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Frequently Asked Questions: SARS-CoV-2 Omicron Variant

What is Omicron?

In late November a group of closely related viruses was identified from Southern Africa which harboured a unique set of mutations, not previously seen with other variants such as Beta or Delta. At the time of writing, Omicron has also been detected in European countries, the Middle East, the United Kingdom and the Asia-Pacific region.

Does it spread more easily?

It is not yet clear whether Omicron spreads more easily from person to person compared to other variants. While there have been increases in case numbers in South Africa around the time Omicron was identified, the exact impact of the variant is still unknown.

Does the clinical presentation differ?

It is not yet clear whether Omicron causes more severe disease compared to previous variants.  There is currently no information to suggest that symptoms associated with Omicron are different from those from other variants.

Can currently available tests detect Omicron?

Yes. The variant was detected through the use of routine PCRs and there is no indication that available PCRs cannot detect the variant. Assays targeting the S-gene of the virus may be able to predict that a sample contains the Omicron variant without sequencing data, but an absence of this proxy signal does not exclude infection with Omicron. The utility of this proxy is therefore limited to surveillance purposes. Furthermore, as this proxy is not available with all commercial assays and the clinical management of Omicron is unchanged from other variants, laboratory reports will not differentiate between Omicron and other circulating variants. Antigen testing is expected to perform as previously as most assays target the nucleocapsid (N) protein, not the S protein.

Is reinfection with Omicron likely?

According to the WHO update of 27 November, Preliminary evidence suggests there may be an increased risk of reinfection with Omicron (i.e., people who have previously had COVID-19 could become reinfected more easily with Omicron), as compared to other variants of concern, but information is limited.

How effective are vaccines?

Data is still limited. Based on the mutation seen in Omicron it is possible that partial immune escape might happen but this was also true for previous variants, where vaccines continued to provide high levels of protection against hospitalisation and death. Vaccines as a crucial measure of risk reduction therefore remains highly recommended.

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SARS-CoV-2 Antigen Test Protocol & Guidance

SARS-CoV-2 Antigen Testing Frequently Asked Questions
What is SARS-CoV-2 antigen testing?

Diagnostic testing for viruses relies on the demonstration of either genetic material of the virus, or protein components of the virus. Reverse-transcriptase polymerase chain reaction (RT-PCR) detects SARS-CoV-2 RNA and is the diagnostic reference standard for COVID-19 due to its high sensitivity. Rapid antigen tests detect structural proteins of SARS-CoV-2 rather than RNA, and thus can also confirms the presence of the virus.

Can the antigen test be used instead of the PCR test?

RT-PCR is more sensitive than other test modalities, including the antigen (Ag) test, for the detection of SARS-CoV-2 as it has the ability to amplify the amount of genetic viral material obtained from a sample. As long as the limitations of antigen testing are borne in mind, it can be used in selected settings to diagnose COVID-19.

Advantages and disadvantages of antigen testing

Compared to RT-PCR tests, rapid antigen test has the following advantages: it is less complex to perform, less expensive and results are available in a shorter time, making it well suited to settings where urgent triage is required. If the goal is to confirm an infection the antigen test is best used when the viral load is at its highest at which time its sensitivity will be optimal. Rapid antigen tests are usually positive in patients with high viral loads, and could therefore aid in identifying highly infectious cases.

Unfortunately, the sensitivity of these tests is lower RT-PCR and rapid antigen tests perform best when used during the early phases of illness when high viral loads are present and individuals are likely to be most infectious. A lack of sensitivity may result in false negative results which can lead to onward transmission or super spreader events, especially in institutionalised settings; as such, negative antigen results need to be confirmed with additional testing under circumstances where infection is likely (see below). Most guidelines also currently advise against the use of rapid antigen tests in asymptomatic patients due to the concern for false negatives.

What kind of sample is required for an Antigen test?

The same samples as are used for a PCR test is required for an antigen test, particularly nasopharyngeal swabs. This is not a blood or serum test. The same biosafety risks remain as for PCR testing and thus staff should wear appropriate PPE, biohazard waste bags should be used and the sample should be taken in a well-ventilated environment.

When can an antigen test be considered?

