Special Pathogens Unit (SPU)

Overview

The Special Pathogens Unit of the National Institute for Communicable Diseases of the National Health Laboratory Service (SPU, NICD-NHLS) is tasked with the laboratory confirmation and investigation of diseases caused by biohazard class 3 and 4 viral agents. These include, amongst others, the viral haemorrhagic fevers (VHF) caused by Crimean-Congo haemorrhagic fever (CCHF); Marburg; Ebola; Lassa fever; Rift Valley fever (RVF) and the

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Staff

Diagnostic Services

Publications

hantaviruses. In addition the Unit is also responsible for the laboratory investigation and confirmation of arboviral disease. Arboviral diseases of public health importance include West Nile fever (WN); dengue fever (DEN); yellow fever (YF), Sindbis (SIN) and Chikungunya (CHIK). Furthermore the Unit is the only laboratory for human rabies testing in South Africa. The Unit operates high (biosafety level 3) and one of the only maximum (biosafety level 4) biocontainment facilities on the African continent. The Arbovirus Laboratory has been accredited by the South African National Accreditation System (SANAS) under ISO 15189 since 2000 (M0029B).

SPU participates and drives several projects that are aimed at the enhancement of regional capacity for outbreak response and diagnosis of VHF. Research interests of the Unit includes development and improvement of diagnostic tools for; the molecular epidemiology of; and the pathogenesis and molecular biology of viruses that cause VHF, arboviral disease; rabies and other emerging zoonoses. The Unit is also actively involved in training of international scientists and others on the topic of diagnosis of VHF and arboviral disease and also contributes to the training of several post-graduate students in the field.

History of the Unit

The Poliomyelitis Research Foundation (PRF) in Johannesburg, which was the main centre for medical virology in South Africa, was consulted by scientists abroad when Marburg disease first appeared in Europe in 1967 in association with monkeys imported from Africa, and again in 1969 when the rodent-borne Lassa fever first appeared as a fatal disease of missionary nurses in West Africa. In 1975, two young Australian tourists became sick in South Africa with what proved to be Marburg haemorrhagic fever after they had been hitchhiking in Zimbabwe, and a nurse became infected while attending the patients in Johannesburg. The sudden emergence of these dangerous new viruses in Africa prompted the development of maximum biocontainment laboratories, and health authorities in South Africa felt the need to construct such a laboratory in the country.

In April 1976, the laboratories of the PRF were transferred to the State Department of Health and reconstituted as the National Institute for Virology (NIV), with Professor OW Prozesky being appointed as the first Director of the new Institute. Professor Prozesky, the Secretary for Health, Mr J de Beer, an architect from the Department of Public Works, Mr CF Beyers, and a consultant engineer, Mr AP Thompson, undertook a tour of microbiological institutes abroad, and on the basis of the information they gathered a biosafety level 4 (BSL4) laboratory was planned and built at NIV. Construction was completed in 1979, and in January 1980 Dr R Swanepoel from Zimbabwe was appointed as the head of a new Special Pathogens Unit to operate the BSL4 laboratory for the purpose of providing a diagnostic and investigatory service for viral haemorrhagic fevers in southern Africa. Within months, a Department of Health Medical Ecology Unit, responsible for monitoring plague activity in rodents, was incorporated into the SPU. In 1981, the Arbovirus Unit at NIV was made part of the SPU, and in 1983 responsibility for the diagnosis and investigation of rabies was allocated to the Unit.

In its second month of operation, in February 1980, the SPU became involved in the investigation of an outbreak of Marburg haemorrhagic fever in Kenya in association with the Special Pathogens Branch of the Centers for Disease Control in Atlanta, USA, leading to lasting cooperation between the two laboratories. In 1981, the first case of Crimean-Congo haemorrhagic fever (CCHF) was recognized in South Africa, and for the next decade work on this disease dominated the research programme of the SPU.

By the end of 2003, the SPU had investigated 4 570 blood and other samples from 2 788 suspected cases of viral hemorrhagic fever in South Africa and its immediate neighbours, plus a further 4 687 specimens from 3 091 patients from 22 countries in the rest of Africa, and 10 countries in Asia and Europe. Important diseases diagnosed included Marburg haemorrhagic fever, Ebola haemorrhagic fever, CCHF, Lassa fever, Rift Valley fever, yellow fever, dengue, West Nile fever, chikungunya and o’nyongnyong. However, the majority of the suspected cases of haemorrhagic fever proved to be more common vaccine-preventable or treatable diseases, and the number of patients investigated does not reflect the actual extent of the epidemics involved. In the most extreme example 4 600 people are estimated to have died in southern Sudan in 1999 from what the SPU diagnosed as louse-borne relapsing fever, which could readily be controlled through the use of an inexpensive antibiotic and insecticide. SPU staff has participated in many missions abroad, sometimes as members of international teams organized by the WHO to respond to epidemics, or to conduct ecological studies to determine the source of infectious agents in nature, such as Marburg and Ebola viruses. Many thousands of specimens from domestic and wild animals and insect vectors have been tested in the course of such investigations. Major missions included trips to the Democratic Republic of the Congo, Gabon, Sudan, Kenya, Somalia, Uganda, Sierra Leone, Guinea, Liberia, Afghanistan and Saudi Arabia.

