COVID-19 Doctors Resources

The World Health Organisation (WHO) was informed about a cluster of pneumonia cases of unknown aetiology in Wuhan City, Hubei Province, China on 31 December 2019. On the 7th of January 2020, a Novel Coronavirus (2019-nCoV) was identified as the causative virus by the Chinese authorities.

The Novel Coronavirus is formally named SARS-CoV-2. The disease caused by the virus is now referred to as COVID-19.

What is the Case Definition/Criteria for Person Under Investigation (PUI)?

A “Person Under Investigation (PUI)” defines a person who may be infected and should be tested. The PUI was updated on 2 April 2020 and now includes any symptomatic patient regardless of travel history or history of close contact with a known or suspected COVID-19 patient.

Current PUI: Persons with acute respiratory illness with a sudden onset of symptoms such as cough, sore throat, shortness of breath or fever [≥ 38°C (measured) or history of fever (subjective)] irrespective of admission status.

The following persons are at highest risk for COVID-19 disease and testing should be prioritised for them:

Persons at a highest risk are those who have an acute respiratory illness and who, in the 14 days prior to onset of symptoms, met at least one of the following epidemiological criteria:

  • Were in close contact1 with a confirmed2 or probable3 case of SARS-CoV-2 infection;


  • Had a history of travel to areas with local transmission of SARS-CoV-2; (NB Affected countries will change with time, consult NICD website for current updates);


  • Worked in, or attended a health care facility where patients with SARS-CoV-2 infections were

    being treated


  • Admitted with severe pneumonia of unknown aetiology or ARDS

1Close contact:

  • A person having had face-to-face contact (≤1 metre) or in a closed space with a COVID-19 case for at least 15 minutes. This includes, amongst others, all persons living in the same household as a COVID-19 case and, people working closely in the same environment as a case.
  • A healthcare worker or other person providing direct care for a COVID-19 case, while not wearing recommended personal protective equipment or PPE (e.g., gowns, gloves, NIOSH-certified disposable N95 respirator, eye protection).
  • A contact in an aircraft sitting within two seats (in any direction) of the case, travel companions or persons providing care, and crew members serving in the section of the aircraft where the case was seated.

2Confirmed case:

  • A person with laboratory confirmation of SARS-CoV-2 infection (using an RT-PCR assay), irrespective of clinical signs and symptoms.
  • Symptomatic cases are considered infectious from 2 days before symptom onset to 14 days after symptom onset.

3Probable case:

  • A PUI for whom testing for SARS-CoV-2 is inconclusive (the result of the test reported by the laboratory) or who tested positive on a pan-coronavirus assay.

Working in a health care facility includes healthcare workers as well as administrative and support staff such as cleaning staff

Please visit the NICD website for the latest case definition

How do patients present and what is the differential diagnosis?

The main clinical signs and symptoms are fever and cough with a few patients presenting with difficulty in breathing and bilateral infiltrates on chest X-rays. Lymphopenia may be present. The differential diagnosis for this syndrome is broad. Consider the possibility of influenza (influenza season in SA typically begins towards the end of May), bacterial pneumonia, tuberculosis and Pneumocystis jirovecii (PCP) if immunosuppressed.

Who should be tested for SARS-CoV-2/COVID-19?

COVID-19 is a category 1 notifiable medical condition that poses a significant public health risk thus private clinicians and laboratories are requested follow the guidelines issues by the NICD and the DOH. Only patients who meet the current NICD case definition and who have been assessed by a clinician (in person or telephonically) will be tested at Ampath. No asymptomatic patients should be tested. The criteria required for a patient to be classified as a “Person under Investigation; PUI” and qualify for testing are listed above.

Note: You do not need permission from the NICD to test for COVID-19. You can refer testing directly to Ampath for patients who meet the case definition. Laboratories are requested to follow the guidelines issued.

Where can I get a Contact Tracing form

Please note that the DOH and NICD no longer require a PUI form to be completed as from 1st May 2020.

This form need be completed to ensure appropriate testing and contact tracing of COVID-19 positive patients. Ampath is not able to process any COVID-19 test request without this completed form.

