Nearly three-quarters of people who have died from COVID-19 had a pre-existing health condition, a Senate committee has been told.

Chief Health Officer Paul Kelly told a parliamentary hearing that 71.2 per cent of all deaths from COVID until October last year also had a pre-existing health condition, such as diabetes, lung disease or heart disease.

Professor Kelly said the most recent death figures only went up until the end of October 2021, and did not include deaths following the start of the Omicron outbreak late last year.

There have been more than 3900 fatalities from COVID-19 since the pandemic began, with half of them occurring in just the past two months.

It comes as the hearing was told the government did not foresee such a large demand for PCR tests as COVID infections spiked when the country reopened late last year.

A deputy secretary in the Department of the Prime Minister and Cabinet said while planning had been undertaken for increased cases, states requiring PCR tests for travel purposes weren’t considered in the process.

“There were so many elements happening at the time, we certainly hadn’t planned that an additional 20 per cent ask of that PCR system would be aligned to test to travel specifications,” Alison Frame told the committee on Wednesday.

“The PCR testing system had performed very well with massively increased capacity in peaks and troughs.”

The deputy secretary said no one in the world had modelled how transmissible the Omicron variant would be, with suspected case increases as restrictions eased remaining manageable within the PCR system’s surge capacity.

“The chief health officers in each jurisdiction said PCR testing was what they would continue to rely on because of the increased reliability of those tests,” she said.

Prime Minister Scott Morrison defended his government’s delayed purchase of rapid antigen tests, saying no health advice predicted a variant for which vaccines wouldn’t work.

Mr Morrison said other countries such as the UK already had supplies of the test because they were dealing with tens of thousands of cases a day, but Australia remained in the position to continue using the more accurate PCR tests.

“Rapid antigen tests are not as good as PCR tests. In the Delta phase, PCR tests were the best thing to do,” he told the Seven Network.

“Omicron changed all of that and no country in the world could avoid Omicron.”

Meanwhile, the medical regulator has issued new guidelines for people using rapid antigen tests.

The Therapeutic Goods Administration said people should not eat, drink, smoke or chew gum for 10 to 30 minutes before collecting saliva for a rapid test due to the potential for an incorrect result.

Deaths continue to climb after what appears to have been the peak of Omicron, with 27 in NSW and 25 in Victoria on Wednesday.

There were also 16 deaths in Queensland and one in South Australia.

The deaths came among more than 11,800 and 14,550 new cases in NSW and Victoria respectively.

There were also 9360 new cases in Queensland, 1723 in South Australia, 666 new infections in Tasmania and 549 in the ACT.

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