Two health units in the Toronto area reported Ontario's fifth and sixth cases of the Omicron coronavirus variant on Thursday.

The two new cases were detected in Durham Region and Halton Region.

Durham Region Public Health said the Omicron-positive individual is a close contact of someone who recently returned to Canada from southern Africa.

"The Health Department is also monitoring other COVID-19 cases under investigation for the Omicron variant based on travel history and working with the province to monitor COVID-19 variants of concern including Delta and Omicron."

It is not clear whether the Durham case is the same one tied to an outbreak at Toronto East Detention Centre.

Toronto Public Health (TPH) said Durham health officials are investigating the Omicron variant case at the Scarborough jail. However, when asked about the case, Durham officials would not provide any further details about their investigation, citing privacy concerns.

TPH said a staff member at the facility tested for the Omicron variant, prompting a COVID-19 outbreak to be declared "out of an abundance of caution."

TPH added that four inmates tested positive for the virus Thursday afternoon, but it is not yet confirmed if the cases are of the Omicron variant.

Meanwhile, Halton Public Health reported late Thursday afternoon that it has one confirmed case and two probable cases of the variant.

The health unit said one of the suspected cases returned from travel to Nigeria and is the close contact of the other two. All three are isolating at home. Halton Public Health added that all close contacts have been identified and advised to isolate and get tested.

"We continue to monitor the situation closely and I urge all residents to be vigilant given the entry of the Omicron variant in our community," Dr. Hamidah Meghani, the region's medical officer of health, said in a statement.

"I encourage all residents to continue to follow all public health measures to prevent the spread of COVID-19 and for everyone who is eligible, to get their two doses of vaccine as soon as possible."

Earlier this week, Ontario officials confirmed four other cases of the Omicron variant in Ottawa, and said nearly 400 people who returned to Ontario from southern Africa over the past two weeks were in mandatory self-quarantine.

The two new cases represent the first known examples of local transmission of the Omicron (B.1.1.529) variant confirmed in the province to date.

Chief Medical Officer of Health Dr. Kieran Moore said there are now 1,800 people under mandatory self-isolation who recently arrived in Canada from one of the ten African countries where the Trudeau government has now banned all foreigners from arriving.

He said it was just a matter of time before more cases are detected in the province.

The province is now moving to perform whole genomic sequencing on all positive COVID-19 samples and the federal government has enacted several new measures to tighten controls around international travel.

Moore said the province is also resurrecting adjustments to the standard PCR COVID-19 test so that it can detect the S-Gene deletion present in most Omicron specimens collected.

S-Gene deletion or S-Gene target failure was used across the province to track the spread of the Alpha (B.1.1.7) coronavirus variant in early 2021.

Moore said the arrival of Omicron adds new haste to the province’s ongoing third dose campaign, now lowered to everyone age 50 and up.

“When Delta overtook Alpha, it took 4 months for that to occur – we may have a shorter window for Omicron given that it is more transmissible,” he said.

He said it was “absolutely unclear” still whether existing vaccines would provide a high degree of protection from severe illness caused by Omicron.

“We don’t expect 100 per cent loss in vaccine efficacy,” he said.