The Centre for Emerging Zoonotic and Parasitic Diseases (CEZPD) was established by the amalgamation of five divisions: the Special Bacterial Pathogens Reference Laboratory (SBPRL), Special Viral Pathogens Division [including the Special Viral Pathogens Laboratory (SVPL) and Arbovirus Reference Laboratory (ARL)], Electron Microscopy (EM), the Parasitology Reference Laboratory (PRL) and the Vector Control Reference Laboratory (VCRL). A sixth division, ARMMOR (Laboratory for Antimalarial Resistance Monitoring and Malaria Operational Research), was established in 2018.
The CEZPD has a competitive track record in providing comprehensive capacity for the differential diagnosis and research of viral haemorrhagic fevers, arthropod-borne diseases, human rabies, anthrax, plague, leptospirosis and other infectious diseases, in particular those of zoonotic origin and public health importance. The centre also offers specialised parasitological diagnostic tests and is involved in the surveillance of drug-resistant malaria and vector control strategies in South Africa.
In order to accomplish its mandate, the CEZPD operates the only positive pressure suit biosafety level 4 (BSL4) facility on the African continent, which places it both strategically and critically in a position to assist in the response of highly dangerous emerging and re-emerging zoonotic pathogens. In addition, to several biosafety level 2 laboratory suites, the CEZPD operates two biosafety level 3 facilities, a transmission electron microscope, several insectaries and a mass-mosquito rearing facility.
The CEZPD contributes actively in the arena of One Health and Laboratory Biorisk Management in South Africa and regionally. CEZPD staff members also contribute to a myriad of training activities including, post-graduate student supervision and both national and international research fellow training.
The objectives of the CEZPD are:
- To be a national and international centre of excellence for emerging and re-emerging zoonotic diseases, especially those categorized as risk group 3 and 4 pathogens;
- To be a national and international centre of excellence for parasitic diseases, especially malaria, schistosomiasis and soil-transmitted helminths;
- To function as a resource for knowledge and expertise to the South African government, SADC countries and the African continent;
- To assist in the planning of relevant policies and programs and to harness innovation in science and technology for the control and prevention of emerging zoonotic and parasitic diseases;
- To support control, surveillance, detection and outbreak response systems for emerging zoonotics and parasitic diseases; and
- To support South Africa’s commitment to the International Health Regulations, One Health and Global Health Security Agenda.
The Special Viral Pathogens Laboratory (SVPL) conducts referral laboratory diagnosis of viral haemorrhagic fevers (VHF) and human rabies. It offers an extensive array of diagnostic tests for the investigation of Crimean-Congo haemorrhagic fever, a VHF that is endemic to South Africa. In addition, the SVPL has the capacity to interrogate suspected cases of VHF such as Ebola virus disease, Marburg virus disease, Lassa fever, related arenaviruses and yellow fever, therein supporting South Africa’s capacity for the detection of cases importing high consequence pathogens. In order to provide diagnostic services and to enable research involving VHF and other risk group 3 and 4 viral pathogens, the SVPL operates biosafety level 3 and 4 facilities. During the Ebola virus disease outbreak in West Africa from 2013-2016 the SVPL offered comprehensive and extensive mobile laboratory support towards the containment efforts in Sierra Leone.
Dog-transmitted rabies is endemic in South Africa, and the SVPL provides diagnostic support for the diagnosis of human cases in the country and elsewhere by conducting tests for ante-mortem and post-mortem investigation of suspected human rabies cases.
Apart from laboratory expertise, the SVPL supports the mission of CEZPD and the NICD to provide surveillance, relevant research and training to support better health outcomes. The SVPL collaborates with various stakeholders to promote One Health, capacity for response to zoonotic disease events, and related policy development. The SVPL is also actively involved in promoting improved laboratory biorisk management in South Africa and beyond, herein contributing to policy development and training.
