South African VHF Guidelines

A suspected viral haemorrhagic fever (VHF) is one of the few events in clinical medicine that sets a defined national machinery in motion. The framework is the National Institute for Communicable Diseases (NICD) guideline, first issued in 1985 and revised in 2015, updated since by outbreak-specific NICD, provincial and laboratory documents from 2024 to 2026. Its purpose is practical: to help a clinician or pathologist recognise a possible case, protect staff and contacts, obtain a safe diagnosis, and trigger the public-health response, while keeping the patient alive. A recurring theme of the guideline is that the fatal nosocomial infections in South African hospitals occurred before isolation precautions were in place, so early recognition and containment are the heart of the pathway.

The 2015 guideline remains the backbone. The newer documents have changed the case-definition approach, the notification route, the name of the reference laboratory and the packaging terminology, and those changes are noted where they apply.

Running through the whole document is the principle of referral: a suspected case is not managed in isolation by the first facility to see it, but is drawn into a system of designated referral hospitals, a national reference laboratory and provincial public-health teams. The receiving facility that first suspects VHF isolates the patient and begins the pathway; whether that patient stays there or moves to a designated centre is a shared decision, taken on the assessed risk, and never made unilaterally.

Background to the viral haemorrhagic fevers

The guideline groups the VHF agents relevant to South Africa by their source, and the practical point of the grouping is that source predicts exposure and therefore who is at risk. Fuller virology and clinical detail for each agent sits in the other articles of this topic; what follows is the local epidemiological and clinical emphasis the guideline itself carries.

Group	Agents	South African relevance
Rodent-associated	Lassa, Lujo, hantaviruses	Lujo emerged locally in 2008; Lassa an importation risk; native African hantaviruses mild
Arthropod-borne	Crimean-Congo haemorrhagic fever, Rift Valley fever; chikungunya, yellow fever, dengue	CCHF and RVF endemic; the flaviviral and chikungunya agents mainly a returning-traveller concern
Bat-associated	Marburg, Ebola	Not endemic; importation and preparedness risk

Rodent-associated viruses

• Lassa fever is endemic to West Africa, not South Africa, and reaches the country only as an importation in travellers or evacuees; it spreads from person to person through body fluids, so an imported case carries nosocomial risk.
• Lujo virus is the region’s own arenavirus, known from a single 2008 nosocomial cluster that began in a patient airlifted from Zambia to Johannesburg and killed four of the five people infected; its reservoir was never identified.
• Hantaviruses are rodent-borne and cause haemorrhagic fever with renal syndrome in the Old World and a cardiopulmonary syndrome in the Americas; South Africa has native African hantaviruses that cause little human disease and does not harbour the severe New World agents.

Arthropod-borne viruses

Crimean-Congo haemorrhagic fever is the commonest indigenous VHF in southern Africa:

• fewer than 10 diagnosed cases a year, chiefly in the drier Northern Cape and Free State where its Hyalomma tick vector thrives;
• acquired from tick bites and from contact with the blood of infected livestock and ostriches at slaughter, so cases cluster in farming and abattoir communities;
• transmissible to hospital and laboratory staff through blood and body fluids, while the animal hosts themselves show only a brief silent viraemia.

Rift Valley fever is primarily a livestock disease that flares in years of heavy rain:

• its last major South African epidemic ran from 2008 to 2011;
• human infection follows mosquito bites and contact with infected animal tissue;
• it is mostly a self-limiting febrile illness with a severe haemorrhagic or encephalitic minority, and has no recorded human-to-human spread.

Chikungunya, yellow fever and dengue are grouped here as arboviruses that can occasionally cause haemorrhagic manifestations. In the South African setting they are chiefly a consideration in the returning traveller, with yellow fever also a vaccination and importation matter. Dengue is diagnosed by molecular testing or antigen detection in the first week of illness and by serology thereafter, remembering that dengue serology cross-reacts with the other flaviviruses, including West Nile, Zika and yellow fever.

Bat-associated viruses

Marburg and Ebola viruses are not endemic to South Africa but are a standing importation and preparedness concern. Both cause severe disease with high case fatality and spread between people through blood and body fluids, and the current driver of preparedness is the 2026 Bundibugyo virus outbreak in central Africa.

The South African record

The local experience is one of rare and mostly imported events, which is exactly why a low index of suspicion is dangerous.

• Marburg reached Johannesburg in 1975 in a traveller who had explored caves in the region, with two secondary cases in a companion and a nurse.
• Ebola was imported once, in 1996, from the Democratic Republic of the Congo.
• Lujo virus emerged in the 2008 Johannesburg cluster already described.
• Lassa fever has been confirmed twice, in 2007 and 2022, both in travellers from Nigeria and both without onward spread.
• The first imported hantavirus case was recognised in 2022.

