Focus Live: Chris Hipkins gives Covid-19 traffic light announcement
Freshly released wastewater surveillance data has added another perspective to New Zealand's Omicron wave – and shown how widespread Covid-19 has become across the country.
Because traces of Sars-Cov-2 can be isolated from what we flush down the toilet – and sometimes survive up to several days after leaving an infected person's body - wastewater-based epidemiology has played an increasingly large role in our pandemic toolbox.
Testing results just released by ESR, and showing data from the week to April 10, reveal how RNA from the Sars-CoV-2 virus was detected at all but one of the 120 wastewater sites the agency screens.
This map shows the location of wastewater sampling sites and results for the week to April 10. Orange shows where the virus has been detected, while green shows where there have been no detections. Source / ESR
That is in stark contrast to the virtual absence of the virus in wastewater sampling, only a matter of months ago, at most spots around the country.
As part of the surveillance, samples are sent from each plant to one of ESR's labs, where scientists can assess the concentration of the virus, and extract viral RNA from it.
When there's enough of the virus in the sample to quantitate, scientists are able to convert that to a viral load of genome copies per day, per person – helping build a picture of infection prevalence in given catchment populations.
National data from this surveillance showed how quantifiable amounts of virus were only being picked up about 10 per cent of sites in the opening weeks of the year.
By mid-February, quantifiable levels were detected at more than a quarter of them. A week later, that proportion had shot up to around two thirds.
This graph shows wastewater sampling results between September and this month. The red shows levels of detections where there was enough virus RNA in samples to be quantifiable. Source / ESR
Around mid-March, it was present at about 90 per cent of them.
In each of the catchments sampled, the data showed how the growth curve of genome copies per person, per day, roughly aligned with rolling, seven-day averages of case numbers.
It also highlighted how that genome rate peaked in Auckland over March, before falling back away by April.
That was also in line with what case numbers officials have reported. The latest data shows how daily cases in the region have tumbled to around 14 per cent of the peak - fewer than 100 daily cases per 100,000.
This map shows how wastewater sampling data has trended alongside reported case numbers in Auckland throughout the Omicron wave. Source / ESR
Elsewhere, the story is different.
As at last week, daily case numbers were likely still rising in the West Coast, and hovering near peak levels in DHB areas like Northland and Southern.
For that reason, some experts questioned whether the entire country was ready to move to the orange traffic light setting.
The Ministry of Health did not release any case numbers on Good Friday, with the Covid-19 case, and number of any fatalities, to be released via a press statement at 1pm Saturday. Health officials confirmed this week that the previous Monday-Friday press conferences would be replaced by press statements until further notice.
The latest results back a recent study that reaffirmed wastewater sampling as a useful surveillance tool for Covid-19.
In it, ESR scientists spent four months sampling wastewater from an Auckland population of about 120,000, where cases were known and uniquely all located in a single managed isolation and quarantine facility.
It showed not only was there a high likelihood of detecting viral RNA in wastewater even if 10 people in a catchment of 100,000 were shedding the virus – but also that the rate of detections could be linked with increasing Covid-19 cases.
As with other modes of surveillance, however, wastewater sampling's role has shifted amid the Omicron wave.
Last month, ESR's Professor Michael Bunce and Dr Joep de Ligt said Omicron had brought about the first time in the pandemic that case numbers had risen high enough to enable quantitation of the virus in wastewater.
"Previously we were at the limits of detection which prevented a gauge on how much virus was present. It was always low," they said.
But they stressed that extrapolating wastewater concentrations into case numbers was difficult and imprecise, primarily because of differences in flow rates, stormwater and population density difference between catchments.
"Trends in wastewater concentrations over a few weeks do provide an indication if Covid-19 is increasing, stable or falling within a given catchment," they said.
