My research focuses on the clinical epidemiology of influenza and other respiratory viral infections in UK and sub-Saharan Africa. This has included SARS-CoV-2 since February 2020.
Acute respiratory infections (ARI) are the commonest cause of illness in all ages, and are also a leading cause of mortality worldwide. The advent of molecular diagnostic tests has led to the growing recognition that respiratory viruses cause a substantial proportion of ARI.
My research aims to:
- Characterise the burden of respiratory viral infections
- Define risk factors for severe disease
- Explore viral-bacterial interactions
- Improve the diagnosis of respiratory viral infections, using next-generation sequencing techniques and evaluating low-cost point-of-care assays
- Develop optimal diagnostic and management pathways to manage patients presenting to hospital with severe acute respiratory illness.
Clinical role: I work as an infectious disease consultant at the Queen Elizabeth University Hospital in Glasgow, and University Hospital Monklands in Airdrie.
Teaching: I supervise medical and PhD students, and teach on the Glasgow Diploma of Tropical Medicine and Hygiene (DTMH), BSc Immunology, BSc Medical Virology and MSc in Critical Care.
Epidemiology of hospitalised influenza in Greater Glasgow
Influenza virus infection causes substantial morbidity and mortality every year. However, the epidemiology of severe hospitalised infection is poor described. In collaboration with the West of Scotland Specialist Virology Centre, we aim to understand the epidemiology of hospitalised influenza and risk factors for severe outcome in Greater Glasgow. Additionally, we are evaluating the impact of rapid influenza point-of-care testing (POCT) on patient care and outcome.
Target enrichment next-generation sequencing to improve diagnosis of respiratory viruses in Malawian adults
A causative organism is seldomly identified in pneumonia due to limitations of existing microbiological tests. This absence of a definitive microbiological diagnosis drives empirical broad-spectrum antibiotic use, thus contributing to growing antimicrobial resistance and poor outcomes. More sensitive diagnostic methods and innovative discovery of pathogens are needed to better characterise the aetiology of pneumonia and thereby effectively target future interventions.
We are applying a novel oligonucleotide probe capture that positively selects and enriches viral sequences for next-generation sequencing via probe hybridisation to respiratory samples obtained from a cohort of adults with hospitalised pneumonia in Blantyre, Malawi. Characterisation of novel, clinically important viruses will inform the development of context-specific viral diagnostic tests that is suitable for use in low-resource settings.
The impact of HIV infection on nasopharyngeal microbiome during respiratory viral infections in Malawian adults
HIV-infected individuals have increased susceptibility and severity of respiratory viral infections, compared to HIV-uninfected persons. We hypothesise that HIV infection and associated disease states leads to alterations in the composition and stability of the nasopharyngeal microbiome, which may contribute to increased incidence and severity of ARI. We are applying novel metagenomics approaches to compare the nasopharyngeal microbiome in HIV-infected and HIV-uninfected adults, before, during and after a viral ARI.
Hospitalised COVID-19 cases in the UK
I coordinate the recruitment of hospitalised COVID-19 cases to the ISARIC 4C study (https://isaric4c.net) and am the academic lead for the sample biobank in Scotland. I am leading the analysis on risk stratification and prognostic score development in hospitalised COVID-19 cases, in addition to bacterial coinfections and antimircobial use within the Clinical Characterisation Work Package. This study is funded by the MRC.
Sero-epidemiology of SARS-CoV-2 in Malawi
I led a prospective cohort study on SARS-CoV-2 exposure among health care workers and community members in Blantyre, Malawi, whcih demonstrated previously unrecognised widespread community transmission dring the first wave. The study was funded by Scottish Funding Council GCRF fund.
We are currently undertaking a longitudinal SARS-CoV-2 seroepidemiology study in an urban and rural setting in Malawi, funded by Wellcome Trust. This is in collaboration with the Malawi Epidemiology and Intervention Research Unit (MEIRU), Malawi Ministry of Health, University of Malawi College of Medicine, Malawi-Liverpool-Wellcome Trust Clinical Research Programme (MLW), and University of Lancaster.
Syndromic surveillance of severe acute respiratory illness in Greater Glasgow (CHARISMA)
I am leading a novel syndromic surveillance to evaluate the contribution of influenza and SARS-CoV-2 to patients with severe acute respiratory illness (SARI) at the Queen Elizabeth University Hospital in 2021/22 winter season. This study aims to generate near real-time surveillance data using an NHS-approved digital data collection tool and multiplex respiratory viral point-of-care test. It is funded by Public Health Scotland.
Research group members
UKRI. Community-based point-of-need integrated diagnostics for SARS-CoV-2. PI - Jon Cooper (2021) £ 375,393
Wellcome Trust. SARS-CoV-2 immunoepidemiology in Wellcome-funded urban and rural cohorts in Malawi: generating evidence to inform regional medium- and long-term decision making. PI - Mia Crampin (2020-2022) £249,544
Wellcome Trust ISSF. Clinical metagenomics in COVID-19. PI - Michael Murphy (2020-2021) £5,000
Scottish Funding Council - Grand Challenges Research Fund. Characterising COVID-19 occupational exposure among healthcare workers through the validation of point-of-care diagnostics (2020). PI - A Ho. £139,395
Chief Scientist Office. Viral and immunological correlates of clinical severity and response to antiviral therapy for COVID-19 (2020-21). PI - Carl Goodyear. £319,473
Chief Scientist Office. Cardiac Imaging in SARS Coronavirus disease-19 (CISCO-19) (2020). PI - Colin Berry. £47,940
Chief Scientist Office. CO-CIN Scotland: Near real-time analysis and reporting of the clinical characteristics of patients admitted to hospital with COVID-19 infection (2020-21). PI - Annemarie Docherty (UoE). £346,500
MRC COVID-19. ISARIC Coronavirus Clinical Characterisation Consortium (2020-21). CI - Kenneth Baillie. £4.9 million
NIHR Urgent Public Health Group – Infection Lead, Scotland (May 2020 – present)
Department of Health and Social Care Advisory Group on Serology testing (May 2020 – present)
European Scientific Working Group on Influenza (ESWI) Influenza Conference Scientific Committee (Jan – Dec 2020)
CVR Genetic Modification Safety Committee (Jan 2019 - present)
CVR Crisis Management Team (March 2020 - present)
University of Glasgow Covid-19 Taskforce (March 2020 - present)
NHS Greater Glasgow Covid-19 R&D Taskforce (June 2020 - present)