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Warning that new Omicron variants in SA are more transmissible

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Two new Omicron variants of COVID-19 detected in South Australia are more transmissible than previous variants and could push case numbers up, a leading epidemiologist warns, as South Australia today recorded 3215 new infections and a drop in hospitalisations.

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In a statement last night, SA Health confirmed one case of Omicron BA.4 and one case of BA.5 had been identified in SA in international travellers, in a sample of tests.

University of SA epidemiologist Professor Adrian Esterman told InDaily today the new sub-variants were 25 per cent more transmissible than Omicron BA.2, which itself is more transmissible than the original Omicron BA.1.

“If it takes hold in Australia then we expect to see case numbers go up and hospitalisations might rise but much more slowly,” he said.

Esterman said the new Omicron sub-variants were as contagious as measles – “our most contagious viral disease”.

The new sub-variants were discovered in SA in the latest whole-genome sequencing results from positive PCR samples reported last week.

“While this is the first time BA.4 and BA.5 have been detected in South Australia, with international borders now open, it is not unexpected to see new variants in our state and across Australia,” SA Health said in its statement.

“These variants have also recently been detected interstate.”

It comes as SA today recorded 3215 new COVID-19 cases, up from 3143 infections yesterday.

There are now 228 people with COVID in hospital – 17 of those in intensive care including two on ventilators – a decrease from the 257 patients who were in hospital yesterday.

Three more deaths of people with COVID have been reported – a woman in her 90s and two men in their 80s.

SA Health said the two new confirmed cases of the Omicron sub-variants had previously been reported as part of the daily numbers, but that genome sequencing is only undertaken on a small sample and results can take several days to be collated and reported.

Expert opinion, however, appears to be divided about whether BA.4 and BA.5 are more infectious than BA.2.

Chief public health officer Professor Nicola Spurrier this morning told ABC Radio Adelaide it was “too early to tell”.

“At the moment we are just watching the epidemiology or the case numbers in South Africa and there is no indication that these are more severe or transmissible,” she said.

“But when the scientists have a look at the particular mutations there is a mutation on the spike protein.

“So at the moment it’s too early to tell but it really is inevitable that we would be getting these variants here.”

Spurrier said there could be more cases of the sub-variants in SA than the two so far detected.

“We’ve just had one case of BA.4 and one case of BA.5 but we don’t do all of the genomics for every single case in South Australia,” she said.

“We focus on people who have needed to be hospitalised, those in ICU, we also have a broader community sample, one from our sensitive settings such as aged care and also we try and have a sub-sample of children.”

Spurrier said people needed three doses of vaccine to protect against Omicron.

“I think people have probably underestimated how sick you get with COVID,” she said.

“We’ve perhaps heard Omicron is less severe: well it’s less severe than Delta but Delta was pretty bad. And you definitely need to have your three doses of vaccine.

“COVID is a nasty infection and whilst you might not need to go to hospital and you might recover at home you can be quite sick and have to spend a few days in bed and people have said the fatigue afterwards and brain fog can be really quite debilitating.”

Esterman said there was “no doubt” that Omicron BA.4 and BA.5 were more infectious than BA.2.

“What they can do is evade immunity a bit better and that’s why they’re more transmissible,” he said. “Just by genetic changes… they look slightly different from previous versions and our immune system doesn’t recognise them.

“If they weren’t more transmissible, why are they taking over in Africa?”

Esterman said the good news was that they did not appear to be more severe.

“In terms of severity, in South Africa reports are that hospitalisation rates haven’t changed,” he said.

The new sub-variants could mean that people are at a greater risk of being reinfected with COVID, however.

“They are more able to evade immunity than BA.2 so the answer is yes… even if you’re vaccinated,” Esterman said.

“The genetic changes make it more difficult for our immune system to recognise it as a foreigner and attack it.”

Spurrier this afternoon told reporters that 898 South Australians had already had COVID more than once during the pandemic.

“But when we look at that in terms of total cases, it’s a reinfection rate of 0.22 per cent so it’s really quite low,” she said.

“But that is likely to increase over time as we have more people have a primary infection and then also there will be a waning of the impact of that infection on your own immunity.”

Esterman said another variant called BA.2.12.1 – which is now “taking over in America” – had also been found in Australia, but not yet in South Australia.

“It accounts for over 70 per cent of all cases in New York State and over 20 per cent of all cases in America,” he said.

“It is also 25 per cent more transmissible than BA.2 and it’s also been found in Australia.”

Esterman said because so many people had already contracted COVID, “I think there’s going to be a broad amount of immunity that’s going to slow down these increases in case numbers”.

He said serology sampling in America of 200,000 people had found that three quarters of all children and half of all adults had been infected with COVID.

“I wouldn’t be at all surprised if we had similar numbers here,” he said.

“When you have that many people who have been infected and recovered you would have some immunity.

“So that’s why I think we will see case numbers up but not to a massive extent because the virus is struggling to find more people to infect basically.”

Esterman said a bigger threat would be the emergence of a totally new variant.

He said the removal of restrictions such as mask mandates was sending a signal that “it’s all over, when it’s not all over”.

“Tomorrow there could be a new variant… one as transmissible as BA.4 and twice as deadly. We simply don’t know.

“A new variant that comes along could be as severe as Delta or more severe than Delta, it’s pot luck.”

Experts are also concerned about the impact of long COVID.

“We’re getting a Tsunami of people with long COVID and no-one’s talking about that,” Esterman said.

“The GPs I speak to are talking about it because they’re seeing patients rocking up at their door with long-term health problems.

“That’s one reason why we need to keep case numbers down and they’re plateauing at very high numbers at the moment.”

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