MRC-University of Glasgow Centre for Virus Research

Specialised Training - Clinical PhD fellows are welcome to take part in the ‘CVR Introduction to Virus Research’ course. In this two-week course, which is designed for all new virology postgraduate research students at the university, scientists from across the CVR and the wider university use their research to explain the many different approaches that can be used for studying viruses here. As well as providing an overview of modern virology and allowing new students to get to know the groups and people they will be working alongside during their PhDs, the course allows our students to join a supportive cohort of new virology researchers in the CVR before beginning their own research work.   

A Global View - It is expected that all programme students will attend a relevant international conference at the earliest opportunity (within 18 months of commencing their PhD).

Global Impact - As a member of the CVR community our students are encouraged to make a difference.  Virology expertise can be urgently required during outbreaks worldwide.  Several CVR PhD students volunteered their services during the Ebola outbreak in Sierra Leone and were presented with the Ebola Medal for Service in West Africa in recognition. Similarly, multiple students have volunteered to be part of the CVR’s COVID-19 response. We always encourage our students to use their expertise for the benefit of humanity and the CVR is proud of the contributions made by our current and former students in response to viral outbreaks.

Public Engagement – A critical responsibility of today’s scientist is to engage the wider community with their research. CVR PhD students have a wealth of opportunities to hone their engagement skills. The Centre’s engagement programme includes blogging and podcasting, schools workshops, activities at community days and the Glasgow Science Festival. We are also embarking on a new programme of patient and public involvement work, including patient forums and science/art collaborations. See our Public Engagement pages to find out more about the sort of work you can get involved with.

Beyond the CVR - As part of a community of collaborative virologists, opportunities exist for collaborative PhD projects with our partner institutions

Transferable Skills Training - As a member of the University of Glasgow postgraduate community, all CVR students have access to a wide range of training opportunities and a professional support network to ensure students get the most out of their PhD.

Your Environment - Glasgow is a vibrant city on the West coast of Scotland, with excellent connections to other areas of the UK and Europe. It has an exciting student and cultural life. The CVR itself is based in the beautiful Garscube campus, easily accessible from the city centre but with views across parkland out to the Campsie Fells. Sports facilities in and outside the University offer a huge variety of activities, with the nearby countryside offering outdoor pursuits such as mountaineering and skiing. The city regularly hosts major events that showcase the region across the world. The University of Glasgow is part of the Russell Group of elite UK institutions and is regularly ranked among the best in the world. To maintain this standard of academic achievement is a key aim of our work, and the CVR PhD students play an important role in this.

Benefits - The UK MRC pays all University fees for MRC programme students. Salary for Clinical Research Fellows will be on the Clinical Academic pay scale £38,704 - £57,349 per annum.     In addition, programme students have access to a flexible travel allowance to facilitate international conference attendance at the earliest possible opportunity.

Your PhD - Your Choice

Research at the CVR spans molecular, structural and cellular levels through to the individual host and affected population, thus integrating molecular and structural virology, cell biology, pathogenesis, epidemiology and mathematical modelling.

Learn about the viruses we study at the CVR.

Clinical PhD Fellows are be encouraged to think about projects in advance of interview. Examples of available projects include: 

Dr Chris Illingworth is interested in better understanding and preventing nosocomial transmission of viral illness. 

The SARS-CoV-2 pandemic highlighted the importance of nosocomial transmission as a key problem in hospitals, with a study at one hospital estimating that as many as 15% of cases in the hospital were caused by this route.  Recent work in viral genomics in the Illingworth group has identified new methods in virus genomics as being of use for understanding outbreaks in retrospect, and tracking outbreaks as they occur in real time.  We carried out a provisional analysis of the role of PPE in nosocomial transmission, studying the consequences of FFP3 mask usage in a hospital in Cambridge.  Via collaboration we have also explored the experience by health care workers of receiving real-time genomic data in real time.  Genomic datasets generated during the pandemic provide a rich resource for retrospective analysis.

The aim of this project will be to explore a broad range of approaches combining genomic and other data to better understand and prevent nosocomial transmission.  Potential avenues of exploration within the project include i) The development and use of simple methods in bioinformatics to better understand evolutionary relationships between viral sequences collected during an outbreak; ii) The use of more advanced methods for network reconstruction to elucidate patterns of viral transmission; iii) The exploration of methods from computational fluid dynamics to understand the role of the hospital environment in promoting or preventing transmission events; iv) Approaches to optimising the communication of genomic data to healthcare workers.

This project will provide training and experience in viral genomics, in bioinformatics, and in the use of quantitative methods for studying data from clinical settings.

