Wednesday 2 December 2020 10:38am
Dr Jemma Geoghegan
It’s inevitable 2020 will be represented in history as the year of COVID-19. A year of sickness and death, of lockdowns and masks, of disruption, confusion, fear and sadness.
Almost all of the connotations are negative, but within this year of unexpected and uncompromising difficulties have come some beacons of hope for a better future. And it is hard to argue anything has shone brighter than the world’s scientific community.
It isn’t just that scientists have had the tools and knowledge to help with this crisis. It’s that, in a manner never experienced before, scientists have made a point of explaining these tools, this knowledge, with the world. They have taken the most extraordinarily complicated work and distilled it into formats that have informed us, educated us, and soothed our concerns.
In New Zealand, one of the standout communicators has been University of Otago evolutionary virologist Dr Jemma Geoghegan. She has become one of the faces of this country’s COVID-19 genome sequencing efforts. And now, as the year comes to a close, Dr Geoghegan has had her future path as a scientist considerably strengthened by being awarded the prestigious Rutherford Discovery Fellowship.
The Otago Bulletin sat down with Dr Geoghegan to find out how she got here.
A child of the eighties, Dr Geoghegan was born and raised in the small Scottish village of Cupar, about an hour outside of Edinburgh. While her hometown was small, even as a toddler her ambitions weren’t. She wanted to dance, and dance well.
Even as a one-year-old she was “weirdly, seriously into dance”, she says. She was good enough to be accepted into the Scottish Ballet, performing on stages from London to Glasgow and Edinburgh.
But at 18 years old she decided life as a ballerina held too many uncertainties and too few opportunities. It wasn’t for her. Her friends were heading to university and, as a small-town girl with a wide-eyed view of the world, she was determined to do the same.
“I always felt I knew I wanted to go to university. I used to train in dance after school for hours every day, so that was kind of competing with schoolwork - I was never top of my class at school.
“But I could see university was definitely the way forward if you wanted to get out of a very small town. Being from a family with a single parent who struggled a lot to bring up four kids, I could see being better educated was very much a way out of struggling financially.”
She applied for six universities and got into all of them, picking the one that “was furthest away from Cupar” - the University of Strathclyde in Glasgow.
“I guess when you’re from a small town, and when I was wee Cupar was really small, I guess I just had a sense of trying to get out of there.”
That sense led her to take a gap year between high school and university, volunteering in rural Sri Lanka, close to the south coast. The year was 2004.
“I was teaching English in a school in the middle of nowhere, a place called Baddegama. It was really rural, a really small town. It had a vocational training centre for women, but also a daycare centre for kids. Basically, their families couldn’t afford to feed them so they came here. So I was looking after kids during the day, teaching English, then teaching English to the women in the evenings.”
The classroom in Baddegama, 2004
The volunteering group was small and had separated into pairs before being stationed around Sri Lanka. As Christmas approached the group arranged to meet up. There were two destinations tossed up - either the south coast seaside resort of Mirissa, or somewhere inland.
“We decided to go, last minute, somewhere inland. And we woke up Boxing Day morning to this news.”
A massive earthquake in the Indian Ocean had triggered a catastrophic tsunami. Nearly quarter of a million people were killed. More than 30,000 of them were in Sri Lanka. The Boxing Day crowds on Sri Lanka’s south coast had been directly in the tsunami’s path. Mirissa had been savaged.
Mirissa beach, 2004, before the tsunami.
“We just got really lucky. It was very surreal. For the days afterwards there were aftershocks and there was just a lot of fear. When someone said ‘run’ there was just panic. And the streets were just, people just running, and the army everywhere, and it was just crazy.
“And even though I was never physically running from a wave, I was running because people were shouting to run. It was just surreal.”
The group of volunteers relocated to Colombo to help however they could.
“We ended up in a warehouse packing supply boxes - rice and soap and clothes and stuff - and loading them onto trucks to try and get them where they were needed. We did that for a few weeks.
“And it became clear I wasn’t going to be able to get back to Baddegama because the road there didn’t exist anymore. And most of the families who’d sent kids there had been completely disrupted.”
She was 18.
She returned to Scotland and to the University of Strathclyde where she soon realised she had the ability to flourish academically.
“I was suddenly achieving really good grades. I felt like I knew how to learn at university, like I knew how to study there. I guess I was a little competitive as well. I wanted to do well.”
She completed her Bachelor of Science (Honours) in Genetics, specialising in Forensic Biology. But another global calamity had arrived - this one financial.
“When I graduated it was the year of the Global Financial Crisis and that whole year was pretty much, the world was going to end.”
The career outlook looked suddenly bleak, and she considered leaving academia and taking up a graduate job in Oxford.
“But one of the things I asked at my interview was about moving up the ladder, ‘how do I get your job’, basically. And they said, well, you’d need a PhD for that.
“But I knew I didn’t want to stay in the UK. I kind of just wanted to get out of there. I thought it would be easiest to do a PhD in an English speaking country - New Zealand, Australia, Canada.
