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How do all the different Covid tests work? (Image: Tina Tiller).
How do all the different Covid tests work? (Image: Tina Tiller).

Covid-19May 5, 2022

PCRs, RATs, and now LAMPs? The different Covid tests in New Zealand, explained

How do all the different Covid tests work? (Image: Tina Tiller).
How do all the different Covid tests work? (Image: Tina Tiller).

What do all the initialisms and acronyms mean? What’s the difference between them all? And how do they work? Naomii Seah clears it up. 

By now, you may have heard that a “new” type of Covid-19 test is being trialled at Auckland Airport as our border fully reopens to visa-waiver countries.

The Lucira test is a type of self-administered Covid-19 diagnostic test, which utilises the loop-mediated isothermal amplification (LAMP) method. Associate minister for Covid-19 response Ayesha Verrall described it as combining “the speed of a rapid antigen test with the accuracy of a PCR”. The tests will be trialled with 30 Air New Zealand staff for three months. Lucira tests will be cheaper than a PCR ($120-$200 when not publicly funded), but more expensive than available RATs ($6-$7 when not publicly funded); Verrall noted that once the trial is completed, they would likely be useful in certain high-risk contexts such as before commencing essential work, in aged-care facilities and as pre-departure tests. 

But what exactly is a LAMP test, and how can a home test be comparable to a PCR, which is conducted in a lab? Why aren’t RATs as accurate as LAMPs or PCR tests? What’s the difference between all these tests? To answer these questions, we first need a quick refresher on PCRs – which were the standard Covid-19 test used in New Zealand until the rollout of RATs in February this year.

How does the PCR work? 

Let’s quickly define some terms. 

First up: RNA. RNA is a molecule like DNA; they’re both genetic markers. DNA is double-stranded and forms its famous helix shape. RNA is single-stranded. Got that?

Covid-19’s genetic marker is RNA. If Covid-19 RNA is present in a sample, we can say that person is infected with Covid-19. 

The issue is that Covid-19 RNA will only be present in trace amounts. Enter PCR, which is a type of “nucleic acid amplification test” – if a person has Covid-19 RNA, a PCR test will replicate that code to measurable levels, confirming infection. 

motorists queueing for Covid-19 tests in the rain in Ōtara
Motorists queue for a PCR test at the Ōtara testing station in 2021 (Photo: David Rowland / AFP)

Here’s where it gets a bit complicated. PCR was invented in the 1980s, to replicate DNA – not RNA. PCR stands for “polymerase chain reaction”. A polymerase is the molecule that does the replication. It works by using an existing bit of DNA as a “blueprint”, copying the sequence over and over again. For the polymerase to work, the DNA needs to be split from its double strand into single strands, which is achieved by heat. This means a PCR test needs to be heated, then cooled, then heated, then cooled to achieve the desired DNA replication. 

But aren’t we trying to find Covid-19 RNA, I hear you ask? Yes! So to run a PCR test, any Covid-19 RNA in the sample must first undergo a separate reaction to create analogous DNA. 

The upshot of all that is that PCR testing for Covid-19 is complicated, requiring multiple steps and heat “cycles” – which is why our testing system broke down as we neared the peak of the omicron outbreak. Advances in PCR also enable us to quantify the starting amount of DNA present in a PCR reaction. In the Covid-19 context, this means PCR enables us to calculate a viral load. It’s a pain in the ass, but it’s accurate. PCRs are no longer the go-to test in New Zealand but still used to confirm infections in people who are particularly vulnerable to becoming seriously ill with Covid, and some countries require a negative pre-departure PCR result for people travelling there.

TLDR: A PCR test confirms Covid-19 infection by replicating and detecting the virus’s genetic material, enabling very accurate diagnosis.

How does a RAT work? 

