Tracking Covid-19 by looking at wastewater

Just-released wastewater data has added a fresh perspective to our Omicron wave, showing that what scientists have learned from sewage sampling has generally matched up with daily case numbers.

ESR’S online Covid-19 wastewater dashboard, which went live last week, enables Kiwis to check what quantity of SARS-COV-2 that scientists are finding in their region — and then compare that to case numbers reported each day.

Because traces of the virus or its RNA can be detected from what we flush down the toilet, wastewaterbased epidemiology has played an increasingly large role in our pandemic toolbox.

As part of the surveillance, samples are sent from each plant to ESR, where scientists concentrate viruses, and extract the 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 — and now the virus was being detected, often in high levels, across all sites monitored nationwide.

“Before February, we were only seeing Covid-19 in a few catchments — mainly in Auckland — but then it really took off,” ESR senior scientist Dr Joanne Hewitt said.

“As Omicron spread across the country, we saw levels go up not just 10 times, but 1000 times, compared with background levels.”

In Auckland, on February 13, there were still just 220 community cases and nearly 387,000 average genomes copies of the virus per person.

But by March 6, at the height of the first wave, those rates had jumped to 10,779 cases and more than 14.2 million genome copies per person per day.

While those genome copies fell back to about 5.2 million genome copies in mid-april, they’d risen again to 12.3 million copies by mid-july, amid a current wave fuelled by the BA.5 Omicron subvariant.

The data showed similar — but slightly different — pictures in other regions.

In Canterbury, where little trace of the virus was being found in wastewater in mid-summer, volumes peaked weeks after Auckland, reaching more than 12.2 million genome copies per person per day on March 20.

As at July 10, that quantity had risen to 28.7 million genome copies per person per day, but then dropped back.

In Wellington, observed quantities stood at 39.7 million genome copies per person per day on July 10 — nearly climbing to the 45.8 million genome copies detected in the region at the peak of the first wave, on March 13.

Nationally, volumes fell slightly from 15.9 genome copies per person per day on March 6, to 5.6 million in mid-june — before climbing again to 13.3 million as at last weekend.

While some experts have speculated this wave may have already peaked, Hewitt said last week’s wastewater results would be informative.