“I didn’t know anything about New Zealand, I didn’t even know a single Kiwi. I googled, found Otago, found my PhD supervisor [Sesquicentennial Distinguished Professor Hamish Spencer, Zoology] and emailed him. It was a completely cold-call email, and he said, ‘well, I’ve got a scholarship you could apply for’.”
When her final grades came through they were good enough to qualify her for the scholarship.
“And I was like, ‘ok, I guess I’m going to New Zealand’.”
Dunedin, New York, Sydney, Dunedin
She was 23, on the far side of the world in a country she knew nothing about, moving into a flat with “a bunch of Kiwis”. But where most might find loneliness, Dr Geoghegan found the opposite.
“In the first week of me arriving we had a party at our flat, and I met my now husband. He’s a Dunedin boy.
“I guess in Dunedin, in New Zealand actually, the people and culture here I find extremely similar to Scotland. In that first week of being here I met really good friends who are still really good friends, I met my husband and his family, and I just felt instantly at home here.”
But she was still nowhere near being an evolutionary virologist, she says.
“I didn’t even think about viruses until my first post-doc. My PhD focus was evolutionary biology, how things evolve from a theoretical modelling perspective.”
On completion of her PhD, her soon-to-be husband won a Fulbright Scholarship to New York. She had a choice - pursue postdoctoral work where she wanted, or follow her partner to New York and accept whatever work she could find.
She decided on New York. She contacted New York University, and eventually connected with a group doing work on HIV.
“They had projects where they were working with the Swaziland government and the Bill and Melinda Gates Foundation, and it seemed like really cool work. So I ended up getting a job there, working on HIV, bringing my knowledge of evolutionary biology into that. And that was my first experience working with viruses.”
Most virologists come at virology from a very clinical perspective, she explains.
“And I saw how I could apply my knowledge of evolution to the subject area. I thought it was important to understand things from an evolutionary point of view and not just a clinical perspective. So it kind of fitted into what I was interested in, completely.”
Once the year was up she was offered the chance to stay on in the US, but together with her partner decided against it.
“It was fun for a while but it was just very full on. The work culture there, especially in academia, was just crazy. You know, people would work all day every day, really long hours, not get paid very well, there was quite a hierarchy structure to it. It was cool in a lot of ways, but the work life balance basically didn’t exist.”
Instead they chose to move to Australia, where Dr Geoghegan worked as a postdoctoral research fellow at the University of Sydney, before getting her own laboratory at Macquarie University in Sydney’s northern suburbs.
“We had a baby in 2019. Sydney is great when you’re young and you don’t have family responsibilities, but when you do, it’s so hard. You spend an hour each way commuting, everything is expensive. Everything is hard, and we didn’t have any family there.
“We’d always wanted to come back to Dunedin and never thought it was possible. But late last year we approached Otago University and luckily there was a job my husband took up, lecturing law here at the university. It was amazing timing really.”
She contacted the University of Otago’s Dunedin-based Department of Microbiology and Immunology, and also spoke to the Institute of Environmental Science and Research in Wellington. The two organisations worked together to jointly fund a position at Otago’s Dunedin campus.
But yet again reasonable plans were about to be altered by a global event.
“This was the very beginning of this year, and as a virologist obviously I was very aware of what was happening in China, in Wuhan specifically. Among the community of virologists we were like ‘this is going to be bad’. But generally, we were blissfully unaware of what the year was going to bring.”
We now know how quickly the COVID-19 situation snowballed for New Zealand and the world, but for Dr Geoghegan her professional life was about to transform.
“New Zealand got our first case at the end of February and me and my colleagues at ESR were keen to sequence the virus genome. So, within a few days, they managed to get that done.”
Genomic sequencing analyses the genetic material of something - in this case a virus. Like humans, viruses have a genome - all their genetic material - made up of lots of letters.
“When we analyse that, when we look at the order the letters appear as, we can compare it to the genome of the other viruses.
“So, if I had a virus it might look slightly different from the virus you’ve got, and we can compare that. Then we can construct a sort of family tree from those samples to see what they’re related to, whether they’re related to each other, and sort of reconstruct the way that those viruses were passed from person to person.”
Amidst the global response to the pandemic it became clear real-time genomic sequencing of the virus was possible, Dr Geoghegan says. That data could then be integrated into the epidemiological data that was helping the pandemic response.
“We applied for funding, and we got it from MBIE [the Ministry of Business, Innovation and Employment]. Our aim was to sequence every positive case in New Zealand and do it in real time.”
During the country’s first wave, as the team was gathering and setting up equipment, that real-time response wasn’t possible.
“But by the time that wave was coming to an end in May we were like ‘we can do this now, we’ve got the capability and the framework, we’ve got people talking to each other who need to talk to each other’. So by the re-emergence in August we were able to do it in real time. So it worked.”
It worked so well, and became such a vital tool in New Zealand’s response to new COVID-19 clusters, that Dr Geoghegan found herself not just looking down the barrel of a microscope, but also looking down the barrel of television cameras.