Click here to download this form.

Why do laboratories not test asymptomatic persons?

The current testing guidelines are developed by the National Institute for Communicable Diseases (NICD), and the South African Department of Health, in alignment with the World Health Organization protocols.

  • A negative laboratory test does not mean that a person is uninfected.
  • A negative laboratory test does not shorten the 14 day quarantine/isolation period. Patients who are asymptomatic and test negative are likely to interpret this as being COVID-free and not self-quarantine. They may go back to work, go to the mall and travel while having an early infection and spread the virus to any close contacts.
  • There is a shortage of laboratory tests in South Africa. All affected countries are trying to access laboratory testing kits and test kits are in short supply. We need to reserve our valuable lab testing resources for those who are sick and in whom the test will have the greater value for the sake of protecting all South Africans.

What safety measures should I implement in my consulting rooms?

In order to contain further transmission of the virus, additional safety measures are needed from clinicians when consulting with patients with suspected COVID-19 infection:

  • Ideally implement a screening process in order to avoid an infectious patient entering your rooms and exposing other patients and staff to the pathogen.
  • Ensure that you have sufficient PPE in your rooms to protect yourself during the consultation.
  • Please refer to the following link for the NICD’s “COVID-19 Quick Reference for Health Workers” for guidance for the necessary guidelines.
  • Ensure that the patient dons a surgical mask prior to entry to protect other people in your consulting area. Ensure that the patient uses a hand sanitiser before entering your rooms.

What should I do if a patient tests COVID-19 positive?

Ampath will inform you of any PCR positive patients and will electronically send the PUI and contact tracing form to the NICD and DOH along with the Ampath laboratory result. COVID-19 is a category 1 Notifiable Medical Condition and thus all Doctors are legally required to notify the DOH of any positive patients in their care.

The DOH is responsible for ensuring patient isolation and contact tracing.

Please provide the following advice to PCR positive patients:

Outpatients with mild to moderate disease should be instructed to self-isolate at home for 14 days and be given appropriate advice about reducing possible transmission to others:

  • Patients should stay in a specific room and use their own bathroom (if possible). Patients should avoid unnecessary travel and unnecessary contact with other people.
  • Where contact is unavoidable, the patient should wear a facemask, and maintain a distance of at least 1 metre (preferably 2 metres) from other people
  • Patients should clean their hands with soap and water frequently. Alcohol-based sanitizers may also be used, provided they contain at least 70% alcohol.
  • Patients should practice good cough and sneeze hygiene, by using a tissue, and then immediately discarding the tissue in a lined trash can, followed by washing hands immediately.
  • Patients should not have visitors in their home. Only those who live in their home should be allowed to stay.
  • At home, the patient should stay in a specific room and use his/her own bathroom (if possible). If they live in shared accommodation (university halls of residence or similar) with a communal kitchen, bathroom(s) and living area, they should stay in their room with the door closed, only coming out when necessary, wearing a facemask if they do so.
  • Patients should avoid sharing household items like dishes, cups, eating utensils and towels. After using any of these, the items should be thoroughly washed with soap and hot water.
  • All high-touch surfaces like table tops, counters, toilets, phones, computers, etc. should be appropriately and frequently cleaned. If patients need to wash laundry at home before the results are available, then they should wash all laundry at the highest temperature compatible for the fabric using laundry detergent. This should be above 60° C. If possible, they should tumble dry and iron using the highest setting compatible with the fabric. Disposable gloves and a plastic apron should be used when handling soiled materials if possible and all surfaces and the area around the washing machine should be cleaned. Laundry should not be taken to a laundrette. The patient should wash his/her hands thoroughly with soap and water after handling dirty laundry (remove gloves first if used).
  • Patients should know who to call if they develop any worsening symptoms, so that they can be safely reassessed.

Please view the latest COVID-19 Clinical Management Guidelines

Where can I refer an out-patient for COVID-19 testing?

Ampath has identified a number of Ampath sites country-wide as designated COVID-19 collection centres. Some of these are “drive-through” type of collection facilities and some are temporary sites. The purpose of these is provide patients with testing facilities outside of our healthcare environments to minimise the risk of spreading the infection to other patients. Please do not send patients to any laboratory located in a hospital.