RAT stands for “rapid antigen test”, and they’re actually a type of lateral flow assay. That’s a fancy term for a common type of chemical test. Pregnancy tests are also lateral flow assays, which is why the two look similar; RATs and pregnancy tests operate on the same principles. RATs were rolled out as the standard Covid-19 test in New Zealand in late February as we neared the peak of the omicron outbreak.

So, what’s an antigen? In the context of a Covid-19 test, it’s a unique marker for the virus. Often, that’s a protein on the surface of the virus. 

A health worker hands out rapid antigen tests at a testing centre in West Auckland on February 24 (Photo: Fiona Goodall/Getty Images)

You’ve likely heard the term “antibody” paired with the term antigen. Antibodies are proteins that bind to antigens. Together, they react to create an antigen-antibody complex. 

RATs contain specially designed antibodies that will bind to Covid-19 antigens in your snot. If you have Covid, an antigen-antibody complex forms where you drip your sample (taken from your nose with a swab, then mixed with an extraction buffer liquid) on the test. Further along the strip, at the T on your test window, another chemical is waiting that will react with the antibody-antigen complex. If you have a high viral load, ie lots of Covid-19 particles and therefore lots of antibody-antigen complex, there will be a strong coloured line. If you’ve got a low viral load, there’ll be a weak coloured line. If your viral load is too low, you might get a false negative. 

RATs can pick up a Covid infection when viral load is high (Illustration: Toby Morris)

As a RAT directly measures the virus in your sample without an amplification step, you’ll need a higher viral load to detect a Covid-19 infection with a RAT than with a PCR.

TLDR: A RAT detects antigens – markers present on the Covid-19 virus itself – so requires more virus particles to detect an infection.

Finally, the question you’ve been waiting for: WTF is a LAMP? 

A LAMP test stands for “loop-mediated isothermal amplification”. There’s that word again: “amplification”. It’s another “nucleic acid amplification test” that detects Covid-19 RNA. 

Like a PCR test, the LAMP test first needs any Covid-19 RNA present to be converted to analogous DNA before replication. But unlike a PCR, it doesn’t need heat to do it. Instead, through some complicated biochemistry, the whole reaction takes place in one container, and at one temperature, cutting the steps needed and the expertise required for a Covid-19 diagnosis. 

For anyone who hasn’t yet seen a Lucira LAMP test, it consists of a tube of liquid into which you put your nasal swab. The tube is then inserted into a single-use battery-powered device that spits out a result within 30 minutes. In simplistic terms, the tube contains all the ingredients needed for DNA replication, and the battery-powered device heats the mixture up to the required temperature. As the reaction occurs, a pH change causes a colour change, which the device monitors. If there’s no Covid-19 RNA in the sample, there will be no reaction and no colour change. 

This puts LAMP tests at a similar level of sensitivity to PCR tests, though the device can’t quantify viral load. 

LAMPs have been successfully used overseas in countries like Canada and Israel for a while now, causing some to criticise the Ministry of Health and the government for their slow uptake here. The Lucira LAMP tests now on trial with Air New Zealand were given an emergency use authorisation by the FDA all the way back in November 2020. National MP Chris Bishop has been advocating for the adoption of LAMP tests since earlier this year after a meeting with Sir Ian Taylor. Taylor believes the Ministry of Health has been slow to act due to confusion over how LAMPs differed from RATs, telling the Otago Daily Times: “How are the public meant to understand the important difference between a LAMP test and a RAT if the ministry’s officials don’t?” 

TLDR: Through some biochemical magic, LAMPs are a user-friendly version of a PCR test, with similar sensitivity, making them more reliable than RATs.

Keep going!
New variant who dis? (Image: Toby Morris / Tina Tiller)
New variant who dis? (Image: Toby Morris / Tina Tiller)

ScienceMay 4, 2022

Siouxsie Wiles: What we know about the BA.4 and BA.5 omicron variants

New variant who dis? (Image: Toby Morris / Tina Tiller)
New variant who dis? (Image: Toby Morris / Tina Tiller)

BA.4 and BA.5 are responsible for a new wave of Covid-19 cases in South Africa. At least one of them has arrived on our shores. So what does the science tell us about these new omicron variants?

