease by age (5-year age groups), sex and country (n=188) based on prevalence data from the Global Burden of Disease (GBD) study for 2017 and United Nations population estimates for 2020. We also calculated the number of individuals without an underlying condition that could be considered at-risk because of their age, using thresholds from 50-70 years. The list of underlying conditions relevant to COVID-19 disease was determined by mapping conditions listed in GBD to the guidelines published by WHO and public health agencies in the UK and US. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity.ResultsWe estimate that 1.7 (1.0 - 2.4) billion individuals (22% [15-28%] of the global population) are at increased risk of severe COVID-19 disease. The share of the population at increased risk ranges from 16% in Africa to 31% in Europe. Chronic kidney disease (CKD), cardiovascular disease (CVD), diabetes and chronic respiratory disease (CRD) were the most prevalent conditions in males and females aged 50+ years. African countries with a high prevalence of HIV/AIDS and Island countries with a high prevalence of diabetes, also had a high share of the population at increased risk. The prevalence of multimorbidity (>1 underlying conditions) was three times higher in Europe than in Africa (10% vs 3%).ConclusionBased on current guidelines and prevalence data from GBD, we estimate that one in five individuals worldwide has a condition that is on the list of those at increased risk of severe COVID-19 disease. However, for many of these individuals the underlying condition will be undiagnosed or not severe enough to be captured in health systems, and in some cases the increase in risk may be quite modest. There is an urgent need for robust analyses of the risks associated with different underlying conditions so that countries can identify the highest risk groups and develop targeted shielding policies to mitigate the effects of the COVID-19 pandemic.Research in contextEvidence before this studyAs the COVID-19 pandemic evolves, countries are considering policies of ‘shielding’ the most vulnerable, but there is currently very limited evidence on the number of individuals that might need to be shielded. Guidelines on who is currently believed to be at increased risk of severe COVID-19 illness have been published online by the WHO and public health agencies in the UK and US. We searched PubMed (“Risk factors” AND “COVID-19”) without language restrictions, from database inception until April 5, 2020, and identified 62 studies published between Feb 15, 2020 and March 20, 2020. Evidence from China, Italy and the USA indicates that older individuals, males and those with underlying conditions, such as CVD, diabetes and CRD, are at greater risk of severe COVID-19 illness and death.Added value of this studyThis study combines evidence from large international databases and new analysis of large multimorbidity studies to inform policymakers about the number of individuals that may be at increased risk of severe COVID-19 illness in different countries. We developed a tool for rapid assessments of the number and percentage of country populations that would need to be targeted under different shielding policies.Implications of all the available evidenceQuantifying how many and who is at increased risk of severe COVID-19 illness is critical to help countries design more effective interventions to protect vulnerable individuals and reduce pressure on health systems. This information can also inform a broader assessment of the health, social and economic implications of shielding various groups.

scholarly journals COVID-19: Second Wave or Multiple Peaks, Natural Herd Immunity or Vaccine – We Should be Prepared

2020 ◽  
pp. 1-8
Author(s):  
Rima Moghnieh ◽  
Dania Abdallah ◽  
Abdul Rahman Bizri
Keyword(s):  
Public Health ◽  
Natural Infection ◽  
Herd Immunity ◽  
Time Frame ◽  
Global Scale ◽  
Public Health Agencies ◽  
The Social ◽  
Health Agencies ◽  
Preventive Public Health ◽  
Novel Coronavirus

ABSTRACT Between December 31, 2019, and August 30, 2020 (date of this article), the novel coronavirus and its corresponding infection, coronavirus disease (COVID-19), increased to more than 25 million cases, and 843 158 deaths have been registered. Countries around the world have been affected, albeit in different levels and intensities. Despite implementations of preventive public health measures, most countries are seriously preparing for 1 or more waves. The threat of this surge is likely to persist until herd immunity is acquired either by natural infection or through vaccination. However, given the time frame needed for herd immunity to occur and the low probability that a vaccine will be available on a global scale by the coming fall and winter seasons, contingency preparedness plans should be established and put in place for the coming days or months. These plans should help mitigate new peaks of the pandemic while relaxing the social isolation rules, patient, public health, and hospital levels. In this article, we discuss recommendations that practicing physicians and public health agencies should provide to individuals, especially those at risk of infection, to take and implement pre-emptive measures in anticipation of the potential next peak of the pandemic.

scholarly journals CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Samuel M. Nicholls ◽  
Radoslaw Poplawski ◽  
Matthew J. Bull ◽  
Anthony Underwood ◽  
Michael Chapman ◽  
...  
Keyword(s):  
Public Health ◽  
Genomic Sequencing ◽  
Sequencing Data ◽  
National Scale ◽  
Surveillance Strategy ◽  
Public Health Agencies ◽  
Continuous Integration ◽  
Digital Infrastructure ◽  
Health Agencies ◽  
The Uk

AbstractIn response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.

