OVERVIEW
OBJECTIVES
FUNCTIONS
CURRENT PROJECTS
LEADERSHIP & TEAM
OVERVIEW
The Centre for Respiratory Diseases and Meningitis (CRDM) is a resource of surveillance, diagnostics, expertise and research in the field of communicable respiratory diseases and meningitis for South Africa and the African continent.
The centre generates data and provides expertise related to respiratory diseases and meningitis of public health importance to the South African National Department of Health, health care providers, regional and international collaborators, to assist with the planning of public health policies and programmes, and response to respiratory disease and meningitis outbreaks. CRDM is also a source of capacity building and formal training within South Africa and the African region.
OBJECTIVES
The objectives of CRDM are:
- To conduct surveillance for communicable respiratory diseases and meningitis within South Africa in order to provide data on the burden, severity and seasonality;
- To characterise (phenotypically and genotypically) pathogens contributing to respiratory diseases and meningitis in order to understand strain relatedness (molecular epidemiology) and guide vaccine development, treatment and prevention policy;
- To monitor trends in antiviral and antibacterial drug resistance in respiratory and meningeal pathogens in order to inform empiric treatment guidelines;
- To monitor the impact and effectiveness of interventions to reduce respiratory diseases and meningitis;
- To provide reference laboratory functions for specialised organism characterisation and identification related to respiratory communicable diseases and pathogens causing meningitis nationally and regionally;
- To identify and characterise novel respiratory and meningeal pathogens with potential to cause outbreaks and to assist with response to respiratory disease outbreaks;
- To be a source of local and regional expertise on respiratory diseases and meningitis;
- To engage in directed and relevant research to answer questions related to regional communicable respiratory disease and meningitis disease problems and their surveillance and management; and
- To build local and regional capacity in epidemiology and laboratory diagnostics for respiratory disease and meningitis.
FUNCTIONS
Syndromic Respiratory Illness Surveillance
CRDM coordinates the following syndromic surveillance programmes: pneumonia surveillance, influenza-like illness (ILI) (including two programmes: systematic ILI at public health clinics and Viral Watch) and the respiratory morbidity surveillance system).
Pneumonia surveillance
Pneumonia is a leading cause of hospitalisation and death in children and adults in South Africa. The National Pneumonia Surveillance Programme (NPSP), started in 2009, includes sentinel syndromic surveillance for severe respiratory illness (SRI) irrespective of duration of symptoms and testing for core pathogens of public health importance, namely, SARS-CoV-2, influenza, respiratory syncytial virus (RSV) and Bordetella pertussis. Surveillance is operational in five provinces. Data from this surveillance programme provides policy makers, clinicians and the general medical community with regular updates on seasonality, trends and the burden of pathogens associated with pneumonia. It also provides strategic information to support planning and monitoring of pneumonia prevention and control activities.
Influenza-like Illness Surveillance
Surveillance for influenza-like illness (ILI) is ongoing at outpatient clinics in three provinces, with plans to expand to cover all provinces with existing pneumonia surveillance sites. In addition, CRDM has a long-standing ILI programme (since 1984), The Viral Watch sentinel surveillance programme. The surveillance programmes provide data on the burden and relative contribution of influenza, RSV, Bordetella pertussis and SARS-CoV-2 to outpatient ILI. Data also allow us to describe the timing and severity of the influenza and RSV seasons and SARS-CoV-2 waves, characterisation of circulating influenza virus strains to guide decisions around Southern Hemisphere influenza vaccine composition, annual estimates of influenza vaccine effectiveness and to detect outbreaks caused by the pathogens included as part of surveillance.
Viral Watch
The Viral Watch programme is an active, prospective sentinel surveillance programme where participating clinicians (mostly private practitioners) submit specimens from outpatients with influenza-like illness to CRDM for testing of SARS-CoV-2, influenza, respiratory syncytial virus and pertussis. Currently, the programme is operational in 8 of the 9 South African provinces. The main aim of the programme is to describe influenza epidemiology in South Africa, to provide influenza strains for global vaccine strain selection and to provide annual estimates of influenza vaccine effectiveness.
The Viral Watch programme was started by the then National Institute for Virology in Johannesburg, South Africa, in 1984. At that time, 12 sites in the central, high-lying Gauteng province were enrolled. Between 1984 and 2004, the total number of sites ranged between 10 and 19. In 2005, amid fears of an impending pandemic, the programme was actively expanded to include new sites in all areas of the country.
