Genomics is the study of an organism's complete genetic code, how it's structured and how
it functions. It can help us understand what happens to viruses like the SARS-CoV2 coronavirus
and its variants. As the virus replicates it picks up genetic changes. Genomics can
be used to track these changes, helping us understand how and where the virus is spreading,
allowing us to fight back against diseases such as COVID-19 which can threaten human
lives and world economies.
I think there is a general feeling amongst those of us who are virologists and sequencing
biologists that this was our time and that we needed to put everything else down and
respond for a pandemic which was causing deaths in our country. COG-UK is a consortium of
people made up of the four public health agencies of the United Kingdom, numerous academic institutions
across the United Kingdom, together with the Wellcome Sanger Institute. We first became
aware of the alpha variant around November 2020. If we look back in our records we'd
sequenced the first alpha variant in September but they were in the country in very, very
low levels. Most of the time mutations in the viral genome are not important, certainly
they usually don't give any advantage to the virus, but there are changes that have been
emerging in SARS-CoV2 which do give the virus a distinct advantage. We know that certain
very successful viruses such as HIV and now SARS-CoV2 have higher mutation rates than
you would otherwise expect in such viruses and this causes major problems. Genomic surveillance
is important because it enables us to look at the genetic code of the virus over time.
We take samples of the virus ideally over a wide geographical area and then when we
take the virus and put it into the sequencing machine we can look at the genetic code and
see what parts of the virus are changing. COG-UK came about following a very early conversation
at the beginning of March 2020 when Sir Patrick Vallance indicated that we needed genomics
capabilities in the country for sequencing the SARS-CoV2 virus.
Well COG-UK has been a brilliant consortium across sequencing groups around the UK. Clearly Cambridge and the Sanger
Center and all of the work that goes on around there has been absolutely pivotal. I mean
it's the centre of much of this. This was a nationwide effort of sequencing everywhere
building on years and years of experience and expertise in and around Cambridge and
elsewhere. Here at the Wellcome Sanger Institute we are receiving positive samples from across
the UK. We are sequencing the samples and we are analysing and sharing the data with
public health agencies. To date we've handled more than 20 million samples and we are currently
processing around 40,000 samples a week. After the samples are sequenced, we analyse the
data and we share the data immediately open access to be analysed by colleagues here at
the Institute, at COG-UK and by colleagues in the public health agencies. So our expertise
is really in interpreting the genetic data that's coming out from COG-UK sequencing centres,
so we first of all make some of these interesting mutations or new mutations in artificial virus
systems and then test the effect on the virus and its behaviour. Well we discovered the
blueprint for how variants of concern actually occur because we had the opportunity to study
an individual who was infected with SARS-CoV2 for a period of about three months. One of
the unique mutations we found in the patient was a deletion or two missing amino acids
in the spike protein and we were intrigued by this so we started looking in the genome
database that was curated by COG-UK and we found huge numbers of this deletion in the
UK and then when we looked more closely at the spike sequences, they were very, very
different from anything that had gone before. In other words there was a new variant that
had emerged. So from the beginning of the pandemic we've been using genomic sequencing
to really try and help us understand how the COVID infection spread between patients in
hospitals and out in the community and that has enabled us as an organization, as a country,
to be able to plan our services accordingly so that we can have the right number of beds
and the right number of staff available and that's been really positive and has helped
us to keep patients safe there is no doubt and has improved patient care across the country.
Control of the global pandemic will require vaccination of the world population but sequencing
needs to be a critical partner there to understand which variants of concern are arising and
whether the vaccines that we're providing to people are fully effective.
It's only a matter of time before another pandemic emerges. It's not a question of if
but when. SARS-CoV2 is the third coronavirus to have crossed into humans within the last
20 years and so there is a high probability that we will be faced with another coronavirus
that crosses into humans potentially from bats or other species. We've learned a huge
amount from this pandemic. I think the biggest advances probably have been to do with sequencing
and identifying the genome of a pathogen. We can do that within hours now. That's very
different from the past and even better than that there are people who can use that information
to create new vaccines also very rapidly. I think genomics is going to revolutionize
clinical medicine in coming years and then I think we're going to increasingly be able
to manipulate treatments and our own immune response to dangerous pathogens and I think
that COG-UK has catalysed that process. COG-UK has shown how the strong academic base in
the UK can come together quickly to solve problems and I think the way in which that
happened is a lesson for the future that we're able to work across boundaries much more easily,
much more readily than people often give credit for. It's been recognized across the world
as the leading place to do this sort of work. I mean at some point the UK was sequencing
50% of all of the viral sequences across the world. That is going to be an important legacy.
It's crucially important that we continue to sequence as we go through this remainder
of the pandemic and as it turns into endemic we need to do that and we need to be ready
to do that for future pandemics. It shows the might of what can be done when scientists
come together to tackle a problem. Incredibly impressive, incredibly high quality and incredibly
focused on the mission and the mission to make sure that as many people benefited from
the science as possible.