Large scale COVID-19 genome sequencing in Norfolk helps manage outbreaks

Published by  Communications

On 1st Oct 2020

Laboratory assistant analysing DNA sequence on computer

An in-depth analysis of the genome sequence of coronavirus circulating in Norfolk, UK by researchers at the Quadram Institute and the University of East Anglia, has mapped the spread of the virus, identified hidden outbreaks and provided insights into the effectiveness of interventions to stop its spread.

Over 1500 COVID-19 genomes representing 42% of positive cases during the first wave of infections were sequenced for this study. Only Australia, Spain, India and the USA have sequenced more genomes than have been sequenced in Norfolk.

Positive coronavirus cases came from the region’s hospitals, community care organisations and drive through testing facilities, and were identified by testing by the National Health Service (NHS) Norfolk and Norwich University Hospital (NNUH) microbiology laboratory.  They were sequenced and examined for tiny changes that indicate different types, or lineages, of the SARS-CoV-2 virus. 

The team identified 100 different lineages in Norfolk, between March and August. There have been multiple separate introductions of the virus into the region, mainly from the UK or other European countries. The number of lineages peaked about 5 weeks after the national lockdown started, with many quickly disappearing, showing that the measures to prevent transmission were working.

Several additional findings were discovered when deeper analysis was performed:

Analysis of samples from an outbreak within a food processing facility were all found to be very highly related, indicating that the virus was spreading between the factory workers.  Identification of the outbreak lineage made it possible to trace the spread of the virus into the community and improve contact tracing efforts.  This helps identify hidden routes of transmission.

Another lineage that appears to be associated only with a group of care homes, but not found in the wider community, has been identified and is currently under investigation.

A collection of hospital-associated cases was found to contain multiple lineages, giving confidence that these were infections picked up in the community, rather than an outbreak within the hospital.

As infections start to rise again, this shows the value of genome-based surveillance at the local level and in support of nationwide control measures.

The Norwich Research Park team is led by Dr Justin O’Grady and Dr Andrew Page, and is one of 19 partners in the UK’s COVID-19 Genomics UK Consortium that was set up in March to track the spread of the virus across the country.

The data are being shared with UK health agencies, as well as academics internationally, as part of the global effort to understand and control COVID-19.

Dr Louise Smith, Director of Public Health, Norfolk County Council said: “It is very exciting that we can use cutting edge technologies such as viral genomic epidemiology to help us manage outbreaks on the ground in real time.  It is immensely valuable to be able to identify whether an outbreak is due to a new introduction of the virus or linked to local cases; and conversely to be able to track the progression of outbreaks out into the general community. I very much appreciate and value this collaboration.” 

“We believe that this gives Norfolk one of the highest genome sequence coverage rates per capita in the world” said Dr Justin O’Grady from the Quadram Institute and the University of East Anglia. “Viral genome sequencing provides much greater resolution than traditional epidemiological methods allowing us to distinguish between different clusters. This is vital information, especially as we move into a second peak of infections.”

“We have quickly put in place a robust, rapid pipeline for SARS-CoV-2 sequencing, with weekly sequencing data fed back into the national effort for pandemic management, whilst also helping local outbreak analyses” said Dr Andrew Page from the Quadram Institute. “These achievements were only possible through the collaborative efforts of scientists, clinicians, data managers and epidemiologists” 

Matching patterns seen elsewhere, most samples came from older people, with only a handful from children. More samples were obtained from females than males, reflecting longer life expectancy patterns but also the large proportion of the NHS workforce who are female. 

This study confirms and adds to our knowledge about this novel coronavirus. The virus has a stable, low genetic mutation rate. A mutation in the spike protein, linked to increased transmission of the virus, came to dominate in Norfolk during the timeline of the study, something that is reflected globally. Also, there was no evidence of reinfection within the region, adding to the evidence that reinfection remains rare, at least for now.

The Quadram Institute researchers are supported by the Biotechnology and Biological Sciences Research Council, part of UK Research & Innovation (UKRI). The COVID-19 Genomics UK (COG-UK) Consortium is supported by funding from the Medical Research Council (MRC) part of UKRI, the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute.

Latest News

Trail runner, view of training shoes, landscape and bright sun
20 Oct 2020

UEA launches new institute for healthier living and ageing

From physical activity and nutrition to stopping smoking, sleep and socialisation, a new research centre has been set up by the University of East Anglia to...

Read more >
Health care worker in PPE knelt against wall with head in hands
16 Oct 2020

The mental health impact of pandemics for front line health care staff

Mental health problems such as Post-Traumatic Stress Disorder, anxiety and depression are common among healthcare staff during and immediately after pandemics –...

Read more >
Cancer cells reproduction
15 Oct 2020

£2 million for UEA’s Future Leaders

From drug discovery to cancer treatment, two University of East Anglia research projects are set to benefit from a UK Research and Innovation (UKRI) award worth...

Read more >
Are you searching for something?
Freshwater carp feeding with sunlight reflecting off of the surface of the water
15 Oct 2020

Australian carp virus plan 'dead in the water'

Plans to release a virus to reduce numbers of invasive Common Carp in Australia are unlikely to work and should be dropped – according to new research involving...

Read more >
Man vaping and exhaling smoke against black background
14 Oct 2020

E-cigs better than gum or patches to help people quit smoking

Electronic cigarettes could increase the number of people who stop smoking compared to nicotine replacement therapy – such as chewing gum and patches – according...

Read more >
09 Oct 2020

UEA community celebrates four awards in Queen's Birthday Honours

Four pioneering female members of the University of East Anglia’s (UEA’s) community have been recognised for their lifelong work in the Queen’s Birthday Honours.

Read more >
Two girls using a tablet
08 Oct 2020

New online hub launched to help keep more than 2 million vulnerable children safe

A digital service designed to help society’s most vulnerable children and young people who are disproportionally at greater risk of online harm has been launched...

Read more >
Tractor fertilizer spreader in young wheat field
07 Oct 2020

N2O emissions pose an increasing climate threat, finds breakthrough study

Rising nitrous oxide (N2O) emissions are jeopardizing the climate goals of the Paris Agreement, according to a major new study by an international team of...

Read more >
Care home worker wearing PPE holding seated elderly woman's hands
07 Oct 2020

Norfolk care homes to benefit from £1.2 million UEA project

Researchers at UEA will be part of a £1.2 million government-funded project to improve care in residential homes, which were hard-hit by the Covid-19 crisis.

Read more >
Dr Michael Houghton receiving his Honorary Graduate degree at UEA
06 Oct 2020

UEA graduate awarded Nobel Prize for Medicine

UEA alumnus and Honorary Graduate Dr Michael Houghton has been awarded the Nobel Prize for Medicine for his work into the discovery of the Hepatitis C virus,...

Read more >