‘Jumping’ viruses: What strains lie hidden in NZ’s own species?

As international scientists try to narrow down the mysterious animal origin of the Covid-19 crisis in China, a leading researcher has begun exploring what unknown viruses may lie within our own species.

Viruses are the most abundant biological entities on Earth – more than a quadrillion-quadrillion individual ones are thought to exist – and the bulk of them remain undescribed.

While seemingly coming out of nowhere, novel or undiscovered viruses often emerge by “jumping” into new hosts.

The global pandemic has shown this sometimes came with catastrophic consequences for human health – but it also posed other threats.

If a new host was an already endangered species, an epidemic could lead to its extinction – while an epidemic in an agriculturally important species could have devastating effects for industries.

In a new study, University of Otago and ESR virologist Dr Jemma Geoghegan will use revolutionary new technology to gain unprecedented insight into viruses within our native and introduced species.

She ultimately sought to tackle what was now an even more urgent question: what made some viruses leap between species, and others stick with their hosts.

“Viruses jump to new hosts a lot but the process is poorly understood,” she explained.

“We have only a limited understanding of the mechanisms that enhance or inhibit virus emergence.”

Before working at the front line of New Zealand’s Covid-19 science response, Geoghegan worked on a series of studies that have shed more light on the picture.

One major finding was that cross-species transmission has played a major role in the evolution for 19 virus families she analysed, while “co-divergence” – where a virus stuck with its hosts, evolving and mutating along the way – remained relatively rare.

Leaps between species were especially frequent in virus families in which genetic material was encoded in RNA rather than DNA – such as coronaviruses like SARS-CoV-2 and closely-related SARS and MERS.

Geoghegan said viruses that “jumped” to humans typically came from other mammals – and New Zealand’s only endemic land species were bats.

In 2014, a team of ESR scientists dubbed “the Virus Hunters” revealed that coronaviruses were present in endangered short-tailed bats.

“Obviously, there’s also a lot of invasive mammals that hang about quite a lot closer to us,” she said.

“But what’s more interesting to me are those viruses that we might find in New Zealand animals like native birds, fish, reptiles and amphibians.

“Because New Zealand has been geographically isolated for millions of years, these may help us better understand that unsampled virosphere – and how they fit into the evolutionary history of viruses.”

While some work had been done here, Geoghegan said it wasn’t extensive – and hadn’t drawn on the next-generation technology she’d be using.

That was meta-transcriptomic RNA sequencing – or what she called “deep” RNA sequencing.

The method, which was driving breakthroughs around the world in virus discovery, could quickly reveal the entire “virome” or virus composition within an individual.

More importantly, it allowed her to pinpoint those ecological traits that aided host-jumping.

“But I also want to provide an assessment of viromes in New Zealand – and therefore new insights into New Zealand’s biodiversity.”

How many New Zealand species did she aim to assess?

“I’m trying to do as many as I can,” she said.

“I’ll be working a lot with Māori researchers and iwi, who are really interested in this work because it helps inform efforts like population restoration.

“Lamprey, for instance, have been affected recently by lamprey reddening syndrome, so I’d like to help understand what is causing the disease.

“Overall, this project will hopefully increase our understanding of how viruses evolve in natural populations.”

She hoped it could also offer some valuable clues to countering the next pandemic.

“An important lesson from the ongoing Covid-19 pandemic is that we need to move faster to curb the spread of disease,” she said.

“I think this is the key to pre-empting full-blown epidemics and limiting their social and economic impact.”

The five-year study is being supported through a Rutherford Discovery grant.

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