Research projects

IPhD self-funded projects (November-April)

Our Integrated PhD combines an MSc and PhD project in a 1+3+1 format.
You can select from the below projects and indentify your chosen MSc from the options listed on the project.

Please note that you can apply for the below PhD projects outwith the IPhD route.

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Barriers to influenza virus cross-species transmission

Supervisor: Massimo Palmarini

MSc choice: Infection Biology (with specialisms) [MSc]

Project outline: Influenza A viruses (IAV) are the cause of a major global health burden in humans and animals. Wild aquatic birds are the main natural reservoir of IAV and are a source of infection for domestic birds, and other species. Spillover of avian IAV into humans results in severe or even lethal disease. These spillover events are typically not followed by extensive human-to-human transmission chains, but they are a risk to global health as they could enable the first step towards human adaptation and the generation of pandemic IAV strains. Multiple barriers have been identified that hamper avian IAV transmission and adaptation in humans including an interferon stimulated gene, BTN3A3, that we recently identified (doi: 10.1038/s41586-023-06261-8). However, several gaps remain in our understanding of how certain avian IAV subtypes/lineages are able to cross the species-barrier and spill over in humans or other mammals. Our laboratory aims to investigate the mechanisms that allow certain avian viruses to spillover into humans using a mixture of virological and evolutionary approaches. Understanding what makes emerging viruses succeed or fail to spillover, and possibly thrive, in human populations are crucial to understand how we manage viral emergence.

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Cryogenic correlated light and electron tomography of virally infected cells

Supervisor: Stephen Carter

MSc choice: Infection Biology (with specialisms) [MSc]

Outline and techniques used: We use cryo-CLEM/cryo-electron tomography (cryo-ET) to study the complex relationships between viruses and the host cell during infection.

Our lab has access to the Scottish Centre for Macromolecular Imagining (SCMI) where we use cutting-edge instrumentation, such as the JEOL CRYO ARM 300 electron microscope and the Leica THUNDER Imager EM cryo-CLEM microscope. This technology allows us to target events that happen deep in the cell so we can see more of the context of virions, including their interactions with cellular organelles.

Ultimately, we want to capture the entire virus life cycle, from assembly of its pieces to maturation (with dramatic internal structural changes), to budding, to fusion with a target cell, and then through more transformations as the viral genome passages into the cell’s cytoplasm, all while hijacking the host cell machinery. We work with a range of viruses, including Rift Valley Fever Virus, Bunyamwera virus (BUNV) and herpes simplex virus (HSV).

Project aims: Developing in situ imaging techniques to image virus infection at high-resolution using cryo-ET. The creation of viral variants that contain and/or can create unnatural amino acids in their own viral proteins and imaging BUNV replication factories using cryogenic focused ion beam (FIB) milling.

References

1. Haney et al. Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles. Nature Microbiology, 2022.
2. Carter, S.D., et al. Sci Adv, 2020. 6(14): p. eaay9572.

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Understanding virus-virus interactions: from cells to populations

Supervisor: Pablo Murcia

MSc choice: Infection Biology (with specialisms) [MSc]

Background and aims: Respiratory viral infections, including seasonal epidemics and pandemics, cause a major disease burden. Multiple viruses can cause respiratory infections, including influenza viruses, coronaviruses, respiratory syncytial virus, rhinoviruses, human metapneumovirus and parainfluenza viruses, to name but a few. Historically, respiratory viruses have been studied in isolation using a one-virus–one-disease approach. Our laboratory carries out a broad research programme that studies the biology of respiratory viruses using a multi-virus and multi-scale approach (i.e. from cells to populations). In published studies, we combined epidemiological and modelling approaches to reveal the existence of positive and negative interactions between respiratory viruses at the epidemiological scale (1). Using experimental approaches, we showed that interferon responses mediate negative interactions in the human respiratory tract (2, 3). At the cellular level, we were the first to show that virus coinfections can generate infectious hybrid particles (4). Our overarching aim is to determine the processes that drive interactions among respiratory viruses at the population, within-host, and cellular levels.

Techniques to be used: Our group offers a truly multidisciplinary research environment. PhD projects align with the group's overarching research aim and are designed around the students' training needs. Wet lab projects include cell culture, classical virology, immunostaining, microscopy, and imaging (2-4) as well as serological assays (5, 6). Dry projects combine epidemiology (7, 8), evolutionary biology, bioinformatics (9) and modelling (1, 10).

