Need for speed
Speed of testing for Covid-19 is a priority, says Gisborne-based DNA scientist John Mackay.
The quicker people infected with this coronavirus can be identified, the quicker they can be quarantined and treated to prevent or reduce transmission.
“We want to take the process from two to three hours to 20 minutes,” says Mr Mackay, the technical director of Gisborne diagnostics and research business dnature.
Mr Mackay is seeking funding for the development of a new method that will greatly speed up Covid-19 detection, and a process that can be used anywhere and without the equipment used in the dnature lab.
The team have already started work on some of the ideas they have for a faster testing process.
“For a number of reasons, in Tairawhiti we have to send away our tests,” said Mr Mackay.
“It can take one to two days to get back results. Taiwawhiti is a community that needs rapid testing.
“We will find a way to help that doesn’t break regulations. Dnature is not registered as a testing lab and I understand the need for the regulation, but we’re in an extreme pandemic situation.
“Tairawhiti needs faster testing and we will find a way to make that happen.”
While his diagnostics and research business dnature is not accredited to do tests, Mr Mackay’s laboratory is the epicentre of New Zealand’s Covid-19 genetic identification methodology and materials.
Dnature has worked up the current gold standard tests as part of its work to improve test sensitivity and to pass this on to the other testing labs, says Mr Mackay.
Further improvements can be made.
“We’re hoping to get funding to bypass the RNA extraction bottleneck.”
That bypass would entail a process in which a swab or patient sample can be turned into something the DNA process can use.
RNA (ribonucleic acid) is a molecule that is involved in coding, decoding, regulation and expression of genes.
DNA (deoxyribonucleic acid) contains the instructions needed for an organism to develop, survive and reproduce.
In the testing procedure, a sample taken by swab from inside a person’s nose is mixed with several solutions in a plastic tube little bigger than a pen lid.
From a second tube, short DNA sequences called primers are mixed with the RNA solution.
A primer is a short strand of DNA that provides a starting point for DNA synthesis. Those strands come from the 30,000 letter-long coronavirus genome identified and published by scientists in China.
If the coronavirus is present in the swab sample solution the Covid primers recognise it and bind with it.
Because dnature began this work before the virus entered New Zealand, the team designed a synthetic piece of DNA to mimic the virus — and built some mistakes into it.
The synthetic piece of DNA is the control component, the sample that remains the same throughout the process.
“In case we need to confirm a result is from the patient, rather than the positive control, this allows us to differentiate between the synthetic virus and the true virus.”
Another tube contains the “copying juice”, the amplification reagents. If the target RNA is the needle in a haystack, the amplification process turns that needle into a haystack of needles.
This nucleic acid amplification test (NAAT) is based on detecting unique sequences in the virus’s RNA by a method called reverse-transcription polymerase chain reaction (rRT-PCR), writes microbiologist and science communicator Siouxsie Wiles in Stuff.
“Because the Chinese released the genetic sequence of the virus so quickly, that allowed tests to be developed and the methods released to the world so any country could do the test if it needed to.
“This is where the US screwed up. They decided to develop their own test instead and that ended up not working properly, which lost them valuable time.”
A PCR (polymerase chain reaction) machine enables a short segment of RNA, the primer, to be synthesised and act as a starting point for new DNA synthesis.
“If the primer binds to the RNA the PCR will make a DNA copy and amplify that DNA.”
While dnature seeks funding and continues to develop sensitivity in the testing process, the team have already started work on the new tests.
Meanwhile, demand from around the country for the reagents coming in from Germany and the US is so high one dnature staff member’s sole role is to manage the flow of the materials to the testing sites.
Before he could begin development of the test method Mr Mackay needed to get hold of the primers himself.
An order to dnature’s US supplier would have taken 10 days to get here.
To speed up delivery he emailed colleague Olfert Landt of Berlin biotech company TIB Molbiol and got an immediate response.
“I said this is a replay of the SARS virus and that I guessed he had assays to send straight away to me.”
An assay is an investigative procedure used to measure the presence of a target entity. In this case, the assay comprised the primers and detection probes premixed into a “just add water” format.
“He said ‘yes, I have them on the shelf.”
Within a few days they were in New Zealand and national testing began.
Now, the race is on to get a faster Covid-19 testing regime in Gisborne.