From 2004 to 2008, the number of participating sites increased from 15 to 170, and by 2008 there were sites in all 9 South African provinces. Practitioners who expressed an interest in the programme during academic events, conferences, and continuing medical education meetings or other forums, as well as practitioners who were referred by colleagues joined the programme. Criteria considered in the selection of health care practitioners included the presence of a motivated clinician, geographic representativeness, a large and diverse patient base, differing patient demographics and socioeconomic conditions, and inclusion of paediatric patients. Data from this surveillance programme enable us to track trends in the seasonality and geographic distribution of influenza, RSV and SARS-CoV-2.
The Viral Watch programme is an important contributor to the establishment of an early warning and monitoring system for emergence of future pandemic viruses in the country. Influenza epidemiological and virological data generated through the program for South Africa contribute to a better understanding of the dynamics of influenza worldwide and in Africa in particular. Specifically data from the viral watch is used to determine the timing of the influenza season as well as the transmissibility each year. It also assists in identifying seed viruses for the production of seasonal influenza vaccines to be used in the southern hemisphere, particularly South Africa.
Respiratory Morbidity Surveillance
The respiratory morbidity surveillance system tracks trends in the number of pneumonia and influenza hospitalizations, using anonymised data from a private hospital group.
Influenza Virus Characterization
CRDM houses a World Health Organisation (WHO)-designated National Influenza Centre (NIC). This is 1 of 142 NICs in 113 countries that form part of the WHO’s Global Influenza Surveillance and Response System (GISRS). The South African NIC works closely with the stakeholders from the National Department of Health and the WHO Collaborating Centres to monitor of the emergence of novel, emerging or resistant influenza virus strains through surveillance activities. The NIC also performs preliminary genotypic and phenotypic characterization of influenza virus specimens circulating in South Africa and ships representative clinical specimens and isolated viruses to WHO Collaborating Centres for advanced antigenic and genetic analysis. The results form the basis for WHO recommendations on the composition of the Northern and Southern hemisphere influenza vaccine each year.
SARS-CoV-2 Genomic Characterisation
CRDM, as part of the Network for Genomics Surveillance of South Africa (NGS-SA), performs genomic surveillance for SARS-CoV-2 in South Africa. The network aims to provide timely scientific data on circulating SARS-CoV-2 variants and rapidly detect newly emerging variants for public health action. Clinical specimens from COVID-19 cases are sent to the NICD, and other NGS-SA labs, from private and public diagnostic laboratories around the country, and are collected through the pneumonia surveillance programme in five provinces (Western Cape, KwaZulu-Natal, North West, Gauteng and Mpumalanga). In addition, CRDM has established DATCOV-Gen, which is a prospective surveillance network linking real-time SARS-CoV-2 genome data to detailed epidemiologic and clinical data on hospitalised cases to allow rapid assessment of severity and clinical presentation of emerging SARS-CoV-2 variants. Genomic data is shared regularly with relevant stakeholders in order to monitor and assess the evolution of SARS-CoV-2 and thereby guide the pandemic response.
Laboratory-based Surveillance (GERMS-SA)
Since 1999, CRDM has conducted national laboratory-based, population-based active surveillance for invasive disease caused by S. pneumoniae, H. influenzae and N. meningitides, and since 2019, Streptococcus agalactiae and Streptococcus pyogenes. Enhanced surveillance occurs at 26 hospital sites (at least one in every South African province) where additional clinical data are collected on each patient with invasive disease. Surveillance data contribute to the evaluation and understanding of the impact of both the pneumococcal conjugate vaccine (PCV) and the Haemophilus influenzae serotype b conjugate vaccine (Hib CV).
CRDM also contribute data on numbers and serogroups of Neisseria meningitidis and support diagnostic testing and outbreak response for suspected cases of meningococcal meningitis. The data allow for descriptive epidemiology of invasive disease and emergence of resistance in these three pathogens. Streptococcus agalactiae, Group B Streptococcus (GBS), causes invasive disease amongst young infants, pregnant women and the elderly. Various vaccine formulations for GBS has undergone clinical trials. Should these become available it would be important to be able to document the burden and serotype distribution of GBS throughout South Africa prior to vaccine introduction.
