Delineating severe coronavirus infection in humans

We lead a £4.1M research program funded by the US Food and Drug Administration to investigate SARS-CoV-2 and MERS-CoV. The project involves national (Universities of Bristol and Oxford and Public Health England) and international partners (King Fahad Medical City, Saudi Arabia and A*STAR, Singapore) to characterise how humans respond to severe coronavirus infection and how this compares to animal models for the development of medical countermeasures (vaccines and antivirals).

Improving coronavirus diagnosis and prognosis

We are part of the DRAGON team, a €11.4M EU funded consortia using artificial intelligence and machine learning to deliver a decision support system for precise coronavirus diagnosis and prognosis. Our role is in sequencing and characterising the host response in people who have COVID-19 and providing data from clinical trials.

Understanding severe COVID-19

We are part of ICECAP led by pathologists and infectious disease clinicians at Edinburgh. This is funded by UKRI. The goal of ICECAP is to study post-mortem tissue from patients who died of severe COVID-19 in order to understand the pathology with a view to identify better interventions. Our role is to characterise SARS-CoV-2 in and from the samples.

MERS-CoV and SARS-CoV-2 molecular virology

Funded by the NIHR we are using information gathered from these projects to investigate the biology of these viruses using cell culture, ex vivo and in vivo models.

Sequencing SARS-CoV-2

We are part of ISARIC-4C (funded by the MRC) and characterise SARS-CoV-2 through sequencing. We are also part of the Liverpool component of COG-UK (funded by UKRI). Our interests are in longitudinal samples and how the virus changes, improving the accuracy of base calling and investigating recombination in the virus.

Human respiratory syncytial virus and influenza virus

We are interested in genetic change in these viruses and how we can use direct RNA sequencing to study modifications on viral RNAs. Another focus is how these viruses interact with coronaviruses during co-infections (that occur in the human population).

Ricin and chlorine and their effect on the respiratory system

Through approximately £400K funding from the Defence Science Technology Laboratory we are investigating how the respiratory system responds to exposure to ricin or chlorine gas.

Ebola virus research program

Working closely with Public Health England, we have a £1.4M research program at Liverpool to look at data from human and animal models of Ebola virus disease. Here we are delineating factors involved in severe infection and predicting outcome. We study the pattern of virus adaptation and viral load with a focus on antiviral therapy.

Underpinning technologies

Many of the lab are CL3 trained and we work at containment for the SARS-CoV-2 work. Our main expertise is in using RNA sequencing, long read length sequencing (Oxford Nanopore), bioinformatics and machine learning to characterise clinical samples. We have several MinIONs and a GridION and work closely with the Centre of Genome Research (CGR). Over the past two years we have invested in dedicated computer power for the laboratory with four servers totalling 736 cores, 3.5 TB of RAM, 316 TB of storage and some GPUs.

Back to: Institute of Infection, Veterinary and Ecological Sciences