Whole-genome sequencing (WGS) provides a vast amount of information and the highest possible resolution for pathogen subtyping. The application of WGS for global surveillance can provide information on the early emergence and spread of AMR and furth...er inform timely policy development on AMR control. Sequencing data emanating from AMR surveillance may provide key information to guide the development of rapid diagnostic tools for better and more rapid characterization of AMR, and thus complement phenotypic methods. This document addresses the applications of WGS for AMR surveillance, including the benefits and limitations of current WGS technologies
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8 January 2021
Sequencing enabled the world to rapidly identify SARS-CoV-2 and develop diagnostic tests and other tools for outbreak management. Continued genome sequencing supports the monitoring of the disease’s spread and evolution of the viru...s. Accelerated integration of genome sequencing into the practices of the global health community is required if we want to be better prepared for the future threats. This document provides guidance for laboratories on maximizing the impact of SARS-CoV-2 sequencing now and other emerging pathogens in the future.
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A COVID-19 virus mutation tracker system (CovMT; appendix) based on SARS-CoV-2 isolate genomes deposited to GISAID to track the worldwide sequencing efforts and the evolution of the mutational landscape of this virus. CovMT, which is updated daily, ...summarises mutations from more than 450 000 isolates into groups of generic virus clades, lineages, and more specific mutation sets we call mutation fingerprints.
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The Committee discussed the implications for preparedness for smallpox-like events reflected by the ongoing COVID-19 pandemic. The Committee noted how quickly diagnostics and vaccines could be developed and deployed when resources and political will were abundant. This rapidity was also due to the f...act that the genetic sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had been shared worldwide. It was noted that in one country SARS-CoV-2 had been reconstructed in a laboratory from the viral genome sequence before the first case of COVID-19 had been reported, highlighting the benefits of synthetic biology technologies for accelerated development of diagnostics as well as the oft-described potential risks. Lessons learned about clinical care during the COVID-19 pandemic were also discussed.
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Background: The human helminth infections include ascariasis, trichuriasis, hookworm infections, schistosomiasis, lymphatic filariasis (LF) and onchocerciasis. It is estimated that almost 2 billion people worldwide are infected with helminths. Whilst the WHO treatment guidelines for helminth infecti...ons are mostly aimed at controlling morbidity, there has been a recent shift with some countries moving towards goals of disease elimination through mass drug administration, especially for LF and onchocerciasis. However, as prevalence is driven lower, treating entire populations may no longer be the most efficient or cost-effective strategy. Instead, it may be beneficial to identify individuals or demographic groups who are persistently infected, often termed as being “predisposed” to infection, and target treatment at them.
Methods: The authors searched Embase, MEDLINE, Global Health, and Web of Science for all English language, humanbased papers investigating predisposition to helminth infections published up to October 31st, 2017. The varying definitions used to describe predisposition, and the statistical tests used to determine its presence, are summarised. Evidence for predisposition is presented, stratified by helminth species, and risk factors for predisposition to infection are identified and discussed.
Results: In total, 43 papers were identified, summarising results from 34 different studies in 23 countries. Consistent evidence of predisposition to infection with certain species of human helminth was identified. Children were regularly found to experience greater predisposition to Ascaris lumbricoides, Schistosoma mansoni and S. haematobium than adults. Females were found to be more predisposed to A. lumbricoides infection than were males. Household clustering of infection was identified for A. lumbricoides, T. trichiura and S. japonicum. Ascaris lumbricoides and T. trichiura also showed evidence of familial predisposition. Whilst strong evidence for predisposition to hookworm infection was identified, findings with regards to which groups were affected were considerably more varied than for other helminth species.
Conclusion: This review has found consistent evidence of predisposition to heavy (and light) infection for certain human helminth species. However, further research is needed to identify reasons for the reported differences between demographic groups. Molecular epidemiological methods associated with whole genome sequencing to determine ‘who infects whom’ may shed more light on the factors generating predisposition.
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The growing understanding of how sequence information can contribute to improved public health is driving global investments in sequencing facilities and programmes. The falling cost and complexity of generating GSD provides opportunities for expanding sequencing capacity; however, challenges to wid...espread implementation remain. This document provides policy-makers and stakeholders with guidance on how to maximize the public health benefit of SARS-CoV-2 genomic sequencing activities in the short and long term as the pandemic continues to unfold. Practical considerations for the implementation of a virus genomic sequencing programme and an overview of the public health objectives of genomic sequencing are covered. This guidance focuses on SARS-CoV-2 but is applicable to other pathogens of public health concern.