While most countries are winding down their testing and sequencing efforts, South Africa has been doing an absolutely stellar job of detecting new Covid-19 virus variants. It was the country that first identified the three original omicron lineages, BA.1, BA.2, and BA.3, back in November last year. Once other countries started to look, they found omicron everywhere.

BA.1 started the initial global omicron wave, followed by the more infectious BA.2. In South Africa they only had one large BA.1 wave. Here in New Zealand, BA.1 and BA.2 arrived and seeded into the community very close together, so we had both at the same time – though BA.2 became the dominant lineage. BA.3 never really took off anywhere. 

Now South Africa has identified two new omicron lineages, BA.4 and BA.5. The data suggests BA.4 originated in mid-December and BA.5 in early January. At the moment, they are responsible for a new rise in cases in South Africa, the country’s a fifth wave of Covid-19. South Africa’s positivity rate – the number of tests that are coming back positive – has jumped from 4% to 20% in the last few weeks. In that time, daily cases have risen from the hundreds to the thousands. 

It’s not clear at the moment whether what’s driving the rise in cases is 1) BA.4 and BA.5 being more infectious, 2) BA.4 and BA.5 having mutations that help them evade immunity even more, or 3) whether everyone’s immunity from the last wave is now waning, making them susceptible to infection again. Given the timing since the last wave, it seems almost certain waning immunity is at play. It’ll be a little while before we know more about the other two options. Because it takes a few weeks for cases to progress to hospitalisations, it’ll also be a while before we know whether these new lineages are more dangerous than the virus already is, at least for people without access to the new antivirals.  

So what do we know about BA.4 and BA.5 at the moment?

The picture below shows a family tree for the Covid-19 virus, going right back to the early version that kicked off the pandemic – referred to as 19A. The omicron lineages are shown orangey-red. BA.1 is referred to as 21K, BA.2 as 21L, BA.4 as 22A and BA.5 as 22B. 22C is another lineage of omicron called BA.2.12.1 which has become dominant in New York State. As you can see from the picture, 22A and 22B both come from 21L, meaning BA.4 and BA.5 have evolved from BA.2.

What made omicron so unusual was the sheer number of mutations it has compared to previous variants of concern like delta, and the ability many of those mutations give the virus to infect people who have already had Covid and/or been vaccinated. They also changed what we call the tissue tropism of the virus. Delta seemed to prefer to infect cells deeper in the lungs, where as omicron is more up in the throat and nose. You can find out more about what mutations BA.1 has here and BA.2 has here

BA.4 and BA.5 are different from BA.2 by about eight to 10 mutations. Some of these we’ve seen before in other variants of concern, like epsilon, and others look like they’ll help the virus bind to its receptor on human cells a little better. One of the most concerning changes in both BA.4 and BA.5 is the L452R mutation. This is a mutation that delta has but BA.1 and BA.2 omicron don’t have. In March, Yahan Zhang and colleagues published the results of their experiments making a version of omicron containing the L452R mutation. Worryingly, they found that L452R enhanced the ability of omicron to infect the lung tissues of mice engineered to have the human version of ACE2 – the receptor the virus uses to infect our cells.

Remember how before I said omicron doesn’t normally infect lung cells so well? Well, the fact BA.4 and BA.5 now have this mutation suggests they’ll be able to infect those deeper lung tissues. Does that mean these new lineages will be able to cause more serious disease than BA.2? Possibly. What we don’t know is how the L452R mutation will behave in combination with the other mutations BA.4 and BA.5 have. Will they cancel each other out, or will their effects be additive?   

How worried should we be about these new variants?

Frankly, I’m worried about all versions of omicron around. All have the capacity to cause serious illness and death, in at least some people. And all have the capacity to cause lingering and debilitating symptoms, aka long Covid. Yes, even the BA.1 and BA.2 lineages of omicron. And that’s before we even factor in what the long-term impact of the damage the virus can do to our various organs even after a mild infection.

