Data and Genomics

Home testing tracking

Imperial College London

A major programme of home testing for COVID-19 is tracking the progress of the infection across England and leading national research. Commissioned by the Department of Health and Social Care, it is being led by Professor Ara Darzi, Paul Elliot and Helen Ward along with a world-class team of Imperial College London scientists, clinicians and researchers, and colleagues at the Imperial College Healthcare NHS Trust. It could also indicate how many have been infected and recovered since the COVID-19 outbreak began by looking for markers – virus antibodies – of previous infection.

Global dataset of all interventions

London School of Hygiene and Tropical Medicine (LSHTM), with the World Health Organisation (WHO)

London School of Hygiene and Tropical Medicine (LSHTM), with the World Health Organisation (WHO), are generating a global dataset of all interventions related to COVID-19 that harmonises existing datasets into one central global dataset. LSHTM has also developed an online interactive tool to map COVID-19 prevalence, deaths and recoveries globally, updated daily. Similarly, an online tracker developed by the LSHTM Vaccine Centre follows COVID-19 vaccine candidates as they progress through the development pipeline and is updated weekly.

Using supercomputers to study the virus

UCL and EU H2020 Computational Biomedicine Centre of Excellence

Professor Peter Coveney, who leads the EU H2020 Computational Biomedicine Centre of Excellence, and his colleagues at UCL, are part of a consortium of 100+ researchers from across the US and Europe, who are using an exceptional array of supercomputers – including the biggest one in Europe and the most powerful one on the planet – to study several aspects of the virus and disease in detail.

Biomarker modelling research

The Francis Crick Institute, Imperial College London, UCL and Institute of Biochemistry, Charité University Medicine, Berlin

Data from COVID-19 patients is also being used in biomarker modelling research that uses a novel high-throughput mass spectrometry platform to identify blood biomarker signatures for predicting the severity of COVID-19. This research is being conducted through a global collaboration across the Institute of Biochemistry, Charité University Medicine, Berlin, The Francis Crick Institute, Imperial College London and UCL.

Symptom Tracker App

King’s College London

A COVID-19 Symptom Tracker App, developed by King’s College London, that has recruited over 3.6 million people across the UK aims to identify how fast the virus is spreading in each area, the highest-risk areas in the country, and who is most at risk, by better understanding symptoms linked to underlying health conditions. This has already generated major insights, including the identification of loss of smell/taste as a significant symptom of COVID-19; discovery that symptoms including fever, fatigue and anosmia, have genetic influences (genetics 50% responsible for the presentation of key symptoms of COVID-19); and development of AI diagnostic to predict COVID-19 without testing, based on symptoms.

Identifing recurrent genetic mutations

UCL 

A study led by the UCL Genetics Institute, identified close to 200 recurrent genetic mutations in the virus, highlighting how it may be adapting and evolving to its human hosts. Researchers found a large proportion of the global genetic diversity of SARS-CoV-2 is found in all hardest-hit countries, suggesting extensive global transmission from early on in the epidemic and the absence of single ‘Patient Zeroes’ in most countries. The study was conducted alongside colleagues from Cirad and Université de la Réunion, University of Oxford and Imperial College London.

International Severe Acute Respiratory Infection Consortium (ISARIC4C) study

Imperial College London, Edinburgh University and Liverpool University

Through the International Severe Acute Respiratory Infection Consortium (ISARIC4C) study, Imperial researchers in collaboration with the Universities of Edinburgh, Liverpool and Imperial are collecting blood samples and clinical data from COVID-19 patients in hospitals across the UK including St Mary’s and Charing Cross Hospitals, part of Imperial College Healthcare NHS Trust. The study is the largest undertaken in Europe and involves a national consortium of researchers that will gather data from more than 15,000 patients. Preliminary analysis of samples confirms that high blood pressure, coronary heart disease, obesity and chronic lung disease are risk factors that can lead to severe cases of COVID-19.

International Global Biobank Meta-Analysis Group

International Global Biobank Meta-Analysis Group and Queen Mary University of London

Our genetic make-up and its links to our reaction to the virus is the focus of the International Global Biobank Meta-Analysis Group, of which Queen Mary University of London is a member. Data is being drawn from volunteers from the East London Genes and Health Study who have been admitted to Barts Health NHS Trust with confirmed severe COVID-19. Overall, the Global Biobanks expect to be able to identify or exclude genes of large effect with around 100 cases and identify those of lesser effect with around 1,000 cases.

Air pollution study

Led by Professor Antonio Gasparrini, researchers are conducting analysis of the effect of lockdown measures in decreasing air pollution in European countries, with related deaths avoided.

Analysis of NHS BAME data

UCL

UCL analysis of NHS data has shown that the likelihood of death from COVID-19 is significantly higher among England’s Black, Asian and Minority Ethnic (BAME) groups than the general population.

Cancer Survival Group

The London School of Hygiene & Tropical Medicine (LSHTM) and Kings Health Partners

Colleagues in the Cancer Survival Group at LSHTM, led by Professor Bernard Rachet, and in partnership with King’s College London and St Thomas’s Trust, are studying the impact of COVID-19 on cancer survival in England, taking into consideration the significant drop in urgent cancer referrals over the course of the pandemic.

Cancer Survival Study

UCL

The COVID-19 emergency in England could result in at least 20% more deaths over the next 12 months in people who have been newly diagnosed with cancer, according to a UCL study with DATA-CAN: The Health Data Research Hub for Cancer in the UK.

