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Department of Veterinary Medicine

Cambridge Veterinary School


My primary interest is in the use the of next generation sequencing platforms (Illumina and MinION) to sequence viral genomes in order to undertake epidemiological research.


My current work focuses on sequencing the genomes of arboviruses (arthropod-borne viruses) such as Dengue virus and Zika virus, isolated from patients with fever across Indonesia. The information provided by these viral sequences can be used to infer where outbreaks are starting and how they are spreading. This information can then be used to inform public health decisions with regards to how to prevent the transmission of these viruses, by taking measures such as targeting certain areas for additional surveillance and vector control.


A primary aim of this project is to implement a method of virus sequencing which is cheap and rapid, so that it can be used in developing countries with limited resources. Therefore an important aspect is that we are directly collaborating with Indonesian researchers.


I believe that international and cross-disciplinary collaboration are the keys to cutting-edge research. To date, I have used my expertise in molecular biology and DNA sequencing in order to collaborate on projects in Africa, Asia and South America, ranging across the fields of microbiology, human and veterinary medicine, ecology and genetics. In turn I have benefitted from working with computer scientists, government employees, clinicians, and chemists. I am keen to form further international and cross-disciplinary collaborations, as my primary goal is to undertake research with a real-world impact, in the form of developing new methodologies and diagnostic tests, and informing public health strategies.



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. McCallum KE, Stubbs S, Hope N, Mickleburgh I, Dight D, Tiley L and Williams TL (2018) Detection and seroprevalence of morbillivirus and other paramyxoviruses in geriatric cats with and without evidence of azotemic chronic kidney disease. J Vet Intern Med, 1-9. DOI: 10.1111/jvim.15097
  5. 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 


 Samuel  Stubbs
Research Associate in Arboviral Sequencing

Contact Details

Email address: 
Not available for consultancy


Person keywords: 
Viral discovery
Host-Pathogen Interaction
Next-generation sequencing
Whole genome sequencing