Scientists’ detective work reveals diversity of coronavirus in NZ
Scientists have completed months of detective work to reveal where New Zealand’s cases of Covid-19 came from at the height of our crisis — with some surprising results.
They found most of the analysed cases that led to others being infected originated from North America, rather than Asia — and that cases that turned up here represented all of Sars-CoV-2’s global genomic diversity.
They’ve also shown there was no sign of Covid-19 circulating in the country before the first case was officially reported.
Decoding or “sequencing” the genetic jigsaw that is the virus’ genome has been a crucial part of the public health response to Covid-19 here and overseas.
Investigating the spread of the virus into a population can leave scientists with a spaghetti-like mess to untangle — but genomic sequencing can quickly tell them where a specific case came from, and pick it apart from other cases in the community.
The speed at which scientists have been able to sequence genomes from positive Covid-19 samples — sequencing work once cost billions and took months — has been among the most impressive feats of the world’s fight against the virus.
In NZ, scientists have completed sequences in less than 24 hours.
This highlights ...how globally connected we are.
Dr Jemma Geoghegan Otago University virologist
In a just-published collaborative study, University of Otago evolutionary virologist Dr Jemma Geoghegan and colleagues have shared data from 649 genome sequences done in New Zealand between February 26 and May 22 — representing about half the cases sampled over that crisis period.
Despite the comparatively tiny size of Covid-19’s incursion here, the team reported 277 separate introductions of the virus, out of the 649 cases.
Of those, they estimated a quarter led to only one other secondary case, while just 19 per cent led to a chain of transmission that could be observed as a lineage. Most of those lineages could be traced back to North America, rather than to Asia where the virus first emerged — which reflected where it was most prevalent during the time of sampling.
The largest NZ clusters were often tied to social gatherings such as weddings, hospitality and conferences.
The biggest of those — which comprised a lineage called B.1.26 and was linked to a “super-spreading” event at a Southland wedding — most likely originated in the United States.
The team also found no evidence the virus had been circulating before NZ’s first case was reported on February 26 — and also that fewer cases were missed later in the country’s epidemic than in early stages.
“It was surprising that, despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population, and this high degree of genomic diversity was observed throughout the country,” Geoghegan said. “This highlights the vast number of introductions and how globally connected we are.”
Geoghegan said genomics gave scientists the power to easily quantify the effectiveness of lockdown measures and border closures. For instance, they found the effective reproductive number of NZ’s biggest cluster was squashed from seven to just 0.2 in the first week of lockdown.
“We can see how interventions stopped virus transmission and also help link more infections to a major transmission cluster than through epidemiological data alone, providing probable sources of infections for cases in which the source was unclear,” she said.
“It is also important to monitor how the virus mutates — this information is vital for any future therapeutics such as vaccines.”
Because our borders remain closed, Geoghegan said, any new incursions of the virus would be from quarantine facilities — as had happened in Victoria, with disastrous consequences.