A security guard working on Sydney’s hotel quarantine has tested positive for the coronavirus.

NSW chief health officer Doctor Kerry Chant confirmed the infection on Tuesday afternoon.

The man is a security guard at the Marriott Hotel, which is also being used to quarantine returned overseas travellers. He has also since worked at Flemington’s Sydney Markets, Parramatta Local Court and Bankstown Central.

“Detective work indicated the most likely source of infection was his acquisition at the Marriott hotel,” Dr Chant said.

“The exact nature of how that infection could have been acquired is a matter under intense investigation as we speak.”

Genome sequencing traced the security guard’s infection to a returned overseas traveller who was staying at the Marriott Hotel at Circular Quay earlier in August.

The guard worked at the hotel on August 3, 4, 7 and 8. The hotel guest was swabbed on August 2 and received their positive result on August 4.

Dr Chant said CCTV footage had been reviewed and police were working with NSW Health to trace the guard’s movements at the hotel.

“Let me tell you, we will not leave any rock unturned in terms of our search for confirming there are no further cases linked to, at this moment, a single case and a security contractor,” she said.

Meanwhile, on the other side of the country, two South Australian women are in custody in Perth after apparently breaching coronavirus quarantine rules.

WA acting police commissioner Gary Dreibergs said the women, aged 19 and 22, would appear in court later on Tuesday.

Police allege the women flew into Perth on Monday night and were refused entry. They were taken to the Novotel to spend the night before being flown home.

They were arrested early on Tuesday after leaving the hotel, against COVID regulations.

“Apprehending these two women was an absolute priority for the Western Australian police,” Mr Dreibergs said.

WA acting police commissioner Gary Dreibergs said the women were arrested early on Tuesday.

Breaches of hotel quarantine have been blamed for sparking Victoria’s devastating second wave of the virus, which has killed more than 200 people.

On Tuesday, a judicial inquiry heard that 90 per cent of Victoria’s current COVID cases could be traced back to just two Melbourne hotels.

Dr Chant said urgent testing had pinpointed the strain of coronavirus the security guard had contracted.

“What that’s identified is that it’s quite a different sequence to the virus associated with the Crossroads [Hotel] and other clusters that NSW is experiencing, which is related back to the Melbourne virus,” she said.

“This is a different virus and matches this person who was quarantined at the hotel.”

The infected Sydney guard was one of 16 mystery cases recorded in NSW in the past four weeks that have concerned authorities.

The state had three new cases of coronavirus in the 24 hours to 8pm on Monday, its lowest daily number in more than a month.

“Even though the daily case numbers have been low, there have been 16 cases in the past four weeks whose sources are not identified or linked to clusters, mainly in western and south-western Sydney,” deputy chief health officer Dr Jeremy McAnulty said on Tuesday.

“So, if you have any cold or flu-like symptoms at all, assume it’s COVID-19 until proven otherwise – isolate and get tested right away. Don’t delay.”

The latest figures come as the City of Sydney was added to a list of the NSW government’s COVID-19 hotspots, where authorities have increased testing and surveillance.

Residents living in the Harbour City local government area have joined other suburbs such as Campbelltown, Bankstown and Fairfield as areas where recent visitors should get tested if they show mild symptoms.

-with agencies