The Perils of Partnership

2019 ◽  
Author(s):  
Jonathan H. Marks
Keyword(s):  
Public Health ◽  
Multinational Corporations ◽  
Separation Of Powers ◽  
Public Health Research ◽  
Noncommunicable Diseases ◽  
New Paradigm ◽  
Public Health Agencies ◽  
Ethical Implications ◽  
Health Agencies ◽  
Public Bodies

Collaboration with industry has become the paradigm in public health. Governments commonly develop close relationships with companies that are creating or exacerbating the very problems public health agencies are trying to solve. Nowhere is this more evident than in partnerships with food and soda companies to address obesity and diet-related noncommunicable diseases. The author argues that public-private partnerships and multistakeholder initiatives create webs of influence that undermine the integrity of public health agencies; distort public health research and policy; and reinforce the framing of public health problems and their solutions in ways that are least threatening to the commercial interests of corporate “partners.” We should expect multinational corporations to develop strategies of influence. But public bodies need to develop counter-strategies to insulate themselves from corporate influence in all its forms. The author reviews the ways in which we regulate public-public interactions (separation of powers) and private-private interactions (antitrust and competition laws), and argues for an analogous set of norms to govern public-private interactions. The book also offers a novel framework that is designed to help public bodies identify the systemic ethical implications of their existing or proposed relationships with industry actors. The book makes a compelling case that, in public health, the paradigm public-private interaction should be at arm’s length: separation, not collaboration. The author calls for a new paradigm to protect and promote public health while avoiding the ethical perils of partnership with industry.

scholarly journals International Perspectives on COVID-19 Communication Ecologies: Public Health Agencies’ Online Communication in Italy, Sweden, and the United States

2021 ◽  
pp. 000276422199283
Author(s):  
Serena Tagliacozzo ◽  
Frederike Albrecht ◽  
N. Emel Ganapati
Keyword(s):  
Public Health ◽  
United States ◽  
Social Groups ◽  
Online Communication ◽  
The United States ◽  
Negative Consequences ◽  
Public Health Agencies ◽  
Communication Ecology ◽  
Health Agencies ◽  
National Public Health

Communicating during a crisis can be challenging for public agencies as their communication ecology becomes increasingly complex while the need for fast and reliable public communication remains high. Using the lens of communication ecology, this study examines the online communication of national public health agencies during the COVID-19 pandemic in Italy, Sweden, and the United States. Based on content analysis of Twitter data ( n = 856) and agency press releases ( n = 95), this article investigates two main questions: (1) How, and to what extent, did national public health agencies coordinate their online communication with other agencies and organizations? (2) How was online communication from the agencies diversified in terms of targeting specific organizations and social groups? Our findings indicate that public health agencies relied heavily on internal scientific expertise and predominately coordinated their communication efforts with national government agencies. Furthermore, our analysis reveals that agencies in each country differed in how they diversify information; however, all agencies provided tailored information to at least some organizations and social groups. Across the three countries, information tailored for several vulnerable groups (e.g., pregnant women, people with disabilities, immigrants, and homeless populations) was largely absent, which may contribute to negative consequences for these groups.

scholarly journals Non-woven materials for cloth-based face mask inserts: Relationship between material properties and sub-micron aerosol filtration

2021 ◽  
Author(s):  
Leigh Crilley ◽  
Brian Malile ◽  
Andrea Angelucci ◽  
Cora Young ◽  
Trevor C. VandenBoer ◽  
...  
Keyword(s):  
Public Health ◽  
Material Properties ◽  
Face Mask ◽  
Respiratory Viruses ◽  
Public Health Agencies ◽  
Aerosol Filtration ◽  
Health Agencies ◽  
Current Guidance

Current guidance by leading public health agencies recommends wearing a 3-layer cloth-based face mask with a middle non-woven material insert to reduce the transmission of infectious respiratory viruses like SARS-CoV-2....

scholarly journals A tale of two parts of Switzerland: regional differences in the impact of the COVID-19 pandemic on parents

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Michelle Seiler ◽  
Georg Staubli ◽  
Julia Hoeffe ◽  
Gianluca Gualco ◽  
Sergio Manzano ◽  
...  
Keyword(s):  
Public Health ◽  
Regional Differences ◽  
Online Survey ◽  
Pediatric Emergency ◽  
The South ◽  
Public Health Agencies ◽  
The North ◽  
Regional Strategies ◽  
Health Agencies ◽  
The Impact

Abstract Background We aimed to document the impact of the coronavirus disease 2019 (COVID-19) pandemic on regions within a European country. Methods Parents arriving at two pediatric emergency departments (EDs) in North of Switzerland and two in South of Switzerland completed an online survey during the first peak of the pandemic (April–June 2020). They were asked to rate their concern about their children or themselves having COVID-19. Results A total of 662 respondents completed the survey. Parents in the South were significantly more exposed to someone tested positive for COVID-19 than in the North (13.9 and 4.7%, respectively; P <  0.001). Parents in the South were much more concerned than in the North that they (mean 4.61 and 3.32, respectively; P <  0.001) or their child (mean 4.79 and 3.17, respectively; P <  0.001) had COVID-19. Parents reported their children wore facemasks significantly more often in the South than in the North (71.5 and 23.5%, respectively; P <  0.001). Conclusion The COVID-19 pandemic resulted in significant regional differences among families arriving at EDs in Switzerland. Public health agencies should consider regional strategies, rather than country-wide guidelines, in future pandemics and for vaccination against COVID-19 for children.

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