Introduction

More than a million people in the UK have endured the unpleasant experience of having their nose and throat swabbed for Covid-19.

For the vast majority, their interest in testing begins and ends with a positive or negative result.

For scientists at the Quadram Institute in Norwich, further analysis can tell them how this unrelenting pandemic is spreading.

COVID-19

It is not an exaggeration to say Covid-19 has impacted virtually everyone – from the major disruption it has wreaked upon modern life to the devastation it has caused families that have lost loved ones.

At best, the virus can range from a mild cold that can tail off with potential long-term effects; at worst, it is ten times more severe than flu and, in some cases, deadly. Its superpower is seemingly in its ability to transmit with ease. Without measures to stop it, such as wearing masks and social distancing, it has proven it can thrive, infecting millions on a global scale.

Though it is common knowledge the pandemic began in the Chinese city of Wuhan in 2019, what is perhaps less known outside the science community is that the virus replicates every month, introducing two new mutations to its 30,000-letter genetic code – forming new lineages of the virus that in effect, create a new branch on the Covid family tree.

These accidental blips are not new strains but minor tweaks to its make-up that enable epidemiologists to track not just the entry of the virus into a population but how and where it came from.

NHS Coronavirus testing

The Quadram Institute is one such team surveilling the evolution and spread of the virus as part of the 21-strong consortium COG-UK, which is funded from £20m of grants from the Department of Health and Social Care, the Wellcome Trust, UK Research and Innovation, and the Wellcome Sanger Institute.

Since the first wave of the pandemic hit the UK in March 2020, Quadram has been at the forefront of genomic sequencing – the science behind taking positive samples identified by testing and extracting the genetic code of the virus.

In part, this success has come from forging a partnership with the local NHS coronavirus testing system, through the Norfolk and Norwich University Hospital (NNUH). Samples from community, hospital and drive-through testing facilities are sent to the NNUH virology labs for PCR tests.

In the NNUH virology labs, genetic material is extracted from the samples. An amplification step increases the testing sensitivity so that very small amounts of SARS-C0V-2 RNA can be detected. A PCR test identifies the presence of the SARS-C0V-2 by matching probes to specific sequences in the virus’ genetic code. The PCR test takes 5-6 hours, but many different samples can be run simultaneously, and multiple machines run 24/7 depending on the demand. Once the results are known, trained NHS staff contact the individuals, usually within 24 hours of them providing the sample.

This gives a simple yes or no answer as to whether there is the virus in the sample, but tells us nothing about its place in the Covid family tree To unlock those secrets, excess genetic material from positive tests goes to Quadram for genome sequencing.

Between March and August 2020, it analysed 1,565 local samples from 1,367 cases: put into context, only five out of 103 countries sequenced more Covid genomes than were done in Norfolk in the same period.

Big Data

One advantage the Norwich, and UK, teams have had is the access to a state-of-the-art cloud-computing infrastructure tailored for microbial genomics. The Cloud Infrastructure in Microbial Bioinformatics (CLIMB)-BIG DATA project is a multi-centre initiative that helps scientists cope with the deluge of data that comes from microbial genome sequencing.

This meant that virtually overnight the COG-UK Consortium had the national infrastructure in place to launch its genome sequencing efforts.

But it’s not just the genome sequences that are being analysed. The researchers need information on who each sample came from to be able to identify patterns and links in the transmission of the virus.

Here the Norwich Research Park Biorepository plays a key role by adapting its usual job of ethically and securely supplying and storing samples for clinical research. As part of the NHS Trust, it has secure access to the data the researchers need, typically age, sex and location, but can withhold anything sensitive or identifiable.

This way, the Biorepository acts as a vital intermediary by providing a streamlined and accurate transfer of relevant data to the Quadram Institute with a rapid turnover and reliable results.

And their findings have been crucial in feeding into the global family tree created when the first coronavirus genome was sequenced in Wuhan.

Genome detectives
Samples from NHS testing are stored in QI until ready for sequencing

Samples from NHS testing are stored in QI until ready for sequencing“The difference [in the genetic code] randomly happens but it lets us track what the changes have been,” says the institute’s head of informatics, Dr Andrew Page. “So if you think about the population, people have different coloured hair and you inherit some traits from your parents – it’s similar with the virus, you can trace it back to its roots.