But I’m also worried about the variants of the virus we don’t yet know about but are almost certainly out there evolving away. Remember that omicron came out of nowhere. At the time BA.1, BA.2 and BA.3 emerged, the world was reeling from the delta wave and wondering how it might evolve in the future. Then omicron appeared and caused the biggest wave of the pandemic so far. Look at the virus family tree again. Omicron is from a completely different branch to delta. Where did it come from, and what’s the chance of another completely different variant emerging? Pretty high, it turns out.

One big problem with the “getting back to normal” phase that most countries have adopted is that it is putting immunocompromised people at high risk of infection. While this is obviously really dangerous for their health, it also has the potential to be really bad for everyone else’s too. Most people who catch Covid-19 will clear the virus in a few days or weeks. But some immunocompromised people are at increased risk of the virus replicating in their cells for many months. This is called a chronic or persistent infection and is different to long Covid where symptoms persist after the virus is cleared. 

Researchers recently reported the case of a 48-year-old woman who had the virus for 335 days. She’s diabetic and in complete remission after having previously had a form of blood cancer. She must have been one of the United States’ early cases as she was first admitted to hospital in April 2020. She was discharged a month later despite still having a fever, cough, and needing extra oxygen. She was PCR tested every three months, sometimes testing positive and sometimes negative. Her symptoms came and went, which sounds an awful lot like long Covid. Then in March 2021, her condition worsened and she was readmitted to hospital. She tested positive, again. 

But here’s the thing. Genome sequencing of the virus from swabs taken during her first hospitalisation in May 2020 and then her second in March 2021 showed the virus was the same variant. But that variant wasn’t the one circulating any more. In other words, she hadn’t been reinfected but had remained infected the whole time. And during that time, the virus infecting her had evolved, developing numerous mutations, including ones affecting the effectiveness of antibody therapies. 

Treatment of Covid-19 has come a long way since the woman was first admitted to hospital, so this time she received antivirals as well as serum from people who’d recovered from infection, which contained their protective antibodies. This time the treatment worked and three months later she was testing negative. We don’t know how rare this is, but another group of researchers, this time from the UK, just put out a press release saying they’d identified nine immunocompromised patients who were chronically infected, the longest for 505 days.

What’s clear is that the next variants of concern are currently evolving all around the world. Because they are evolving in both healthy and immunocompromised people, we’ve no idea what the next variant of concern might actually be. It may be one of these new omicron lineages, or it may be a form of delta, or it may be a version of the virus that was circulating a year or more ago.

We need to keep public health protections in place and strengthen our Covid surveillance

Researchers from the US have recently shown that large super-spreader events also contribute to the emergence of new variants. They found that most new highly infectious variants will fizzle out if they only infect a few people. But if these variants meet a super-spreading event, they are much more likely to gain a foothold in the community. That means as well as doing our best to reduce community transmission and stop the virus from infecting immunocompromised people, we need to reduce the chances a large gathering will turn into a super-spreading event. That should help delay or even prevent the emergence of at least some new variants of concern. 

What worries me is that we likely won’t even know the next new variant has emerged unless or until there are cases in a country like South Africa which is still testing widely and routinely doing genome sequencing. The reality is that PCR testing and genome sequencing are expensive, so most countries are dismantling their testing systems as part of “getting back to normal”, or making people pay for previously free tests, further reducing uptake. The Guardian reports the head of global diagnostics alliance FIND, William Rodriguez, as saying that despite the world experiencing the omicron wave over the last four months, “testing rates have plummeted by 70% to 90% worldwide”. The widespread use of rapid antigen tests means fewer samples suitable for sequencing too. 

As the director-general of the World Health Organisation, Dr Tedros Adhanom Ghebreyesus, puts it: “When it comes to a deadly virus, ignorance is not bliss.”

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