Covid 19 coronavirus: Why New Zealand might never know how virus came back

It's the mystery that's captured our collective imagination - and experts suspect we'll never know how Covid-19 slithered back into New Zealand.

Yet, beyond revealing the single weak point where the incursion happened, they say failing to solve the case won't make much difference to the country's ongoing fight against the virus.

Nearly 90 new cases of Covid-19 have now been linked back to the new cluster, which itself stemmed from an "index case" - a 50-year-old man working at Mt Wellington's Americold coolstore, with no history or link to overseas travel.

Contact tracers have been trying to work backwards from that index case, who tested positive on August 11, in hopes of finding the "primary case" - or the person who brought the virus into the country in the first place.

Yesterday - more than a week and 175,000 tests since the start of the outbreak - Prime Minister Jacinda Ardern shared some details on how exhaustive that process had been.

Virtually all of the country's border and managed isolation staff have been tested in the past 10 days, and so far there had been no additional cases, outside the mystery infection of a maintenance worker at Auckland's Rydges hotel.

"We have asked those who have been our earliest known infections in this cluster whether they have any links to overseas travel, airline crew or border workers, to try to establish links through contact tracing," she said.

"But this hasn't turned up anything."

At Americold - the Mt Wellington coolstore that the outbreak has been traced to - officials have been tracing a list of contractors who have visited the worksite, and also carried out testing at the port where Americold's containers were received.

"We have even undertaken environmental testing at the Americold site and checked our sequence against the one from an Americold outbreak in Melbourne, but none of this to date has provided any answers," Ardern said.

University of Auckland microbiologist Associate Professor Siouxsie Wiles says it's quite possible we'll never get any further.

"It that a big deal? From the testing we've done so far, it looks like this is a pretty tight cluster - so I would say, no," she said.

"What we have lost is the opportunity to know how it happened, or what gaps need plugging.

"But at the same time, we have to remember that nothing is 100 per cent guaranteed to work all of the time."

Having ruled out the possibility of the virus entering the country through frozen goods at Americold, scientists and authorities are now more or less settled on the explanation of a hidden, person-to-person chain of infection.

"I still think the most likely source of the cluster is that it came in via a border worker somewhere - whether at an airport, a port, or a quarantine facility - and it's then gone a few more steps in a chain before it arrived with the worker at Americold," University of Canterbury mathematician and modeller Professor Michael Plank said.

"Tracing backwards does get harder as you go, simply because it's difficult for people to remember who they were in contact with last week, as opposed to the week before."

Traces of the virus from earlier infected people might have also now vanished, leaving the trail cold - although it was possible antibody testing could still pick that up.

What can we infer about this chain from the fact no other positive cases were detected before August 11?

While New Zealand modelling has suggested that, without controls in place, the virus could be capable of spreading from one person to another three on average, Plank said it was common for an infection to result in just one other.

"I'd add we don't know for sure that there aren't any other clusters lingering out there, but the fact we've done a lot of testing does give us a lot of confidence there aren't."

Dr Jemma Geoghegan, an evolutionary biologist and virologist at the University of Otago and ESR, remained confident the outbreak wasn't linked to New Zealand cases from months ago.

"We did have this lineage in New Zealand way back in April, but both the genomic and epidemiological data we have doesn't link this new cluster to those old cases," she said.

"We know that there are a substantial number of people around the world who get really sick with this disease, and in my view it's very unlikely it could have gone undetected for several months."

Genomic sequencing of the latest samples revealed the lineage - called B.1.1.1 - as one with strong connections to coronavirus in Australia, the UK and other countries.

But, having analysed more than two dozen samples from positive cases that have been isolated in quarantine facilities, ESR scientists still haven't found any local recent matches.

Geoghegan stressed that scientists carrying out sequencing work on those samples didn't have all the puzzle pieces they needed.

Around 40 per cent of the samples, for instance, didn't contain enough genetic material to be able to construct a full genome.

She agreed with other scientists' conclusions about being able to track down the primary case.

"I think there's a good likelihood that we might not ever find out."

Ardern said there were other possibilities - albeit less likely - and authorities would keep hunting.

"But just as was the case in our first wave of infections, we may not find all the answers for this cluster," she said.

"We have, however, learned valuable things that have led to improvements in our response.

"So as long as we have the cluster contained, we can still lift our restrictions eventually."