Under conditions where infection with the virus is likely (like the current stage of the pandemic or in hotspot areas) and the chances that the patient could be infected is high, the antigen test could help to make the diagnosis if a PCR results will not be available in 48h. These scenarios are regarded as having a high pre-test probability of infection. People that could be screened will include:

  • Symptomatic patients
  • Patients from an environment where an outbreak is ongoing e.g. in care homes
  • High risk patients e.g. health care workers
  • Patients with a known contact (symptomatic or asymptomatic contact)

A positive outcome under these conditions may be regarded as confirmation of an infection. The recommended 10-day isolation period should follow on such a positive antigen test (under these conditions).

A negative antigen test under these conditions should ideally be confirmed with a more sensitive PCR test or alternatively repeat antigen testing in 2-3 days as the chances are high that the patient is indeed infected (thus a false negative antigen test result). Patients with unidentified infection may be the source of onward transmission or super spreading events.

If the conditions were different e.g. the area does not have a high COVID-19 prevalence, or the patient’s individual chances of being infected is low, a positive antigen test should be confirmed with a PCR test to avoid unnecessary isolation. These are called low pre-test probability scenarios. A negative antigen test rules out a highly infectious state and would not require additional testing in most settings. However, it is advised that the patient’s context is taken into account, and that PCR confirmation be considered in settings where the impact of the occasional false negative result will have a significant impact. If PCR is not available, concern over the lower sensitivity of the antigen test can be partially alleviated by repeat testing within 2-3 days after a negative result, especially in settings such as staff of health care facilities.

Patients with a very low chance of being infected include:

  • Asymptomatic patients
  • Patients with no known contact
  • People routinely screened (e.g. workplaces other than health care facilities)
For an asymptomatic patient after a confirmed exposure, how does one interpret the antigen test outcomes?
  1. Antigen positive

The patient may be considered as infected, and appropriate treatment initiation and infection prevention and control measures should be followed including a 10-day isolation period, similar to a diagnosis by RT-PCR

  1. Antigen negative

The patient still needs to quarantine for 10 days because of the exposure to a known contact despite a negative test result, irrespective of whether an antigen test or PCR test was performed. Super spreader events may occur should a patient be shedding viruses which was not picked up by the less sensitive antigen test. Retesting of patients within the quarantine period is generally not indicated unless the patient develops symptoms.

COVID-19 Testing for diagnostic purposes

Covid 19 request form JAN 2022

COVID-19 Request Form
Updated January 2022

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Frequently Asked Questions: COVID-19 & Antibody Testing

Who is at risk of getting COVID-19

 People at highest risk for contracting SARS-CoV-2 (which causes COVID) are:

  • people in areas with ongoing local transmission
  • healthcare workers caring for patients with COVID-19, and the contacts of these HCWs
  • close contacts of infected persons
What symptoms will I have with COVID-19?

Most people who get this disease will have very mild symptoms, like having a cold. Some people may not have any symptoms at all.
People who do develop symptoms generally have the following:

Fever • Headache • Sore throat • Cough • Muscle aches. • Many people may present with a loss of smell and/or taste.

In the minority of cases an individual may develop severe symptoms such as difficulty breathing or shortness of breath, persistent pain or pressure in the chest, or diarrhoea. If this happens, it is imperative that medical attention is sought and that you go to the hospital.

How does it spread?

Person to person contact is the main way the virus spreads. This is either through close contact or by the spread of droplets when someone who has the virus coughs or sneezes on you.

Close contact means that you had face-to-face contact within 1 meter (without a mask) or were in a closed space, for more than 15 minutes with a person with COVID-19. This contact should have happened while the person with COVID-19 was still “infectious”, i.e. from 2 days before to 10 days after their symptoms began.

Generally, if you are more than 2 meters away, the droplets won’t reach you, and should not be able to infect you. However, those droplets can land on surfaces, such as tables, door handles, or any other surface. The virus can survive on the surface for a long time if not thoroughly cleaned (currently estimated to be between 7-9 days if not cleaned adequately and depending on the type of surface).

If you touch that contaminated surface with the virus and then touch your face, especially your eyes, mouth or nose, you could become infected.

Can I have contracted the virus but have no symptoms?

Yes you can. If you are infected but show no symptoms, you might still be infectious to other people and it is therefore very important to keep to recommendations on hand hygiene, wearing of masks and social distancing.

What tests are done to diagnose COVID-19?