Click here to view Ampath’s designated COVID-19 collection centres.

How long will the test take and what is the cost?

The COVID-19 test is an RT-PCR (reverse transcriptase PCR) test and will take up to 24 hours before you receive a result. You will receive your results immediately on completion via our Ampath Doctors Results App if you are registered. To register please go to: Lab Results

There is a single exit price in place for all patients of R850.00 incl. VAT. Medical schemes are reimbursing and will be billed at the negotiated scheme rate.

Should I be using rapid antibody or antigen COVID-19 tests in my rooms?

No, there is insufficient evidence and experience with these rapid tests at this point in time. As such, Ampath does not currently recommend the use of rapid point-of-care serology tests for the diagnosis of COVID-19. This position may change once the performance of these tests have been evaluated and we have guidelines in place to direct the appropriate use of these tests.

Click here to refer to the following National Pathology Group statement regarding COVID-19 rapid tests.

What specimen should be collected for COVID-19 PCR?

For out-patients, a nasopharyngeal and / or an oropharyngeal swab is required for COVID-19 PCR testing. Please refer out-patients to a designated COVID-19 testing centre rather than collecting specimens in your rooms to limit exposure to you and your patients. A lower respiratory tract specimen is preferable for hospitalised patients as upper respiratory tract specimens in these patients can give false negative results.

What does a negative COVID PCR result mean?

A negative PCR result does not does not always rule out a SARS-CoV-2 infection. A false negative result can be seen with early infections or if the specimen was not correctly collected. In patients admitted with a LRTI, throat swabs may be PCR negative and you should repeat the test on a specimen such as a tracheal aspirate or BAL.

What is the clinical management of suspected or confirmed COVID-19 disease?

Please refer to the NICD’s “Clinical management of suspected or confirmed COVID-19 disease” guideline. This can be accessed at: Clinical Management of COVID-19 disease

There are a number of experimental drugs that have been shown to be of possible benefit for the treatment of infected patients such as chloroquine and lopinavir. These are currently not in routine clinical use and their efficacy is being studied in various randomised controlled trials. We will keep you abreast of developments on this front.

When can a patient with COVID-19 de-isolate?

Current data based on small numbers of patients investigated, suggests that viable virus is shed up until approximately day 8 following onset of symptoms in SARS-Cov-2- infected patients. Viral RNA may be detected by PCR for longer (typically up to 12 days) although shedding of viral RNA does not always equate to shedding of viable and infectious virus.

Current guidelines recommend that persons with mild and moderate COVID disease, de-isolate 14 days after onset of symptoms. COVID-patients with severe disease will shed virus at higher loads and for longer and thus should only de-isolate 14 days after clinical stability has been achieved (e.g. 14 days after supplemental oxygen was stopped).

In summary, the recommendation has changed from two consecutive negative results to no testing with the following de-isolation criteria:

Patients can be de-isolated:

  • 14 days after their initial positive test in asymptomatic patients; or
  • 14 days after the onset of their symptoms in mild cases, or
  • 14 days after achieving clinical stability in severe disease

Click HERE for the NICD Clinical Management of Suspected or Confirmed COVID-19 Disease

What should I advise a patient who requests a medical certificate to certify them “COVID-19 free”

  • An employer cannot force a patient to have a laboratory test to prove that they are not infected before you can work. A negative lab result does not means that a patient may not be infected. Anyone with possible exposure who is asymptomatic should self- quarantine for 14 days.
  • A negative laboratory test result, if performed on a person who is well, does not constitute a medical certificate to certify a patient COVID free. There is no such thing as a “COVID-free medical certificate”.

External Resources

The National Department of Health and National Institute of Communicable Diseases (NICD) have developed clinical guidelines for health workers. You can also find more information on the NICD website: Clinical management of suspected or confirmed COVID-19 disease guideline

Please also see the WHO for daily situation reports with affected countries.

You can also find more information on the NICD website COVID-19 Resources

For additional assistance or information, kindly contact your local Ampath Pathologist.