COVID-19 testing: a 2023 update

We need to keep an eye on which lineages are circulating, so that if there's a sudden rise in a particular emergent strain, or an increase in severity is noted, that we know what's going on and we know early.

[Music] Welcome to the Australian Prescriber Podcast. Australian Prescriber, independent, peer-reviewed, and free.

COVID testing used to dominate our lives. It was one of the most visible cornerstones of an intensive test, trace, and isolate public health strategy in 2020 and 2021 especially. Perhaps rarely, if never before, had infectious diseases testing been so prominent in our society. However, since that time at the beginning of the COVID pandemic, our understanding of COVID testing strategies has become more sophisticated. But where do we stand now in terms of practice, and what can we learn from it? I'm David Liew, your host for today, and we're back with the Australian Prescriber Podcast. I'm very glad to welcome Ella Meumann to the podcast today. She's an infectious diseases physician, and she's written an article in Australian Prescriber on Testing for COVID-19: the 2023 Update. Ella, thanks for joining us.

Thanks for having me on the show.

So Ella, before we really get into this, let's just take a step back and ask, what's happening with COVID now, especially regarding variants of concern?

To recap, for the first couple of years of the pandemic, the case numbers in Australia were low, until our borders opened towards the end of 2021, at around the time of the Omicron wave. And since that time we've had widespread community transmission in Australia, with several waves arising from the various Omicron sublineages. This year we did have an increase in cases in May, so early winter, not quite winter, but a gradual decline since then. Since the start of the pandemic, genomic surveillance for SARS-CoV-2 has been conducted through AusTrakka and the Communicable Diseases Genomics Network, a national public health laboratory group, and they've been tracking emerging variants. So since the borders opened, the various Omicron sublineages have dominated, and more recently there's been the emergence of several recombinant sublineages, and these are lineages arising from the exchange of chunks of genetic material between strains, and these recombinant lineages are now dominating.

So which sublineages are particularly a problem right now, and where do they stand compared to the sublineages that we were looking at before?

There are several of these designated by the Pango designation, which is a nomenclature system for SARS-CoV-2 lineages and sublineages. And the ones that are circulating now begin with the letters XBB, and then various numbers depending on the sublineage. So there are several so-called variants of interest as assigned by the WHO, such as XBB.1.5, XBB.1.16, and EG.5, which is an XBB descendant, that are circulating.

So the sublineages, why does that matter to us?

Genomic surveillance is important because we need to keep an eye on which lineages are circulating, so that if there's a sudden rise in a particular emergent strain, or an increase in severity is noted, that we know what's going on and we know early.

It's often said, if we don't look then we won't know.

That's exactly right.

Let's talk about things at a patient level first, and then we'll get onto the genomics. Rapid antigen tests. They've become the mainstay of our approach to COVID testing. Tell me a little bit about them. Should we still be relying on them? How effective are they with the current sublineages?

Rapid antigen tests were a really important tool, particularly around the time the borders opened when case numbers were very high and laboratory PCR testing capacity, or nucleic acid amplification testing capacity, was saturated. And so these provided a way in which people in the community could test themselves and have a result within 15 to 30 minutes and be able to enact an appropriate treatment or public health response to having been diagnosed. So particularly at that time, they were vital.

They do have some limitations. The sensitivity of these rapid antigen tests is lower than for nucleic acid amplification tests or PCR tests. Patients with very early infection may be negative and may require repeat testing in 24 to 48 hours, or a nucleic acid amplification test as a more sensitive test to confirm the result. These days with lower case numbers, there is laboratory capacity for PCR or nucleic acid amplification testing, and being a more sensitive test than RAT, where it's feasible, that's a better test to do.

So maybe you can tell us a little bit about why rapid antigen tests have inferior sensitivity to PCR testing. Does that have to do with the way that we collect the tests, or is it really something a bit more technical than that?

