Covid 19 coronavirus: Genome-sequencing could be the key to avoid lockdown

If the source remains elusive, branches of Covid-19 transmission could be spreading in the city and even around the country. Photo / 123RF

ANALYSIS:

A lot potentially hinges on tomorrow's results of the genome sequencing for the Auckland woman - New Zealand's new mystery Covid case.

If they show a link to a case in a managed isolation facility close to her workplace or home, the outbreak will be contained more easily and Auckland may well avoid any lockdown.

If the source remains elusive, branches of Covid-19 transmission could be spreading in the city and even around the country.

In the meantime, 100,000 people in the Auckland CBD are essentially being asked to be in quasi-level 3, minimising contacts and movements, and wearing a mask and keeping physically distant if they leave home.

The source remains the biggest missing piece of the puzzle, but others include the number of as-yet-undetected cases, and how far their movements might have spread the virus.

So far the woman is the only case and she has only three close contacts - a colleague and two friends.

She has a small circle of work colleagues, and while there are dozens of residents at the Vincent Residences, where she lives, she herself lived alone, as did one of her identified close contacts.

Locations of potential transmission where the woman and her close contacts visited are all in the Auckland CBD.

For that reason, Covid-19 Response Minister Chris Hipkins said there was no evidence of "enhanced risk" outside the CBD, hence the localised quasi-lockdown.

Covid-19 Response Minister Chris Hipkins said there was no evidence of "enhanced risk" outside the Auckland CBD. Photo / Mark Mitchell

That's not to say there are no potential vectors for transmission outside the CBD. She was in a customer-facing position at the A-Z Collection store. Diners sitting near her at the Red Pig restaurant might have caught and taken Covid-19 to another region. Her Uber drivers might have become infected and passed it to other passengers.

The new case in Auckland is a woman in her 20s who works at A-Z Collections in Auckland's High St.

And if any of the common areas in the Vincent turn out to be hotspots for infection, then the potential for the virus to have already spread in all directions is much greater.

The Government is counting on the chances of any of that happening to be slim to none. The last thing Prime Minister Jacinda Ardern wants is a Melbourne-like outbreak, where initial restrictions were a few suburbs shy of where they needed to be.

Indeed Ardern pointed to Melbourne whenever a more localised lockdown was called for during the Auckland August outbreak, which had already spread across the city and into the Waikato by the time it was detected.

Back then, we only had about 20 per cent of MIQ cases genomically sequenced - pretty poor in terms of shedding light on what remains an elusive source.

Now we are at 55 per cent. More importantly, recent cases in MIQ facilities close to the woman's home and work have been sequenced.

So far the response has followed Ardern's rapid response plan, with immediate and localised restrictions while further information is sought.

The plan shows the likelihood of lockdown depending on what happens in the coming days.

If genomic sequencing points to a source and there are only a few new cases, a move to level 2 or even staying at an enhanced level 1 is likely.

If not, and more cases and contacts pop up, level 3 lockdown looms - though it might remain very localised, depending on cases' movements.

A harder call would be if the source remained a mystery, but very few new cases were found. What should happen if undetected transmission is likely but there's little evidence of it?

The call for CBD dwellers to wear masks has again raised the question of why the Government hasn't mandated it for public transport and flights at level 1, as well as compulsory QR scanning.

Hipkins suggested that doing so might see public compliance crumble, but now might be the time to move; Kiwis are more likely to keep the faith when the prospect of lockdown looms.

He also helpfully gave an indication of whether there will be good news or bad news between now and tomorrow's update.

If there is a change to alert levels, it will be fronted by Ardern.