References

1. S. Nickbakhsh et al., Virus-virus interactions impact the population dynamics of influenza and the common cold. Proc Natl Acad Sci U S A 116, 27142-27150 (2019).
2. K. Dee et al., Human Rhinovirus Infection Blocks Severe Acute Respiratory Syndrome Coronavirus 2 Replication Within the Respiratory Epithelium: Implications for COVID-19 Epidemiology. J Infect Dis 224, 31-38 (2021).
3. K. Dee et al., Influenza A and Respiratory Syncytial Virus Trigger a Cellular Response That Blocks Severe Acute Respiratory Syndrome Virus 2 Infection in the Respiratory Tract. J Infect Dis 227, 1396-1406 (2023).
4. J. Haney et al., Coinfection by influenza A virus and respiratory syncytial virus produces hybrid virus particles. Nat Microbiol 7, 1879-1890 (2022).
5. E. C. Hughes et al., Severe Acute Respiratory Syndrome Coronavirus 2 Serosurveillance in a Patient Population Reveals Differences in Virus Exposure and Antibody-Mediated Immunity According to Host Demography and Healthcare Setting. J Infect Dis 223, 971-980 (2021).
6. M. Manali et al., SARS-CoV-2 Evolution and Patient Immunological History Shape the Breadth and Potency of Antibody-Mediated Immunity. J Infect Dis 227, 40-49 (2022).
7. S. Nickbakhsh et al., Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections. Epidemiol Infect 144, 2064-2076 (2016).
8. S. Nickbakhsh et al., Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019. J Infect Dis 222, 17-25 (2020).
9. F. Thorburn et al., The use of next generation sequencing in the diagnosis and typing of respiratory infections. J Clin Virol 69, 96-100 (2015).
10. C. Mair et al., Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Comput Biol 15, e1007492 (2019).

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Overview

The MRC-University of Glasgow Centre for Virus Research (CVR) sits within the School of Infection and Immunity. The CVR is the largest virology-focussed research centre in the UK and brings together a critical mass of researchers studying human and animal viruses and viral diseases.

The CVR provides excellent facilities and opportunities for cross-disciplinary projects and the delivery of a comprehensive programme of training in contemporary, multi-disciplinary, virology research. The Centre includes research programmes in arboviruses, Epstein Barr virus, feline calicivirus, herpes viruses, hepatitis C virus, influenza, retroviruses and papillomaviruses.

 Cross cutting research themes and expertise include:

• antiviral immunity
• virus discovery
• viral bioinformatics, mathematical modelling and genomics to guide new approaches to the understanding and management of viral infections
• structural biology/cryo-electron microscopy and viral evolutionary dynamics
• molecular virology to in vivo pathogenesis
• virus-cell interactions
• viral immunology
• viral ecology
• viral oncology
• clinical and veterinary virology
• viral diagnostics 
• virus epidemiology

Our excellent facilities underpin a bench to bedside approach that will equip you with training complementary to a range of career options, and you can tailor your study pathway to the precise aspects of infection and immunology that suit your objectives. Through their research interests in drug development, vaccines and diagnostics, many of our project supervisors have strong links with industry.

Study options

PhD

• Duration: 3/4 years full-time; 5 years part-time

Individual research projects are tailored around the expertise of principal investigators.

Integrated PhD programmes (5 years)

Our Integrated PhD allows you to combine masters level teaching with your chosen research direction in a 1+3+1 format. 

International students with MSc and PhD scholarships/funding do not have to apply for 2 visas or exit and re-enter the country between programmes. International and UK/EU students may apply.

Year 1

Taught masters level modules are taken alongside students on our masters programmes. Our research-led teaching supports you to fine tune your research ideas and discuss these with potential PhD supervisors. You will gain a valuable introduction to academic topics, research methods, laboratory skills and the critical evaluation of research data. Your grades must meet our requirements in order to gain entry on to your pre-selected PhD research project. If not, you will have the options to pay outstanding MSc fees and complete with masters degree only.

Years 2, 3 and 4

PhD programme with research/lab work, completing an examinable piece of independent research in year 4.

Year 5

Thesis write up.

MSc (Research)

• Duration: 1 year full-time; 2 years part-time

MD (Doctor of Medicine)

• Duration: 2 years full-time; 4 years part-time (for medically-qualified graduates only)