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The University of Southampton

Professor Ian Clarke BSc, PhD

Professor of Molecular Microbiology/Virology

Professor Ian Clarke's photo

Ian Clarke was appointed to the Chair of Molecular Microbiology/Virology in 1998. He graduated in Microbiology from the University of Leeds in 1979 and completed his PhD in Molecular Virology at the University of Warwick in 1982 studying genomic variation in rotaviruses. He worked as a research scientist in the food industry before appointment to a ‘new blood lectureship’ at the University of Southampton in 1984. Subsequently he has held various positions at Southampton including Director of Division and is currently head of the Molecular Microbiology group.

Ian leads a research team that is interested in host-pathogen interactions with special emphasis on intracellular pathogens and diseases for which there are currently no effective vaccines. He has particular focus on Chlamydia and enteric viruses. The Chlamydia research group is specialized in chlamydial molecular biology, genomics and evolution. In Chlamydia research Ian collaborates with Prof. Bentley Fane (BIO5 Arizona, USA), Dr. Peter Marsh (Southampton), Prof. Kyle Ramsey (Midwestern, USA), Dr. Suneeta Soni (Brighton), and Prof. Nick Thomson (Sanger, Cambridge). He is currently Chair and co – organizer of the European Society for Chlamydia Research to be held in Oxford 2016 ( Together with Prof. Thomson Ian has established the first global biobank of C. trachomatis isolates with matched genome sequences ( Ian has also retained interests in human noroviruses with the aim of understanding their role in foodborne diseases and in developing a norovirus vaccine. The Southampton virus was the first norovirus to be characterised at the molecular level (published in Science). The group have subsequently developed the first reverse genetics system for noroviruses and the long term aim is to adapt human norovirus to growth in cell culture. Ian collaborates with Dr. Chris McCormick (Southampton) on DNA-based delivery of viral genomes, with Drs. Morgan Herod (Leeds) and Prof. Vernon Ward (Otago, NZ) on the properties of the non-structural proteins. Ian was chair of the ICTV Calicivirus study group (2009 – 2015). His research group is based within the Faculty of Medicine and comprises both clinical and non-clinical scientists with postgraduate students. Potential students, postdoctoral scientists or clinician scientists who are interested in joining his group are encouraged to contact Professor Clarke.


BSc, Microbiology University of Leeds (1979)
PhD, University of Warwick (1982) "Genomic variation rotaviruses"

Appointments held

2013 - present Director, sub-Division, Infection and Immunity

1999- 2013 Head, Molecular Microbiology Group

2004– 09 Director, sub-Division of Tissue, Infection and Repair

2001– 04 Director, Molecular Microbiology and Infection

1998- 01 Director, Division of Cell and Molecular Medicine

Research interests

The development of genetic technologies and their application to understanding gene function is the fundamental research programme. Ian is also interested in applying basic research findings for epidemiological studies (network tracing and analyzing population prevalence) and the development of point of care testing.


Research Projects

Systemmatic gene knock-outs of the C. trachomatis genome

Collaborator: Prof Nick Thomson (Sanger, Cambridge)


A simple, reproducible, robust cell culture system for human noroviruses

Collaborator : Prof. Vernon Ward (Otago, NZ)



Green fluorescence of transformed chlamydia trachomatis. Wang et al 2011.
Green fluorescence of transformed chlamydia trachomatis. Wang et al 20
Chlamydial Research Group

The ability to diagnose accurately and rapidly treat Chlamydia infections is necessary to reduce the burden of this disease. We are involved in a major programme to define the nature and extent of diversity in C.trachomatis with the overall research goal of understanding the role of C.trachomatis in complications of infection such as infertility and pelvic inflammatory disease. This work is multidisciplinary and involves many international partners most recently (August 2013) we have been supported by the Wellcome Trust to develop a biobank of C. trachomatis. Our genomics programme is supported by the Wellcome Trust and is performed in partnership with the Sanger Centre, Prof Nick Thomas. We also have funding from the HPA for investigating the epidemiology of C.trachomatis in the UK and work in close partnership with the Southampton HPA laboratory, Dr Peter Marsh. The Chlamydia research group is also a joint partner with the Department of Chemistry in a work programme funded by the Technology Strategy Board, together with industrial partners to develop a point of care test for C.trachomatis. Our basic cell and molecular biology research is also funded by the Wellcome Trust to develop transformation protocols and use plasmid-based chlamydial genetics to understand virulence. Our long term plans are to develop a vaccine to C.trachomatis. We have research partners in both Israel Dr. Simona Kahane -(Ben Gurion University) and USA (Prof. Bentley Fane - BIO5 University of Arizona, Prof Kyle Ramsay - Midwestern University).