Against this background of imported single cases, endemic Crimean-Congo haemorrhagic fever and the 2008 to 2011 Rift Valley fever epidemic stand out as the indigenous events.

Recognising and diagnosing a suspected case

Clinical recognition and case definitions

The 2015 guideline recognises a suspected case through a low, moderate and high risk classification of the patient, combining the clinical picture with the exposure history:

• a low-risk patient has a VHF-compatible febrile illness but no relevant exposure and no bleeding;
• a moderate-risk patient adds a rural or tropical exposure, or contact with animals, ticks or mosquitoes, or an indirect link to a VHF case;
• a high-risk patient is either severely ill with fever and haemorrhage, or has a definite VHF exposure, such as a health worker who falls ill within the incubation window of caring for a confirmed case.

The relevant exposure window is about two weeks for the arboviral agents such as Crimean-Congo haemorrhagic fever and three weeks for Lassa, Marburg and Ebola. This grading is still used in hospital to decide how intensively a patient is isolated and whether they are retained or transferred.

Current NICD practice supplements this with virus-specific suspected and probable case definitions, issued and revised for each outbreak. Their strength is that they keep the symptom criteria deliberately broad while pinning down the epidemiological link, a defined outbreak area and an exposure within the incubation window, and requiring that malaria be excluded. The 2026 Bundibugyo definition is a worked example: it asks for acute fever of 38 degrees Celsius or higher, or one of a list of common symptoms, together with travel to a named outbreak area and contact with a case in the previous 21 days, or else an unexplained malaria-negative multisystem illness. Because these definitions are virus- and outbreak-specific and change with each alert, the current NICD case definitions should be consulted directly rather than any single one being treated as fixed.

Differential diagnosis

Malaria is the priority exclusion and must be actively ruled out, since it is far more common in the same patients and the two can coexist. The guideline also lists typhoid, tick-bite fever, leptospirosis, bacterial septicaemia, viral hepatitis and the haematological malignancies among the conditions confused with VHF, and a blood smear, blood cultures taken before antibiotics, a full blood count and liver enzymes all help separate them. Specialised VHF testing is not an exposure screen and is not indicated for a well returning traveller without a compatible illness.

The routine clinical-pathology pattern helps weigh the possibilities, though none of it is specific:

• towards VHF: a low platelet count, a low or falling white cell count, raised aminotransferases and deranged clotting;
• towards another diagnosis: a positive malaria smear, a neutrophil leucocytosis pointing to bacterial sepsis, or the blast cells of an acute leukaemia.

The difficulty is that early VHF and severe malaria can look alike and can coexist, so an abnormal result never replaces the exposure history, and a plausible alternative diagnosis is pursued in parallel rather than instead.

Laboratory verification

Confirmation rests on tests that identify the virus directly, and the specimen handling is as important as the assay. The standard submission for a live patient is one clotted-blood tube and one EDTA tube, with the completed case investigation form; any specimens already sent to other laboratories before VHF was suspected must be traced and redirected, because they are both a hazard and an early diagnostic opportunity. Samples are kept cold and whole blood is not frozen. For a death in which VHF must be excluded, minimal specimens are taken under reference-laboratory and forensic guidance rather than a full autopsy. Crucially, the reference laboratory accepts a specimen only after prior consultation, through the hotline, with an NICD medical officer and the receiving laboratory, so a sample is never simply dispatched unannounced.

The packaging is the point most changed since 2015. Suspected VHF specimens are Category A infectious substances, triple-packaged to United Nations number UN2814 under International Air Transport Association packing instruction 620, a higher standard than the routine diagnostic category, and moved only by prior arrangement.

Feature	Suspected VHF specimen	Routine diagnostic specimen
Classification	Category A infectious substance	Category B
United Nations number	UN2814	UN3373
Packing instruction	IATA PI620	IATA PI650
Movement	Triple packaging, prior arrangement, dedicated courier	Standard triple packaging, routine transport

Confirmatory testing is done only by the NICD Special Viral Pathogens Laboratory, within the Centre for Emerging Zoonotic and Parasitic Diseases, which is the only biosafety level 4 laboratory in Africa and carries the former name Special Pathogens Unit in the 2015 guideline. Its menu is a fluorescent antibody test and enzyme-linked immunosorbent assay for antibody and real-time polymerase chain reaction for viral genome, with a GeneXpert cartridge assay for Zaire ebolavirus specifically. A pitfall carried over from the 2015 guideline is that an early specimen negative on antigen, genome and antibody can still grow virus in culture days later, so an early negative must be backed by a convalescent antibody sample before VHF is confidently excluded.