In recent years, an increasing number of emerging and re-emerging arthropod borne (arbo) viruses have become pathogens of public health importance, largely due to the unprecedented expansion of the geographical distribution of the arthropod vectors and changes in their virulence and trends global climate change. There are more than 500 recognized arboviruses, of which more than 130 are known human pathogens. The Arbovirus Reference Laboratory (ARL) performs reference diagnostic services for endemic and exotic mosquito-borne viral diseases, including Rift Valley fever, West Nile fever, chikungunya, dengue and Zika fever. Furthermore, the laboratory is involved in surveillance and other projects studying the ecology and prevalence of arboviruses in specific areas that previously served as epicenters for large outbreaks, or where exotic viruses are likely to be introduced from neighboring countries. Discovery, detection and characterization of unknown and known arboviruses, which will result in better preparedness for possible future emergence or re-emergence, is an important part of the laboratory’s function. The laboratory also operates a recently-renovated insectary facility to study the competence of South African mosquito species to transmit endemic and exotic arboviruses.
The Special Bacterial Pathogens Reference Laboratory (SBPRL) houses a biosafety level 3 facility that deals with a variety of high-consequence bacterial pathogens and other zoonoses. The laboratory conducts specialised human diagnostics for anthrax, plague, botulism and leptospirosis, and also serves as a reference laboratory for other high-consequence pathogens such as Brucella, Francisella tularensis, and Burkholderia, and is the World Health Organization Regional Reference Laboratory for Plague in the SADC region. The SBPRL is also involved with a number of surveillance activities. The laboratory conducts plague surveillance in susceptible rodent populations in the City of Johannesburg and Nelson Mandela Metropolitan (Port of Coega, Eastern Cape Province) in order to alert public health authorities to any increased human plague risk. The laboratory is also involved with sero-surveillance studies for bacterial zoonoses (brucellosis, leptospirosis, Q fever and bartonellosis) in patients with undifferentiated fever, and brucellosis in high-risk populations (abattoir workers, (para) veterinary professionals, and farming communities).
The Parasitology Reference Laboratory (PRL) provides a specialised parasitology reference service for routine diagnostic medical laboratories. The laboratory offers specialised parasitological diagnostic and confirmatory tests. Certain important parasitic pathogens are targets of its surveillance, research and teaching activities. With the current drive towards malaria elimination in South Africa and its neighbours, the PRL focuses on improving malaria case management by raising the standard of malaria diagnosis, both in routine laboratories (microscopy) and at point-of-care (rapid diagnostic tests). Another way the PRL supports the national strategy for elimination, is through training, outreach and quality assessment of diagnostic laboratories. A regional malaria slide bank that provides training material and quality assessment for diagnostic laboratories has been established with international funding and is assisting southern African countries with their malaria elimination efforts. Research and development of new identification techniques for human parasites, particularly application of PCR and sequencing, include projects on opportunistic diseases such as Pneumocystis pneumonia, cryptosporidiosis, microsporidiosis, toxoplasmosis, and free-living amoeba infections, as well as improved identification of helminths. Other major areas of interest are soil-transmitted helminths and schistosomiasis (bilharzia), now that these are now designated notifiable medical conditions.
Malaria is the major vector-borne disease in Africa, killing close to one million people annually, most of them children under five years old. In South Africa, malaria transmission is confined to the low-lying north-eastern border regions of the country. The Vector Control Reference Laboratory (VCRL) focuses on those Anopheles mosquito species responsible for malaria transmission and houses a unique collection of live mosquito colonies of the four most important vector species in Africa namely; Anopheles gambiae, An. coluzzii, An. arabiensis and An. funestus, as well as the minor vector An. merus and the non-vector An. quadriannulatus. Insecticide susceptible and resistant strains of these species provide the VCRL with a unique resource for research into insecticide resistance. These resources and substantial in-house expertise place the VCRL in a unique position to provide operational support to the National and Provincial malaria control programmes, to offer collaborations with international institutions investigating similar problems and to play a role in influencing policy decisions on vector control strategies in the southern African region. In addition, the VCRL houses the largest museum collection of African arthropods of medical importance in Africa, the third-largest such collection in the world. The University of the Witwatersrand has recognised the high level of expertise in the VCRL and it now forms part of the Wits Research Institute for Malaria.
