The best tests for this Delta outbreak – Expert Q&A

The place of testing in our current Covid-19 response is being widely discussed – but which tests are best: PCR or rapid antigen? Saliva or nasal swab?

Essential workers transiting in and out of Auckland will have to be tested weekly and the Government continues to ask all symptomatic people – especially Aucklanders – to get tested.

The SMC asked experts to comment on the state of play with Covid-19 testing.

Associate Professor James Ussher, Department of Microbiology and Immunology, University of Otago​ and Consultant Clinical Microbiologist, Southern Community Laboratories, comments:

How do New Zealand’s testing needs change at this stage of the outbreak, compared to earlier? What might be the best strategy or optimal mix for NZ of the technologies currently available?

“Firstly, I’d say that we’re past the surge, but we need to maintain higher levels of testing for surveillance, so everyone who has got symptoms should be tested. But as we are past the surge, and with Auckland in Level 4, the outbreak is much more contained, so it’s important to focus testing on people who have symptoms suggestive of Covid-19 or who have been at locations of interest. We’ve also got people crossing the Auckland border, where there’s a role for asymptomatic surveillance testing. There are also discussions around whether we should have asymptomatic testing of frontline workers such as healthcare workers, but I’m uncertain of the role of this at present. It is important ​to distinguish between Auckland and other parts of the country where the risk differs considerably. Even in Auckland, the risk is much more contained now with lockdown than it was in the early days of this outbreak. We’re seeing fewer people testing positive where it’s a surprise, which is good news.

“As far as the testing approach goes at the moment, while we’re trying to regain elimination, I think PCR is the test of choice. I don’t see rapid antigen tests as a primary test at this stage. They’ve got an uncertain role while we are seeking to regain elimination because they are less sensitive, even in the acute stages [of infection], than PCR testing. We currently have zero tolerance for missing an infection. I think nasopharyngeal swabs for symptomatic people, and people who’ve been in locations of interest, remains the preferred method and the gold standard.

“There is certainly a role for saliva PCR testing for surveillance, and it’s currently being rolled out to border staff, but it could also be used for surveillance around the Auckland border and, if the Government was wanting to go down that route, for regular asymptomatic screening of healthcare workers.

“The reason I say nasopharyngeal swabs are still the preferred specimen to collect on symptomatic patients or those who have been in locations of interest, is because there are a number of meta-analyses that have shown that the nasopharyngeal swab is either equivalent to or has a slightly better sensitivity than saliva. Nasopharyngeal swabs are also a specimen that is quick and easy to collect, whereas saliva takes a few minutes to collect. For patients who are symptomatic or have been at a location of interest, where the testing is high-stakes, you would want saliva collection observed to make sure that an appropriate volume of sample was collected and that the person had not been eating, drinking, or smoking in the half hour prior to collection.

“Observed collection of a saliva specimen is actually going to take longer to collect than nasopharyngeal swabs. I think one thing that’s missing from the discussion around saliva testing is that the reason we saw the queues in Auckland was not the process of taking a swab. Taking a swab is extremely quick; it’s getting all the person’s details, entering them into the system, and labelling the specimen that takes time – and that needs to be done regardless of specimen type. Also, the processing in the lab is essentially the same process, whether you’re processing a saliva [specimen] or a nasopharyngeal swab. Regardless of whether you do extraction or not, the length of time in the lab is pretty similar.

“The other thing that is important to note is that, in a surge situation, the saliva can’t be pooled, whereas you can pool nasopharyngeal swabs, so there’s greater capacity to test nasopharyngeal swabs in a surge.”

What is different with testing under Delta?

“With Delta, there’s more virus present, and it’s present earlier, meaning people can transmit earlier. All the PCR tests can easily detect Delta and we have seen higher amounts of virus in patients with Delta infection. While you might expect that rapid antigen tests would be more sensitive in infections with Delta because of the higher viral load, that hasn’t necessarily played out overseas. I think that’s a ‘watch this space’.

“Because of the shortened serial interval between people getting infected and passing the virus on to someone else, it’s critical to try to optimise the turnaround times of testing as much as possible. I think as Sydney has demonstrated, even with their gold standard test-and-trace system, it’s really hard to get on top of Delta with that alone.”

What are we learning from overseas?

“I think what’s important to highlight is that we’re in a very different situation than most countries in the world at the moment in that we’re seeking to regain our elimination status. Hence, we need the most sensitive tests to detect infection, but as we move to open our borders and accept SARS-CoV-2 transmission in the community, there will be a much greater role for the likes of rapid antigen tests and saliva PCR. For example, rapid antigen tests could be used prior to attending school or attending major events. There’s a lot of experience being developed with these sorts of surveillance methods overseas that’ll be critical for us to learn from as we move past an elimination strategy. I think we’re in a fortunate position that we can learn from much of what’s occurred overseas.”

Conflict of interest statement: Associate Professor Ussher is Science Director of the Government-funded Vaccine Alliance Aotearoa New Zealand – Ohu Kaupare Huaketo, a partnership between the University of Otago, the Malaghan Institute and Victoria University of Wellington. He is also on the Government’s COVID-19 Vaccine Science and Technical Advisory Group. He works part-time as a Consultant Clinical Microbiologist for Southern Community Laboratories, part of the APHG group.

Professor Michael Plank, Te Pūnaha Matatini and University of Canterbury, comments:

“New Zealand’s testing strategy has been centred on PCR testing of nasal swabs. This is sometimes referred to as ‘gold standard’ because it is the most accurate form of test. However, there are other testing methods that can be useful in specific situations.

“Saliva testing is a different way of collecting a sample, which is then tested by PCR. Most research shows this has comparable accuracy as nasal swabs. Saliva testing would be a good option for people who need to be tested regularly, e.g. border workers and arrivals in MIQ. Because it is less invasive, saliva testing could be done more frequently, e.g. every 1-2 days. This would actually give better protection than weekly nasal swabs because it is more likely to pick cases up early, so they can be isolated before they have a chance to pass the virus on.

“The other type of test is a rapid antigen test, sometimes called a lateral flow test, which come in the form of a self-contained test kit. They are less accurate than PCR tests and are more likely to miss infections particularly in the very early or late stages of infection. However, they have the advantage that provide results quickly (usually within half an hour) and do not require lab processing.

“Rapid antigen tests are not recommended for people who have symptoms, who should get a PCR test. But widespread use of rapid antigen tests in asymptomatic people would be very helpful in the current outbreak as an extra form of surveillance. For example, these could be used regularly for essential workers and for people crossing the Auckland boundary. In the UK, rapid antigen test kits are widely and freely available. New South Wales also uses them for essential workers. They shouldn’t be relied on to catch every last case, but they could be very useful as an additional layer of Swiss cheese in our system.”

Conflict of interest statement: I am partly funded by MBIE for research on mathematical modelling of COVID-19.