Immediate action after clinical diagnosis

The first steps run in parallel and should not wait for confirmation:

• isolate the patient and apply barrier precautions;
• inform hospital management and the infection control team;
• give any life-saving treatment and manage fever;
• telephone the 24-hour NICD hotline (0800 212 552) for a risk assessment, which is how the reference laboratory is engaged and testing arranged;
• notify the local and provincial Communicable Disease Control Coordinator.

Staff, ambulance, laboratory and cleaning contacts are listed at this point, and a senior clinician decides whether to retain the patient or transfer them to a designated referral hospital.

Management of VHF patients

Medical management

Treatment is largely supportive, but two specific measures have a place in the guideline.

• Ribavirin is used for Lassa fever and haemorrhagic fever with renal syndrome and is given for post-exposure prophylaxis of Crimean-Congo haemorrhagic fever in exposed staff, although more recent appraisal regards its therapeutic benefit in Lassa and Crimean-Congo haemorrhagic fever as unproven.
• Immune convalescent plasma has an established role in Argentine haemorrhagic fever when given early.

Beyond these, supportive care is the mainstay: careful attention to circulating volume and electrolytes, blood products, and organ support, with corticosteroids, non-steroidal anti-inflammatory drugs and aspirin avoided.

Clinical-pathology monitoring

The managing hospital’s own laboratory should be able to run the tests that exclude other diagnoses and monitor the patient: a full blood count, a malaria smear, blood cultures, coagulation studies, liver and renal function, electrolytes and a cross-match. The work is done by a small team of experienced staff, with any aerosol-generating step performed inside a biosafety cabinet and under enhanced protective equipment, and clinically essential tests are never withheld while VHF is being excluded. In Crimean-Congo haemorrhagic fever a set of early laboratory values, including a markedly low platelet count and high aminotransferases and prolonged clotting times in the first days, predicts a fatal outcome.

Isolation precautions

Effective isolation does not require sophisticated engineering. The minimum is an isolation room with an ante-room for putting on and taking off protective equipment, and South African experience across more than two hundred VHF patients has shown that standard isolation without negative-pressure ventilation is adequate.

The protective equipment is put on and taken off with a trained partner watching, and comprises:

• a gown or coverall and a plastic apron;
• an N95 respirator and eye protection;
• a double pair of gloves, and boot covers.

Powered respirators are reserved for high-hazard procedures such as intubation.

Disinfection and decontamination

Decontamination uses chlorine at two strengths: 0.5% (5,000 parts per million) for spills, body fluids, surfaces and used equipment, and 0.05% (500 parts per million) for skin and lightly soiled items, made up fresh each day, with a contact time of at least 30 minutes for spills.

Disposal of corpses

A body is washed with the stronger chlorine solution, its orifices sealed, and it is placed in double impervious bags and kept refrigerated until the diagnosis is settled, then cremated or buried under supervision. Under the National Health Act a post-mortem examination to establish the cause of death may be authorised by the practitioner in charge without relative consent.

Notification and control of outbreaks

Notification

VHF is now notified as a Category 1 Notifiable Medical Condition through the Notifiable Medical Conditions application, the change that most clearly supersedes the 2015 route of a telephone call within 24 hours and a paper form within five days. Notification through the app sits alongside the hotline call for a risk assessment and the telephonic alert to the local and provincial Communicable Disease Control Coordinator, so the reference laboratory and the public-health system are engaged together. The national department in turn notifies the World Health Organization where the International Health Regulations require it.

Transfer and importation of patients

The decision to move a patient is taken jointly by the referring clinician, the receiving centre and the reference laboratory, weighing the patient’s assessed risk against the hazard of transport:

• a low-risk patient may be moved without an ambulance, by ordinary transport with simple precautions;
• a moderate or high-risk patient is carried by a dedicated ambulance whose crew wear protective equipment, whose surfaces are protected, and which is decontaminated afterwards, with powered respirators available for any procedure en route.

Importation is a distinct scenario. A patient arriving by air who is recognised as a possible case is managed with Port Health at the airport, the aircraft, control tower and passenger manifest all part of the response so that fellow travellers can be traced. The same principle applies to arrivals by land or sea, where Port Health at the border post or harbour coordinates isolation and referral. In each case the point of entry acts as a control point, not merely a place of arrival.