It's to do with the nature of the assays themselves. So a nucleic acid amplification test, in a general sense, these are very sensitive assays. They detect the genetic material, so either the RNA or DNA, in a clinical specimen, and they're able to detect very small amounts of the material. What they do is, following DNA or RNA extraction, there's a series of thermal cycles which result in amplification and then detection of the assay target. Whereas a rapid antigen test, that's detecting an antigen component of the virus itself through a lateral flow immunoassay, and so it's detected visually. And there's no amplification of material as part of that step, and so it's a less sensitive approach, but still has reasonable sensitivity. To be eligible for registration on the TGA, the last I looked, the minimum sensitivity compared to a nucleic acid amplification test required for registration was at least 80%. So not too bad, but they will miss some cases.

I'm glad that we've got greater accessibility to PCR testing now. And what you've said really makes a lot of sense in terms of trying to understand cycle thresholds and other things that we've started to become familiar with as we've had better access to PCR testing.

Yeah, that's true. So I mentioned the nature of PCR tests is through a number of thermal cycles that result in amplification of the gene target. The cycle threshold is the first one of those cycles at which the PCR product is first detected. So the higher the amount of pathogen genetic material in the specimen, the lower the cycle threshold will be. So it's inversely related to the viral load, essentially.

These cycle thresholds vary between PCR assays. There's a huge number of PCR assays out there, each with different gene targets, and the cycle thresholds aren't comparable between assays. And that's why we don't report those in our pathology reports for PCR tests. However, they can provide some helpful information sometimes. A very high cycle threshold, for example, 35 cycles or higher, that could either indicate very early infection, or it could indicate persistent low-level shedding of non-viable viral fragments following an infection. And that can occur for a number of weeks following acute infection.

So if you have a PCR result that's positive with a very high cycle threshold, the recommendation would be to repeat that test in the following 24 to 48 hours. If there's a drop in cycle threshold, that would be consistent with acute infection. However, if it's persistently very high, then that could indicate potentially past infection. However, these results need to be interpreted in the clinical and epidemiologic context, in terms of the patient's symptoms, their comorbidities, and so forth. So there's not really a hard and fast rule for interpreting these, and they're not routinely reported.

So overall, this lab-based nucleic acid amplification testing, PCR testing, when should we be using this clinically? What role does it play in our clinical armamentaria?

PCR testing or nucleic acid amplification testing is the most sensitive method to diagnose COVID-19, and would be the recommended test for patients in hospital for high-risk contacts or healthcare workers, where there are serious consequences if you miss a diagnosis so, for example, where there might be a false-negative RAT.

Often it gets suggested that patients who have negative rapid antigen tests should have a PCR done if they've got really obvious symptoms, if they've got clinically evident infection. What do you think of that strategy, and do you think that's something that we'd be carrying with us as we go forward?

If a patient is suspected to have COVID-19 and they have a negative RAT, then ideally you should do a PCR test or a nucleic acid amplification test to confirm that result. An alternative strategy, if a nucleic acid amplification test isn't available, would be to repeat the RAT in 24 to 48 hours.

One of the other advantages of a PCR test is that we can get genomic data, which we obviously can't get from rapid antigen testing. How widespread is genomic testing in everyday PCR testing, and how much should we be doing?

That is one consideration. In the first two years of the pandemic, a very large proportion of COVID-19 cases had a specimen sent for genomic sequencing, and that's because at that time we were tracking and tracing every case, whereas once the borders opened, there wasn't the capacity to sequence all cases. And so a genomic sequencing strategy was developed by the Communicable Diseases Genomics Network, prioritising cases with severe disease, cases with reinfection or recurrent infection or persistent infection, returned travellers, and also outbreak investigations. These are the priority specimens, and there's ongoing genomic surveillance as we discussed earlier, tracking the variants and so forth.

That brings me on to this discussion about other winter viruses as well. We're increasingly in a world where a patient might present with symptoms that could easily be not just COVID but influenza or other winter viruses. Seems like we're looking at testing which can increasingly capture all of those in a single swab.