Although positioned within the CEZPD, the Electron Microscopy (EM) laboratory functions as a core facility for the NICD, also providing transmission electron microscopy services further afield. Diagnostically, EM provides rapid viral screening of clinical specimens and cultured isolates, and is crucial for microsporidial identification. As an applied technique for researchers, EM is used for the phenotypic characterisation of viral constructs and diverse pathogens (viral, bacterial, parasitic and fungal), ultrastructural details of pathogenesis, microbiocide descriptions/applications, and morphological investigations into the vectors of communicable diseases.
Distinguishing between imported and locally-acquired malaria cases in South Africa
The accurate classification of malaria cases as either locally-acquired or imported is essential for the selection of the appropriate elimination strategies. In South Africa, malaria cases are currently classified based solely on travel histories obtained from malaria patients or their close family members. Unfortunately, these travel histories are often incomplete and inaccurate, and even when complete histories are available, they frequently do not allow for accurate identification of the source of infection. This lack of accurate information on the source of malaria infections is preventing the implementation of appropriate interventions to halt residual transmission, impeding South Africa’s progress towards malaria elimination.
Recent advances in sequencing technology now enable the integration of molecular characterization into routine malaria surveillance activities to provide critical intelligence on case classification and guide intervention implementation. With funding the Bill and Melinda Gates Foundations and in collaboration with Africa CDC, the Elimination Eight and University of California-San Francisco, ARMMOR is investigating the impact of establishing a genomic surveillance platform for accurate classification of malaria cases in eliminating districts of South Africa.
Biosurveillance for bat and rodent-borne zoonoses
In an effort to understand infection dynamics in rodents and bats, a research program was established to investigate emerging zoonotic viral diseases of possible public health significance. This research programme, in collaboration with the Biosurveillance and Ecology of Emerging Zoonoses research group (Leadership of Prof. W. Markotter) at the Centre for Viral Zoonoses and the University of Pretoria, is focused on development of diagnostic capacity, epidemiology, pathology, pathogenesis and ecology of zoonotic pathogens in humans and animals. Interdisciplinary research projects with a One-Health approach aim to identify intervention strategies for effective disease control and prevention.
Development of rabies diagnostic assays for low resource settings
Rabies is a fatal and neglected disease mostly affecting children in the developing world. To assess the true burden of disease, routine and accurate diagnosis of rabies is required, this however, has been shown to be a major limitation in developing countries that are plagued by limited diagnostic capability that leads to poor surveillance, underreporting and misdiagnosis. Since diagnostic tests in the developing world will be reliant on resource availability and simplicity there is a strong focus on point-of-care tests. This project is focused on the development of isothermal amplification assays with detection using lateral flow devices in collaboration with the Biosurveillance and Ecology of Emerging Zoonoses research group (Leadership of Prof. W. Markotter) at the Centre for Viral Zoonoses and the University of Pretoria. These assays will allow for adaptation and implementation in low resource settings for rabies diagnosis.
Improving laboratory diagnosis of viral haemorrhagic fevers in Africa
Several viral haemorrhagic fevers (VHF) are endemic to the South Africa (for example Congo Crimean Haemorrhagic Fever; CCHF) and to the African continent, including Ebola virus disease (EVD) and Lassa fever (LF). Laboratory diagnosis of these diseases is complex and the differential diagnosis is broad ranging. Part of the mandate of the Special Viral Pathogens Laboratory, is to improve the diagnostic capacity for VHF’s locally and on the continent. Laboratory diagnosis have migrated from classical virological investigations to nucleic acid detection methods. Confines to diagnosis of VHF’s, include the need to perform investigations rapidly & the need for immunological investigations to monitor immunological responses to infection & for surveillance investigations. The development & validation of immunoreagents is more complex than molecular assays, thus the lag in availability. A further challenge for making immunoreagents is that most VHF causing viruses are classed risk group 4 pathogens, requiring maximum containment facilities when handling.