The public-health response and contacts

Once a case is notified, the provincial Communicable Disease Control Coordinator leads the response, with immediate responsibilities to:

• confirm that the event meets the case definition;
• convene an outbreak-control team where needed;
• identify and trace contacts;
• secure isolation and laboratory capacity;
• keep the facility and the public informed.

Contacts are then placed under active observation, meaning each is seen by a named official rather than trusted to self-report. Temperature is recorded twice daily from the last contact, and the period depends on the agent: 21 days for the filoviruses, Lassa and Lujo, and 14 days for Crimean-Congo haemorrhagic fever, whose incubation is shorter, while Rift Valley fever needs no such observation. Any contact who develops a fever of 38 degrees Celsius or VHF symptoms is isolated and managed as a suspected case. An outbreak is declared over once twice the observation period has passed since the last exposure.

The coordinator also carries longer-term responsibilities once the acute event is contained: reviewing and auditing how the response was handled, feeding the lessons back into practice, sustaining the training of clinical, laboratory and ambulance staff, and strengthening surveillance so the next case is recognised sooner. Laboratory and clinical staff who suffer a needle-stick, splash or protective-equipment breach are logged and monitored the same way as contacts, with first aid, occupational-health review and incident recording.

Communication with the media

Public communication is part of outbreak control, not a distraction from it. A VHF alert attracts intense attention, and inaccurate or contradictory reporting can spread fear, deter contacts who fear stigma, and undermine the response. The guideline calls for a single designated spokesperson, coordinated with the NICD and the departmental communications office, giving accurate and timely information while protecting patient confidentiality. The aim is to inform the public and health workers honestly, correct rumour early, and leave the clinical and public-health teams free to work.

Facilities and the referral centre

A designated VHF referral centre is built around an adaptable isolation unit: an isolation room with an ante-room for putting on and removing protective equipment, ideally with separate clean and dirty routes, and an observation room for high-risk contacts. Around it the centre needs:

• a quarantine facility for contacts under active observation;
• a refrigerated mortuary for a body held pending diagnosis;
• an on-site laboratory able to run the essential monitoring tests under enhanced precautions;
• trained clinical, nursing, infection-control and laboratory staff, a senior clinician authorised to accept transfers, and a trained ambulance service with protective-equipment stocks.

South African experience is reassuring on one point in particular, that a unit of this kind does not need negative-pressure engineering to be safe, so an adaptable general facility can serve rather than a purpose-built high-containment ward. In the Western Cape the provincial pathway routes a suspected case to Tygerberg Hospital, through its infectious diseases specialist and the NICD hotline, with the provincial coordinator notified and the contact list forwarded.

What has changed since 2015

Much of the 2015 guideline stands: confirmatory testing at the national reference laboratory, supportive care as the mainstay, isolation until VHF is excluded, the clotted-and-EDTA specimen pair, the chlorine concentrations, the contact-observation periods and malaria as the priority differential. The substantive updates are the following.

2015 baseline	Current (2024 to 2026)
Notify as a category A disease (telephone within 24 hours, form GW17/5 within 5 days)	Category 1 Notifiable Medical Condition through the NMC application
Several reference-laboratory numbers, hotline 082 883 9920	Single 24-hour NICD hotline, 0800 212 552
Special Pathogens Unit	Special Viral Pathogens Laboratory, within the CEZD
Triple packaging described in principle, AW-series labels	Named Category A, UN2814, IATA PI620
Low, moderate and high patient screen as the front-line recognition	Retained in hospital, supplemented by virus- and outbreak-specific suspected and probable case definitions

References and recommended reading

• National Institute for Communicable Diseases. National Guidelines for Recognition and Management of Viral Haemorrhagic Fevers. NICD; 2015. The national baseline for case recognition, laboratory handling, isolation and outbreak response.
• National Institute for Communicable Diseases, Special Viral Pathogens Laboratory. Guidelines for the Specialized Laboratory Investigation of Suspected Ebola Virus Disease in South Africa. NICD; updated 30 September 2024. The current reference for notification, specimen submission, Category A packaging and the test menu.
• National Institute for Communicable Diseases. Bundibugyo Virus Disease Preparedness: an update for physicians, emergency practitioners and laboratorians. NICD; updated May 2026. The current suspected-case definition and response steps.
• National Institute for Communicable Diseases. Viral Haemorrhagic Fevers: Frequently Asked Questions. NICD; updated October 2023. The consolidated South African orientation source for the local outbreak record, endemic-disease burden and the specimen-consultation rule.
• Western Cape Department of Health. Procedure for Suspected Ebola Virus Disease in the Western Cape Province. The provincial referral pathway to Tygerberg Hospital.