“And by looking at these changes, we can track the spread – who has viruses that are similar and who has ones that are different. By looking at these changes, we can track the spread and assign an identifier – so we can tell, say, that a virus that was circulating in Europe has come into the UK.

“Using genomics we can work out these hidden links.”

This is exactly what happened when the institute was asked to sequence samples from a chicken processing facility in Norfolk that experienced an outbreak in August 2020. The team was able to provide results to Norfolk and Norwich University Hospital within 24 hours which not only allowed public health bodies to begin managing the outbreak quickly, but also provided intelligence as to how it was introduced into the workforce.

“The most closely-related viral genomes in the global family tree were from Portugal,” says Professor  Justin O Grady, Quadram group leader and professor at the University of East Anglia.

“We were able to say definitively that [the samples] were all the same and nothing like anything we’d previously seen in the region. And we were able to say that they were quite likely to have originated from Portugal, because that’s what the genomic information – the lineage – told us.

“When we reported that information to the hospital and Norfolk Test and Trace, they were amazed we could say that.”

Using science to join the dots is not dissimilar to detective work and it’s possible that without it, the origins of the factory outbreak would have remained something of a mystery. Certainly, in this instance, modern epidemiology methods enabled scientists to locate links between lineages of the virus – something you can’t do normally, says Dr Page.

“In the past, people would use traditional epidemiology in that they’d talk to people and say, ‘where have you been and who’ve you talked to’ and try to work out a map like that. The public health team went into the factory and nobody reported having travelled. So traditional epidemiology failed there.

“But [the genomic epidemiology] told us that someone had travelled and brought it in because [the lineage] was the only place in Europe it had been seen in the previous two months.”

Public Health
"The genomics gives us confidence that our strategy and approach is evidence-based" - Dr Louise Smith, Norfolk's Director of Public Health

For Norfolk’s director of public health, Dr Louise Smith, the information provided confidence in how to manage the outbreak.

“It was our first example of being able to prove we had a point-source outbreak – that it had happened in the factory and that the transmission was the same lineage amongst everybody, which supported the strategy that we took to isolate quite large cohorts of staff,” she explains.

“It’s very challenging for a business because in the early days of an outbreak, they’re almost in wishful thinking [mode], saying it’s because lots of people in the community have coronavirus.  The genomics gives us confidence that our strategy and approach is evidence-based and when we see certain patterns that it is likely to be transmission in the workplace. It confirmed our strategy and approach.”

Spotting the transmission is, however, very different to preventing its spread. The genomics has proved its travelled beyond Norfolk’s borders despite the early intervention.

“We’ve seen it pop up in random places – someone went up to the north, and to Essex, and you can see little spreads of it everywhere,” says Dr Page.

“That’s the power of genomics, you can link all these things together, it tells you the real story – not the one people tell you.”

It is not the only instance in which the institute has been able to identify links and provide actionable intel from sequencing positive pillar one tests, which are carried out in hospitals, care homes and some workplaces. A combination of investigative work and lateral thinking uncovered a previously unidentified transmission between six care homes in the Norfolk-Suffolk region, which is now being scrutinised by public health officials.

“We get basic data about the people we test – their age, their sex and the first part of their postcode,” says Prof O’Grady. “So, we were like, OK, the lineage we found in that [first] care home is heavily concentrated in older people in the region and in certain pockets of it.

“When we looked at that in more detail, we asked the hospital whether there was any chance there were other cases from other care homes and we found that there were.”

Though it is possible to identify outbreaks, it is not so simple to identify the exact point of transmission. In the case of the care homes, the possibilities were numerous.

“It may have been that a healthcare worker picked it up and moved around from one to place to another, or that patients from those different care homes were in the same hospital and picked it up then were sent back to their care homes,” says Prof O’Grady. “There are multiple ways this could have happened, but no-one knew it happened until we applied genomic epidemiology to it.”

Reassurance
“The COG-UK initiative to provide whole genome sequencing of SARS-CoV-2 provides improvement in hospital functioning by aiding Infection Prevention and Control... as well as reduction of transmission of the virus from hospitals to the community” - Dr Samir Dervisevic, consultant virologist at NNUH.

Being able to feed back this type of information has been crucial in helping to manage the spread between workforces, according to Dr Smith. She says Public Health has been liaising with employment agencies to identify the links between staff who typically move between workplaces to help stop possible transmission.