There are two different kinds of tests; one to make the diagnosis of an acute infection and one which may help to show a previous infection.

To diagnose an acute infection a test (PCR) is used which picks up the presence of the virus by looking for the genetic material of the virus. For this test we will collect a throat and/or nose swab or other type of sample and forward it to our laboratory for testing. The private laboratories (e.g. PathCare) and South African National Health Laboratory Service laboratories have the capability to perform this test.

The test takes about 48 hours to process. You will receive a SMS with your result stating whether the virus was DETECTED OR NOT DETECTED. We will contact your doctor with your results as well. Please wait for your doctor to contact you.

Are there any preventative measures I can take against contracting the virus?

There is currently no vaccine available to prevent SARS-CoV-2 infection, but we urge you to get vaccinated against the flu, as this will strengthen your immune system.

Risk of infection and transmission can be reduced by:

  • Reducing personal contact (e.g. by no longer shaking hands).
  • Cleaning your hands before touching your eyes, nose or
  • Properly cleaning your hands after coughing or
  • Avoid using handkerchiefs and rather use a tissue and discard
  • Wearing a mask in public areas

People at high risk for severe disease can further decrease their risk by:

  • Stocking up on supplies to avoid going into public places often, or have other people bring supplies to your home.
  • Often washing your hands with soap and water.
  • Stay home as much as possible.
  • Avoid large gatherings of people.
Do I need to routinely use a face mask?

Face masks are required to lower risk of infection and transmission. Facemasks prevent the spread of droplets and can help to prevent that you touch your own face when your hands might be contaminated.

How is COVID-19 treated?

There is no specific treatment for COVID-19. Symptomatic treatment may be given, for example to reduce fever, muscle aches and sore throat.

If symptoms are severe (e.g. if an individual requires oxygen due to difficult breathing) treatment should not be managed at home and will need to take place in hospital.

What do I do if I’m concerned I have COVID-19?

Contact your doctor. If your symptoms are mild, it might be sufficient to stay at home and treat your symptoms, keep hydrated and get lots of rest. Currently the recommended period of time to stay at home is 10 days, as you could be infective for this amount of time. Keep practicing good hygiene at home and clean surfaces regularly.

Should I get tested for the virus?

If your symptoms are mild, no, it is not necessary to be tested but consult your doctor for advice. However, if you have to be in contact with other people and you are unsure whether your symptoms are due to SARS-CoV-2, testing is recommended to inform your contacts and avoid further spread.

What do I do if I have been in contact with someone with a SARS-CoV-2 infection?

If you have been in contact with somebody with confirmed or probable COVID-19, you should self-isolate for 10 days.

Get plenty of rest, and stay hydrated by drinking enough fluids. If you develop any symptoms, contact your doctor and:

  • Practice good cough etiquette when coughing or
  • Clean your hands after coughing or
  • Wear a mask

If you feel short of breath, or have difficulty breathing, go to the nearest hospital. If possible, please try to phone ahead and inform the hospital/clinic/GP to tell them that you are coming.

Wear a face mask to prevent transmission to other patients and healthcare workers.

How do I explain COVID-19 to my child?

Manuela Molina created this short book to support and reassure our children, under the age of 7, regarding the COVID-19. This book is an invitation for families to discuss the full range of emotions arising from the current situation. It is important to point out that this resource does not seek to be a source of scientific information, but rather a tool based on fantasy.  Get the book here

What is SARS-CoV-2 IgM?

The SARS-CoV-2 IgM test is a blood test to detect IgM antibodies against SARS-CoV-2. Different types of antibodies circulate in the blood. In response to an infection, IgM antibodies usually appear first, followed by IgG antibodies. Therefore in theory when IgM is detected, it suggests a recent infection. However, IgM can sometimes remain detectable for months after the initial infection. Therefore doctors would interpret the results of IgM testing in conjunction with their clinical findings.

What is the purpose of testing for SARS-CoV-2 IgM?

SARS-CoV-2 IgM has limited utility, on its own, as a diagnostic test for COVID-19, because a positive result does not necessarily indicate current infection, whilst a negative test does not rule out current or past infection. This is why these tests are not widely used in South Africa. However, due to the so-called “second wave” of COVID infections around the world, some countries require an IgM test as an additional measure (in conjunction with PCR) in an attempt to further limit the risk of imported cases.