Streptococcus pyogenes or Group A streptococcus (GAS) is associated with a range of infections including skin infections, pharyngitis and more severe invasive disease (endocarditis, septic shock syndrome and necrotizing fasciitis). Rheumatic heart disease (non-infectious complication of GAS) notifications are being reassessed with the new notifiable medical condition legislation in South Africa. These data will enable us to describe and better understand the epidemiology of GAS in our setting.
WHO/AFRO Supported Surveillance for Vaccine Preventable-Invasive Bacterial Diseases (VP-IBD)
CRDM serves as a regional reference laboratory (RRL) for the WHO Regional Office (WHO/AFRO), Immunization and Vaccine Development Cluster, which is part of the WHO/AFRO (VP-IBD) surveillance network. Cerebrospinal fluid samples are submitted from eleven countries (mostly SADC) for molecular detection and serotyping/grouping of S. pneumoniae, H. influenzae and N. meningitidis. Data are reported back to countries and WHO AFRO. Training and site assessments are also provided to improve surveillance capacity in these 11 countries.
Notifiable Medical Conditions Surveillance System
CRDM partners with the national Notifiable Medical Conditions (NMC) surveillance system, which is tasked with providing timely, accurate data of diseases that are of public health importance. These diseases may pose significant public health risks that can result in disease outbreaks or epidemics with high case fatality rates both nationally and internationally.
CRDM partners with the Outbreak Response Unit (Public Health Surveillance and Response Division/NICD). They are tasked with providing technical support for all aspects of communicable disease outbreak investigation and control in the nine provinces of South Africa, with special emphasis on optimising the role of laboratory services during these events. The Unit ensures constant communication with stakeholders such as the Department of Health, medical practitioners, media and the general public.
CRDM takes a proactive approach to public health education and capacity building, emphasizing a commitment to addressing pressing health challenges. Activities range from conducting surveillance training across various sites in South Africa to organizing laboratory workshops focused on pathogen detection and sequencing. CRDM provides advisory, technical and epidemiological support and training, both locally and continent-wide, assisting with training of among others medical technologists, medical scientists, epidemiologists, public health and microbiology registrars and South African Field Epidemiology Training Programme (SAFETP) residents. The centre has a strong focus on supervising and mentoring MSc and PhD students, and also contributes to lectures and course facilitation at The University of the Witwatersrand.
CRDM has an active research agenda in the field of respiratory diseases with a focus on the burden of disease, risk groups for severe illness and transmission, as well as assessment of the impact and effectiveness of interventions to reduce respiratory disease burden. Research studies conducted at CRDM ranges from ground breaking prospective household cohort studies to seroprevalence and healthcare utilisation surveys.
CURRENT PROJECTS
The aim of this platform is to identify and monitor acute respiratory tract infections (ARI) which may potentially include influenza, RSV and COVID-19. CoughWatchSA is designed to be a long-term surveillance platform for respiratory diseases beyond COIVD-19 and is not similar to the contact-tracing apps released by the National Department of Health. This platform may assist in the early detection of the onset of the influenza season in 2022 and potentially any subsequent waves of COVID-19. Participants in KwaZulu Natal, Western Cape and Gauteng may be linked to a pilot study that will allow for the home-based testing for influenza, RSV and COVID-19. This pilot study is called CoughCheck and will provide laboratory confirmations for suspected cases from CoughWatchSA participants who are eligible. CoughWatchSA will run as a pilot for the remainder of this year and will be officially launched as a complementary surveillance platform to current disease surveillance systems from 2023 onwards.
The Prospective Household observational cohort study of Influenza, Respiratory Syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa (The PHIRST Study) was a prospective cohort study in a rural and urban site from 2017-2018, with approximately 100 new households enrolled each year and followed up for 10 months. Nasopharyngeal swabs were collected twice-weekly from consenting household members irrespective of symptoms and tested for influenza virus, respiratory syncytial virus (RSV), B. pertussis and S. pneumoniae using a real-time reverse transcription polymerase chain reaction. We collected and tested over 100,000 nasopharyngeal swabs and over 7,000 serum samples. Although the follow-up of the cohort has stopped, we are currently doing serology testing and analysis.
The PHIRST study is a collaboration between the National Institute for Communicable Diseases (NICD), Johannesburg, South Africa; University of Witwatersrand, School of Public Health, Johannesburg, South Africa; United States Centers for Disease Control and Prevention, Atlanta, United States of America (USA); Perinatal HIV Research Unit, Johannesburg, South Africa; MRC/Wits Rural Public Health and Health Transitions Research (Agincourt), Bushbuckridge, South Africa; Medical Research Council (Environment and Health Research Unit), Johannesburg, South Africa and the ISI foundation, Italy.