“A business may only have told us about their main substantive workforce, so it reminds us to ask, ‘what about your temporary, agency-based staff?’” she explains.

“The obvious place to go to is the employer’s recruitment agent, because often they’re placing people for shifts in different factories and on different days of the week. Then we start to find links between [for example] abattoirs and care homes, simply because people… are working in different businesses.”

Genomic epidemiology has confirmed not only the presence of the virus but informed public health officials as to whether control measures are working in care settings. In one case, the Quadram was able to confirm the lineages were only present in care workers and not their patients – meaning, as Dr Page explains, that “all the basics, such as masks and hand-washing” were working.

It is not the only instance in which science has provided reassurance. When Ipswich Hospital was worried about a possible transmission in the wards, Prof O’Grady was able prove otherwise.

“What we found out was that they had multiple lineages in the wards which were very similar to what was circulating in the community,” he says.

“That basically meant people who were testing positive in the hospital had come in with the virus, not because they all got it from each other in the [wards]. It put the hospital’s mind at ease that their infection control processes were working appropriately – in that case, they were getting it right.”

“The COG-UK initiative to provide whole genome sequencing of SARS-CoV-2 provides improvement in hospital functioning by aiding Infection Prevention and Control efforts and clarifying intra-hospital transmission events as well as reduction of transmission of the virus from hospitals to the community” says Dr Samir Dervisevic, consultant virologist at NNUH.

Quadram and NNUH are now looking at using genomics to identify hospital spread of SARS-CoV-2 within 24 hours.

“The rapid deployment of genome sequencing in outbreak situations would greatly aid the effort to reduce the risk of the spread of infection amongst our vulnerable patients as well the staff,” he adds.

“This type of intervention would not only help patient management but would provide as accurate as possible analysis of intra-hospital transmission.”

The Quadram has not only identified new lineages and clusters of the virus into the region, but also instances in which they have disappeared completely – another form of reassurance. By August, the number of lineages had reduced from 100 to one because the virus had been unable to thrive, says Dr Page.

“A lot disappeared totally because [areas] had been in lockdown and the virus couldn’t infect anyone. So, we do know that some measures were extremely successful,” he explains.

Furthermore, Quadram has found no evidence of secondary infections, adds Prof O’Grady. What continues to be rewarding is the application of their work to help get the virus under control.

“The hospital finds it extremely useful; Test and Trace finds it extremely useful; Public Health finds it extremely useful,” says Prof O’Grady. “But what’s really great is to see direct translation of science – we do a lot of scientific research and it’s not every day that your science is translated into something useful. Doing something in the lab at the bench and then two days later seeing that information being utilised to help control the spread of the virus – that is very satisfying.”

Second wave
"If setting up our epidemiological sequencing work through COG-UK in March 2020 felt like a world record-breaking sprint, the rest of the year evolved into a scientific ultra-marathon" - Professor Justin O'Grady

However, there is reason to be cautious – in contrast to the avalanche of samples it sequenced during the first wave is the sobering knowledge that this had dropped to a handful in the summer.

“I do analysis every week from pillar one tests about how many clusters and distinct new genomes are coming into the area and how it’s growing, and which are related,” says Dr Page. “And we can build the picture very quickly – are things just ticking over? – which was the case in early September.

“But at least they know what’s related and what’s not and what’s new and what to keep an eye on. It gives them real intelligence to fight the pandemic.”

Dr Smith says these seemingly “random” introductions are actually highlighting a number of different issues.

“Just occasionally a case will be identified that just seems completely unconnected, so it’s here and then in the Midlands and then the south-east,” she says. “Those missing links in the generations of the virus transmission is what the genomics is highlighting.

“It is definitely telling us something – which is either about compliance and engagement with Test and Trace or it’s because we have these asymptomatic transmissions.” 

This intelligence became even more important in the autumn, as the period between the second and third national lockdowns led to a very significant rise in the spread of the disease. Between October and December 2020, the team sequenced over than 7,000 samples, more than treble the amount  analysed in the previous six months.

Prof Justin O’Grady says: “If setting up our epidemiological sequencing work through COG-UK in March 2020 felt like a world record-breaking sprint, the rest of the year evolved into a scientific ultra-marathon. After the first wave we knew we’d need to create more capacity so that we could handle increases in cases and still meet the demands we would face.”