How long can the SARS-CoV-2 IgM stay positive?

The SARS-CoV-2 IgM may remain detectable for several weeks after the initial infection.

What does it mean if the IgM is positive but the PCR is negative?

A positive SARS-CoV-2 IgM result indicates an acute or recent infection. Some patients don’t produce any antibodies, while in others the IgM antibodies may remain detectable for prolonged periods. The presence of IgM does not necessarily indicate current infection. Many patients will have a positive IgM with a negative PCR, indicating an infection with SARS-CoV-2 some time in the recent past (weeks to months), and are most likely not infectious anymore.

What does it mean if the SARS-CoV-2 IgM is negative?

A negative SARS-CoV-2 IgM result could be as a result of never being infected, or the person may have been infected some time ago and the antibodies are no longer detectable. A negative IgM could also occur in patients who are infected with SARS-CoV-2, but the antibodies have not developed yet. Some patients may never produce detectable antibodies.

What are the chances of false positive and false negative SARS-CoV-2 IgM results?

All tests performed in accredited laboratories are extensively validated to ensure that results are accurate and reliable. Rigorous quality assurance protocols are in place to ensure the reliability of laboratory results. Therefore the chances of false results are very low. However, with any test, there is always the risk of potential false positive or false negative results, for which there are numerous causes. This applies to all laboratories.

Can one test positive for SARS-CoV-2 at one lab, then test negative at another lab? Which result is correct?

Yes. It is possible that by the time the second test is performed, that the antibodies may have waned to an undetectable level. In addition, it is not always possible to make direct comparisons between different laboratories. Different laboratories may use different types of tests, and may have different quality assurance protocols. It is usually not possible to say which result is the correct one.

What should I do if my IgM is positive and my PCR is negative?

This scenario most likely indicates an infection in the recent past, where antibodies are still detectable. This means that the person is most likely not infectious anymore. Since IgM testing is only performed for travel purposes, patients may have to re-test until a negative result is obtained. There is no way to tell for sure how long the IgM antibodies will still be detectable in your blood. Re-testing in 7-10 days may be appropriate, although it is not guaranteed that the result will be negative by then. If the person is symptomatic, they should consult their doctor. Continue practicing preventative measures such as hand hygiene, social distancing and wearing a mask.

Why is my PCR positive when I do not have any symptoms and why is the PCR negative when repeated within a few days?

The RT-PCR which Pathcare performs on platforms like ABBOTT, Roche, Seegene and Thermo Fisher is highly specific meaning false positives are unusual. We do however see false negatives as these assays may lack sensitivity.

There are also other factors that may influence the result like:

-Quality of the specimen (broncho-alveolar lavage specimen is better than sputum which is better than a nasal swab which is better than a throat swab or saliva)

-Whether the patient is asymptomatic or not i.e. low viral load vs higher viral load (high CT value vs low CT value)

-Timing of sample where PCR turns positive about 48 hours before symptoms develop and then generally stays positive for about 10 days from time of symptom development. However, in a fair number of patients we are seeing persistence of positive PCR results for weeks or even months after they had Covid and that includes patients who had asymptomatic infection. This is a reflection of non-infectious viral RNA fragments that gives a positive PCR result but it does not reflect transmissibility. This is not a false positive PCR result but it may reflect the presence of non-viable virus.

-At the tail end of infection, intermittent viral shedding is seen which causes discrepant PCR results if the PCR is repeated within a few days of each other.

CV19 is generally transmissible for 48 hours before symptoms develop till about 8 days after symptoms developed. When screening asymptomatic patients and the result is positive, one does not know whether that is a true current infection or merely persistence of a positive PCR in a healthy patient that had previous asymptomatic or mild infection.

Our clinical advice is if you test positive, stay home for 10 days and do not retest as the virus is generally not transmissible beyond D10. If you retest you will see persistent positive results in some patients, but that is just viral RNA fragment persistence and not viable virus. We generally only advise retesting in previously positive patients after 90-days, should such a patient again present with viral respiratory symptoms.

Asymptomatic infection is more common than symptomatic infection and it is not surprising to see that asymptomatic patients test positive with PCR. Follow the 10-day rule of self-isolation if a patient tests positive, and do not retest as the second test does not alter decision making.