Almost all of Victoria's second wave of COVID-19 cases can be traced back to overseas travellers in two hotels, an inquiry into the quarantine program has heard.
Department of Health and Human Services epidemiologist Dr Charles Alpren confirmed on Tuesday "99 per cent" of the state's current coronavirus infections were linked to the Rydges on Swanston and Stamford Plaza hotels.
He said the Rydges hotel outbreak started with a family of four who returned from overseas on 9 May.
They were moved to the hotel on 15 May and all four tested positive to COVID-19 by 18 May.
On 25 May, three hotel staff members were diagnosed with COVID-19.
By mid-June, a total of 17 staff and their close contacts had tested positive.
The virus then made its way out into the community.
Meanwhile, some 46 workers from the Stamford Plaza and their close contacts were found to have caught COVID-19 from a man who returned from overseas on 1 June and a couple who returned on 11 June.
Having analysed the genomic sequencing of 5395 active cases, Dr Alpren said 3,594 could be linked to the Rydges hotel.

The Stamford Plaza Hotel on in Melbourne Source: AAP
The outbreak is also linked to another 24 clusters.
"It is likely that a high proportion, approximately 99 per cent of current cases of COVID-19 in Victoria have arisen from Rydges or Stamford," Dr Alpren said.
"However, I cannot be very precise in the number or proportion to have arisen from each outbreak separately.
"It is likely that the large majority - I said in my statement approximately 90 per cent or more - of COVID-19 infections in Victoria can be traced to the Rydges Hotel."
He said the DHHS had seen "no evidence of any other transmission" outside the hotels.
"That's not to say that there are no other transmission events that could be there. But because there are very few people now coming into Victoria who potentially offer new sources of importation of the virus, it is less and less likely," Dr Alpren said.
In late May, when the virus first broke out of hotel quarantine, 19 people in Victoria had died from COVID-19.
The state's death toll now stands at 351, with almost 7500 cases active.
The inquiry continues.
Metropolitan Melbourne residents are subject to Stage 4 restrictions and must comply with a curfew between the hours of 8pm and 5am. During the curfew, people in Melbourne can only leave their house for work, and essential health, care or safety reasons.
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