A review has described New Zealand's genome sequencing effort as "world-leading" – but has still found room for improvement in steering the clever technology against Covid-19.
Genome sequencing creates a "genetic fingerprint" of a virus that's infected a person, and can help public health officials untangle different cases involved an outbreak through their genetic sequences.
In New Zealand's first wave of Covid-19, scientists sequenced the genomes of 649 separate cases to reveal nearly 300 different introductions from different parts of the world.
Sequencing proved just as crucial in the August outbreak, helping pick apart Auckland community cases – effectively informing the response to the cluster in real time.
"There were several instances where we were reassured that seemingly unconnected clusters were actually closely linked," Prime Minister's chief science adviser Professor Juliet Gerrard wrote in a post introducing the just-released review.
"There were other times when the specific mutation in a sequence significantly narrowed the search for the contact tracers.
"Without that information, we would have been in the dark about whether new cases lacking a known link to the cluster were due to another source, or were in fact linked to the community outbreak."
The review, carried out by Environmental Protection Authority chief scientist Professor Michael Bunce, noted that half of Covid-19 cases that had received positive PCR tests had been sequenced.
New Zealand also stood as one of the few countries to publish a nationwide genome study.
But Bunce found there was a need to build capacity, speed up the delivery and processing of samples, and improve how genomic data is reported.
"The speed at which samples are shipped and genomes can be sequenced remains a priority if genomic data is going to be useful in real-time contact tracing and cluster analysis," he found in the review.
There was further potential to further develop capacity to ensure there was no single point of failure that would disrupt the flow of genomic data when it might be needed urgently.
Bunce also found the reporting of genomic data could and should be improved.
That included embedding a "priority system" for genomic analysis that could rapidly report viral lineages from "urgent" samples to contact tracers, along with more consistent data presentation, and a closer working relationship between different scientists and officials.
Despite the high rate of sequencing, Bunce also found that missing genomic data from positive samples would continue to hamper efforts to pinpoint the sources of any outbreaks that might escape border quarantine.
"There is room to improve both processes and priorities in this area," he said, adding that protocols should be put in place to sequence all samples that tested positive.
"This may require multiple samples be taken for every MIQ person, alternatively, rapid follow-up testing as soon as a positive PCR result is recorded."
Those samples that failed to yield full viral genomes should be analysed using shorter fragments of the genomes, he said, ensuring that a viral strain could still be determined from even small sections of the virus.
More broadly, New Zealand needed to embrace genomic tools for the long-term monitoring of viral evolution.
"This is not simply an academic exercise, rather there is a pressing need to monitor the viral lineages that are circulating - akin to seasonal influenza tracking," he said.
"This is vitally important once a vaccine is deployed in Aotearoa New Zealand and border restrictions are relaxed. Genetic characterisation of circulating lineages needs to become routine practice."
Finally, he found a need to better communicate the science of genomics to the public.
"Given the public interest in this science, there is an opportunity to explain and educate about the wider benefits of genomic testing and technologies, including how vaccines are made and tested."
ESR chief scientist Brett Cowan said the Crown research institute had been using genome sequencing and bioinformatics long before the pandemic and investing in technology and expertise.
"Obviously, the pandemic has called for higher levels of investment and speed for our scientists to provide solutions in this unique situation," he said.
"ESR has made sizable investments in genome sequencing, including the purchase of a GridION to enable the fast throughput needed to have rapid impact.
"The review applauds our efforts thus far, and those of our collaborators, but calls for the science to keep moving and we are living that advice."
ESR scientist Dr Joep de Ligt said he and colleagues were now working with a large number of experts around the country, from clinical microbiologists to epidemiologists.
"Sequencing is proving to be a valuable tool for New Zealand and we also want people to engage and understand it," he said.
"Providing this information to the public for them to understand and dissect through platforms like NextStrain will help bring understanding and through that trust about the use of these technologies."