A strain of whooping cough spreading has been sequenced, but scientists are finding it hard to track where it has come from.

Public health officials were urgently trying to sequence the strain to see if it is unusually deadly after three babies died from the disease, also known as pertussis, this year.

Environmental Science and Research bioinformatics and genomics senior science lead Joep de Ligt told RNZ a sample from a young child showed the strain was likely covered by the current vaccine, according to newly finished sequencing.

“The vaccine will still work based on the typing that we’ve done. So you can do antigen typing. So that’s part of the bacteria that is seen by the immune system, and we can then see if that is part of the current vaccine that is offered... For the sample we have analysed, we could see that it is likely covered.”

The disease was “quite hard to get a culture from” and it was therefore “quite hard” to trace its spread, de Ligt said.

“So there’s not historic data available, or at least not a lot. So it’s not like with Covid that we could say that it had come in on a boat or something like that.”

Vaccination for pregnant women: ‘We’ve really, really dropped the ball badly’

Meanwhile, Te Whatu Ora has written to doctors and midwives this week, asking them to prioritise vaccinating pregnant women to protect babies.

It also released a report saying some immunisation rates for under-fives were “dire”.

University of Auckland vaccinologist Helen Petousis-Harris told RNZ dwindling child immunisation rates against diseases like whooping cough were “really unfortunate”.

Vaccinologist Helen Petousis-Harris says there are moves to address low rates of pregnant women being vaccinated against whooping cough. Photo / RNZ

• Vaccinologist: It's important pregnant women in second-trimester are vaccinated against whooping cough
• Concerns about whooping cough vaccination levels after three baby deaths
• Immunisation system failing children in vulnerable communities- report

“It’s a real worry. Because this winter, we could see some real resurgence in some diseases that actually are preventable.”

Petousis-Harris believed Aotearoa had not taken whooping cough vaccination drives seriously enough.

“I think we’ve really, really dropped the ball badly on it. But over a long period of time, actually. So it’s not just recent, but it’s across time.

“We started this programme of vaccinating pregnant women back, it was about 10 years ago now. We’ve never really achieved very good coverage and that’s because there wasn’t enough effort that went in across the board to get that coverage up.

“There are now moves, and big, really strong moves, to try and improve it and address it. But I think the most important message is if you’re pregnant, or know somebody pregnant, make sure they’ve had this booster because this disease is out there. It can be lethal in small babies.”

It was now an “emergency” situation, Petousis-Harris said.

She hoped “we can have some good long-term solutions and won’t see this happen again in the future, but at the moment, we’ve got a long way to go, before we can consider this problem solved”.

She also acknowledged it was a difficult time to ramp up vaccinations when health services were “under the pump” - coping with other winter illnesses spreading, Covid, and staffing problems.

“The workforce shortage is one of the big issues... People [having difficulties] being able to access the services has become a growing problem.”

-Sam Olley and Felix Walton, RNZ