These guidelines describe the clinical management of cases of COVID-19 disease, including clinical care in and outside of health facilities, and are intended for use in both public had private sectors. The guidelines are developed by the Clinical Guidelines Subcommittee of the National Department of Health’s Incident Management Team. They are informed by rapid medicine reviews conducted by the National Essential Medicines List Committee’s Subcommittee on COVID-19, as well as advisories provided by the Ministerial Advisory Committee on COVID-19. 

The guidelines are presented as modules in order to facilitate and expedite updating of individual sections in future.

The National Department of Health is committed to providing regular updates for guidelines, as knowledge regarding strategies to address COVID-19 develop both globally and in South Africa.

  1. Guidance on the use of antigen self-tests
  2. Update on testing eligibility
  3. Revision of guidance on reporting of results

Version 5 (Aug 2020)

Epidemiology and clinical characteristics

  • The mean incubation period for COVID-19 is 4-5 days. Patients may be infectious for 2-3 days prior to the onset of symptoms. 
  • The strongest risk factor for severe disease is advanced age. Other risk factors include cardiopulmonary comorbidities, obesity, HIV, and diabetes mellitus.
  • The spectrum of COVID-19 clinical presentations include asymptomatic infection, a respiratory tract infection that may range from mild to severe, and atypical manifestations such as diarrhoea, skin manifestations, hyperglycaemic syndromes and large vessel strokes.


  • PCR-based tests are recommended for the diagnosis of acute COVID-19 infection. Upper respiratory tract samples should be sent on all patients. Sputum or (if the patient is intubated) bronchoalveolar lavage samples should be sent when available.
  • Due to very poor sensitivity within the first 1-2 after symptom onset, serology is not recommended for the diagnosis of acute COVID-19 infection.

Management of the patient with asymptomatic or mild disease

  • Patients who are asymptomatic or who meet criteria for mild disease can be managed at home provide they can safely self-isolate.
  • Patients who self-isolate at home should be given strict advice on how to reduce possible transmission to others.
  • Paracetamol is recommended for symptomatic treatment of patients with fever or pain in preference to nonsteroidal anti-inflammatory drugs (NSAIDs).

Respiratory support for hospitalised COVID-19 patients

  • Supplemental oxygen remains the mainstay of therapy for most hospitalised patients. Target SpO2 ≥90% in non-pregnant adults, titrating to reach targets by means of a nasal cannula, simple face mask or face mask with reservoir bag.
  • The use of the prone position in non-intubated, conscious patients who are hypoxaemic may be beneficial.
  • Patients who have respiratory failure despite maximal facemask oxygen should be promptly identified and evaluated for possible escalation of respiratory support. Possible modalities include high flow nasal cannula oxygen, continuous positive airway pressure, or intubation and mechanical ventilation.

Drug Therapy

  • Dexamethasone is recommended for patients requiring supplemental oxygen or mechanical ventilation.
  • Heparin venous thromboembolism prophylaxis is recommended for all hospitalised patients. Therapeutic dosing is suggested for patients requiring ≥60% supplemental oxygen, or those with a D-dimer >6 times the upper limit of normal.
  • Due to remdesivir’s high cost and marginal benefit, routine use of the drug in hospitalised patients with COVID-19 is not recommended in the public sector outside of clinical trials.

Palliative Care of patients with COVID-19

  • Palliative care of COVID-19 patients includes the alleviation of symptoms that are causing distress, and the promotion of a dignified death.
  • The most common physical symptoms requiring palliation include breathlessness, anxiety, increased secretions, cough and fever. These can be at least partly alleviated via the judicious use of symptomatic treatment.

De-isolation and return to work

  • Symptomatic patients with mild disease (not requiring hospitalisation for COVID-19) can be de-isolated 10 days after the onset of their symptoms, provided their fever has resolved and their other symptoms are improving.
  • Hospitalised patients with moderate-severe disease (who require hospitalisation due to COVID-19) can be de-isolated 10 days after achievement of clinical stability (i.e. from when they are not requiring supplemental oxygen and are otherwise clinically stable).
  • Asymptomatic patients can be de-isolated 10 days after their test.
  • Repeat PCR testing is NOT required in order to de-isolate a patient and is not recommended.

Infection prevention and control (IPC)

  • Appropriate personal protective equipment when in close contact with COVID-19 cases includes standard, droplet and contact precautions.
  • Aerosol-generating procedures require aerosol precautions to be taken, including the use of an N95 respirator or equivalent.

*Please note*
The interim guidelines are based on what is currently known about the Coronavirus Disease 2019 (COVID-19). The National Institute for Communicable Diseases will update these interim guidelines as needed and as additional information becomes available.