Deputy Premier John Barilaro says the detection of COVID-19 in Merimbula's sewage was of a "high level" indicating the presence of someone in the community with the virus.
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He spoke to regional journalists on Wednesday after the sewage surveillance result was announced in the morning along with the updated figures of vaccinations and positive cases for NSW.
Mr Barilaro outlined that surveillance of sewage systems can often find low levels of the virus which disappear.
However, the Merimbula sample contained a high enough level that "clearly shows that someone is in the community with the virus".
As yet there has not been a positive case confirmed in the Bega Valley, and the detection in the shire's sewage does not necessarily indicate a currently infected local.
Mr Barilaro indicated it may have been a visitor to the area, particularly due to the Far South Coast's proximity to Canberra.
"We still have authorised workers [moving between regions] - truck drivers, construction workers, health workers and people in disability can do that.
"We also had the mass exodus out of Canberra when their lockdown approached.
"Anything could've triggered this [sewage fragments in Merimbula].
"My concern is there is still a level of movement out of Canberra and maybe even Sydney. I can't quantify that, but it's a concern."
Meanwhile, Mr Barilaro also said vaccinations would be "ramped up" across southern NSW as a result of the concern.
"We will be ramping up vaccinations in Bega, Queanbeyan and Goulburn - up to three or four times the number they are doing in a day," he said.
He said he was awaiting advice from the Southern NSW Local Health District on the capacity of the three southern hospitals to increase their vaccination rates, with updates expected by Friday.
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