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Department of Veterinary Medicine

Cambridge Veterinary School

Studying at Cambridge


Samuel Stubbs

Samuel Stubbs

The virome during immunosuppression

Supervisor - Prof Jonathan Heeney


I am a PhD student in the Laboratory of Viral Zoonotics at the Department of Veterinary Medicine, University of Cambridge. I am supervised by Prof Jon Heeney (Uni of Cam) and Dr Helen Baxendale (Papworth Hospital). My work is funded by an MRC CASE studentship in collaboration with Novartis.

Prior to my PhD, I was employed as a research assistant in viral discovery at the Laboratory of Viral Zoonotics, University of Cambridge (Prof J Heeney). This project utilised a next generation sequencing and bioinformatic approach to search for novel viral pathogens in tissue samples from human patients with idiopathic disease.

I graduated with a BSc in Biology from Southampton University in 2009 and completed an MSc in The Control of Infectious Diseases in Animals at the Royal Veterinary College, University of London in 2010. I undertook my MSc research project at the Institute for Animal Health, Pirbright where I compared, optimised and validated a PCR-based diagnostic test for Capripoxvirus to be used by the international reference laboratory.

Subject groups/Research projects

Infection and Immunity:

Research Interests

Immunosuppressed populations are increasing in size and now represent a significant portion of the population. Therapeutic immunosuppression in particular has become prevalent as a life-long treatment option for solid organ transplant recipients and those with autoimmune diseases. Hospitalisation of these patients due to infectious complications is common. Viral infections in immunodeficient individuals are often more severe and more likely to persist. However, routine diagnostics for these patients are generally limited towards bacteria and only a limited range of viruses. Therefore, the results of these diagnostics provide us with little information regarding the true impact of viruses on the immunosuppressed population.

We are using DNA sequencing to investigate viruses that infect immunosuppressed patients. Unlike the use of traditional diagnostic tests we need not make assumptions as to which viruses might be present as DNA sequencing has the ability to detect all viruses in a sample simultaneously.


  • Common variable immunodeficiency
  • Microbiome
  • Immunology
  • Viral discovery
  • Host-Pathogen Interaction
  • Virology
  • Next-generation sequencing
  • Infection
  • Whole genome sequencing

Key Publications

  1. Stubbs S, Oura CA, Henstock M, Bowden TR, King, DP and Tupperainen ES. (2011) Validation of a high-throughput real-time polymerase chain reaction assay for the detection of Capripoxviral DNA. J Virol Methods 179: 419-22.
  2. Daly GM, Bexfield N, Heaney J, Stubbs S, Mayer AP, Palser A, Kellam P, Drou N, Caccamo M, Tiley L, Alexander GJ, Bernal W and Heeney JL. (2011) A viral discovery methodology for clinical biopsy samples utilising massively parallel next generation sequencing. PLoS ONE 6(12): e28879.
  3. Daly GM, Stubbs S, Leggett RM, Rowe W, Wilkinson M, Ramirez-Gonzalez RH, Caccomo M, Bernal W and Heeney J (2015) Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data. PLoS ONE 10(6): e0129059.
  4. Riesle-Sbarbaro SA, de Vries SPW, Stubbs S,
    Amponsah-Mensah K, Cunnigham AA, Wood JLN & Sargan DR (2016) The complete mitochondrial genome of Epomophorus gambianus (Chiroptera: Pteropodidae) and its phylogenetic analysis, Mitochondrial DNA Part B, 1:1, 447-449, DOI: 10.1080/23802359.2016.1181993