A virologist says it's "hugely significant" that there's no genomic match between the new cases and any in MIQ - potentially pointing to a missing link in the community or a leak from elsewhere at the border.
Genome sequencing creates a "genetic fingerprint" of a virus that has infected a person, allowing health officials to untangle or link up different cases.
Sequencing proved especially crucial in the August outbreak, and also in New Zealand's more recent community incursions, providing officials more confidence the virus had been isolated and stamped out.
But in the latest case, there was no genomic match with any positive cases detected in managed isolation and quarantine (MIQ).
ESR and Otago University virologist Dr Jemma Geoghegan said that fact was "hugely significant".
"It's why the city went into lockdown, because there's no physical or genomic link that we can immediately identify in a way that links this case back to our border - and that's very concerning," she said.
"It's kind of like going back to [the Auckland August cluster], where we've had this lineage in MIQ before - but it's not a direct link.
"So we're either missing people in this chain of transmission or it's another source of leakage from the border, and not through MIQ.
"Right now, there are lots of pieces to the puzzle still missing and it's possible that we might not find an answer, as we didn't in August."
She added it was positive that testing so far hadn't revealed any further hidden community cases.
ESR's bioinformatics lead, Dr Joep de Ligt, agreed it was possible there could be an "in between step" missing.
"It's another line of evidence indicating that we have to be cautious, and that we have to take those precautions that are now being taken," he said.
"We just need to do everything we can to find those missing links - and in the meantime also make sure that it doesn't spread further."
De Ligt said scientists had attempted to sequence almost all positive cases that had been detected at the border.
Some of those samples carried a low viral load of the virus, making it harder to render a complete genome.
"But even in those where we have a partial genome, we looked for those specific mutations that are present in these cases - and we haven't found a link."
Some other samples that were collected recently were still to be sequenced.
"So if there are any clues to be found, we will know as soon as possible."
The latest cases come as ESR recently expanded its sequencing work to its Mount Albert Science Centre in Auckland.
Since opening late last month, the centre has now sequenced a number of SARS-CoV-2 genomes over 12 sequencing runs.
The first sample was received on January 25 - when urgent work was needed to sequence the cases involved in last month's Northland scare - and the latest included Sunday's cases.
Until last month, sequencing at the Auckland centre had been carried out for research and development of sequencing methods for forensic applications.
The Auckland team, which work alongside scientists at ESR's Kenepuru Science Centre in Wellington, includes staff with expertise in the DNA and RNA profiling of case samples.
ESR has also provisioned its Christchurch facility for any urgent samples needing sequencing that come from the South Island.