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Mike Bunce, a geneticist and top scientist at the Environmental Protection Authority, is the author of a new report on the role of genomics in responding to Covid-19.
Genome sequencing enables health experts to better understand if and how cases are linked.
Professor Bunce says during the first wave of the pandemic, genome sequencing was not a priority and only half of positive test samples from managed quarantine facilities were sequenced.
Therefore, it was not possible to rule managed quarantine in or out as the source of the outbreak - but it seems most likely.
Professor Bunce told RNZ's Morning Report programme we should be doing everything possible to close gaps in genomic surveillance.
"We should be doing everything possible to get a genomic sequence from every single managed isolation and quarantine sample."
This might mean taking more than one swab type, he said.
Genomic technologies need to also be adapted to deal with highly degraded samples like the ones seen in managed isolation, he said.
"I think we can say with 100 percent certainty that this second wave has come across the border, it's still an outstanding question whether it's come through people or through goods."
Genomic surveillance, when integrated with contact tracing, can provide a better surveillance net to understand transmission chains, he said.
"Using these genomic technologies, trying to understand who might have given it to who and take unknown samples where we don't have links to people and draw those lines."