Environmental Science and Research data has picked up Delta hotspots in both Wellington and Dunedin, and the Southern District Health Board yesterday confirmed it was dealing with cases of it, as well as Omicron.
"Both are active in the southern district, although the vast majority of cases are Omicron," a spokeswoman said.
Delta is much more transmissible than the original strains of Covid and also more virulent, and was the strain for which the SDHB had devised its most recent plans.
However, those plans were revised after the emergence of Omicron, which is much more transmissible than Delta but less virulent.
Omicron is eventually expected to swamp Delta, but for now the SDHB was unaware how many cases of each it faced.
"Due to the increasing number of cases across the country, only a small sample of cases are undergoing whole genome sequencing," the SDHB spokeswoman said.
The latest SDHB update yesterday confirmed 484 total Covid-19 cases in Otago and Southland.
While Queenstown remains the location with the most cases, 244, case numbers in Dunedin have been rising rapidly and yesterday jumped by 48 to 187.
There were 239 close contacts in isolation in the district, which included 70 in Queenstown Lakes and 157 in Dunedin,
Multiple local locations of interest were released yesterday, including flights to or from Dunedin and Queenstown.
Over the weekend both Otago Polytechnic and the University of Otago confirmed some of their students had contracted Covid-19, and yesterday two of Dunedin’s largest high schools, King’s and Queen’s, also announced they had cases.
Testing numbers in Otago and Southland reflected the increasing number of cases, 2272 people having been tested as at 4pm yesterday.
Of those, 1560 were swabbed in Dunedin, 337 in Queenstown and 197 in Invercargill.
University of Otago Wellington epidemiologist Prof Michael Baker said it was still "a work in progress to understand how Delta and Omicron interacted with each other".
"In general the fitter viruses do eliminate the others because it all comes down to how many copies of yourself you can make, but it is possible that you could have multiple variants circulating, as with normal influenza we often have two or three strains circulating at any one point."
"It could be that each virus could find its own niche and we won’t have total replacement but in general, internationally, Omicron has largely displaced Delta."
If Delta was able to maintain a significant foothold in Dunedin it could pose a problem for the local health system as a higher proportion of Delta cases eventually required hospital care, Prof Baker said.
Nationally, the Ministry of Health reported a total of 2365 cases of Covid-19 yesterday, slightly down from the 2522 reported on Sunday.
However, that dip likely reflected the usual lower testing rates during the weekend.
Prime Minister Jacinda Ardern warned yesterday she did not expect the current outbreak to peak until mid to late March.
"Our seven-day average for cases is 1667 and we are predicting cases will continue to double every three to four days," Ms Ardern said.
She said restrictions such as vaccine passes and gathering limits would begin to be eased after outbreaks peaked.
