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1
COVID-19: Training slides based on guidelines for case-finding, diagnosis, management and public health response in South Africa
Centre for Respiratory Diseases and Meningitis and Outbreak Response
National Department of Health, South Africa
(2020)
C2
Outline
• Welcome and objectives
• Microbiology, epidemiology and clinical presentation
• Surveillance for imported cases including case definitions
• Laboratory diagnosis • Infection prevention and hospital readiness
• Patient
...
flow and actions required at each step
• Co-ordinating a public health response
more
This study addresses part of the Terms of Reference for a scoping report ‘An analysis of approaches to laboratory capacity strengthening for drug resistant infections in low and middle income countries’. It has been produced as a separate report
...
because it is also very relevant for a second study ‘Supporting Surveillance Capacity for Antimicrobial Resistance: Regional Networks and Educational Resources’. This study compares antimicrobial surveillance systems in three low and middle income countries in order to describe the components of these systems and to understand which surveillance models are best suited to particular contexts. Ghana, Nigeria and Nepal were selected as study countries because they cover different continents and include one ‘fragile’ context (Nigeria). Brief information from Malawi is also included.
more
Interim guidance, 6 October 2021
Direct detection of SARS-CoV-2 viral proteins (antigens) in nasal swabs and other respiratory secretions using lateral flow immunoassays (also known as rapid diagnostic tests, RDTs) offers a faster and less expensive method to test for SARS-CoV-2 than the reference
...
method, nucleic acid amplification tests (NAATs). This interim guidance offers recommendations on the priority uses of antigen-detecting rapid diagnostic tests (Ag-RDTs) in specific populations and settings, including (i) for primary case detection in symptomatic individuals suspected to be infected and asymptomatic individuals at high risk of COVID-19, (ii) for contact tracing, (iii) during outbreak investigations and (iv) to monitor trends of disease incidence in communities. Ag-RDTs meeting minimum performance requirements can be used outside of clinical and laboratory settings, including in communities, by trained operators in accordance with instructions. The guidance additionally provides recommendations on implementation, product selection and storage.
more
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
...
ion patterns, early detection of SARS-CoV-2 variants inside each country is critical to complement the epidemiological and virological surveillance
9 February 2021
more
Following review of evidence and advice from the Technical Advisory Group (TAG) on Tuberculosis (TB) Diagnostics and Laboratory Strengthening, the World Health Organization (WHO) announces that current WHO recommendations for the use of interferon-
...
gamma release assays (IGRA) are also valid for Beijing Wantai’s TB-IGRA and Qiagen QuantiFERON-TB Gold Plus products. This expands the range of tests available to detect TB infection. Full details are provided in this WHO policy statement.
more
This document aims to provide interim guidance for microbiology and virology experts, other laboratory professionals, laboratory managers, infectious disease programme managers, public health profes
...
sionals and other stakeholders that provide primary, confirmatory or advanced testing for SARS-CoV-2, including genomic sequencing, or are involved in making decisions on establishing or scaling up capability and capacity to detect and characterize circulating SARS-CoV-2 variants.
more
As of 14 December 2021, a total of 19 laboratory-confirmed human rabies cases has been reported in South Africa for 2021. The cases are from Eastern Cape, KwaZuluNatal and Limpopo provinces. In addition, four probable rabies cases were reported from
...
KwaZulu-Natal and the Eastern Cape provinces. A probable case of rabies is defined as a person who has had a history of contact with a suspected or confirmed rabid animal and has developed an acute encephalitis with hyperactivity and paralytic signs and symptoms that progressed and resulted in death, usually by cardiac or respiratory failure, typically within ten days.
more
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 Na
...
tional Public Health Institutions (NPHIs) and/or Refe-
-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.
more
n October 2019, WHO convened the first meeting of the Buruli ulcer laboratory network (BU-LABNET) in Yaoundé, Cameroon, bringing together 11 laboratories from nine countries at the Pasteur Centre of Cameroon (CPC), the network’s Coordinating
...
Centre. The network was formally established at this meeting (1) and its members were those present. The objective of BU LABNET is to improve diagnosis of Buruli ulcer based on polymerase chain reaction (PCR) using standardized testing protocols, involving external quality assurance programmes and sharing knowledge among member laboratories.
more
The aim of the meeting was to broaden the network’s initiatives. Preliminary work involved integrating laboratory testing for skin NTDs other than Buruli ulcer, such as cutaneous leishmaniasis, mycetoma, leprosy and yaws, while extending the netwo
...
rk’s reach to encompass additional laboratories.
more
The course is divided into four thematic modules:
1. General information; 2. Laboratory diagnosis; 3. Plasmodium species identification and parasite counting; 4. Microscopy quality assurance. To update and review the basic concepts of epidemiology
...
and laboratory diagnosis of malaria, as well as the corresponding quality controls.
more
Exploring the application of Large Language Models and other AI
techniques to the European Crisis Management Laboratory analyses
based on the WHO Bench Aids for the diagnosis of intestinal parasites;
Tutor’s Guide: perform specific laboratory techniques; identify intestinal parasites by genus and species; quantify helminth eggs in faeces by Kato-Katz procedure.
Responding to a polio outbreak. Guidelines
recommended
The occurrence of a case of wild polio in a previously polio free area as presently in Syria, whether through importation, laboratory accident, or mutation of vaccine virus (VDPV), should be considered a public health emergency, that requires a rapi
...
d and high quality response as utmost priority
more
The 6th edition of the essential medicine list has been developed based on the 5th edition list of essential medicines, the National Standard Treatment Guidelines and Protocols 2013, list of laboratory commodities and List of Consumables used in pub
...
lic health facilities.
more
Package and approaches in areas of intense transmission of Ebola virus
World Health Organization
(2014)
Ebola interventions: The intervention to combat Ebola aims to stop human-to-human transmission. The package is composed of five elements necessary to control the spread of the disease: care to patients, contact monitoring, safe burials, laboratory
...
support and social mobilisation.
The document also describes key information on Ebola virus disease, patient care, contact tracing and monitoring, safe and dignified burial, laboratory diagnosis.
more
A survey was conducted in countries in all six WHO regions and focused on the building blocks that are considered prerequisites to combat antimicrobial resistance: a comprehensive national plan, laboratory capacity to undertake surveillance for resi
...
stant microorganisms, access to safe, effective antimicrobial medicines, control of the misuse of these medicines, awareness and understanding among the general public and effective infection prevention and control programmes.
more
The document outlines comprehensive guidelines for managing cholera outbreaks in South Africa, focusing on prevention, diagnosis, treatment, and public health measures. It emphasizes the importance of rehydration therapy, sanitation, clean water access, and community involvement to control the sprea
...
d of the disease. It also provides protocols for handling outbreaks, including case identification, laboratory confirmation, and multi-sectoral coordination to reduce morbidity and mortality rates.
more
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, and 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.
more
WHO Information Note on Revised Cholera Kit
recommended
The WHO Cholera Kits 2020 provide essential medical and logistical supplies for responding to cholera outbreaks. Designed to support the first month of an outbreak, the kits include treatment supplies for 100 patients, laboratory testing materials,
...
investigation tools, and infrastructure components for patient care. The six kit types cover central, peripheral, and community-level treatment, along with resources for surveillance and outbreak response. The document also outlines recent modifications, ordering procedures, and recommendations for deployment in high-risk areas.
more
