How do you know if you have Omicron? What happens once you’ve taken a PCR test?

The UK Health Security Agency (UKHSA) explains how suspected or confirmed Omicron cases find out if they have the variant.

Mobile Covid testing unit. (Pic credit: Bruce Fitzgerald)

Covid testing is a crucial stage to fight and contain coronavirus as it helps to curb the spread of the virus and prevent further transmission.

How do you know if you have the Omicron variant?

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The NHS Test and Trace laboratories are rolling out new technologies to quickly detect Covid-19 mutations which indicate whether positive test samples contain known variants.

The technology, which is known as ‘genotype assay testing’, is expected to halve the time it currently takes to pinpoint whether a positive Covid-19 sample contains a mutation indicative of a known variant of concern, and will then be used in addition to standard Covid-19 testing to quickly identify cases.

Genotype assays work along with existing surveillance that uses genomic sequencing to look for variants in Covid-positive samples.

Genomic sequencing surveillance will continue to identify new variants and strains of the virus.

According to the UKHSA, if you have taken the PCR test and you are suspected or confirmed to have the Omicron variant, you will usually be contacted by NHS Test and Trace via a phone call and warned to self-isolate.

How do the laboratories test for Omicron?

There are hundreds of thousands of swabs that are processed in laboratories across the country every day. We have now gotten used to the procedure of taking a Covid test at home or at a test site, but the technique at a laboratory is one that is not well known to the public.

The purpose of laboratory-based techniques is to diagnose people with symptoms, test close contacts of those who have tested positive for coronavirus, help detect variants of concern, to better understand how the virus spreads and confirm rapid test results.

The following step-by-step process relates to PCR testing and processes will differ slightly between laboratories.

1. Double-bagged test samples arrive at the laboratory in sealed plastic containers, each one with its own unique barcode.

2. A laboratory operator in PPE removes the sample from the bags, inside a biosafety cabinet. The cabinets have negative air pressure so that no aerosol particles can be released into the room.

3. The operator ensures that the sample is successful in that there is enough liquid in the tube and the barcode is correctly placed.

4. The next part of the process involves removing the liquid from the sample tube and mixing it with a chemical that kills any living virus so that it is safe to handle. The sample is then prepared for ribonucleic acid (RNA) removal, where any genetic material that can be found in the sample is extracted.

5. The samples are then added to a machine that uses magnetic substances to extract and wash the RNA. The purified RNA is then put on ice inside a heated container to keep it stable.

6. Plates of purified RNA are removed from the ice and mixed with a number of chemicals called ‘reagents’. They are then put into a polymerase chain reaction (PCR) machine.

7. PCR testing works by cycling the RNA samples through multiple temperatures, many times. Each cycle triggers a chain reaction that causes the genes (if there are any) to replicate and emit a detection chemical which tells us if coronavirus RNA is present in a sample.

8. As soon as the PCR reaction has been run, the results are carefully checked before being released and uploaded to the laboratory’s Laboratory Information Management System (LIMS), then sent to the National Pathology Exchange (NPEx). This is where the laboratory result is matched with the initial sample barcode and subject record.

9. All of the results are sent to the NHS Business Services Authority (BSA) who sends out email and SMS results to the person who booked the test. For England-related results, NPEx matches them to an NHS number and GP record where possible.

The chief executive of the UK Health Security Agency, Dr Jenny Harries, said: “We are continuing our efforts to understand the effect of this variant on transmissibility, severe disease, mortality, antibody response and vaccine efficiency. Vaccination is critical to help us bolster our defences against this new variant - please get your first, second or booster jab without delay.

“The guidance on vaccination is changing to help all of us bolster our defences in the face of this new variant. Everyone should complete a primary course as soon as possible - for most this will be a first and second dose. For some more vulnerable, a third dose is available.

“Following the change in JCVI advice today, a booster dose for everyone over 18 years is now recommended and will be available at a minimum of three months from your last primary course jab. Please take up this offer as soon as you are eligible to protect yourself, your families and your communities.

“It is very likely that we will find more cases over the coming days as we are seeing in other countries globally and as we increase case detection through focussed contact tracing. That’s why it’s critical that anyone with Covid-19 symptoms isolates and gets a PCR test immediately.”