Teagasc’s role in fighting Covid-19: Samples, sequencing and making sense of the situation

Teagasc on Covid-19: “I know from the general public it seems like this is dragging on forever and it’s very slow progress…it feels like that for us too, sometimes. But, in reality, the scientific collaboration worldwide has been outstanding.”

It is just over a year since the World Health Organization (WHO) China Country Office was informed of cases of pneumonia of an unknown cause.

Two and a half months later, Covid-19 was characterised as a pandemic. This virus, that had once been unknown and foreign to so many people, made itself comfortable in people’s lives; it welcomed itself into society, communities, homes. It destructed life as we knew it, before the average person even extensively knew about it or understood it.

One of the key dates for many scientists and health experts around the globe was January 12, 2020 – when China publicly shared the genetic sequence of Covid-19, according to the WHO.

Science, sequencing and making sense of the situation

The virus that causes Covid-19 – SARS-CoV-2 – contains genetic information that changes over time. By sequencing the virus RNA (ribonucleic acid), as members of the Irish Coronavirus Sequencing Consortium explain to AgriLand, “we can track these changes, also known as mutations, and map the spread of the virus across Ireland”.

The Irish Coronavirus Sequencing Consortium is funded by Science Foundation Ireland and led by Professor Paul Cotter of the Teagasc Food Research Centre at Moorepark and APC Microbiome Ireland.

There are various partners in the consortium, including Teagasc research centres, universities, hospitals, labs, and private companies.

The consortium sequences the RNA of viruses isolated from samples of patients who have lab-confirmed infections of Covid-19, using the latest technology from Oxford Technology.

‘We’re focusing on clinical samples’

“There’s one particular cohort that’s led in UCD [University College Dublin] called the All Ireland Infectious Disease Cohort and they have people who can ask patients for consent and get all the documents signed off on, which allows us to then continue to sequence their samples,” Professor Paul Cotter explained to AgriLand.

“We’re focusing on clinical samples, and then the NVRL [National Virus Reference Laboratory], which is part of the consortium, is the one exclusively working on the community samples – so people who aren’t in hospital, who are just going for standard testing.

“The samples we get are samples collected quite recently in the last week or so, and we can then relay that information back to the origins, a particular clinician in the hospital from which it came, and then we can also feed that into those accumulating the national information to see what’s going on overall.”

As more infections take place around the globe, the likelihood increases of variants arising that are more prone to transmission in humans. New variants that were detected in the UK and South Africa garnered much attention over the Christmas period.

Professor Cotter said that the shear number of samples increased, which means there was more to be sequenced.

‘Any experience gained from this would be transferable’

As Professor Cotter points out, some may wonder why Teagasc is involved with this.

“We had the infrastructure, the expertise, those to analyse all this data onsite to do other things that relate to food and agriculture,” he continued.

So, because all the medics in the hospital labs were so busy just looking after patients and doing standard testing, we had the capacity to help out.

“The sequencers that we have do things like studies on microbiomes, a lot of what Teagasc does is work with food companies, or consumers to see what impact different foods have on the gut.

“We do a lot of things like study cheeses and fermented foods and establish what bacteria are doing good things and adding nice flavours; looking at probiotics to determine what their health promoting activity is; looking at soil microbes and fertiliser; and rumen and methane production.

“All of those technologies are applicable to viruses and viruses of animals and plants and so on and, obviously, to coronavirus as well – so that’s why we were able to roll it out and make it available so quickly.”

Dr. John Kelly, colleague of Professor Cotter, added that due to technological advancements, “that framework, that capability, means that across the globe, the response is there” in a way that couldn’t have been possible a number of years ago.

“Sometimes the general public thinks there’s an element of basic research and development that goes into it and so on, but when things like this happen, you can see why that basis, why that network, why that capability is really important to be able to respond and help whether it be the vaccine development side, sequencing side, or analysis side.”

‘I know from the general public it seems like this is dragging on forever’

Dr. Fiona Crispie, through her extensive work on this with the consortium, instills hope with the knowledge that so far, it looks like the vaccines that have been developed “would still work” despite the new variants.

“So far, the good news is even this new UK variant, it looks like the vaccines that have been developed would still work,” Dr. Crispie explained.

“That’s why it’s very important to do that sequencing, to see our new variants coming up the whole time.

Hopefully by summer we’ll have some return to some sort of normality. But, that’s why we need to keep monitoring it, to make sure that a new one doesn’t arise.

“I know from the general public it seems like this is dragging on forever and it’s very slow progress…it feels like that for us too, sometimes. But, in reality, the scientific collaboration worldwide has been outstanding.

“If you think about the 1918 flu, the cause wasn’t even identified until the 1930s whereas, within a couple of weeks of China admitting there was a problem in Wuhan, the genome of this virus was sequenced and published internationally.

“People are sharing data on an unprecedented scale, and things have moved incredibly fast on a scientific level.”