A report obtained by Newshub says there are "blind spots" and "gaps" in our surveillance of COVID-19 at the border.
It's raised concerns that if new variations of the virus arrive here they could get established and spread in the community without us knowing.
The Institute of Environmental Science and Research (ESR) COVID-19 lab in Porirua is one of the engine rooms for tracking the virus. But tracking it is dependent on having samples.
"If we do have gaps, you know we could be unlucky and actually see new variants come in and new variants develop overseas and we can't see it in New Zealand yet because it's hiding in a pocket where we don't have great surveillance," said Professor Mike Bunce, ESR principal scientist and genomics lead.
And New Zealand does have gaps, according to an ESR genomics insights report obtained under the Official Information Act.
ESR needs a minimum of 10 PCR tests to sample from each district health board (DHB) per week. The report states that "failure to hit these targets results in genomic blind spots" and "low sample numbers means studying these variants under NZ conditions is difficult as is making inferences about the size/shape of any future wave that might result".
"Because of our gaps in genome sequencing, it could be weeks before we detect something that's spreading in the community in our genomic surveillance and we don't know what the next variant looks like," said Dr Jemma Geoghegan, Otago University evolutionary virologist.
The next variant could, of course, be more severe, but the rate of samples sent for checks varies.
The genomics report, written on June 15, shows Canterbury and Southern DHBs are doing well, sending 177 and 129 PCR tests to ESR every week.
Counties Manukau and Waikato are lower down the list, referring 21 and 25 samples respectively.
Six DHBs are not hitting the target. Wairarapa sent just one, Tairawhiti, West Coast, and Lakes didn't do much better. Hawke's Bay and Whanganui sent just seven PCRs.
"For the most part, we've got great surveillance across the country but there is some patchiness into some areas and we're constantly working on that to improve that," said Prof Bunce.
Analysing a whole genome sequence allows scientists to identify what variant they're dealing with and how it functions.
You need PCR samples to be loaded into a machine to unravel the information. But in the two weeks to June 3, only 57 percent of PRC border cases were sent to ESR. In the fortnight to June 10, 66 percent were sent.
And in the same time period, if you look at PCRs taken from sick people in hospital, just 32 percent of samples made their way to ESR.
Dr Geoghegan said that must improve.
"It is worrying that some DHBs are not referring samples to ESR for sequencing."
COVID-19 Response Minister Dr Ayesha Verrall said the system isn't perfect, but it's still helping identify trends.
"We are, however, going to try and lift that rate of coverage with the whole genome sequencing."
The report states there is currently "insufficient data" to robustly estimate the growth of different variants.
What is known is Omicron BA.2 is most prevalent, but BA.2.12.1 is also circulating, as are BA.4 and BA.5. These three emerging variants are the ones to watch.
"Of those three it looks like Omicron BA.5 is going to be the one that wins the gunfight," Prof Bunce said.
"Our estimate from our modelling suggests that will become the most dominant variant in New Zealand probably in mid to late July."
And that in itself will be a challenge in mid-winter. BA.5 is more transmissible and better at beating the vaccine.
Wastewater sampling is also being used to establish trends in COVID-19 variants, but this surveillance method has limitations as the results produced are retrospective.
Middlemore clinical microbiologist and infectious diseases physician Dr Susan Morpeth told Newshub the variation in the number of PCRs being sent to ESR is due to a combination of factors.
She said some samples can't be sequenced due to their low viral load and that some hospitals use tests that cannot be used for whole genome sequencing.
She said there's variability in labs having sufficient staff to package and ship samples regularly and staff sickness is also impacting labs, especially smaller ones.