22 Feb 2024

Covid-19 testing in a time of subvariant soup: What you need to know

5:14 pm on 22 February 2024
Express corona test. Positive covid antigen test.

Photo: 123rf.com

With Covid-19 restrictions long gone and an uncertain supply of rapid antigen tests beyond June, some are asking whether diagnostic testing remains worthwhile. And, more urgently, whether it is still reliable.

In early 2020, scientists were able to sequence the full genome of SARS-CoV-2, the virus causing Covid-19. This information has allowed countries to map viral transmission around the world and track the emergence of new variants.

We know the virus has a propensity for big, evolutionary leaps. It is always looking for new ways to evade our immunity.

We saw Omicron replace Delta as the dominant strain in early 2022. From Omicron came BA.2.86, nicknamed Pirola, carrying a high number of mutations on the spike protein - the part of the virus that helps it infect human cells.

And from Pirola came JN.1.

Just before Christmas, JN.1 was responsible for about 10-15 percent of infections, according to ESR surveillance data.

The variant contributed to Aotearoa New Zealand's fifth wave of Covid, with hospitalisations peaking just before the new year. Tuesday's data showed more than nine in 10 cases over the previous fortnight were caused by JN.1 or one of its derivatives.

Do tests still work?

Yes. Several experts told RNZ new variants seem to be detected as well as their predecessors with current diagnostics.

A bit of background: A test's sensitivity refers to its ability to accurately identify the pathogen in an infected person. Test specificity indicates its ability to correctly identify patients who aren't sick. High sensitivity means avoiding false negatives, and high specificity means avoiding false positives.

"RATs are highly sensitive with respect to identifying people who are currently infectious," said Dr Andrew Old, deputy director-general of Manatū Hauora's Public Health Agency. This was because the tests detected the nucleocapsid protein, or the "shell" of the virus. This tended not to change from variant to variant.

JN.1 in particular has very few mutations in the nucleocapsid protein, meaning it's "highly unlikely there will be a change in sensitivity or accuracy of RATs", Old added.

PCR tests and RATs work in different ways. The former, also known as molecular tests, search for specific snippets of the virus' genetic material. The latter look for pathogen protein. In this article, we are not going to dive much deeper than that into how they work.

PCR tests are more sensitive, while RATs are likelier to miss infections especially in people with no symptoms.

"Their main limitation is they won't pick up an early infection," said Otago University public health professor Michael Baker.

But a bigger viral load generally means a bigger risk of being contagious. So even if you feel OK, a positive RAT means you should stay home.

"Most people who are very infectious will have an unambiguous positive line," Baker said.

Why test?

There are three main reasons to test at home, Baker told RNZ.

For the elderly and people with underlying health conditions, a positive test can unlock access to treatment. Namely, antiviral medication Paxlovid, known to reduce severe illness and hospitalisation from Covid.

In August, the previous government scrapped the remaining Covid-19 restrictions. However, people who test positive are still recommended to isolate for five days.

"That's the second big reason testing is important," Baker said. "If you know you've got Covid, hopefully you'll be more motivated to have five days, at a minimum, of self-isolation."

Covid is not a common cold. It remains the country's biggest infectious disease killer, twice as deadly as influenza.

Finally, RATs are a useful screening tool. Not necessarily all the time, but - particularly during a Covid wave - it can be a good idea to test before visiting a rest home, for example. Or before attending a conference or another large, indoor event.

Monitoring variants

At-home RATs can quickly let you know if you have Covid, but not what variant. PCR tests, however, can be sequenced to provide that information.

ESR has two main streams of surveillance: wastewater and clinical samples.

ESR science leader, genomics and bioinformatics David Winter told RNZ on Tuesday that over the past two weeks, 90 percent of cases have been caused by Omicron subvariant JN.1.

"Our focus now becomes, what's next?"

Overseas, there is interest in BA.2.87.1, a variant with many mutations first identified in South Africa. It has not been detected in New Zealand.

Winter - who works with clinical samples - said that occasionally a new variant was harder to sequence.

"But overall, the sequencing is going to be robust to the changes we're seeing and there's capacity to tweak it if necessary."

So, what's next?

At the end of 2023, Te Whatu Ora had distributed 125-odd million free RATs for use by healthcare providers and the public.

With the country's current stocks due to expire in March, the public health agency recently purchased a further five million tests.

National Public Health Service head Nick Chamberlain said RATs will continue to be widely available to the public at no cost until the end of June.

No decisions have been made about their supply beyond that date.

"We strongly encourage people to make the most of the continued free access, and to keep testing if they feel unwell or think they may have Covid-19," he said in a statement.

"We also encourage them to report their RAT result, as confirmation of a positive result enables people to be connected with any help and support they might need and provides vital insight on the number of active Covid-19 cases across the country."

In 2021, a rapid review of Covid testing in New Zealand said the interest in diagnostic testing by the public, politicians, and scientists has been "unequalled".

It is fair to say interest has waned among the first two groups, at least.

"There's no talk of Covid-19, it's disappeared from communications from health authorities," Baker said. "Unless people are in the know, they're not accessing the resources available. And it's creating a huge inequity."

He, along with colleagues, has called for a comprehensive respiratory infection strategy.

"We need testing as part of an integrated, cohesive approach to Covid and as part of a broader, respiratory infection strategy."

A Te Whatu Ora spokesperson told RNZ decisions regarding Covid testing advice beyond mid-2024 were yet to be made.

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