New Zealand labs process some 5000 Covid-19 tests each day. Photo / Don Thomas/RNZ
New Zealand labs process some 5000 Covid-19 tests each day. Photo / Don Thomas/RNZ
New Zealand labs churn through an astonishing number of Covid-19 tests each day.
With our total tally nearing the million mark, labs around the country are processing just over 5000 samples daily.
As Auckland's outbreak showed, that could be quickly scaled up to 20,000 - but it was gruelling, painstakingwork.
And contrary to popular belief, it wasn't automated, with a number of manual steps that lab technicians had to repeat up to thousands of times each day.
"The risks of occupational overuse and burnout among laboratory scientists is very real," said Dr Joshua Freeman, clinical director of microbiology and virology at Canterbury District Health Board.
"This threatens the sustainability of our public health response. For this reason, labs are putting a lot of ongoing work into eliminating manual steps from processing and testing Covid specimens."
New Zealand's standard method of testing for Covid-19 remained what's called polymerase chain reaction, or PCR.
That 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.
PCR tests require technical expertise, have to be carried out in labs, and typically take as long as 24 hours to provide results. Photo / Dom Thomas/RNZ
Last week, the World Health Organisation announced an initiative to make available to low and middle income countries what are called rapid antigen tests.
These tests detect specific proteins - antigens - on the surface of the virus that causes Covid-19.
They're seen as attractive as they're easy to use, might not need to be performed in a laboratory, and provide results as quickly as 15 to 30 minutes.
By contrast, PCR tests require technical expertise, have to be carried out in labs, and typically take as long as 24 hours to provide results.
Why haven't these tests been deployed here and elsewhere already?
"A major reason has been concern about the accuracy of these tests and, until recently, there were little data on their performance," explained Professor David Murdoch, a clinical microbiologist and infectious diseases physician at Otago University.
"We now know rapid antigen tests are less sensitive than PCR at detecting cases of Covid-19, and may fail to detect fewer than 20 per cent of cases."
In other words, he said, they could produce a relatively high proportion of false-negative results.
That meant scientists had to weigh up the benefits of ease of use and rapid turnaround times, with the risk that more cases could be missed.
"There is a valid argument that people who have a positive rapid antigen test are most likely to have high levels of the virus and are more likely to be infectious to others," he said.
"However, it is still unclear just how confident we can be that a person with a negative rapid antigen test is not infectious."
Saliva and serology tests
Saliva tests could be carried out without the invasive nasal swabs many Kiwis will now be used to. Photo / Mark Mitchell
Scientists at ESR have been exploring the potential for saliva tests, which may prove more sensitive and effective and less invasive than nasal swabs.
It's already been suggested our border workers could be excellent candidates to use rapid and minimally invasive techniques, such as the SalviaDirect method developed by Yale University researchers, and just approved by the US FDA.
Border workers might submit a saliva sample each day, or every few days, along with routine temperature checks and health questionnaires.
But Freeman didn't see saliva testing as currently viable for lab processing, given specimens required extra manual steps to homogenise and liquefy the sample.
Even after being homogenised, there remained big unanswered questions about whether high volumes of specimens could be reliably processed on the available automated instruments.
"So when comparing the merits of saliva over nasopharyngeal swabs, consideration needs to be given to the implications for our laboratory scientist workforce and realism about what's practically achievable in the laboratory setting," Freeman said.
"Saliva may certainly have a niche role as an alternative to nasopharyngeal swabs, but a lot more work is required before we know whether high volume saliva testing is a realistic option."
Serology tests, meanwhile, were blood tests that could show if a person may have once had been infected without knowing, revealing hidden chains in outbreaks with mystery sources.
They also had the potential to identify those who were infected within a few minutes, allowing them to self-isolate and avoid infecting others.
"These are becoming more important as the pandemic progresses and we look to find those people who have had the disease but didn't know they were ill," ESR chief executive Peter Lennox told the Herald last month.
"We are awaiting ethics around a study in the serology area, so keep your eyes peeled for this."
Wastewater tests
Researchers at ESR test wastewater samples from managed isolation facilities. Photo / Dom Thomas/RNZ
Another area being further explored by ESR was the potential for wastewater stations to be used for community-level surveillance of Covid-19.
The approach - called wastewater-based epidemiology - has already been used in New Zealand to study other viruses, and even illegal drug use.
Recent studies have suggested that live traces of the virus can be isolated from the faeces and urine of infected people, and can sometimes survive for up to several days after leaving the body.
The concept was being pushed by many prominent Kiwi scientists, including Otago University's Professor Neil Gemmell, who is part of an ESR-led group just awarded $1.6m to begin research.
"The main message is that the research is progressing but the data from the collection of samples are not yet actionable," Lennox said.
"The overall goal long-term is for robust and reliable tools for detection in sewage, that can be used to identify any unrecognised Covid-19 infections in New Zealand.
But before that could be done, a proper methodology needed to be developed, and wastewater samples were recently collected from Auckland and other places for analysis.