Centre for the Mathematical Modelling of Infectious Diseases (CMMID)

The London School of Hygiene & Tropical Medicine (LSHTM)

Led by Professor Graham Medley, the Centre have been mapping the virus since the earliest days of the outbreak. Data and analysis are open to collaborators globally. Key research can be found here. The CMMID and Professor John Edmunds recently secured £500,000 funding from UKRI and NIHR to support this vital work in real-time forecasting, scenario analyses and behavioural surveillance.

Clinical Effectiveness Group (CEG)

Queen Mary University of London

Leveraging the power of the real time Discovery Data Service, the CEG provides information for integrated primary and secondary health care and anticipates and supports population health management and health system responses to COVID-19. This has entailed linking hospital COVID-19 test results to GP data, creating reports for the London SitRep, and developing dashboards to report COVID-19 by demography, geography and outcomes.

Clinical trials

UCL

Alongside the above sequencing pipelines, the Pathogen Genomics Unit and UCL Genomics Hub are also working on a number of clinical trials that will look at within-host variation of the virus in relation to drug treatment (notably, favipiravir, ISARIC and remdesivir).

COG-HOCI Study

UCL

This study is co-led by UCL and Imperial at the UCL Genomics Hub is testing whether delivering sequencing results back to infection control teams, quickly, can improve the control of hospital acquired infections in both patients and staff.  This has the potential to inform how we manage other epidemic viral infections in the future also.

CogStack

King’s Health Partners

CogStack offers rapid, real-time analysis of patient records from major NHS Trusts using AI and Natural Language Processing to address urgent clinical questions. Early findings include on the impact of on outcome of severe COVID-19 infection, the effects of ARBs, ACEIs and statins on clinical outcomes of COVID-19 infection among nursing home residents, and much more.

COVID-19 Genomics UK (COG-UK) initiative

UCL and Imperial College London

A national study led by Public Health England, supported by the UCL Genomics Hub, to provide national COVID-19 sequencing to inform public health planning – the results of which feed directly to SAGE. The Hub is one of the few centres in London that provides viral sequencing and can help predict and measure where there might be break downs in control measures and cause increased spread to the rest of the UK.

COVID-19 mobile app review

The London School of Hygiene & Tropical Medicine (LSHTM)

Led by Dr Sharon Cox and Chris Grundy. LSHTM is undertaking a survey to conduct a rapid review of the availability and basic functionality of mobile applications designed to collect COVID-19 related data from the general public.

DELVE group

UCL and Imperial College London

Findings from the ‘Data Evaluation and Learning for Viral Epidemics (DELVE)’ group, a multi-disciplinary team convened by the Royal Society to support a data-driven approach to learning from the different approaches countries are taking to managing the pandemic. The report, co-authored by Professor Dame Anne Johnson at UCL, highlight that the speed at which tests are completed, results delivered and contact traced, public compliance and the ability to identify a large proportion of cases, will be crucial to the success of the Test and Trace programme.

FORECAST study to establish the importance of smell and taste changes in people with COVID-19 infection

UCL

In partnership with UCLH and the Whittington, this study will examine if people with new loss or reduced sense of smell and/or taste without fever and/or persistent cough have COVID-19 infection and if people with COVID-19 who report smell/taste changes have more or less severe disease than people with COVID-19 without these changes.

Historical coronaviruses study

UCL

Using historical data, a UCL research team found that levels of infection from three common coronaviruses appear to have followed a seasonal pattern in England, with peaks occurring during winter and broadly at the same time as influenza.

Oxford Nanopore genome sequencing

King’s Health Partners

To prevent hospital transmission, the KHP genome sequencing facility has sequenced over 250 COVID-19 isolates to identify ward clusters and are contributing to a national clinical trial assessing the impact of sequencing on the prevention of hospital transmission (COG-HOCI).

SAPPHIRE

UCL

COVID-19 in pregnancy appears to cause a relatively mild form of the disease. It is not known what proportion of pregnant women may be infected but asymptomatic, putting maternity workers at additional risk of viral transmission. The aim of this study is to determine the proportion of pregnant women and maternity health care workers have previously been or are currently infected with COVID-19 without symptoms.

SARS-CoV-2 diversity study

UCL

A UCL-led study involving the analysis of virus genomes from over 15,000 Covid-19 patients from 75 countries has shown that none of the SARS-CoV-2 mutations currently documented appear to increase transmissibility.

TB Modelling and Analysis Consortium (TB-MAC)

The London School of Hygiene & Tropical Medicine (LSHTM)

Members of TB-MAC are estimating and mitigating the impact of COVID-19 on the global tuberculosis burden to support global and country level decision makers, using a previously-calibrated model to estimate the impact of COVID-19 lockdown interventions on tuberculosis, considering the impact on both TB transmission from reduced social contact, and health service delivery via reduced case finding and treatment success.

Virological analysis and behavioural study of healthcare workers

UCL

Re-instigating a previous protocol which examined symptomatic and asymptomatic influenza in HCWs at UCLH in 2017/8. The study that will examine rates of SARS-CoV-2 acquisition in HCWs using the previous methodology, and an exploratory one in a rural hospital in South Africa; Hlabisa Hospital.

Global Biobank work

Queen Mary University of London

Our genetic make-up and its links to our reaction to the virus is the focus of global biobank work at Queen Mary. Data is being drawn from volunteers from the East London Genes and Health Study who have been admitted to Barts Health NHS Trust with confirmed severe COVID-19. Overall, the Global Biobanks expect to be able to identify or exclude genes of large effect and identify those of lesser effect.