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The growing understanding of how sequence information can contribute to improved public health is driving global investments in sequencing facilities and programmes. The falling cost and complexity of generating GSD provides opportunities for expanding sequencing capacity; however, challenges to wid...espread implementation remain. This document provides policy-makers and stakeholders with guidance on how to maximize the public health benefit of SARS-CoV-2 genomic sequencing activities in the short and long term as the pandemic continues to unfold. Practical considerations for the implementation of a virus genomic sequencing programme and an overview of the public health objectives of genomic sequencing are covered. This guidance focuses on SARS-CoV-2 but is applicable to other pathogens of public health concern.
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Representative, quality, timely and continuous genetic surveillance of SARS-CoV-2 is critical to the COVID-19 outbreak response. This document provides practical guidance to Global Influenza Surveillance and Response System (GISRS) laboratories and other relevant national laboratories to move beyond... virus detection to genomic sequencing of SARS-CoV-2 PCR positive materials obtained from sentinel surveillance of influenza-like illness (ILI), acute respiratory infection (ARI) and severe acute respiratory infection (SARI). It contains considerations on sample selection for sequencing, numbers of viruses to be sequenced, metadata and timeliness for sharing genetic sequence data (GSD) and opportunities for technical support.
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Genomic sequencing has been an essential tool in generating virological data, driving the laboratory response, and better understanding the dispersal and evolutionary patterns of SARS-CoV-2. In addition to the characterization of the global circulation patterns, early detection of SARS-CoV-2 variant...s inside each country is critical to complement the epidemiological and virological surveillance
9 February 2021
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This technical guidance aims to provide guidelines to laboratories and relevant stakeholders in the European Union (EU), European Economic Area (EEA) and other countries in the WHO European region in making decisions on establishing sequencing capacities and capabilities, in making decisions on whic...h technologies to use and/or in deciding on the role of sequencing for SARS-CoV-2 diagnostics, research, outbreak investigations and surveillance. It addresses the most used sequencing technologies and their applications and proposes a central standardisation process to analyse and report the findings of SARS-CoV-2 genetic characterisations.
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The Strategy provides a high-level unifying framework to leverage existing capacities, address barriers and strengthen the use of genomic surveillance in the detection, monitoring and response to public health threats. Genomic surveillance is part of the broader surveillance and laboratory system, a...nd its implementation should reinforce end-to-end capacities including sample collection, diagnostics, data sharing and analysis. The strategy aims to facilitate the connectivity between different disease control programs and surveillance networks. This interoperability will strengthen the cross-cutting essential public health laboratory functions underpinning genomics holistically. The strategy articulates the overarching goal, objectives and strategic actions needed. These are dependent on commitments from countries, partners and WHO for their implementation.
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WHO-2019-nCoV-genomic_sequencing
Для того чтобы помочь разобраться с детской психиатрической генетикой, мы сначала представим основные концепции общей генетики. Это послужит краткой ознакомител...ной информацией о том, как психиатрические проблемы передаются от родителей их детям. Далее мы обсудим важность обследования семей так, чтобы можно было получить информацию как о генетике, так и о влия-нии окружающей среды. Затем мы опишем разные типы научных исследований в генетике и расскажем, как интерпретировать их результаты.
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published in: Viruses 2016, 8, 161
Climate change, increasing population densities, and intensified globalisation in trade, travel and migration are among the most important factors shaping the 21st century. Each impacts upon population health and the risk of infectious disease, particularly those originating at the human-animal-envi...ronmental interface. The recognition that many risk drivers of infectious disease fall outside of the typical domain of the health sector creates the challenge of identifying and pursuing priorities for cross-sectoral action aimed at strengthening global health security. In response, the One Health concept has emerged, as have related initiatives addressing Planetary Health and Biodiversity and Human Health. From a public health perspective and operationally speaking, the One Health approach offers great potential, emphasising as it does cooperation and coordination between multiple sectors. Yet despite having been a focal point for discussion for over a decade, numerous challenges facing the implementation of One Health preparedness strategies remain. While some are technical, related to the requirement for innovative early warning systems or new vaccines, for example, others are institutional and cultural in nature, given the transdisciplinary nature of the topic. There have thus been calls to address One Health from multiple perspectives, from ecology to the social sciences. In order to further explore this issue and to identify priority areas for action for strengthening One Health preparedness in Europe, ECDC convened an expert consultation on 11–12 December 2017.
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