Covid-19: How New Zealand's testing strategy was defeated, and how saliva testing can help
Friday, 19 November 2021
Early on in the Delta outbreak Rodney Jones saw something in the testing numbers that made him very nervous.
Tests are a sample of a population, so if 0.1 per cent of all tests are positive then there is a good chance you are capturing all of the positive cases with your testing.
However, if the positivity rate is higher than this then there is a good chance you are not.
The problem was, even with a lower rate of testing in Auckland, the positivity rate in South Auckland in September was 1 per cent, 10 times Jones’ comfort threshold.
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It hit 1 per cent first amongst Pasifika communities getting tested, then among Māori.
Jones, a principal at Wigram Capital advisers who also advises the Government on some Covid-related matters, thought there was a need to massively ramp up the nation’s testing capacity by four or five times the number of tests a day, the problem was we couldn’t.
“We didn’t have the armoury we needed, you need rapid testing.”
New Zealand’s testing regime is currently far from rapid. In answers to written Parliamentary questions Covid-19 Response Minister Chris Hipkins reported numbers showing it took more than 24 hours to process one third of all Covid-19 tests.
In this case processing doesn’t include how long it takes staff to transport the samples to the lab, instead it goes from the time a sample is received at the lab to the time a result is entered into a computer system.
The main laboratory network contracted to do a lot of the work, Asia Pacific Healthcare Group (APHG), controls 75 per cent of the pathology market, and is warning people leaving the country that they shouldn’t expect their Covid-19 tests to be processed within 72 hours.
An APHG spokeswoman says the company is “comfortable” with its testing times, and says other labs are also involved in PCR testing – although she won’t comment on whether APHG labs are the ones taking more than 24 hours to process tests.
New Zealand businesses are now facing up to the challenge of keeping their workplaces free of infection while vaccinations get up to speed and the testing network remains stretched.
It is a similar situation to the one University of Illinois professor of chemistry Martin Burke, and others at his institution, faced in 2020.
The University wasn’t facing the Delta strain then, but they were trying to figure out a way to open up their 48,000 strong campus with no vaccine available.
The University of Illinois ranks highly on academic rankings of United States universities, but it also has another ranking its leaders are less keen to promote: it is one of the country’s top campuses for student parties.
“We were thinking, OK, we're going to bring back 35,000 undergraduates from all over the country in the world, right back to Champaign Urbana, in August of 2020,” Burke says.
The multidisciplinary team looking into it used physics-based models to figure out how different measures like testing, mask wearing and social distancing might affect their ability to re-open.
Their focus was on keeping the “R” number below one, and they started adding and subtracting variables.
They discovered something crucial quickly, social distancing and masking wouldn’t get that R value below one, but doing that alongside frequent testing would.
“If you had a really good sensitive test, and you're testing everybody twice a week, the modelling showed you would catch people early, and many people you would catch before they had symptoms, and you would help, therefore get them out of the population.”
Which was great in theory, but not very realistic at the time.
PCR testing as the most accurate form of testing for Covid-19, but testing 48,000 people twice a week would probably require a testing rate of 20,000 a day – a testing capacity similar to what we have for our entire population of 5 million people.
“There was no test available that could do that, and as you know, at that point, the only thing is really available was the nasal swab test, and good luck trying to convince everybody to do nasal swabs twice a week.”
The issue wasn’t just how painful nasal swabs were, but how long it took to disassemble and process them in the lab, along with the cost of all the reagents needed – all very expensive things for a single university campus.
Burke credits Kiwi expat Anne Wyllie, of the Yale School of Public Health, with a scientific discovery around the detection of Covid-19 in saliva.
The research enabled his team to create a Covid-19 saliva testing and isolation system that would see the campus run so many Covid-19 PCR tests that it accounted for 1 to 3 per cent of all tests run in the US on some days.
A key part of this was a heat treatment step, which cut out a number of time-consuming and expensive parts of the process.
By heating a saliva sample you deactivate the virus, allowing you to test the sample without the kind of precautions needed when dealing with a live virus, and you can automate more steps.
Illinois students were tested twice a week, those who tested positive needed to isolate within 30 minutes of receiving a result, more frequent testing (three times per week) was used when a spike in positive tests was detected within a particular group or area, this helped them pickup Covid-19 cases from people attending parties in defiance of campus rules.
Later, when vaccines arrived, testing was dropped as a compulsory requirement except for unvaccinated students and people in high-risk living environments.
Throughout the pandemic, including after Delta arrived, the campus has suffered no hospitalisations or deaths, before Delta it had also got its case numbers down to zero.
The University of Illinois has its critics, most notably Daniel Simons, a psychology professor who has criticised the university for how long it took to ramp up capacity to the promised 20,000 a day (he says it took a while for them to scale up the logistical operation).
However, even Simons doesn’t criticise the test, instead he calls it “impressive”.
Yet Burke’s test has become the unexpected target of political controversy in New Zealand.
Illinois Covid Shield is used by Rako Science. While Rako Science is widely used in the private sector, including by Amazon while filming the Lord of the Rings (Amazon required a diagnostically validated test to satisfy film insurance guidelines), and the New Zealand Olympic Team, it has been snubbed by the Ministry of Health.
The Ministry of Health rejected Rako’s bid for a border worker saliva testing contract and chose APHG through a procurement process that has been heavily criticised by the Auditor-General for the conflicts of interest involved.
However, corporate leaders are looking for alternatives to the public testing system, and they’re looking to rapid antigen tests and providers like Rako Science for them.
Napier Port has introduced a 100 per cent vaccination policy and saliva testing using Wyllie’s SalivaDirect protocol (which operates along similar lines to Burke’s).
They aren’t using Rako Science, but have done it by establishing a miniature lab of sorts at the port using Ubiquitome testing machines and specialist medical staff. It will be compulsory for employees to get tested three times a week.
Napier Port Chief Executive Todd Dawson says it is a cheaper and more accurate option than rapid antigen testing, even with the extra people you have to hire to run it.
High accuracy means Covid-19 can be picked up before workers become infectious, which can stop them spreading it to others.
“We’re not going to wait around for the Government to provide something because, quite frankly, we’ll be waiting forever,” Dawson says.
However, it also means some Napier Port employees may end up taking five Covid-19 saliva PCR tests a week.
If they have chosen the Government’s saliva testing programme they will take two ministry-approved saliva tests, then three tests with Ubiquitome machines.
While government-provided tests can take days to arrive, Adam Harvey, marine and cargo operations general manager, says port workers will take a test after they finish their shift and get a result before they start work next day.
“This is about early detection and having them not come into work infectious.”
Jones says the Ministry of Health is too strongly opposed to developing the kinds of testing tools we will need for the next phase of our Covid-19 response.
He believes we need the ability to deliver 100,000 tests a day in New Zealand, and he sees no other way than to rely on some form of rapid test – even if it produces more false positives and negatives.
“We’re never going to return to elimination, so that’s over. That was fantastic for 18 months, but that’s now over.
“We're going to have to develop a toolkit that is much more comprehensive and much more sophisticated.”
What riles Jones up is just how much of the recent debate has focused on the possibility of everyone getting a summer holiday rather than what happens in autumn when it is colder, school is in full swing, and more people are indoors.
“We should be much more worried about ‘what does 2022 look like’, what does the winter look like, how are we going to manage living with this, are we building the toolkit today?
“And the answer to that, right now, is no.”