Ongoing projects at the SVPL include the NRF Thuthuka funded project on the “development of immunoreagents & assays for the investigation of the viral haemorrhagic fevers, Lassa fever & Ebola virus disease”. The scope of this project covers the development of a recombinant antigen based enzyme linked immunosorbent assay (ELISA) & Point of Care (POC) rapid test for LF & EVD, respectively. The project is focused on using recombinant proteins, which can be safely & conveniently produced under biosafety level 2 conditions, as immunoreagents. The unit is also running a Poliomyelitis Research Foundation (PRF) funded project that is evaluating the utility of a metagenomics approach to the pathogen identification, using the MinION sequencing device. The MinION could be a useful tool help prompt identification of the infectious agent and be used for differential diagnosis of VHF’s in clinical samples. Both these projects build on our capacity to diagnosis VHF’s using newer molecular and serological technologies.
Investigating the natural ecology, epidemiology and socio-economic impact of Rift Valley fever in South Africa
Expanding on the 5-year Understanding Rift Valley Fever in the Republic of South Africa project (2014-2019), Reducing the Threat of Rift Valley Fever (RVF) through Ecology, Epidemiology, and Socio-Economics (2019-2024) is an ongoing project coordinated by the National Institute for Communicable Diseases, the University of Pretoria and EcoHealth Alliance to investigate the impacts of RVF virus (RVFV) and improve the capacity to predict local outbreaks. The project will look at the socio-economic consequences of RVF on individuals and on national levels, and will combine its prior findings with satellite-collected meteorological data to create an early warning system. The initiative encompasses a 40,000-square-kilometer area in the Free State and Northern Cape provinces of South Africa, including the areas severely afflicted by the RVF outbreak in 2010-2011.
In the Free State, the research is continuing key long-term studies on i) the RVFV infection rate in sheep between outbreaks, ii) how long antibodies last in sheep following Smithburn vaccine vaccination, and iii) seasonal dynamics in mosquito populations. Since 2019, the project has also been doing research in a 1,000-square-kilometer area of northern KwaZulu-Natal (KZN), where only a few small RVF outbreaks had previously been identified but there has been recent evidence of infections in domestic ruminants and people. In 2022, household surveys and mosquito sampling will begin.
Surveillance for arboviruses in South African populations
Arboviral infections are becoming increasingly important public health threats. Rising global temperature is altering rainfall patterns worldwide, changing the conditions under which disease carrying mosquitoes flourish and these carriers move into regions where they previously could not survive. Syndromic sentinel surveillance sites in public health facilities for mosquito-borne viruses were established in 2018-2019 in the uMkhanyakude Health District, KwaZulu-Natal, South Africa in collaboration with international partners. This area was selected because of the presence of mosquito vectors competent in transmitting arboviral infections, adequate human populations to sustain transmission and cross-border migration with neighbouring countries (e.g., Mozambique and eSwatini). A Rift Valley fever virus (RVFV) serosurvey confirmed recent exposure and indicated endemic circulation of RVFV in humans residing in this area. The study indicated that RVFV infections in northern KwaZulu-Natal could be misdiagnosed or underreported, highlighting the urgent need for improved diagnostic testing and awareness of RVF and other arbovirus diseases in this part of South Africa. Using these surveillance samples for arbovirus seroprevalence studies (including but not limited to Zika virus, dengue virus, chikungunya virus, West Nile virus, Rift Valley fever virus and Usutu virus), will give a better understanding on which arboviruses are circulating in these surveillance sites. The data will guide us to set up a larger surveillance system to determine the disease burden of arboviruses and whether to implement diagnostic testing for specific arboviruses in the Arbovirus Reference Laboratory.
Identifying the entomological drivers of malaria transmission in South Africa
Malaria incidence in South Africa is currently low owing to well-coordinated provincial malaria control programs. Malaria transmission however persists despite the implementation of control interventions. This is due to the continuous importation of Plasmodium parasites and the perennial presence of several major and secondary mosquito vector species in endemic areas. Tackling residual transmission therefore requires additional vector control strategies while maintaining the effectiveness of the core intervention – indoor residual spraying (IRS) using specially formulated insecticides. Selection of any additional vector control methods should be evidence based, which means it is necessary to obtain information on key indicators, especially for the lesser-known vector species. These indicators include their feeding, resting and breeding characteristics, and their insecticide susceptibilities. The aim of this project is therefore to collect essential malaria vector surveillance and control indicators for all vector species in South Africa, and to obtain critical information on the transmission dynamics of residual malaria in low-incidence settings where cases are sporadic.