Primary objectives
- To estimate the community burden of influenza and RSV, including: (i) the incidence of influenza and RSV infection in the community; (ii) the symptomatic fraction associated with influenza and RSV infection; (iii) the severity associated with symptomatic infections; and (iv) the fraction of individuals with symptomatic infection seeking medical care.
- To assess the transmission dynamics of influenza and RSV infections in the community, including: (i) the estimation of the household secondary infection risk (SIR), serial interval and length of shedding; (ii) the estimation of transmission of infection between age groups within the household and possibly the community; and (iii) the estimation of the effective reproductive number (Rt) and its variation over time in the community.
Importance
The PHIRST study will improve our understanding of the community burden of influenza, RSV, pertussis, tuberculosis and pneumococcal infection in South Africa. It will also provide data on the carriage prevalence of meningococcus, diphtheria and group A streptococcus. The data generated from this study will also provide important information on the transmission dynamics of influenza, RSV, pertussis and pneumococcus in the community allowing to better strategize interventions (including targeted vaccination strategies) and evaluate their potential impact.
For more info: CRDM website
Click below to read more
Contact details
Prof Cheryl Cohen
Tel: 011 386 6593
Email: cherylc@nicd.ac.za
The Prospective Household study of SARS-CoV-2, Influenza, and Respiratory Syncytial virus community burden, Transmission dynamics and viral interaction in South Africa (the PHIRST-C Study) study builds on a previous study, the PHIRST study, that was implemented in 2016-2018 and focused on the community burden and household transmission of influenza, respiratory syncytial virus (RSV), Bordetella pertussis and pneumococcus.
In light of the ongoing corona virus disease 2019 (COVID-19) pandemic, PHIRST-C will be conducted to help us understand the community burden, transmissibility potential and clinical features of illness associated with severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection. PHIRST-C is a prospective household cohort study where we follow up 200 households, 100 in a rural community in Mpumalanga Province, and 100 in an urban community in the North West Province. Participants in the study are visited twice-weekly for ten months to collect nasal swabs to test for SARS-CoV-2, influenza, RSV and pertussis; and to collect information on symptoms and healthcare seeking. Results will help us identify how many individuals are infected by SARS-CoV-2, how many of these experience symptoms, seek care, are hospitalised and die. Blood is collected every two months during this period to look for SARS-CoV-2 antibodies, signalling that someone was infected with the virus and their immune system reacted to that infection. To help us understand the reduction of antibodies in individuals that were infected, we will also be collecting blood every 2 months for an additional 12 months from participants who tested positive for SARS-CoV-2 in the initial follow-up period, helping us understand for how long someone may be immune to the virus after they were infected.
Overall, PHIRST-C will help us understand who is more at risk for being infected with the virus and becoming severely ill, how long someone may stay infectious, if someone can be re-infected, what proportion of infections occur without any symptoms and to what extent individuals without symptoms can transmit the virus, how SARS-CoV-2 is influenced by other respiratory viruses such as influenza and RSV. We will also examine how age and HIV-infection affect all of the above areas. This information can then in turn be used to inform the design and duration of measures to contain the virus.
Primary objectives
- To estimate the community burden of SARS-CoV-2, including:
- the incidence of SARS-CoV-2 infection in the community as determined by polymerase chain reaction (PCR) and serologic assays;
- the correlation between individuals that seroconverted for SARS-CoV-2 and tested positive by PCR;
- the incubation period and the symptomatic fraction associated with SARS-CoV-2 infection;
- the spectrum of severity associated with symptomatic infections;
- the fraction of individuals with symptomatic infection seeking medical care; and
- the effect of the interaction of SARS-CoV-2 with influenza and RSV on disease severity.
- To assess the transmission dynamics of SARS-CoV-2 infections in the community, including:
- the estimation of the SARS-CoV-2 household secondary infection risk (SIR), generation time and length of shedding;
- the estimation of the probability of transmission of SARS-CoV-2 infection between individuals (both symptomatic and asymptomatic/presymptomatic) within the household and potentially the community;
- the estimation of the SARS-CoV-2 effective reproduction number (Rt) and its variation over time in the community; and
- the effect of the interaction of SARS-CoV-2 with influenza and RSV on transmission dynamics.