“I had never been on TV before, I didn’t think I’d ever want to do TV. I guess at the start of this I wanted to be involved because I could see we had the capability of doing genomic sequencing in real time. And now we have lots of people who know what genomic sequencing is.
“It’s very rewarding being a part of science communication when people see the value in what you’re doing. And I think the value in this has been made quite clear now. So it feels very rewarding to know that, you know, even my mother-in-law knows what genomic sequencing is now!”
While Dr Geoghegan’s work shows the virus mutating, there is no evidence those mutations are making it more benign, she says.
“Because a virus’ main goal is to transmit to a new host, to find a new cell to replicate, and so if it’s doing that really well there’s no pressure for it to change the way it causes disease. I think the fact that a reported 40 per cent of people are asymptomatic but infectious has made this thing as huge as it is, you know? That’s the scary thing.”
In October Dr Geoghegan was one of 10 New Zealand early-to mid-career researchers to be awarded a 2020 Rutherford Discovery Fellowship. The prestigious Royal Society Te Aparangi award not only comes with a hefty financial benefit - $800,000 over five years - it also carries considerable prestige.
“It’s a privilege to be associated with the Royal Society, to be an ambassador for the Royal Society now I am a Rutherford Fellow. And I think internationally science in New Zealand has got a stellar reputation, especially with this pandemic response and listening to science. It’s just a privilege to be a part of it.
“I’ve looked at the past fellows and how [this award] has really made their career. It has really changed the trajectory of their career. And I really hope that’s the case here.”
Dr Geoghegan’s winning research is entitled ‘Ecological barriers and drivers of virus emergence’.
“I’m really interested in how viruses evolve, and they often do that by jumping to a new host. This new coronavirus evolved by jumping from an animal into humans; we don’t know what animal it jumped from, but we know that several wildlife species have a similar relative - bats and pangolins and other animals too.
“The vast majority of new, novel virus infections in animals, in plants and in humans have jumped from a different species. There’s ecological and genetic barriers to host jumping, and we don’t know what those barriers are. And we don’t know how these barriers hinder or promote virus emergence. And that’s what I want to better understand.”
We’re only at the beginning of our journey towards fully understanding viruses, she says.
“Our focus on viruses has really only been on viruses that affect humans, or that affect plants and animals that are economically important. But there is a plethora of viruses that exist in nature that don’t seemingly cause disease. But they exist.
“So when we do virological surveys of natural ecosystems and animals in nature, we can begin to fill our gaps in knowledge of the evolutionary history of viruses. Maybe we can detect where viruses that do infect hosts that we care about have come from, and begin to understand how often they’ve jumped hosts in the past.”
Does this mean we’re in for a steady and gradual increasing of what we know about viruses? Or are we at the precipice of a giant leap forward? Dr Geoghegan is emphatic.
“It’s going to explode. It already has in the last couple of years with the advent of next generation sequencing technologies. Before, with virus discovery, you kind of had to know what you’re looking for, you had to grow it in a lab and culture it. And it would take a long time to do that. Now you can sequence the total RNA in an organism and find viruses.
”And what we’re finding is that most of them don’t seemingly cause disease but they are present and are replicating and infecting hosts and jumping to new hosts too. It’s an extraordinary time to be in virus discovery, because everywhere you look you find new viruses.”
New viruses are being discovered that don’t look at all familiar to us, in places we didn’t know much about before.
“They’ve probably been evolving for hundreds of millions of years and don’t actually share anything similar with known viruses, we can’t recognise them as viruses.
“I think it’s in the unsampled bits of nature that we’re going to find viruses we didn’t know existed. They’re probably there, we just can’t recognise they’re there. And I think we’re going to get better at doing that. We’ve got to get better at doing that.”
But there is going to be “a next pandemic”, she says.
“Coronaviruses, particularly, seem to jump to humans a lot. The last five coronaviruses that have emerged in humans have done so in the last 20 years, and three of them have been pandemics. So it’s going to happen again.
“We need to generate more knowledge about these viruses that exist in the world, because if we already know about them then perhaps treatments could be preemptive, rather than reactive. So, there’re definitely things we need to learn.”
For Dr Geoghegan, that thirst for learning is as strong as ever. And she’s standing tall in a field where discovery is constant.
“It’s exciting because we’re in a discovery phase. It’s not going to last forever, but I get to ride this wave of discovery and everything is exciting because you find a new virus and you’re like 'oh my god’.
“We've found viruses, for example in fish, related to human viruses we didn’t know existed in any other host before. It’s just all really exciting.
“What I want to do with this Rutherford opportunity is sample hosts that have never been sampled before. Because New Zealand is an extraordinary place where you have all this native fauna and the animals here, most of them, the native ones, they only exist in New Zealand. And because of their geographic isolation they’ve been separated for a long time.
“For example, I’m hoping to sample tuatara virome, and discover viruses in there that are ancient relatives of viruses in other hosts we know about. I think that’s the most exciting thing about doing science in New Zealand.”
And, despite a life laced with global roaming, it is New Zealand where she intends to stay. This is where her family is. This is where her house is - bought just after lockdown. The rambling days are over, she says.
“Dunedin is home.”