Why did New Zealand's latest community case test negative for Covid-19 after arriving in the country, but positive a week later? Could it have been a historical case? Could it have caused a new outbreak? And why didn't the vaccine clear the infection? Jamie Morton explains.
Our newest community case - an Air New Zealand crew member - returned a negative test shortly after arriving into Auckland from Tokyo on February 28, before receiving a vaccination shot on Wednesday, and finally testing positive at the weekend.
Health officials say the most likely scenario was the person was exposed overseas and therefore, most likely was either incubating, or infectious with, the virus before being vaccinated later in the week.
But there's also a possibility the infection may have been a historical one.
An old case?
It's understood the positive sample had a cycle threshold (CT) value that made for a "weak positive".
These samples could point to the case being early in their infection - which might be more unlikely in this case - or viral debris lingering from an earlier infection, weeks or months ago.
Out of 239 cases confirmed in New Zealand this year, 37 have been historical.
Otago University epidemiologist Professor Michael Baker said it wasn't uncommon for such cases to test negative and later positive.
He said it could come down to which parts of the person's respiratory tract was picked up by a given swab test.
ESR and Otago University virologist Dr Jemma Geoghegan added that a weak positive sometimes also didn't reflect the case itself - but how the sample was handled and processed.
She said results of genome sequencing expected tomorrow could tell us whether the case did happen to be a historical one.
If so, the next step would be to try to match to any positive cases previously recorded at the border.
To detect the presence of viral genes in a sample, scientists use what's called a polymerase chain reaction, or PCR, test.
This involved searching for the virus' genes in a sample taken from the person being tested - usually with a swab from the nose or throat that Kiwis are now familiar with.
Importantly, these tests could not determine whether or not infectious virus was present - or if indeed the patient was infectious at all.
While studies have suggested the infectious virus was more likely to be cultured in samples strongly positive by PCR, virus could still be cultured from weak samples.
Scientists could get an idea of how much virus was present in a sample by looking at the Ct value - and the lower that value was, the more copies of the virus was present.
Sometimes, the tail of PCR positivity was so long that low levels of the virus could linger for several weeks or even months.
The infection window
In the first few days after infection, a PCR test would typically come back negative.
"So if you have a test in a point in time where you don't have detectable virus, it doesn't mean you're necessarily negative."
Once the virus became detectable, the amount of it rapidly increases - making for a lower Ct value - before decreasing over the next few days to weeks.
Even still, it wasn't possible to accurately time the infection or determine infectivity with a PCR test, which needed to be taken in context with a patient's symptoms, exposure history, and previous test results.
Geoghegan said the lag between exposure, infection and having enough virus present to test positive was one reason why pre-departure testing couldn't always be relied upon.
One study she co-authored showed how a number of a passengers on one flight turned in negative pre-departure tests - yet were nonetheless infectious.
"In [the latest case], it could have also been that they were actually negative, but got the virus the next day," she said.
"Nonetheless, it's important to stress that a negative test only means that it's not detectable at that point in time.
"The Ministry of Health has caught on to this now, by requiring people to get tests when they are identified as a contact in the community."
Lucky in lockdown?
Health officials maintain the public health risk was low from the case, because she had limited contacts.
Auckland also happened to be at alert level 3 for much of the time she would've been infectious.
"Having not been in lockdown, there would have been higher chances of onward transmission - and we could be dealing with a larger cluster," Covid-19 modeller Professor Shaun Hendy said.
The likelihood of that would've depended on the person having been infectious enough - the "80-20 rule" suggests 80 per cent of disease transmission events in an epidemic are caused by 20 per cent of people - and whether they'd attended large "super-spreader" events.
Had New Zealand been at level 1 or 2, Hendy said it was difficult to say what the "R" value - or the average number of people that one infected person passed the virus on to - would have been.
"If we were forced to guess, we'd probably say something like 1.5."
What about the vaccine?
If the case did happen to be infected when they received their shot last Wednesday, that didn't mean the vaccine would have purged the virus.
The Pfizer vaccine the crew member received has been shown to provide some protection against symptomatic infection from 12 days after the first dose, increasing to 95 per cent protection from seven days after the second dose.
Therefore, taking it after infection was unlikely to provide any protection against the development of symptoms and disease.
"After you are vaccinated it takes the body at least a week to get those protective antibodies pumping out so you won't be protected straight away," University of Auckland vaccinologist Associate Professor Helen Petousis-Harris said.
"Also, while most people who get the vaccine will be well protected, there will be a few people who do not respond as well."
Keeping up our other prevention behaviours, she said, had to go hand-in-hand with vaccination for a while as long as this virus was widely circulating in the world.
Vaccine Alliance Aotearoa New Zealand clinical director Dr Fran Priddy said that was a "critical point".
"We don't know how effective any of these vaccines are at preventing infection. We know they are effective at preventing disease, hospitalisation and death," she said.
"So even vaccinated people need to keep up with routine Covid prevention measures. They could still become infected and spread to others.
"We should have better information on how well the vaccines prevent spread in the near future, but for now everyone needs to follow the same preventive measures."
Petousis-Harris meanwhile pointed out the vaccine itself couldn't cause any infection.
"There are no viruses or any other infectious material in the vaccine. In fact, this vaccine has been made entirely without the virus."
Air crew clampdown needed
Experts say the case ultimately highlighted a remaining weakness at New Zealand's border.
"Air crew are working in a high-risk environment without full personal protective equipment," said Associate Professor James Ussher, of Otago University's , Department of Microbiology and Immunology.
"While there are currently risk mitigation measures in place, both during air travel and at overseas destinations, these are insufficient to prevent infection, as demonstrated by this case."
Along with vaccination of air crew, he argued procedures should be reviewed and tightened to reduce the risk of introducing the coronavirus to New Zealand.
"This should include reconsideration of the isolation period for air crew on return to New Zealand, and the frequency of the testing regimen."
The Ministry of Health was considering whether there needed to be more restrictions on international crew.
"We are going through a process ... of whether we need to up the ante on different countries," Prime Minister Jacinda Ardern said today.
Under Covid rules, air crew members are required to undergo Covid-19 testing every seven days.
All Air New Zealand air crew returning to New Zealand after flying on "higher-risk" routes need to self-isolate in a prearranged hotel for 48 hours.
Los Angeles and San Francisco are currently designated as higher-risk routes. Japan is not considered a high-risk route.
Once they have returned a negative test, they can leave the hotel.
Baker said the fact the staff member had been picked up with a routine test was good news.
But he acknowledged that the lack of isolation on arrival - of airline staff - was worrying.
"Throughout the pandemic, it's always been a source of concern - the fact that we have a very different process for aircrew.
"They have never gone through the standard process that other returning travellers do - which is ...14 days in MIQ and two or even three tests now.
"There have been reasons for that. But it's obviously an area of vulnerability."