Norovirus replication in the differentiated epithelial cells of the tips of villi in the distal jejunum.  Otto et al 2011.
Norovirus replication
Norovirus Research Group

Norovirus research in Southampton has been established for over 20 years . Work is focused on the ‘Southampton virus' one of the prototype human noroviruses and characterization of this virus represented the culmination of many years work to pinpoint the causative viral agent of epidemic non bacterial gastroenteritis. This advance allowed the characterisation of other noroviruses leading to the identification of the most prevalent norovirus in the world, the so called GII.4 viruses. The prototype of these viruses ‘Lordsdale virus' came from a patient at the Southampton General Hospital. The immediate research goal of the team is to develop a cell culture system that supports human norovirus replication using Southampton and Lordsdale virus. We are also engaged in a programme to understand the basic biology of noroviruses using the murine virus as a model system, this work is performed in collaboration with Professor Vernon Ward (University of Otago) and makes use of the first reverse genetics system for noroviruses developed jointly between Otago and Southampton. In collaboration with Professor Jon Cooper (UCL) we are determining the structure of human norovirus proteins with the aim of developing novel antiviral agents. We also have a long term collaboration with Dr. Peter Otto at the Friederich-Loeffler Institue in Jena to investigate the pathogenesis of norovirus infection. Noroviruses are a major source of environmental contamination and we are funded by the food standards agency to develop highly sensitive diagnostics for noroviruses.

Research group

Clinical and Experimental Sciences

Affiliate research group

Infection and Immunity Research group

Postgraduate student supervision

(22 completed PhDs)

Current PhD Students

Clare Labiran
Cate Winstanley 

National and International responsibilities

Chair, Calicivirus study group, International Committee on the Taxonomy of Viruses (2nd term 2012 - 2015)
Chair scientific committee, European society for Chlamydia research (2012 - 2016)

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Book Chapters

  • Clarke, I. N., Estes, M. K., Green, K. Y., Hansman, G. S., Knowles, N. J., Koopmans, M. K., ... Thiel, H-J. (2012). Caliciviridae. In A. M. King, M. J. Adams, E. B. Carstens, & E. J. Lefkowitz (Eds.), Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses (pp. 977-986). Oxford, GB: Elsevier.
  • Clarke, I. N. (2011). Evolution of chlamydia trachomatis. In A. Nahmias, D. Danielsson, & S. Beckman Nahmais (Eds.), The Evolution of Infectious Agents in Relation to Sex (pp. E11-E18). (Annals of the New York Academy of Sciences; Vol. 1230, No. 1). Chichester, GB: Wiley. DOI: 10.1111/j.1749-6632.2011.06194.x
  • Salim, O., Lambden, P. R., & Clarke, I. N. (2011). Norovirus. In C. Tidona, & G. Darai (Eds.), The Springer Index of Viruses (pp. 245-250). New York, NY: Springer New York. DOI: 10.1007/978-0-387-95919-1_36
  • Clarke, I. N. (2010). Chlamydial transformation: facing up to the challenge. In Chlamydial Infections (pp. 295-304). San Francisco, US: Twelfth International Symposium on Human Chlamydial Infections.
  • O'Connor, C. D., Clarke, I. N., & Skipp, P. (2006). Quest for complete proteome coverage. In I. Humphery-Smith, & M. Hecker (Eds.), Microbial Proteomics: Functional Biology of Whole Organisms (pp. 27-38). (Methods of Biochemical Analysis; Vol. 49). Hoboken, US: John Wiley & Sons. DOI: 10.1002/0471973165.ch3
  • Clarke, I. N., & Lambden, P. R. (1997). Viral zoonoses and food of animal origin: caliciviruses and human disease. In O-R. Kaaden, C. P. Czerny, & W. Eichhorn (Eds.), Viral Zoonoses and Food of Animal Origin: A RE-Evaluation of Possible Hazards for Human Health (pp. 141-152). (Archives of Virology. Supplement; Vol. 13). Berlin, DE: Springer Verlag.


Personal tutor BM5/BM6

BM5. Delivers lectures and group teaching that introduce virology and microbiology and also specialist lectures in enteric virology, hepato-virology, respiratory virology and neurovirology.

Professor Ian Clarke
Phone: (023) 8120 6975 Email:

Room Number: SGH/LC70/MP814

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