Sterile Insect Technique feasibility study
Malaria transmission in South Africa is limited to the low-altitude border regions in the Limpopo, Mpumalanga and Kwazulu-Natal provinces. Despite a concerted effort to eliminate malaria in these provinces, local transmission has remained relatively steady over the past decade. The failure to eliminate malaria transmission in South Africa has necessitated a reflection on current malaria control strategies, especially vector control interventions. It has become apparent that IRS as a standalone vector control tool, though sufficient for effective control, is unlikely to achieve malaria elimination without supplementation. There is therefore a need to look for additional vector control strategies. The main objective of this study is to assess and establish proof of concept for using the Sterile Insect Technique (SIT) as a vector control strategy. The long-term goal of the SIT project is to establish an industrial-scale mass rearing facility capable of producing and sterilizing sufficient numbers of sterile male mosquitoes to support a larger area-wide field programme in malaria affected areas in the country and region.
Serotonergic pathway effect on Anopheles species
Understanding important behavioral characteristics and their underlying physiological processes in Anopheles malaria vector species is a necessary step toward targeted control methods. The neurotransmitter serotonin and/or the serotonergic pathways influence physiological and behavioral processes in several insect species, including heart rate contraction, metabolism, eclosion, locomotion, aggression, learning and memory, appetite, food seeking behavior, flight behavior, blood feeding, odorant attraction and reproduction. It has been demonstrated in some Anopheles species that the D7 proteins, which are salivary molecules, act as serotonin receptors, with five of the D7 receptors binding with strong affinity to serotonin. The D7 receptors are part of the odorant binding protein family that are expressed in Anopheles species. Given the fact that the serotonergic pathway plays an important role in insect physiology and behavior and that the D7 proteins in Anopheles gambiae bind to serotonin, we consider it useful to study the role of the serotonergic pathway in Anopheles vector species as a possible target for an additional vector control tool.
Mosquito infection studies
In collaboration with the WITS Research Institute for Malaria at the University of the Witwatersrand, we are now able to infect Anopheles mosquitoes with Plasmodium malaria parasites. This system is a unique resource in South Africa for novel studies on host-parasite interactions, paving the way for collaborations with other stakeholders on malaria transmission-blocking technologies. Using this system, we can also investigate those bionomics influencing the susceptibility of mosquitoes to malaria infection.
LEADERSHIP AND TEAM
Acting Centre HEAD: Dr Jacqueline Weyer
Dr Jacqueline Weyer is a Principal Medical Scientist at the Centre for Emerging and Zoonotic Diseases at the National Institute for Communicable Diseases.
Here she leads a team of scientists tasked with the laboratory investigation (diagnostics and research) of human rabies, viral heamorrhagic fevers and other emerging zoonotic disease of concern to the health of the South African public.
Weyers completed her PhD in Microbiology at the University of Pretoria and was employed as a Research Fellow with the Rabies Unit of the Centers for Disease Control and Prevention in Atlanta Georgia from 2004 to 2005. In 2006 she was awarded the L’Oreal-UNESCO, Department of Science and Technology Woman in Science Award: PhD Fellowship for Life Sciences. And in 2018 she was awarded the degree Master of Public Health, cum laude from the Sefako Makgatho Health Sciences University in South Africa.
In the past 10-years, Weyers has authored and co-authored more than 40 scientific papers in peer-reviewed journals, and seven chapters in books, and achieved a National Research Foundation C2 rating in 2017. Jacqueline has been appointed as Extraordinary Lecturer at the University of Pretoria and has been involved in supervision of 14 BSc Hons or MSc research studies, one MPH and four PhD students.
In 2020, she was appointed as Lecturer in the School of Pathology at the University of the Witwatersrand. She serves on several national committees and working groups pertaining to laboratory biosafety and biosecurity, rabies and other zoonoses, One Health. Her interests include the laboratory diagnostics, epidemiology, pathogenesis and host interactions of rabies virus and other zoonotic viral pathogens that cause disease of public health importance in South Africa.