Covid-19: Behind the scenes of genomic sequencing in Wellington's own backyard

Covid-19: Behind the scenes of genomic sequencing in Wellington’s own backyard

Hidden in plain sight, a group of scientists in Porirua – some wearing lab coats, some more at home in jeans – carry out some of the most important work in the fight against Covid-19.

Genomic sequencing is at the heart of contact tracing, although most New Zealanders hadn’t heard those words until after the first wave.

ESR Bioinformatics lead Dr Joep de Ligt​​ and his team, Dr Una Ren and Matt Storey, work around the clock to map the chain of transmission for every single case of Covid-19 in New Zealand.

Their building is straight out of the 1980s, a warren of corridors and stairwells. There are drawings by de Ligt’s kids on the bookshelf, a small 3D model of a coronavirus molecule on the next shelf.

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ESR bioinformatics lead Dr Joep de Ligt demonstrates the software which maps the chains of transmission of local cases, just like a complex family tree.

ROSA WOODS/Stuff

ESR bioinformatics lead Dr Joep de Ligt demonstrates the software which maps the chains of transmission of local cases, just like a complex family tree.

These scientists knew from the beginning this work would be important. During the first lockdown they tested samples, mapped chains of transmission, and added to their database, funding it all themselves.

Then they laid all their data on the table at the Ministry of Health, and explained how they could help.

The ministry now relies on this work, and funds it jointly with the Ministry of Business, Innovation and Employment’s Covid-19 Innovation Acceleration Fund.

At the moment, ESR in Wellington is the main player in this field. Samples can be sequenced elsewhere, but the results are usually sent to Wellington for analysis and mapping.

The robot responsible for pipetting and mixing solutions with the inert virus – capable of doing 84 at a time – at the ESR lab in Porirua.

ROSA WOODS/Stuff

The robot responsible for pipetting and mixing solutions with the inert virus – capable of doing 84 at a time – at the ESR lab in Porirua.

Equipment is easy to obtain, but the people with expertise are invaluable, and scarce.

“New Zealand can say we’ve sequenced nearly every case,” de Ligt said. That meant a near-conclusive map of cases, with every chain of transmission shown as a line on a diagram, like a family tree.

Other countries around the world were doing this too. Australia and some smaller Pacific islands were also able to track every case and map them.

But for countries overwhelmed with thousands of cases a day, it wasn’t a priority. The United Kingdom was sequencing about 30 per cent of its cases, de Ligt said – impressive considering its volume of daily cases could reach more than 20,000.

New Zealand was in a sweet spot; a manageable amount of cases, with real value to be gained by knowing where they came from.

Joep de Ligt talks to Prime Minister Jacinda Ardern about the different Covid-19 genomes in New Zealand, during an ESR tour in August. (File photo)

Dom Thomas/Getty Images

Joep de Ligt talks to Prime Minister Jacinda Ardern about the different Covid-19 genomes in New Zealand, during an ESR tour in August. (File photo)

The first sequence was produced on March 9. Since then, ESR had done the bulk of the work – 1289 of a total 1296 sequences – with one other by Otago University, and sic by Massey University.

The case of the Auckland AUT student who tested positive on November 12 was the fastest turnaround so far in New Zealand and, according to de Ligt, likely the fastest in the world.

Overseas, a sample could take anywhere from 24 to 48 hours to sequence. In New Zealand, with the pedal to the floor, it took around 10 hours.

Since samples often travelled from around the country to the lab in Wellington, ESR is planning to equip and train the teams in its Christchurch and Auckland centres to perform the same service, to shorten delivery times even further.

This would also provide alternatives if something happened to the Wellington base, be it disastrous like an earthquake or fire, or simple as a power outage.

A Covid-19 molecule, shown here as an enlarged 3D replica, has spikes on the outside which attach themselves to a human cell, and transfer their contents – RNA.

ROSA WOODS/Stuff

A Covid-19 molecule, shown here as an enlarged 3D replica, has spikes on the outside which attach themselves to a human cell, and transfer their contents – RNA.

The science

When a coronavirus sample lands in the hands of ESR scientists, taken by swabbing the nose and throat of a person with symptoms, it has already tested positive for Covid-19.

The person it came from should already be in self-isolation, and perhaps there is already some indication of whom they caught it from.

Or perhaps everyone is scratching their heads, workplaces thrust into lockdown, and staff at the Ministry of Health are calling hushed, hurried meetings.

RNA, like DNA, is a long ladder of chemical compounds; adenine (A), uracil (U), guanine (G) and cytosine (C). They pair up to form a double helix structure, A always joining with U, and C with G.

These letters change due to mutation. Because of the way Covid-19 RNA mutates, scientists know they can expect a change in the code once every two weeks.

The closer one person’s virus resembles another known case, the more likely it is they caught it from that person.

Last week, the AUT student’s sample was identical to another known case.

De Ligt and his team spend most of their time in the office rather than the lab, comparing one sequence to the next.

ROSA WOODS/Stuff

De Ligt and his team spend most of their time in the office rather than the lab, comparing one sequence to the next.

The process

A positive sample begins its quest for an answer by being turned from a live form of the virus, into one which cannot infect people.

According to ESR chief scientist Dr Brett Cowan​​, “we explode it, and then we cook it”. Simple, when you put it like that.

Cowan spends a lot of his time explaining things in layman’s terms. While it can be interesting to the public, more importantly, it helps if those co-ordinating health responses and contact tracing understand the process.

The membrane around the outside of the virus is burst open, spilling the genetic data. The spikes on the membrane’s surface are the parts that latch onto human cells, and allow the RNA, the code of the virus, to transfer and infect. Without the membrane, the RNA can’t enter a cell.

The sample is then heated to a temperature that will damage everything but the RNA – a second line of defence.

ESR chief scientist Dr Brett Cowan, holding a 3D printed replica of the virus Covid-19, is well-versed in explaining the science of viruses to the public.

ROSA WOODS/Stuff

ESR chief scientist Dr Brett Cowan, holding a 3D printed replica of the virus Covid-19, is well-versed in explaining the science of viruses to the public.

Once the sample is no longer infectious, the RNA is isolated from the other junk collected in a sample – pollen, dust, or bacteria in the nose of the test subject.

The only part of the sample they were interested in, said de Ligt, was the RNA. “We don’t want to learn about the person.”

In any sample, there isn’t enough RNA present to produce a result at this stage. The RNA needs to be replicated millions, if not billions of times.

Then a robot transfers the virus into a cocktail of chemicals. This machine, which costs around $30,000, can transfer up to 84 samples at a time – that’s a sample of inert Covid-19 RNA from 84 different people.

For a country like New Zealand, which rarely had more than a handful of positive cases a day, the robot was not intended to speed up the process.

Rather, it meant everything was done systematically, with no risk of mixed-up samples. Some samples are still pipetted by hand – such as the single case of the AUT student.

The next stage is to run it through a machine called a GridION​, which costs around $100,000, and can sequence the RNA into the string of As, Us, Cs, and Gs.

The machine spits out the code, and the scientists move in to analyse the results.

Coding is a big part of the process. Here, de Ligt enters the data from the machine into the mapping program, to see the bigger picture of community transmission.

ROSA WOODS

Coding is a big part of the process. Here, de Ligt enters the data from the machine into the mapping program, to see the bigger picture of community transmission.

By comparing one sequence with every other on file, they can pinpoint the person it most closely resembles, and then the epidemiologists and contact tracing teams take over.

“We take data, and turn it into actionable intelligence,” Cowan said. “We have the end of the chain, and sequencing gives us the beginning.”

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