Another busy time for the Unit was during the last 2 months of 1996, when a major outbreak of CCHF among workers at an ostrich abattoir caused the European Union to ban importation of all ostrich products from South Africa, thereby threatening the continued existence of a major industry. While still testing samples from hundreds of abattoir workers, the SPU had to study the nature of experimental CCHF infection in ostriches to provide information so that the Department of Veterinary Public Health could promulgate regulations designed to prevent the virus getting into ostrich products, thus making it possible for the ban to be lifted. Meantime, Ebola haemorrhagic fever was diagnosed in a nurse in Johannesburg, and a frantic search ensued to locate the source patient who proved to be a doctor from Gabon who had sought treatment for his illness in South Africa. This in turn led to a major exercise to identify and monitor health care workers and others who had been in contact with the 2 patients. Tragically, the nurse died but further spread of the infection was prevented.

SPU staff member working in the BSL 4 facility.

In 2003 the SPU became involved in performing diagnostic tests on suspected cases of severe acute respiratory syndrome (SARS), but fortunately the disease was not confirmed in southern Africa. Most recently the Unit has played an important role in investigating the occurrence of human infections with highly pathogenic avian influenza A H5N2 virus followed by an outbreak of the disease in ostrich population in the Eastern Cape in May 2004.

In 2008, the Unit was involved with the laboratory and field investigation of a local nosocomial outbreak of a previously unreported arenavirus haemorrhagic fever during September and October 2008. The index case was a female travel guide based in Lusaka, Zambia. She was evacuated for medical attention to a hospital in Johannesburg, South Africa after a 10 days of illness which was at the time clinically diagnosed as septicaemia, possibly typhoid. The patient passed away the day after being admitted to the Johannesburg hospital without a confirmed diagnosis. Three secondary cases involved a paramedic that was attending the index case during the medical evacuation, a nurse who cared of the index patient and a hospital cleaner who cleaned the ward. One tertiary case, and the only survivor of the outbreak, was a nurse that had contact with the paramedic. Once the epidemiological link between case 2 and the index case was realized, extensive differential laboratory testing for VHF was carried at SPU- NICD on specimens for cases 2, and also 3, but without any positive results. The first indication that an arenavirus was the etiological agent followed immunohistochemistry testing of liver biopsies by the CDC. These results were confirmed by PCR and virus isolation at SPU and the CDC. Subsequently all cases were confirmed by PCR and virus isolation. IgM seroconversion could only be shown in case 5. Specimens for the index case were not available locally and were forwarded from Zambia for retrospective testing to the CDC. In collaboration with the Colombia University and CDC the full genome sequencing study was undertaken which results confirmed that the outbreak was caused by a novel Old World arenavirus.

Contact us

Please direct any queries via one of the following:

Postal address: Private Bag X4, Sandringham 2131, South Africa

Physical address: 1 Modderfontein road, Sandringham 2192, South Africa

Queries	Telephone	Email
General	+27113866382
Laboratory	+27113866336 (Special Pathogens) +27113866391 (Arbovirus) +27113866376
Medical (outbreaks, VHF, rabies or arboviral disease)	+27828839920 (24 Hour NICD Hotline for clinical Advise) +27113866336

Staff

Head of Department
Prof JT Paweska (BVSc, DVSc, Doctor habilitatus)

Deputy
Dr J Weyer (PhD)
Medical Scientist

Consultant
Prof R Swanepoel (BVSc PhD DTVM MRCVS)

Departmental Secretariat
Mrs LJ Dos Santos

Special Pathogens Laboratory

Mrs PA Leman, PA (BSc Hons)
Medical Scientist / Laboratory Manager

Mrs AA Grobbelaar (MSc)
Medical Scientist

Mrs J Croft (Dip Med Lab Tech)
Medical Technologist

Mr T Taleng (Dip Med Lab Tech)
Medical Technologist

Mr CT Ndou (BSc)
Medical Technician

Mr NB Magome General worker)
Mrs SG Nkomo(General worker)

Arbovirus Laboratory

Mr A Kemp (MSc)
Medical Scientist / Laboratory Manager

Mr P Jansen van Vuren (MSc)
Medical Scientist

Miss CA Le Roux (BSc Hons)
Medical Scientist

Mr TE Chaane
Laboratory Assitant, Intern

Mr R Nkoana (General Worker)
Mr D Tigedi (General Worker)

