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 circulat
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ion patterns, early detection of SARS-CoV-2 variants inside each country is critical to complement the epidemiological and virological surveillance
9 February 2021
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The Practical manual on laboratory strengthening, 2022 update provides practical guidance on implementation of WHO recommendations and best practices for TB laboratory strengthening. It is an updated version of the GLI Practical Guide to Laboratory Strengthening published in 2017 and provides the la
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test practical guidance on use of newly recommended diagnostics as well as guidance in key technical areas, including quality assurance and quality management systems, specimen collection and registration, procurement and supply-chain management, diagnostic connectivity, biosafety, data management, human resources, strategic planning, and model algorithms. The key changes are:
inclusion of recent or updated WHO recommendations for tests to diagnose TB and detect drug resistance;
alignment with the latest WHO critical concentrations for phenotypic drug-susceptibility testing (DST) and the new definitions of pre-XDR-TB and XDR-TB;
updated information on building quality-assured TB testing and management capacity using the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) approach (Score-TB package1);
updated information on assessing, analysing and optimising TB diagnostic networks; and
updated information on the use of next-generation sequencing (NGS) to detect mutations associated with drug resistance for surveillance purposes.
The document also provides references to resources and tools relevant for work on laboratory strengthening.
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PLOS ONE | DOI:10.1371/journal.pone.0133869 July 28, 2015, p.1-16
Any individual that meets the suspected case definition of monkeypox should be offered testing in appropriately equipped laboratories by staff trained in the relevant technical and safety procedures. Confirmation of monkeypox virus infection is based on nucleic acid amplification testing (NAAT), usi
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ng real-time or conventional polymerase chain reaction (PCR), for detection of unique sequences of viral DNA. PCR can be used alone, or in combination with sequencing. The recommended specimen type for laboratory confirmation of monkeypox is skin lesion material, including swabs of lesion surface and/or exudate, roofs from more than one lesion, or lesion crusts.
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Copenhagen, Denmark, 24–25 August 2017
Interium guidance, 25 June 2021Timely and accurate diagnostic testing is an essential tool in preventing and controlling the spread of COVID-19. This document describes recommendations for national testing strategies and the use of PCR and rapid antigen tests in different transmission scenarios of t
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he COVID-19 outbreak, including how testing might be rationalized in low resource settings. All testing should be followed by a strong public health response including isolating those who test positive and providing them care, contact tracing and quarantine of contacts.
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A role for nuclear techniques
Antimicrobials play a critical role in the treatment of human and animal (aquatic and terrestrial) diseases, which has led to their widespread application and use. Antimicrobial resistance (AMR) is the ability of microorganisms to stop an antibiotic, such as an antimic
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robial, antiviral or antimalarial, from working against them. Globally, about 700 000 deaths per year arise from resistant infections as a result of the fact that antimicrobial drugs have become less effective at killing resistant pathogens. Antimicrobial chemicals that are present in environmental compartments can trigger the development of AMR. These chemicals can also cause antibiotic-resistant bacteria (ARB) to further spread antibiotic resistance genes (ARG) because they may have an evolutionary advantage over non-resistant bacteria.
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The Central African Republic is at a major turning point in its history. The country
is just emerging from a very violent conflict, during which thousands of human lives were lost and one-third of the population was displaced. After
a three-year transition, and with the support of the internationa
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l community, authorities successfully created the conditions required to conduct credible presidential and legislative
elections. Central African citizens mobilized to express their desire for peace and to break
with the cycle of past violence. Their exemplary democratic maturity ensured the electoral
process was peaceful, despite palpable tensions. The welcome given Pope Francis in Bangui in
November 2015 and visible reconciliation efforts demonstrate the population wishes to turn
the page on this conflict.
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The role of environmental contamination in transmission of COVID-19 virus is currently not clear. This protocol has been designed to determine (viable) virus presence and persistence on fomites in various locations where a patient infected with COVID-19 is currently receiving care or being isolated,
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and to understand how this may relate to COVID-19 transmission events in these settings. It is therefore important that it is done as part of a comprehensive outbreak investigation and that information obtained by environmental studies is combined with the results of epidemiological, laboratory and sequence data from COVID-19 patient investigations.
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For Children and their Families
October 2015
Africa CDC Institute of Pathogen Genomics (IPG) was launched in November 2019 and operates under the Division of Laboratory Systems and Networks.
IPG coordinate the implementation of molecular diagnostics, pathogen genomics and bioinformatics in National Public Health Institutions (NPHIs) and/or Re
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fe-
-rence Laboratories (NRLs) across Africa.
Africa CDC and APHF are coordinating a continental initiative to maximize the benefits of molecular approaches and pathogen genomics for more effective
outbreak preparedness, prevention, response, and for the control and elimination of endemic diseases in Africa. One of Africa CDC’s flagship initiative is the Africa
Pathogen Genomics Initiative (Africa PGI), a partnership that aims to strengthen laboratory systems and enhance genomic surveillance by equipping the continent’s
public health institutions with the tools, training, and data infrastructure.
About the Project
In 2023, 166 outbreaks and public health events were reported in Africa. This calls for a resilient laboratory systems for timely detection and reporting of current and future outbreaks. This project aims to scale up molecular diagnostic and genomic sequencing-based detection and characterization of outbreaks.
Africa CDC is working with Member States to develop guidance, diagnostic algorithm, training and capacity building to enable outbreak detection, and reporting to inform public health response.
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doi: https://doi.org/10.1101/2020.10.28.20221143
This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
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,
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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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Given the circulation of the variant of clade I of mpox virus (MPXV) in the African Region, which is associated in the African Region with sustained transmission and the occurrence of cases in a wider range of age groups, including children, the Pan American Health Organization/World Health Organiza
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tion (PAHO/WHO) encourages Member States to remain vigilant to the possibility of introduction of this variant in the Americas, and to continue their surveillance efforts, including genomic sequencing of detected cases, with special emphasis on high-risk groups.
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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
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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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Временные рекомендации
9 августа 2021 г.
Цель данного документа - описать минимальный набор мероприятий по эпиднадзору, рекомендуемых на национальном уровне для вы
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вления и мониторинга относительной распространенности вариантов SARS-CoV-2, и наметить набор мероприятий для характеристики и оценки риска, создаваемого этими вариантами. Также приводится набор показателей для стандартизации мониторинга и публичной отчетности о циркуляции вариантов.
Документ предназначен в первую очередь для национальных и субнациональных органов здравоохранения и партнеров, поддерживающих внедрение эпиднадзора за вариантами SARS-CoV-2.
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The World Health Organization (WHO) recognizes the challenges countries face for maintaining their COVID-19 response while addressing competing public health challenges, conflicts, climate change and economic crises.
It remains critical for national programmes to continue to offer testing for COVI
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D-19 in line with three main objectives: reduce morbidity and mortality through linkage to prompt care and treatment, reduce onward transmission and track the evolution of the epidemic and the virus
itself.
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Application of a One Health approach .
The present guidance was developed with the support of the WHO Advisory Group on Integrated Surveillance of Antimicrobial Resistance (AGISAR) to assist countries and other stakeholders in the establishment and development of programmes of integrated surveillan
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ce of antimicrobial resistance in the foodborne bacteria (i.e., bacteria commonly transmitted by food) by taking a One Health approach.
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