Covid 19 Omicron outbreak: New sequencing weapon to pinpoint cases shows promise, but has limits

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A major new strategy in the fight against Omicron has been welcomed but could face severe strain if case numbers overwhelm contact tracers.

Urgent whole genome sequencing - used to identify and link the genetic fingerprint of individual infections, and confirm variants like Omicron - will now be prioritised for any unlinked community cases and those involving border-related workers.

Previously, whole genome sequencing was prioritised for international arrivals, who would now also be assumed to be carrying the globally-dominant Omicron.

Meanwhile Health Minister Andrew Little said today he was confident the health system could cope, despite modelling indicating New Zealand could face between 5000 and 50,000 Covid cases a day.

It comes as Auckland Hospital doctors have been told they may be asked to return to work five days after testing positive for Covid.

A memo from senior management, obtained by RNZ, also says staff may be drafted into other roles to help cover staffing gaps - and leave could have to be cancelled.

Hospital bosses expect up to a quarter of staff could be off work for some time as the outbreak spreads.

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Te Pūnaha Matatini complex systems researcher Dr Dion O'Neale said it was just about impossible to know how widespread Omicron was right now.

"It's almost certain that this is going to take off and get big," the physicist said.

He welcomed the move to broaden sequencing, which could determine the similarity of infections from different people.

But its effectiveness in weeks ahead would rely on an intricate series of other events, and ultimately, it seemed likely contact tracing would have to be refined.

Dr Dion O'Neale says the expansion of sequencing is a positive move, but Omicron case numbers could still overwhelm contact tracing. Photo / Supplied

O'Neale said once hundreds or thousands of cases were appearing, contact tracers would have to make judgment calls on who to track down, and who to ignore.

"It depends how vigorously you're contact tracing."

He said in last year's Delta outbreak, the tracing system was stretched at about 100 daily cases.

But then, interviews with contacts were extensive.

O'Neale said in an Omicron scenario, investigators might be told an unknown person shared a bus with a positive case.

"Do you spend half a day trying to track down that person, or do you say: We're going to move on?"

And some contact networks will be much simpler to pin down, he said.

"For example, if someone was infected and they were at work, it was relatively easy to contact trace who they were at work with."

Dr James Hadfield, Wanaka-based sequencing expert with Seattle's Bedford Lab, said the expansion of whole-genome sequencing was a crucial step.

"It's hugely important. The cost is worth every penny," he said. "There is a lag but the information is so valuable."

A common PCR swab test can be sent to Environmental Science and Research, which then conducts sequencing.

"One of the things that genome sequencing allows us to do is to identify whether a positive case at the border, at the community, is Delta, is Omicron."

Hadfield said in every country, sequencing faced limits.

"If we are in a situation where we have thousands of Omicron cases a day in New Zealand, we don't have the sequencing capacity to sequence that many cases."

People queue outside the Auckland City Doctors on Queen Street, central Auckland. Photo / Michael Craig

And Hadfield said most rapid antigen test users would never get their results sent for genome sequencing.

The rapid tests, or lack thereof, have sparked intense political debate, with the National Party saying the Government had been hopeless at helping businesses get the kits.

And Hadfield said despite the attention Omicron was getting, the Delta strain still posed a threat.

"We are potentially going to have to deal with simultaneous Delta and Omicron outbreaks."

Most current evidence suggested Omicron is more transmissible than Delta, but is less frequently producing severe illness.

University of Otago epidemiologist Professor Michael Baker said the Government was currently applying the same approach to Omicron as it did to Delta.

"We've applied a tight suppression to Delta and it's worked remarkably well," he said.

He said whole genome sequencing could now be used on every Omicron case, but probably not for much longer.

Worst case scenario 50,000 daily cases

Health Minister Andrew Little said it was not the first time in the past two years that people said the health system would be overwhelmed and it had coped.

Speaking to Tim Dower on Newstalk ZB, Little said it did have a short-staffed workforce but not to the tune of the figures he saw reported yesterday.

"I've certainly been advised we have shortages, but we have coped very well."

The Government was doing the best it could to keep the pressure off the health system including lockdowns, mask wearing and taking a cautious approach.

Little said the health effects of Omicron were not as severe as Delta.

If pressure increased elective surgeries would be put off to look after people very sick with Omicron.

At its peak New Zealand would have between 5000 and 50,000 cases a day and that was the worst case scenario we had to prepare for, he said.

New Zealand was also taking precautions that other nations such as the UK and Australia didn't take.

On restructuring the DHBs, he said the system was crying out for restructuring.

A lot of work happening under the reforms was already under way and the 20 DHBs were all working together as one.

Prime Minister Jacinda Ardern on Sunday said the fight against Omicron would be phased, with the first stage when daily cases do not exceed 1000.

The second phase is transitional, adjusting the focus to those at greater risk of severe illness from Omicron.

The third stage, if cases are in the thousands, will redefine tracing, contacts and isolation requirements.

It is expected the Government will reveal some third stage details tomorrow.

The new Omicron cases reported yesterday included eight in the Nelson-Tasman region, five in Auckland, and one in Palmerston North.

Other Covid-19 cases included four each in Kaitaia and the Waikato.

Meanwhile, staff and residents at an Auckland aged care facility in Flat Bush were tested after a worker who tested positive was linked to the current Omicron outbreak.

A new drive-through vaccination centre will open today in west Auckland to accommodate increased demand for booster doses.

The Northern Region Health Co-ordination Centre said the centre on the corner of Gunton Drive and Tawhia Drive in Westgate will open from at 11am.

From tomorrow, it will operate from 8.30am to 3.30pm, every day.