How does a new Covid-19 variant respond to tests?
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Covid-19 variants: will the reliability of tests be affected?

By Chloe Kent 20 Jan 2021 (Last Updated January 25th, 2021 14:16)

Emerging variants of an infectious virus are to be expected, but new, more transmissible forms of Covid-19 cropping up around the world have been an understandable cause for concern. Could these variants impact the way we test for the disease? Medical Device Network takes a closer look.

Covid-19 variants: will the reliability of tests be affected?
The chance of an emergent Covid-19 variant evading testing is highly unlikely. Credit: Shutterstock

Covid-19 variants represent a confusing factor in the spread of the pandemic. From the UK and Brazil to South Africa, the US and now Germany, mutant strains of Covid-19 have been causing concern wherever they emerge.

SARS-CoV-2 mutations are unfortunately to be expected – mutating is part and parcel of what viruses do, and the Covid-19 virus has been mutating ever since it emerged. Most of these mutations don’t substantially change the virus and some might actually be to its detriment, causing the variant to die out.

“Viruses mutate all the time, but we are only interested if it changes their features or how they behave,” says University of Kent professor of molecular medicine Dr Martin Michaelis. “We see this with influenza – every year, we need a new vaccine.”

But as pressure on the virus increases and it has fewer eligible hosts, it’s forced to evolve into forms that can still transmit. For now, the new strains of Covid-19 do not appear to increase the severity of the illness, but evidence suggests that they are more easily transmissible – though estimates for quite how much range wildly.

Could the new variants evade testing?

The new strains and mutations are identified by taking samples from positive patients for background observation of the genetic code. As such, the chance of an emergent Covid-19 variant evading tests is highly unlikely.

Currently, the most widely used tests for Covid-19 are polymerase chain reaction (PCR) and lateral flow tests (LFTs).

“As you have a sample of the virus strain you should be able to detect it,” says PrescriptionDoctor.com general practitioner Dr Giuseppe Aragona. “Lateral flow tests are less accurate than PCR in general, so PCR would be the best and most accurate way of testing the emerging variants. I would not think there would be any issue with testing, especially with PCR, as any virus strains will be picked up.”

PCR tests work by taking an upper respiratory specimen, most commonly a nasopharyngeal swab. Reverse transcriptase and DNA polymerase enzymes are added to the sample, and make many copies of any viral RNA present in the sample. This is so that enough copies are present that the presence of the virus can be detected when the sample is then tested.

Primers and probes are then deployed, attaching themselves to specific sequences in the virus’s genetic code, which can then signal that the sample is positive. These primers and probes are designed to target specific segments of the virus’s genome that are unlikely to change over time.

Michaelis says: “I don’t think PCR will ever be an issue, because with PCR you pick the most conserved areas of the genome of a virus. You don’t go for something like the spike region which binds to receptors because that will change, as this is where antibodies will bind, but something that is conserved. The current PCR that we have doesn’t even discriminate between SARS-CoV and SARS-CoV-2, because so much is conserved between the two viruses that they are 80% the same.”

LFTs are not as accurate as PCRs, and don’t work in quite the same way. An LFT for Covid-19 works similarly to a pregnancy test, with a liquid sample coming into contact with an absorbent pad fitted with components which react to the SARS-CoV-2 virus. Even so, experts believe it is again unlikely that these tests will be thwarted by new viral variants.

“Most [LFTs] are actually based on the nucleocapsid protein,” says Michaelis. “It’s much more stable than the spike protein. So again, the risk is not that big.”

What about vaccines?

Currently, researchers are testing the first crop of vaccines against the new variants, and we should know in the coming weeks whether or not they’re still effective.

There is good reason to be optimistic here – the vaccines are designed to generate an immune response to multiple different parts of the virus, which means a lone mutation is unlikely to render a vaccine ineffective. Even if the antibodies generated by immunisation become unable to recognise one element of the SARS-CoV-2 virus, they will still be able to recognise the others and dispatch it.

Eventually, the virus probably will mutate enough to evade the vaccines in their current form, but this isn’t as dire as it sounds – we see this happen every year with the flu, where developing a new jab is a standard part of vaccine manufacturers’ annual workload. But it doesn’t appear we’re at that stage just yet, and any necessary tweaks to the vaccines won’t take nearly as long as the experimental candidates took to develop.

Now the bare bones of developing a Covid-19 vaccine have been laid out, any necessary updates should be fairly straightforward.