E
very day at the Wellcome Genome
Campus, boxes with frozen samples
leftover from COVID-19 tests arrive.
Couriered from the Lighthouse Laboratories
undertaking the tests in communities across
the UK, over 17 million samples have been
handled so far.
With one of the largest genome sequencing
facilities in the world, much of our capacity
has been turned over to the SARS-CoV-2 virus,
as a sequencing hub of the COVID-
Genomics UK consortium (COG-UK).
Together, the consortium has sequenced
over 200,000 virus genomes from the UK.
Virologists around the globe are using
the data to understand the spread, and the
biology, of the SARS-CoV-2 virus. We spoke
to Dr Jeffrey Barrett, Director of the COVID-
Genomics Initiative at the Sanger Institute,
about the work.Tracking the spread
Tracking the virus within a hospital, town,
country or across the world is possible
because genomes mutate. Letters in the
genome sequence change as organisms
replicate. Individual virus sequences can
be placed on a phylogenetic tree, much like
a family tree. Researchers can use this data
to determine the relatedness of different
viruses. The analysis can help identify chains
of transmission, super spreading events and
fast-growing variants.
To be useful for public health officials,
genomic analysis must be available as close to
real time as possible. Outbreaks and changes
to the virus need to be swiftly identified, and
then interventions deployed to contain them.
It is a huge logistical challenge to sequence
and analyse thousands of genomes that
quickly, every day. In each box from the
Lighthouse Laboratories there are hundreds
of positive samples among thousands of
negative ones. Laboratory, technical, software,
logistic, and scientific teams at Sanger have
worked to handle the millions of samples, and
there is now the capacity to sequence 10,virus samples a week. A new £2 million
robotic system has just been installed to
speed things up even further.
“Researchers in COG-UK use the virus
genome data at a local scale, to support
public health officials. This crucial work
is helping to inform infection control
procedures, as well as uncover previously
hidden routes of transmission,” says Jeff.
“We’re also constantly monitoring the
national sequence data for mutations that
might impact the behaviour of the virus.
COG-UK identified a new variant, B.1.1.7,
in the South East of England in late 2020. Its
prevalence has rapidly increased. This new
variant was unlike any others we’d seen – it
has many more mutations,” explains Jeff.Advertorial Paid for by
Sequencing COVID
By Alison Cranage, Science Writer at the Wellcome Sanger Institute
New variant
Many of those mutations affect the spike
protein of the virus, which binds to our cells.
Analysis has now confirmed that B.1.1.
is around 50% more transmissible than
previous variants. The increased
transmissibility helped explain the rapid
rise in cases in the UK at the time.
“We are continuing to work around the
clock to sequence and monitor the virus,
and we immediately pass information to
public health officials and those who need it.
The next big question is about vaccines – will
the virus mutate to escape? No data so far
suggests it can escape the current vaccines.
But sequencing will rapidly alert us if it does,
plus it will inform the next generation of
vaccines, should they be needed.”
Jeff re-joined the Sanger Institute in July
this year, to lead the coronavirus analysis
work. He had previously worked in the
Human Genetics department for 10 years.
He was then the founding director of Open
Targets, before moving to become Chief
Scientific Officer at Genomics PLC in 2017.
I asked what made him come back.
“I wanted to put large-scale genomics to
use in the pandemic,” he says. “I wanted to
help. It’s all anyone wants to do, isn’t it?” ❚Genome sequencing
is a vital tool in
tracking new
variants of the
SARS-Cov-2 virusDAN^ ROSS^ (HTT
PS
://WWW.DAN-
ROSS
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)