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Professor Ian N Clarke BSc, PhD

Professor of Molecular Microbiology/Virology

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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. Ian started his academic career as a ‘new blood lecturer’ in microbial pathogenesis at the University of Southampton in 1984.

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. The Chlamydia research group researches focusses on basic science with expertise in chlamydial molecular biology, genetics, genomics and evolution. Ian collaborates with Prof. Bentley Fane for structural biology and phages (BIO5 Arizona, USA), Prof. Kyle Ramsey -Chlamydial pathogenesis (Midwestern, USA) and Prof. Nick Thomson  genomics - (Sanger, Cambridge).

The team also have translational science interests and collaborate with Dr. Peter Marsh on diagnostics and epidemiology (PHE) and Dr. Suneeta Soni (BSMS).

Ian was president and co – organizer of the European Society for Chlamydia Research held in Oxford 2016. Together with Prof. Thomson Ian has established the first global biobank of C. trachomatis isolates with matched genome sequences.

Ian retains an interest in virology, here his specialism is enteric viruses. 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.


B. Sc. (Hons) Microbiology, University of Leeds, 1979

Ph.D. Molecular Virology, University of Warwick, 1982

Career History

Lecturer in Microbial Pathogenesis 1984 - 1989

Senior Lecturer 1989 – 1997

Reader 1997-1998

Professor/personal chair 1998 – present

1998- 01 Director, Division of Cell and Molecular Medicine

2001– 09 Director, sub-Division of Tissue, Infection and Repair

1999-2015 Head Molecular Microbiology Group

Research interests

Ian pursues a basic science, academic research programme which is founded on the development of genetic technologies and their application to understanding gene function. 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.

PhD Supervision

23 Completed PhDs as principal/1st supervisor

Current students

Emma Cousins 2017 - 2021

Chloe Manning 2017 - 2021


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 we have been supported by the Wellcome Trust to develop a biobank of C. trachomatis isolates from around the world. Our genomics programme is supported by the Wellcome Trust and is performed in partnership with the Sanger Centre, Prof Nick Thomas. We are funded by the PHE to investigate the epidemiology of C.trachomatis in the UK and work in close partnership with the Dr Peter Marsh. Our basic cell and molecular biology research is funded by the Wellcome Trust to develop plasmid-based chlamydial genetics to understand virulence. Our long term plans are to develop a vaccine to C.trachomatis. We have research partners in Israel Dr. Simona Kahane -(Ben Gurion University) and USA (Prof. Bentley Fane - BIO5 University of Arizona, Prof Kyle Ramsay - Midwestern University).

Genetically transformed C. trachomatis expressing the green fluorescent protein
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


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 N Clarke
Phone: (023) 8120 6975 Email:

Room Number : SGH/LC70/MP814

Professor Ian N Clarke's personal home page
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