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Professor Pablo Murcia leads a multidisciplinary team that brings together virologists, mathematicians, diagnosticians, bioinformaticians and structural biologists to study interactions between respiratory viruses at different scales (from cells to populations). Work from our group based on the analyses of diagnostic data collected from the Glasgow patient population showed that virus interactions impact the epidemiology of respiratory viruses and the patterns of coinfections at the patient level (Nickbakhsh et al., PNAS 2019; Nickbakhsh et al., JID 2020). Using 3D-cultures of respiratory epithelium, we also showed that the interferon response mediates negative interactions between SARS-CoV-2 and rhinovirus, influenza virus, and respiratory syncytial virus (Dee et al., JID 2021; Dee et al., JID 2022). Finally, studies on interactions between influenza and respiratory syncytial virus at the cellular level, led to the discovery of hybrid virus particles, a novel type of viral pathogen (Haney et al., Nature Microbiology) whose impact on infection biology is completely unknown. 

Viral respiratory coinfections represent ~10% of all viral respiratory infections and most of them occur in children under five years of age. RSV is a major respiratory pathogen that affects mainly children and is frequently detected in viral coinfections. It is unclear why viral coinfections are more common in children than in other age groups, and why RSV is more common than other viruses in coinfections. Possible explanations are that children mount weaker innate immune responses than adults, and that RSV modulates the innate immune response in a way that facilitates viral coinfections. This project aims to address those two knowledge gaps by comparing the response to RSV infection and RSV/HRV coinfection in paediatric and adult patients. Results from this work will provide important insights on the impact of age on the response to RSV infection and coinfection. Characterising the host response to viruses in patients is critical to identify markers associated with susceptibility to viral infection and/or altered disease outcomes.

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Dr Chris Boutell and Professor Alfredo Castello are working to define the host-cell immunological response and barriers to MPOX infection.

MPOX (formerly known as monkeypox) is a disease caused by the MPOX virus (MPXV), a zoonotic pathogen transmitted from rodents to humans. Since January 2022, the WHO has reported a significant global rise in MPOX, totalling 86,309 confirmed cases and 107 deaths from 110 Member States across six WHO regions (https://worldhealthorg.shinyapps.io/mpx_global/). A high proportion of these cases have been reported from previously non-endemic regions, including Europe and the Americas (Thornhill et la., NEJM, 2022; Lum et al., Nat Rev Immunol, 2022). While MPOX is typically self-resolving, MPXV infection of the young or immunocompromised can lead to severe disease and increased likelihood of fatality. Human-to-human transmission occurs through contact with infected skin lesions, bodily fluids, and large respiratory droplets. Although smallpox vaccination and antiviral therapy (tecovirimat) can reduce MPOX replication and transmission, these countermeasures are not widely available or accessible in most countries. Thus, there is concern that MPXV may establish an endemic foot hold around the globe leading to an increase in MPOX morbidity and mortality within vulnerable groups. This MRC-funded Clinical Fellow (CF) project will investigate the host-cell tropism and immunological barriers to MPXV infection employing a range of two- and three-dimensional tissue culture model systems. Utilising a combination of genomic (RNA-seq) and proteomic technologies, this project will investigate whether strain dependent MPXV adaptation influences the kinetics of MPXV replication, activation of innate immune pathways, and sensitivity to immune suppression by the interferon response. This project will actively collaborate with our internal and external MPOX consortium partners to rapidly disseminate its findings in response to an ongoing outbreak.

This project will provide extensive training in infectious disease research across multiple technological platforms and research disciplines. The CF will actively participate in an existing collaboration between the Boutell group (CVR), other UKRI MPXV consortium members, and members of the CVR from Tissues to Molecules; Host-Cell Response to Infection programme to rapidly disseminate its research findings. This project will enable access to specialist knowledge and equipment not commonly found within an individual host institution or laboratory, for example BCL3 containment facilities, high-resolution light microscopy imaging, and bioinformatic support/training (MRC-UoG CVR). Outputs from this project will aid in the identification and characterisation of immune barriers and antiviral compounds that may restrict the replication or future re-emergence of zoonotic pathogens. 

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Professor Emma Thomson focuses on the use of NGS and functional assays to identify and investigate viruses that present a risk to human health in the UK and Uganda. Two projects are offered.

Project 1: The orthonairoviruses CCHFV, Dugbe virus and Nairobi Sheep Disease virus are common in Uganda and other surrounding countries. A novel virus in the same family called Macira virus has also been identified recently, from tick collections in Uganda, by the Thomson group. The aim of this project is to investigate the role of cross-specificity in serological responses to these viruses by carrying out neutralisation assays using a non-infectious VLP system. Further, we will carry out a survey of ticks in Uganda to identify these viruses and to identify factors that may affect their distribution across the country.

Project 2: The group have recently identified a virus called adeno-associated virus 2 (AAV2) in children with otherwise unexplained hepatitis. The aim of project 2 is to investigate the immune response to AAV2 in children affected by this condition using ELISpot, flow cytometry, peptide binding assays and mass spectrometry.

