It's "impossible" to say if Victoria had eliminated coronavirus community transmissions before the botched hotel quarantine program.
But testing shows no evidence of the original virus in genetic modelling.
At least a significant number of Victoria's current second wave cases could be linked to the program, now being investigated by a former top judge.
Chief Health Officer Brett Sutton says he first learned of problems with hotel quarantine from media reports, but only realised it was responsible for a "significant proportion" of the second wave's cases when genomic reporting was released.
It might never be clear if hotel quarantine is entirely to blame, with Prof Sutton declaring it's impossible to tell if the state had completely eliminated community transmission before the problems were discovered.
"We've got genomics for many cases in Victoria at the moment," he said.
"There's no evidence of original virus in the genomic report, but we haven't tested everyone."
Not everyone can grow the virus, and a genetic fingerprint is not always available even where the virus can be grown, meaning evidence can't be examined, he says.
"But where we do, there is evidence of virus that goes back to February, March, April," Prof Sutton said.
The $3 million hotel quarantine inquiry, led by former Family Court judge Jennifer Coate, is now due to begin on August 17.
Premier Daniel Andrews is not answering questions about the inquiry, saying he wants the government to be at arm's length to avoid "self-assessment".
Prime Minister Scott Morrison said a national dashboard of data, used to examine outbreaks nationally, had been updated with information from all states.
On whether that modelling should be released publicly, he said chief health officers were already being transparent, providing a wealth of information each day.
On July 1, Mr Andrews said genomic sequencing had traced a big proportion of coronavirus cases to breaches in the hotel quarantine program.
Australian Associated Press