Retesting of COVID-19 swabs suggests Omicron arrived late November

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Almost 1000 coronavirus swabs re-tested for the Omicron variant show no evidence the strain was circulating in NSW before November 23, leading health officials to believe an international arrival is the source of the south-west Sydney cluster.

As Omicron variant infections grew to 31 on Tuesday, pathologists continue to genomically sequence old tests and scan wastewater across the state to detect traces of the newly arrived strain.

St Peter Chanel Primary School at Regents Park is one of two schools linked to a cluster of Omicron cases in south-west Sydney.Credit:Peter Rae

“It looks like we haven’t had an unknown spread of the variant or unrecognised cases of Omicron in the community before November 23,” a spokesperson for NSW Health said. “And now what we are doing is checking all positive swabs for the strain with a second PCR test to make sure we try and capture them all.”

With 20 cases now linked to a local cluster across two Regents Park schools and a climbing gym, Sydney Catholic Schools have given their principals the choice of switching to remote learning early, or continuing until the end of term four.

Some have decided to take the option, some haven’t.

Parents at St Pius Catholic Primary School in Newtown were told in a letter on Tuesday that the school would be doing remote learning for the final three days of term, from next Monday until December 13.

“There is an understandable concern that Christmas with family and friends could be impacted by a potential exposure,” a letter to families said. “This change to the program is to provide those families who are concerned with potential exposure or have particular vulnerabilities in their family the option to have their students learn from home.”

Thirty-six of all new cases reported – a mix of old COVID-19 variants and Omicron – were children aged nine and under. Children under 10, who are too young to be vaccinated against COVID-19, have been the age group most likely to catch the virus over the past month, making up roughly one in five cases recorded in the past 30 days.

On Tuesday, Chief Health Officer Kerry Chant confirmed the likely source of the south-west Sydney Omicron cluster was a person who had recently spent time in Nigeria, arriving in Australia on November 23 before isolation requirements were re-introduced.

Dr Chant said health authorities were “keeping a close eye” on the 31 Omicron cases in the state, 11 of whom are recent overseas arrivals. However, none of the cases were in hospital.

NSW’s 20 locally acquired cases are all linked to transmission at two schools and a climbing gym in the Regents Park and Villawood areas, mostly among school-aged children.

“It’s expected that the numbers linked to this cluster will rise as further results are confirmed over the coming days,” Dr Chant said.

Several other confirmed Omicron cases, including a Central Coast woman who had spent time in South Africa and a Chatswood family who health authorities believe could have caught the virus while on their flight from Doha, were in the community before testing positive. However, no onward transmission of the variant has been reported.

ANU infectious diseases specialist Associate Professor Sanjaya Senanayake said it was “reassuring and somewhat surprising” that Sydney’s locally acquired Omicron cases were all linked, given others who caught the variant overseas had been in the community while infectious.

However, he said it was too early to infer much from the variant’s hospitalisation rate.

“It’s only around day 10 of the illness that they really end up in hospital,” he said, noting Australia’s Omicron infections were less than a fortnight old.

When looking at data from places abroad like South Africa, where Omicron was first discovered under two weeks ago, Dr Senanayake said it was important to remember Australia has had a world-leading response to the pandemic, with high vaccination rates, as well as other measures such as mask-wearing and QR code check-ins to speed up contact tracing.

“It would be unusual for a virus to become less virulent … but now we are seeing cases in western countries with high rates of vaccination [like the UK and the Netherlands] we will start to get some good data,” he said.

James Wood, a mathematician at UNSW’s School of Public Health and Community Medicine, said recent data from South Africa raises some concerns about the speed of the variant’s spread in a population with high levels of previous infection.

“Within a couple of weeks it seems likely that South Africa will have a large national epidemic in a country that has three big waves of infection. It looks like Omicron evades our immune response to some extent and that raises some concern,” he said.

However, Dr Wood said despite a spike in hospital admissions in South Africa’s Gauteng province, deaths have not increased as rapidly as in the initial stage of their Delta wave.

“We aren’t sure why that is. It could be people infected with Delta have immunity and aren’t getting as sick. Or it could be something different about the variant.

“There is concern about transmissibility and if the R value rises well above 1 we would see rapid rise in cases. Even if the variant is much less severe it will still put pressure on the health system.”

There were 260 new COVID-19 cases reported in NSW on Tuesday, including more than 200 in metropolitan Sydney. Two deaths were reported.

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