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Dr Antonia Ho, Dr Ana da Silva Filipe and Dr Joseph Hughes are interested in using next-generation sequencing to better understand viral causes of severe respiratory infections in UK and Malawi, with an aim to improve patient diagnosis and treatment

Acute lower respiratory tract infection (LRTI) causes 2.4 million annual deaths worldwide. Despite the availability of state-of-the-art, multiplex molecular tests in resource-rich diagnostic laboratories, the causative organism of these infections is seldom identified due to the limitations in microbial tests. This lack of definitive diagnosis often results in the overuse of antibiotics with poor outcomes and contributes to growing antimicrobial resistance. More sensitive diagnostic methods and pathogen discovery approaches are needed to better characterise the aetiology of LRTIs and thereby effectively target future interventions.

Metagenomic sequencing is an untargeted approach to detect viruses, bacteria, fungi and eukaryotic parasites across a range of patient specimens, which can aid in the diagnosis of infectious diseases when more conventional assays fail. Untargeted high-throughput sequencing is particularly useful for the identification of viruses, as these lack an universal conserved region to enable targeted pan-viral amplification, unlike bacteria. This approach has therefore been valuable for the discovery of new viruses and the identification of divergent strains. Metagenomics-based pathogen detection is also powerful when diverse pathogens co-contribute to disease development, as it allows the identification of viral-viral or viral-bacterial co-infections. Furthermore, this approach can also provide single-nucleotide resolution of pathogen genomes enabling the identification of mutations associated with severe disease or drug-associated resistance mutations, e.g., oseltamivir in influenza. Thus, untargeted pathogen sequencing is a useful resource to guide “precision microbiology” strategies.

Two prospective adult cohorts with detailed clinical metadata have been sampled: 1) adults (aged >18 years) hospitalised with LRTI in Blantyre, Malawi (BASH-FLU study); 2) adults (aged >16 years) hospitalised with severe acute respiratory illness in Glasgow, Scotland (CHARISMA2 study). Despite extensive microbiological tests, no aetiological pathogens were identified in up to one third of patients. We plan to focus our investigation on these samples by performing untargeted sequencing on these respiratory samples. The aim of the project is to systematically identify and classify the respiratory viruses and microbiomes of these patients, which will aid aetiological characterisation of severe respiratory infections in Malawi and UK, compare the aetiologies from the two settings, and improve understanding of associations between viral infections and disease outcome.

We hypothesise that a proportion of LRTI with unknown aetiology may be due to: 1) respiratory viruses untargeted by the multiplex real-time polymerase chain reaction (RT-PCR); 2) genotypes or variant strains that are sufficiently diverged from the target RT-PCR to fail amplification or; 3) viruses of zoonotic origin.

This project will provide training and experience in clinical epidemiology, viral genomics and bioinformatics. Importantly, it will generate knowledge that can improve diagnosis and management of patients with LRTI. 

Clinical PhD fellows are welcome to take part in the ‘CVR Introduction to Virus Research’ course. In this two-week course, which is designed for new virology postgraduate research students at the university, scientists from across the CVR and the wider university use their research to explain the many different approaches that can be used for studying viruses here. As well as providing an overview of modern virology and allowing new students to get to know the groups and people they will be working alongside during their PhDs, the course allows our students to join a supportive cohort of new virology researchers in the CVR before beginning their own research work.

Eligibility

We are looking for skilled and motivated clinically qualified medical doctors from any specialty at pre-consultant (usually registrar) level, with an interest in infectious diseases or clinical virology to undertake a higher degree (PhD) and pursue an academic career. The position is also open to suitably qualified nurses with suitable qualifications and demonstrable interest in research. 

Applicants for this competitive programme are expected to have:

• a primary medical or nursing qualification
• GMC or NMC registration and licence to practice
• demonstrable interest in infectious disease research 

Applications from all medical and surgical specialities are welcomed. Applicants should be in a training position (not necessarily with a training number); candidates at consultant grade will not be considered.

As these are MRC-funded pre-doctoral fellowships, residence requirements apply. 

Application Process

Vacancies will be posted here when live. Further information will be available online at: https://www.gla.ac.uk/explore/jobs/. 

Positions will be available in 2024 and 2025 but not 2016 or 2027. 

Clinicians can start their PhD in advance of the science fellows – i.e. between August and October.

Interview Process

Following selection for interview, you will be invited to come to Glasgow to visit the CVR. Reasonable travel expenses will be reimbursed and accommodation made available as required. 

Whilst at the CVR, time will be spent visiting the laboratories, meeting Programme group leaders and current CVR students, and being interviewed. If you receive an offer, we will ask you to decide whether to join the CVR within a reasonable timeframe, according to your circumstances. 

Any questions about the programme or eligibility requirements should be directed to ruth.jarrett@glasgow.ac.uk