Impact
This study will provide essential information on the natural history of the virus that will impact decisions on optimal strategies for the containment and mitigation of the current and potential future epidemics of SARS-CoV-2 locally, regionally and globally.
Contact details
Prof Cheryl Cohen
Tel: 011 386 6593
Email: cherylc@nicd.ac.za
The household transmission study (HTS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease (COVID-19), is a case-ascertained, prospective, observational household transmission study of household contacts of index cases from two urban communities in the North West Province (Klerksdorp) and the Gauteng Province (Soweto). In order to better understand the transmission dynamics of SARS-CoV-2 in households with HIV-infected and HIV-uninfected COVID-19 index cases, we screen individuals consulting at primary healthcare facilities for respiratory illness or suspected COVID-19 and test them for SARS-CoV-2. If someone tests positive for SARS-CoV-2 and reports to be the first person with respiratory or suspected COVID-19 symptoms in their household, we approach their household for enrolment in the HTS. Following enrolment, nasal swabs are collected from the index cases and their household contacts three times per week for 6 weeks’ post-enrolment to test for SARS-CoV-2, irrespective of presence of symptoms. We also collect serum at enrolment and the end of the follow-up period to test for antibodies to SARS-CoV-2. The HTS started in October 2020 and will continue until August 2021, and will help us understand if compared to HIV-uninfected individuals, HIV-infected individuals shed SARS-CoV-2 for longer, or if there is a difference risk of transmitting the virus to household contact, and to determine the incubation period and the proportion of SARS-CoV-2 individuals that have symptoms.
Primary objectives
- To determine the time period (range and median) in days that HIV-infected and HIV-uninfected index cases continue to shed SARS-CoV-2 from respiratory specimens after symptoms onset using real-time reverse transcription polymerase chain reaction (rRT-PCR) and viral culture.
- To determine the temporal variations of SARS-CoV-2 viral-load in respiratory specimens from HIV-infected and HIV-uninfected index cases using reverse transcriptase polymerase chain reaction (rRT-PCR).
- To determine the secondary infection risk (SIR) in household contacts of HIV-infected and HIV-uninfected index cases.
- To determine the serial interval (SI) for SARS-CoV-2 transmission from HIV-infected and HIV-uninfected index cases.
- To determine the antibody response to SARS-CoV-2 early-post infection among HIV-infected and HIV-uninfected index cases.
Impact
This study will provide essential information on the natural history of the virus, also considering how it may differ between HIV-infected and –uninfected individuals. This will impact decisions on optimal strategies for the containment and mitigation of the current and potential future epidemics of SARS-CoV-2 locally, regionally and globally.
Contact information
Dr Sibongile Walaza
Email: sibongilew@nicd.ac.za
The Healthcare Utilisation and Seroprevalence of COVID-19 (HUTS) study is a cross-sectional community survey being conducted in three communities serviced by healthcare facilities where severe respiratory illness (SRI) and influenza-like illness (ILI) surveillance is conducted in South Africa (Mitchell’s Plain, Pietermaritzburg and Klerksdorp) during and after the second wave of SARS-CoV-2 infections in South Africa. The study aims to explore the healthcare seeking behaviour for and cost of respiratory illness during the pandemic and to estimate SARS-CoV-2 community seroprevalence and the COVID-19 knowledge, attitudes and practices (KAP) of the selected communities. The study will complement data from inpatient and outpatient syndromic surveillance conducted in the same target communities to document the clinical spectrum of illness, including the proportion of asymptomatic, mild, severe and fatal cases, both medically and non-medically attended. Serology testing for SARS-CoV-2 is important in order to better quantify the number of COVID-19 cases, including those that may have been asymptomatic or recovered without having been tested. Public health action is guided by the incidence of infection, and therefore understanding the full burden of infection and potentially immunity, is important. Surveillance of antibody seropositivity in the South African population will allow inferences to be made about the extent of infection in the community.
Objectives
In three communities in South Africa, Klerksdorp North West Province, Pietermaritzburg KwaZulu-Natal and Mitchells Plain Western Cape, address the following:
Primary objectives:
- Characterize healthcare seeking behaviour for respiratory illness during the first wave of the COVID-19 pandemic
- Determine the proportion of mild and severe respiratory illnesses that were not medically attended during the epidemic period
- To estimate the household and community economic burden of respiratory illness during the first wave of the epidemic
- To describe the economic impact of mitigation measures on households during the first wave of the epidemic
- Describe knowledge, attitudes and practices related to COVID-19 in the community, including prevention
- Determine the seroprevalence of antibodies to SARS-CoV-2 following the first wave of the pandemic, by age group and HIV-infection status.