Animal Unit

Mrs B Mogodi (Dip Animal Tech)
(Chief Animal Technologist)

Maseko, J (General Worker)
Seema, L (General Worker)

Sibiya, S (General Worker)
Mavhungu, MS (General Worker)

BSL-4 Engineering / Workshops

Mr Z Masuku (B Ing, LTS Consultant)
Mr R Mabilo (Artisan)
Mr P Mokoena (Assistant Artisan)

Diagnostic Services

The Special Pathogens Unit is the referral laboratory for laboratory confirmation of viral haemorrhagic fevers, arboviral disease and rabies (in humans). Serology and virus isolation of arboviruses are performed in compliance to ISO 15189:2003 (SANAS accreditation number: M00029B).
The following diagnostic tests are available:

Table 1: Diagnostic tests for viral haemorrhagic fevers and other biosafety level 2 and 4 pathogens

Pathogen	Specimen required	Test/s performed
Ebola virus Marburg virus Lassa virus Crimean Congo haemorrhagic fever virus Hantaviruses	Clotted blood / serum	ELISA, IgM Indirect immunofluorescence, IgG and IgM PCR Virus isolation
SARS coronavirus	Clotted blood Throat swabs Stool	PCR ELISA

Table 2: Diagnostic tests for arboviral disease

Pathogen	Specimen required	Test/s performed
Chikungunya virus Dengue virus Rift Valley fever virus Sindbis virus West Nile virus Yellow fever virus	Clotted blood (or serum) (Cerebrospinal fluid for encephalitic cases)	HAI ELISA, IgM Indirect immunofluoresence, IgG and IgM PCR Virus isolation

Table 3: Diagnostic tests for human rabies

Specimen	Test/s performed	Comments
Saliva (and Cerebrospinal fluid)	PCR Virus isolation	Only clinical patients Saliva preferred
Nuchal biopsy	PCR	Only clinical patients. Ante- or post mortem
Serum (or clotted blood)	Indirect immunofluorescence	In addition to saliva/cerebrospinal fluid for clinical patients For post vaccinal immunity determination
Brain	Direct immunofluorescence PCR Virus isolation	Post mortem testing Gold standard

Table 4: Diagnostic tests for rickettsia infection (Tick bite fever)

Pathogen	Specimen required	Test/s performed
Rickettsia conorri (Tick bite fever)	Whole blood (EDTA/purple cap)	PCR* Indirect immunofluorescence IgG and IgM
Other Rickettsia	Whole blood (EDTA/purple cap)	PCR*

* PCR has diminished sensitivity when patient has received antibiotic treatment

Publications

Recent publications by members of staff

Publications by members of SPU staff during 2009

Ahmed J, Bouloy M, Ergonul O, Fooks AR, Paweska J, Chevalier V, Drosten C, Moormann R, Tordo N, Vatansever Z, Calistri P, Estrada-Pena A, Mirazimi A, Unger H, Yin H, Seitzer U. International network for capacity building for the control of emerging viral vector-borne zoonotic diseases: ARBO-ZOONET. Eurosurveillance 2009; 14 (12): 1-4.

Anyangu AS, Gould LH, Sharif SK, Nguku PM, Omolo J, Mutonga D, Rao CY , Lederman E, Schnabel D, Sang R, Paweska JT, Katz M, Hightower A, Njenga MK, Feikin DR, Breiman RF. Risk factors for severe Rift Valley fever infection in Kenya, 2007. American Journal of Tropical Medicine and Hygiene, in press.

Briese T, Paweska JT, McMullan LK, Hutchison SK, Street C, Palacios G, Khristova ML, Weyer J, Swanepoel R, Egholm M, Nichol ST, Lipkin WI. Genetic detection and characterization of Lujo virus, a new hemorrhagic fever-associated arenavirus from southern Africa. PloS Pathogens 2009; 4 (5): e1000455, 1-8.

Burt FJ, Paweska JT, Ashkettle B, Swanepoel R. Genetic relationship among southern African Crimean-Congo haemorrhagic fever virus isolates and evidence for occurrence of reassortment. Epidemiology and Infection 2009; 23: 1-7.

Heise MT, Whitmore A, Thompson J, Grobbelaar AA, Paweska JT, Madrick K, White L, Swanepoel R, Burt FJ. An alphavirus replicon derived candidate vaccine against Rift Valley fever virus. Epidemiology and Infection 2009; 137: 1-10.

Jansen van Vuren P , Paweska JT. Laboratory safe detection of nucleocapsid protein of Rift Valley fever virus in human and animal specimens by a sandwich ELISA. Journal of Virological Methods 2009; 157: 15-24.

Le Roux CA , Kubo T, Grobbelaar AA, Jansen van Vuren P, Weyer J, Nel LH, Swanepoel R, Morita K, Paweska JT. Development and evaluation of a real-time reverse transcription-loop-mediated isothermal amplification assay for rapid detection of Rift Valley fever virus in clinical specimens. Journal of Clinical Microbiology 2009; 47:Njenga 645-651.

