As COVID-19 batters Australia’s hospitals and public health system, New South Wales no longer has the resources to test the strain of every case.
NSW Health tweeted in December it will only undertake genomic sequencing for Omicron variants in cases where it will make a “clinical difference” to a patient’s care due to the high number of cases in the state.
“For instance, where it will inform treatment choices as some therapies work with Delta but not for Omicron, and in situations where it will inform public health action,” they added.
Since its emergence in November, Omicron has quickly become the most dominant strain in the country, muscling out Delta in Queensland, Victoria and NSW.
The most recent PCR sample analysis by Victoria’s Department of Health indicated 86 per cent of cases in the community were of the Omicron variant.
SBS News understands analysis is underway to determine the percentage of Omicron cases among hospital patients in the state, while Queensland Chief Health Officer John Gerrard said the state is currently seeing a "95 per cent" prevalence of Omicron.
NSW chief health officer Dr Kerry Chant on Wednesday said that results from a pathology company had shown about 90 per cent of the cases are Omicron and about 10 per cent are Delta.
Members of the public queue in their cars for PCR tests at a clinic at North Ryde in Sydney. Source: AAP
“In early December, from the first to the seventh, 90 per cent of the cases that were sequenced in ICU were Delta and 10 per cent were Omicron,” Dr Chant told reporters.
“And then progressively in the week of the 29th of December to the fourth of January, we've seen that shift to 33 per cent of Delta and 67 per cent of Omicron.”
The importance of differentiating strains
Dr James Trauer, head of epidemiology modelling at Monash University’s School of Public Health and Preventive Medicine, believes it’s important to distinguish between variants.
Unlike state and territory governments in Australia, the UK and France have both been publishing regular updates on the number of Omicron cases circulating in the community.
In recent months, the UK has released frequent overviews and summaries of case data for Omicron that focuses on confirmed cases.
France, meanwhile, introduced a new screening strategy on 20 December allowing for better detection of suspected Omicron cases.
“It makes a difference in terms of our hospital planning and … in terms of how people might want to approach the epidemic,” Dr Trauer told SBS News.
But Dr Trauer acknowledges there isn't the capacity to test the strain of every single COVID-19 infection.
Healthcare workers are seen arriving to an aged care facility in Melbourne in 2021. Some aged care workers say their facilities were not prepared for Omicron. Source: AAP
To combat the lack of resources, he said random testing could help give a rough estimate of the proportion of cases in each state and territory.
“Due to rapid antigen tests ... There are a whole lot of people for whom there is no swab in the lab for genotyping to be done,” he said.
“But it is worth having a better approach to this because it will give us a better idea of where the pandemic is heading.”
Infectious Diseases physician and microbiologist Dr Peter Collignon said genomic sequencing is already occurring for most people in hospital and intensive care in Australia.
“Generally, you will do it on people in hospital and [those who are] severely ill and then a sample of your general population, because it's not worthwhile and, in fact, logistically impossible when you have huge numbers of strains to do it on all of them,” he said.
Dr Collignon said while Omicron is believed to be less severe but more contagious than Delta, the spectrum of symptoms for each strain is similar.
“The vaccines seem to be equally effective at stopping you dying and stopping you getting into hospital with both variants,” he said.
Dr Collignon said as the focus has shifted to living with the virus, rapid antigen testing has become increasingly important - unlike genomic testing, RAT kits do not test for the strain of the virus.
People arriving at Sydney International Airport in Sydney Source: AAP Image/James Gourley
“We need to change our focus from the number of cases to the consequences of the virus,” he said.
“Once you get a lot of cases in the population, you're not going to really measure all the cases accurately anymore.
“What you need to measure is the number of people coming into hospital and ICU and dying from COVID.”
Dr Trauer said he believes restrictions should be reintroduced in NSW to lessen the burden on hospitals. He said this could include the cancelling of crowds at potential super spreader events.
"I'm plugging for a little more to be done over the next few weeks and then once we see the peak begin to come down again we can relax again and be confident we're headed towards a more positive state of affairs," he said.
Dr Collignon believes, over the next few years, Australia will need varying restrictions depending on the consequences of the virus.
"Those who are fully vaccinated and particularly young, there should be [fewer] restrictions on them than unvaccinated because it's the unvaccinated that are disproportionately filling hospital beds," he said.
SBS News has contacted Victoria's Department of Health, Queensland Health and NSW Health for comment.