Secondary objectives:
- Provide a more accurate estimate of the burden of COVID-19 in the community by adjusting facility-based surveillance data for healthcare seeking behaviour
- Assess the sensitivity of sentinel surveillance for COVID-19 at each site
- Identify risk factors for SARS-CoV-2 infection including age, HIV infection and underlying illnesses
- To estimate the SARS-CoV-2 infection case-fatality ratio through triangulation with COVID sentinel surveillance and mortality data
- Determine the seroprevalence of antibodies to other respiratory viruses such as influenza, respiratory syncytial virus and other human coronaviruses
Impact
Understanding community healthcare utilization, KAP and economic burden on households associated with the COVID-19 pandemic is key to guide containment and mitigation measures in local settings and globally. In addition, understanding the disease burden of COVID-19 and groups at increased risk of severe COVID-19 is key to inform mitigation guidelines for ongoing and potential future epidemics.
Contact information
Dr. Nicole Wolter
Email: nicolew@nicd.ac.za
The Centre for Respiratory Diseases and Meningitis (CRDM) houses a World Health Organization (WHO)-designated National influenza centre (NIC). This is 1 of 142 NICs in 113 countries that form part of the WHO’s Global Influenza Surveillance and Response System (GISRS). The South African NIC works closely with the stakeholders from the National Department of Health and the WHO Collaborating Centres to monitor the emergence of novel, emerging or resistant influenza virus strains through surveillance activities. The NIC also performs preliminary genotypic and phenotypic characterisation of influenza virus specimens circulating in South Africa and ships representative clinical specimens and isolated viruses to WHO Collaborating Centres for advanced antigenic and genetic analysis.
Importance
We submit results on the advanced antigenic and genetic analysis to WHO Collaborating Centres and these data form the basis for WHO recommendations on the composition of the Northern and Southern Hemisphere influenza vaccine each year. We also serve as a technical resource on influenza-related matters to the National Department of Health.
Contact details
Dr. Nicole Wolter
Tel: 011 555 0305
Email: nicolew@nicd.ac.za
The RSV Global Online Mortality Database, abbreviated as RSV GOLD, is the first global registry for children younger than 5 years dying with RSV infection. The aim is to identify clinical and socioeconomic characteristics of children dying from RSV infections to identify important risk factors for child mortality due to RSV and to ultimately combat RSV-associated childhood mortality. Data is extracted year from the existing national syndromic surveillance and submitted. There are 51 countries participating and the project is funded by the Bill and Melinda Gates Foundation.
Importance
Globally, approximately 33.1 million episodes of RSV- associated lower respiratory tract infection occur each year, about 10% of these will be hospitalised and nearly 200 000 will die. An improved understanding of risk factors for RSV-associated mortality will help recognize the potential impact of the various types of vaccines that are under development. Providing policy makers with this data will assist in establishment of a vaccine policy for RSV. Ultimately, the goal of this project is to combat RSV-associated childhood mortality.
Contact details
Dr Jocelyn Moyes
Tel: jocelynm@nicd.ac.za
The Centre for Respiratory Diseases and Meningitis (CRDM) also provides a special diagnostic service to clinicians for pathogens which are not tested for routinely in other National Health Laboratory Service and private laboratories, or when clusters of severe respiratory disease or meningitis are identified throughout the country. Tests offered include avian influenza, seasonal influenza and RSV subtyping, B. pertussis, C. diphtheriae, group A streptococcus, group B streptococcus, Legionella spp, Middle East Respiratory Syndrome Corona Virus (MERS-CoV) as well as panels for community- and hospital-acquired pneumonia, atypical pneumonia, neonatal sepsis, and bacterial and viral meningitis. Requests for diagnostics are to be discussed with the laboratory (contact details below) and should be accompanied by the submission form that can be found HERE.
Importance
By providing diagnostic testing to clinicians, we can assist in finding the correct course of treatment for patients and also to identify clusters of cases which may need investigation.