The Department for Health and Social Care’s Testing Innovation Fund backed the COG-UK consortium in expanding whole genome sequencing of positive SARS-CoV-2 virus with £12.2million in extra funding.

The Quadram’s share of this was put to purchasing new equipment and employing extra staff, but the team also focused on honing their processes to maximise the throughput of samples.

By increasing capacity, optimising the processes and develop a unified lab pipeline, one or two scientists can now process more than 1,000 samples in just a couple of days, depending on the urgency and response needs.

Variants of Concern

The genomic surveillance capacity has shown its value in finding and tracking Variants of Concern (VOCs). These are variants that stand out from the many others that are constantly appearing because they may affect virus properties like transmissibility.

One variant (the Alpha variant) associated with a major surge in cases in Kent first appeared in Norfolk in November 2020 and by the first week in December, it accounted for 45 per cent of all positive samples in the community.

Dr Andrew Page says “There have been at least seven independent introductions of the virus into the county, all happening in November. There are likely many more, but these are the ones we can put our finger on because they are distinct. This tells us that there is a continuous flow of the new variant into our region, rather than a one-off introduction.

Some of these introductions will go nowhere, people will get sick, self-isolate and that transmission chain ends. In other cases, a single introduction can cause a huge number of subsequent cases. This appears to have happened in Wymondham in south Norfolk in November, with a distinct mutation allowing us to track that outbreak.”

The variant of concern first identified in South Africa can only be identified currently by genome sequencing. A small number of cases were picked up in Norfolk, traced back to travel or contacts of travellers to South Africa. Where these links to travel haven’t been found, more expansive surge testing locally directed is deployed.

The future
"COG-UK’s ambition is to develop a sustainable and long-term sequencing capability across the UK than can be used for both Covid-19 and for other pathogens.” - Dr Sharon Peacock, director of COG-UK

Dr Sharon Peacock, director of COG-UK, says Quadram’s “powerful” analysis of local outbreaks has made it instrumental in contributing to the national picture and that a key part its legacy will be in its continued research.

“Prof O’Grady is creating some really important methodologies and the work he’s doing is important because if you can’t get the methodology right, then you’re going nowhere,” she says. “And Dr Page is undertaking a national review of genomics in relation to care homes to submit to [government advisory body] SAGE about what sequencing in care homes actually needs, which is a key piece of work.

“You think lightning doesn’t strike twice in the same place but it’s possible. COG-UK’s ambition is to develop a sustainable and long-term sequencing capability across the UK than can be used for both Covid-19 and for other pathogens.”

Locally, Dr Smith is hoping the Quadram Institute will continue to play a major role in helping to rid the region of Covid for good.

“The ambition is we’ll get a lid on it, we’ll get the virus suppressed and the numbers will go down, but we’re going to be managing this virus for a very long time,” she says. “So the intelligence about how the virus is passing through the community is going to be become even important when the numbers are small and we’re trying to drive out the last remaining cases.

“We’re only just getting started on this, it’s got massive potential.”

Sequencing team

Photos by Jason Bye

Thanks to the NHS staff from the Norfolk and Norwich University Hospital for access to the testing facility and Virology Labs.

Meet the Quadram Institute and NRP Biorepository team members working as part of COG-UK to sequence SARS-CoV-2 genomes:

Dr Evelien Adriaenssens

Dr Nabil-Fareed Alikhan

Alp Aydin

David Baker

Dr Andrew Bell

Roxy Brunton-Sim

Professor Ian Charles

Dr Leonardo de Oliveira Martins

Dr Maria Diaz

Ebenezer Foster-Nyarko

Dr Rachel Gilroy

Ana Victoria Gutierrez

Dr Thanh Le-Viet

Dr Gemma Kay

Professor Robert Kingsley

Dr Anastasia Kolyva

Hannah Limbach

Dr Martin Lott

Dr Alison Mather

Lizzie Meadows

Dr Justin O’Grady

Dr Andrew Page

Sophie Prosolek

Steven Rudder

Caelum Spearing

Dr Rachael Stanley

Dr Ana Tedim

Dr Nicholas Thomson

Alexander Trotter

Professor John Wain

Dr Mark Webber

Joel Wood

Dr Muhammad Yasir

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