Yeah, that's right. So for the first couple of years of the pandemic, other viruses, particularly influenza A and influenza B, disappeared essentially altogether. However, once the borders reopened, as you would expect, these viruses re-emerged, and have been circulating over the last 2 winters. Most laboratories offer multiplex nucleic acid amplification testing, which are assays able to detect a number of viral pathogens, and some also include bacterial pathogens as well. And this allows syndromic diagnosis and identification of the most common viral pathogens with just one test. So these have been recommended the last couple of winters. More recently, there have been some rapid antigen tests for influenza A and B approved by the TGA. Similar to the test for SARS-CoV-2, there are some minimum performance requirements, such that they have to have minimum sensitivity and specificity. However, as for SARS-CoV-2, they are less accurate than the nucleic acid amplification tests.

We've had influenza for a long time, but we haven't had rapid antigen tests for influenza until now. Is this something that we've learned from our COVID experience? I’m sure there are a number of things that we've learned from our COVID experience that might be applicable to other winter viruses.

The COVID-19 pandemic really was an exceptional situation, and there have been a number of lessons learned around implementation of diagnostic testing and scaling of diagnostic testing for respiratory viruses. I think one of the keys to successful management of the pandemic was the early availability of the full genome sequence of SARS-CoV-2, which enabled the design of nucleic acid amplification tests. And so we had sensitive and specific tests available from very early on. Australia's lucky that we have a really robust regulatory system for pathology testing. However, there were appropriate provisions made for emergency development and rollout of tests, and the existence of the Public Health Laboratory Network and Communicable Diseases Genomics Network enabled sharing of expertise, sharing of control material for test validation and development, development of a quality assurance program for comparison of laboratory performance. And this really was key to us being able to diagnose and trace those early cases and control the pandemic.

From a genomics perspective, the infrastructure for genomic sequencing had been in development at the various public health laboratories. The AusTrakka platform, which is used for genomic sequence sharing, was in development, and the pandemic accelerated that, and it was rolled out from very early on, enabling inter-jurisdictional data sharing. So all of this was vital for our test, trace, and isolate approach to public health management.

However, at the time that the borders opened in late 2021 and with that Omicron wave, that's when the rapid antigen testing really became important, and the ability for patients to test themselves, and having the regulatory framework that enabled TGA registration of those tests, rolling those out meant that we were able to continue diagnosing cases even when the laboratory and nucleic acid amplification testing capacity had been reached. Since that time, as case numbers have dropped, I think the rapid antigen tests are potentially a little bit less important, but they still have a role.

Where antigen testing for other viruses fits in the scheme of things, I think it’s still not 100% clear, because at the end of the day, the nucleic acid amplification tests are more sensitive and a better test really for diagnosing those viruses, if it's available.

Let me take a little pivot there and ask you about something which is quicker than a conventional lab-based PCR, but is obviously more sensitive than a rapid antigen test, and that's point-of-care nucleic acid amplification testing. Have we learned a little bit about how we might use that kind of technology better? Has that technology advanced during the COVID pandemic? And do you think that fits into our overall long-term strategy?

That's a really important point. Certainly point-of-care tests for SARS-CoV-2 were important in some settings, particularly emergency departments and remote clinics, for example. So that assisted with infection control decisions in emergency departments, where there were limited single rooms or negative pressure rooms, for example, and also for remote clinics where there's a delay in testing associated with specimen transport. Having sensitive and specific nucleic acid amplification tests that were easy to use, but importantly operated under the NPAAC [National Pathology Accreditation Advisory Council] governance requirements for point-of-care tests, so still with important quality measures in place, having those point-of-care tests available was really helpful and I think did prevent transmission in some instances.

It sounds like we've learned a lot about testing for viral respiratory infections throughout the COVID experience so far. Do you think that this really informs a way that we deal with the next viral respiratory infection epidemic or pandemic?

I think definitely. What we've learned is the importance of rapid development and rollout of high-quality diagnostic tests, but with appropriate quality management of that testing in place is really important for being able to diagnose cases, and then subsequently enact the appropriate public health response.

I'm very glad that you and your colleagues are doing the great work that you are. So thank you so much, and thank you for joining us on the podcast today.

Thanks so much.

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The views of the guests and the hosts on this podcast are their own and may not represent Australian Prescriber or Therapeutic Guidelines. I'm David Liew, and once again, thank you for joining us on the Australian Prescriber Podcast. [This interview was conducted on 28 August 2023.]