Contact details
Dr Nicole Wolter
Tel: 011 555 0352
Email: nicolew@nicd.ac.za
Dr Mignon du Plessis
Tel: 011 555 0387
Email: mignond@nicd.ac.za
The South Africa – Pittsburgh Public Health Genomic Epidemiology (SAPPHGenE) Training Program was established as a collaborative effort between the University of Pittsburgh (Pitt) in the United States, and the National Institute for Communicable Diseases (NICD), Johannesburg, South Africa.
The programme involves the multidisciplinary training of young South African health and academic researchers from historically-disadvantaged backgrounds, focusing on the genomic epidemiology of respiratory disease-causing bacterial and fungal pathogens of importance in South Africa and globally.
The overall aim is to improve the public health genomics scientific capacity in South Africa and ultimately in Africa, by implementing genomics characterization to improve the swift detection and control of healthcare and community outbreaks, understanding transmission dynamics, monitoring of antimicrobial resistance and impact of immunization programs.
The programme directors are Professor Lee Harrison, head of the Epidemiology and Medicine as well as the Microbial Genomic Epidemiology Laboratory at Pitt, and Professor Anne von Gottberg, section lead of the Centre for Respiratory Diseases and Meningitis (CRDM) at the NICD. The programme involves a multidisciplinary group of experienced mentors at three training sites: Pitt, the Centres for Disease Control and Prevention (CDC) in Atlanta, and the NICD. Trainees are a combination of full-time and part-time post-graduate (MSc and PhD) degree candidates, of which degrees will be provided by the University of the Witwatersrand, South Africa.
Contact details
Prof Anne von Gottberg
Tel: 011 555 0316
Email: annev@nicd.ac.za
LEADERSHIP AND TEAM
Cheryl Cohen is a Professor in Epidemiology at the University of the Witwatersrand and head of the Centre for Respiratory Diseases and Meningitis. She qualified as a medical doctor at the University of the Witwatersrand and is a Fellow of the College of Pathologists of South Africa in the discipline of Microbiology.
She obtained an MSc qualification in Epidemiology from the London School of Hygiene and Tropical Medicine in the United Kingdom and a PhD from the University of the Witwatersrand. In her position at the NICD, she works closely with the National Department of Health to generate evidence that may guide government policy in the control and management of respiratory diseases.
In 2009 she led the establishment of a national surveillance programme for severe acute respiratory infections in South Africa and is the epidemiology lead for national pneumonia surveillance and invasive bacterial infections that cause pneumonia.
Cohen leads a team who are dedicated towards researching respiratory diseases. The team largely focuses on the burden of disease and risk groups for severe illness, in addition to assessing the impact and effectiveness of interventions that may reduce respiratory disease burden. She is a member of several national advisory committees and several international World Health Organization working groups, mainly related to influenza and other respiratory viruses. Her research has been funded through the NICD and also partly through grants from the South African Medical Research Council, the UK Foreign, Commonwealth and Development Office, the Wellcome Trust, the US Centers for Disease Control and Prevention (CDC), Programme for Applied Technologies in Health (PATH) and Sanofi Pasteur
South African Department of Health to generate evidence to guide policy with regard to the control and management of respiratory diseases. She led the establishment of a national surveillance programme for severe acute respiratory infections in South Africa in 2009 and is the epidemiology lead for national surveillance for pneumonia and invasive bacterial infections causing pneumonia. She heads up a team with an active research agenda in the field of respiratory diseases with a focus on the burden of disease and risk groups for severe illness, as well as assessment of the impact and effectiveness of interventions to reduce respiratory disease burden. She is a member of several national advisory committees as well as several international World Health Organization working groups, mainly related to influenza and other respiratory viruses.
Contact details
Prof Cheryl Cohen
Tel: 011 386 6593
Email: cherylc@nicd.ac.za
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Office Administrator
Mpho Ntoyi
Tel: +27 11 386 6450
Email: mphon@nicd.ac.za
Principal Pathologist
Prof Anne von Gottberg
Email: annev@nicd.ac.za
Principal Medical Scientist
Dr Mignon du Plessis
Email: mignond@nicd.ac.za
Medical Epidemiologist
Dr Sibongile Walaza
Email: sibongilew@nicd.ac.za
Medical Epidemiologist
Dr Jocelyn Moyes
Email: jossmoyes@gmail.com
National Influenza Centre Director
Dr Nicole Wolter
Email: nicolew@nicd.ac.za
