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Public Health nursing and immunisation vaccinators and administration staff were doing much of the work at present, southern vaccine rollout incident controller Hamish Brown said.
This was affecting the Southern District Health Board’s MMR vaccination catch-up campaign, B4 schools check, HPV vaccinations and other school-based programmes.
"This is also using staff who would also support contact-tracing work for Covid-19 cases."
Before Good Friday, about 3800 people in the South from the border workforce, their household contacts and frontline health workforce had received their first Pfizer-BioNTech jab.
"There have been a few teething problems, as you can imagine with an operation of this scale, but our teams have been able to resolve issues as they have cropped up, and on the whole the clinics have run very smoothly," Mr Brown said.
However, in a report to be considered by the Southern District Health Board on Thursday, Mr Brown said a national Covid-19 vaccination booking system was at least a month away and southern health officials were relying on electronic diary Outlook calendar in the interim.
"There is currently no robust booking system in place, and the existing hospital booking system does not meet the requirements for the programme.
"An interim booking system...has been put in place to manage the immediate need to book in household contacts for the next few weeks."
Southern and other DHBs had worked together to find a suitable booking system and discussions were ongoing with a possible provider, Mr Brown said.
Significant work was also still needed to recruit and support the staff who would make the vaccine rollout work.
"This remains one of the most critical constraints impacting on our ability to upscale the volume of vaccination delivery."
Mass vaccination of the general population is due to start in July, and Mr Brown said numerous staff needed to be appointed within the next two months.
Also still to be resolved was how the highly vulnerable people who lived in or worked at aged care residential facilities would be vaccinated.
An added complication was the need for the Pfizer vaccination to be stored at a very low temperature.
"To date we have received vaccine with about a three-day shelf life," Mr Brown said.
"The SDHB’s high number of remote rural populations...provides added challenges under the current logistics limitations."
Another complicating factor could be if a transtasman travel bubble comes into effect, a decision Government is set to make an announcement about tomorrow.
Should it be approved and flights resume to Queenstown, the resort would need exit and entry screening to be staffed seven days a week, and a regular Covid-19 testing programme would need to be set up.
"A workforce needs to be in place to ensure that this does not impact on either Covid-19 vaccination staffing or Covid-19 contact-tracing work, he said.
"Workers and their household contacts will also need to be prioritised to be vaccinated."
In Invercargill, clinics are being run at the WellSouth offices and Murihiku Marae, and Mr Brown’s report said the Victoria Room in the city’s municipal chambers was the preferred site for another clinic.
Queenstown clinics are to start this Saturday and a Te Anau clinic from April 13.
Meanwhile, there were five new cases of Covid-19 in managed isolation yesterday and none in the community.
In a statement, the Ministry of Health said it was also reporting that one previously reported positive Covid-19 case has been reclassified as not a case following further testing and investigation.
"They have been assessed as an historical infection which has been recorded in their home country, and therefore has been removed from New Zealand’s case numbers."