K M, Paweska J, Wanjala R, Rao CY, Weiner M, Omballa V, Luman ET, Mutonga D, Sharif A, Panning M, Drosten C, Feikin DR, Breiman RF. Using field quantitative real-time reverse transcription-PCR test to rapidly identify highly viremic Rift Valley fever cases. Journal of Clinical Microbiology 2009; 47: 1166-1171.

Paweska JT . Host gene expression triggered by West Nile virus infection. In: Yang, D (ed). RNA viruses: host gene response to infections. World Scientific Publishing Co Pte Ltd, ISBN 9789812833792, 2009, 391-413.

Paweska JT, Jansen van Vuren P, Kemp A, Swanepoel R, Buss P, Bengis RG, Gakuya F, Breiman RF, Njenga MK. A recombinant nucleocapsid-based indirect ELISA for serodiagnosis of Rift Valley fever in African wildlife. In; Proceedings of the FAO/IAEA International Symposium on Sustainable Improvement of Animal Production and Health, Vienna Aus

Paweskatria, June 8-11, 2009. JT , Sewlall NH, Ksiazek TG, Blumberg LH, Hale MJ, Lipkin IW, Weyer J, Nichol ST, Rollin PE, McMullan LK, Paddock CD, Briese T, Mnyaluza J, Dinh T-H, Mukonka V, Ching P, Duse A, Richards G, de Jong G, Cohen C, Ikalafeng B, Mugero C, Asamugha C, Malotle MM, Nteo DM, Misiani E, Swanepoel R, Zaki SR and Members of the Outbreak Control and Investigation Teams. Nosocomial outbreak of novel arenavirus infection, southern Africa, Emerging Infectious Diseases 2009; 15: 1598-1602.

Swanepoel R , Burt FJ. Bunyaviridae. In: Zuckerman A, Banatvala J, Griffiths P, Mortimer P, Schoub B, eds. Principles and Practice of Clinical Virology 6th Edition. Chichester: John Wiley and Sons, 2009. Swanepoel R , Paweska JT. Crimean-Congo haemorrhagic fever. In: Palmer SR, Soulsby EJL, Torgerson P, Brown D, eds. Zoonoses , Oxford: Oxford University Press (in press).

Swanepoel R , Paweska JT. Rift Valley fever. In: Palmer SR, Soulsby EJL, Torgerson P, Brown D, eds. Zoonoses , Oxford: Oxford University Press (in press).

Towner JS, Amman BR, Sealy TK, Reeder C, Comer JA, Kemp A, Swanepoel R, Paddock CD, Balinandi S, Khristova ML, Formenty PBH, Albarino CG, Miller DM, Reed ZD, Kayiwa JT, Mills JN, Cannon DL, Greer PW, Byaruhanga E, Farnon EC, Atimnedi P, Okware S, Katongole-Mbidde E, Downing R, Tappero JW, Zaki SR, Ksiazek TG, Nichol ST, Rollin PE. Isolation of genetically diverse Marburg viruses from Egyptian fruit bats. PLoS Pathogens 2009; e764

Venter GJ, Wright IM, Van Der Linde TC, Paweska JT. The oral susceptibility of South African field populations of Culicoides to African horse sickness virus. Medical and Veterinary Entomology 2009; 23: 367-378.

Venter M, Burt FJ, Blumberg L, Fickl H, Paweska J, Swanepoel R. Cytokine induction after laboratory acquired West Nile Virus infection . New England Journal of Medicine 2009; 360:1260-1262 .

Venter M, Human S, Zaayman D, Gerdes GH, Williams J, Steyl J, Leman PA, Paweska JT, Setzkorn H, Rous G, Murray S, Parker R, Donnellan C, Swanepoel R. Lineage 2 West Nile virus as a cause of fatal neurological disease in horses, South Africa. Emerging Infectious Diseases 2009; 15: 877-884.

Venter M , Steyl J, Human S, Weyer J, Zaayman D, Blumberg L, Leman P, Paweska J, Swanepoel R. Zoonotic transmission of West Nile virus during autopsy of a horse with neurological symptoms in South Africa. Emerging Infectious Diseases , in press. Weyer J , Rupprecht CE, Nel LH. Poxvirus-vectored vaccines for rabies – a review. Vaccine 2009; 27: 7198-7201

Wölfel R, Paweska JT, Petersen N, Grobbelaar AA, Leman PA, Hewson R, Georges-Courbot M-C, Papa A, Heiser V, Panning M, G ϋ nter S, Drosten C. Low-density macroarray for rapid detection and identification of Crimean-Congo hemorrhagic fever virus. Journal of Clinical Microbiology 2009; 47: 1025-1030.