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An Interdisciplinary Research Centre at the University of Cambridge
Human evolution


Charlotte is a lecturer in the Department of Genetics, leading the Virus Genomics group.

As an undergraduate she studied Human Sciences at the University of Oxford before a PhD in Molecular Biology at the Wellcome Sanger Institute. Charlotte has also worked at the UCL Institute of Child Health, and the Department of Medicine here in Cambridge.

Charlotte has an interest in how human genetic and immunological variation shape viral diversity, and how viral diversity in turn influences human evolution.

Research interests

I study the evolution and diversity of double-stranded DNA viruses, human pathogens causing diseases as diverse as respiratory infections and fever to chronic nerve pain and cancer. Whole-genome sequencing allows us to track the spread of viruses in space and time; but it also allows us to detect drug resistance, to see the emergence of novel recombinant strains and to study the ancient evolution of successful human pathogens.



Key publications: 

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. L Meredith, W Hamilton, B Warne, C Houldcroft, M Hosmillo, AS Jahun et al. Lancet Infectious Diseases, 2020.

Assessing anti-HCMV cell mediated immune responses in transplant recipients and healthy controls using a novel functional assay. CJ Houldcroft, SE Jackson, Lim, E Y, GX Sedikides, EBM Remmerswaal et al. Frontiers in Cellular and Infection Microbiology, 2020.

Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination. J Cudini, S Roy, CJ Houldcroft, JM Bryant, DP Depledge, H Tutill, P Veys et al. Proceedings of the National Academy of Sciences, 2019.

Identification of novel adenovirus genotype 90 in children from Bangladesh. CJ Houldcroft, MA Beale, MA Sayeed, F Qadri, G Dougan, A Mutreja. Microbial Genomics, 2018.

Inferring the hominin origin of herpes simplex virus 2 from fossil, epidemiological and phylogenetic data. Underdown SJ, Kumar K & Houldcroft CJ. Virus Evolution, 2017. doi: 10.1093/ve/vex026

Clinical and biological insights from viral genome sequencing. Houldcroft CJ, Beale M & Breuer J. Nature Reviews Microbiology, 2017. doi: 10.1038/nrmicro.2016.182

Severe Epstein–Barr virus infection in primary immunodeficiency and the normal host. Worth AJJ, Houldcroft CJ and Booth C. British Journal of Haematology, 2016. doi: 10.1111/bjh.14339

Detection of Low Frequency Multi-Drug Resistance and Novel Putative Maribavir Resistance in Immunocompromised Pediatric Patients with Cytomegalovirus. Houldcroft CJ et al. Frontiers in Microbiology, 2016. doi: 10.3389/fmicb.2016.01317

Neanderthal Genomics Suggests a Pleistocene Time Frame for the First Epidemiologic Transition. Houldcroft CJ & Underdown S. American Journal of Physical Anthropology, 2016. doi: 10.1002/ajpa.22985

Host genetics of Epstein–Barr virus infection, latency and disease. Houldcroft CJ & Kellam P. Reviews in Medical Virology, 2015. doi: 10.1002/rmv.1816

Host Genetic Variants and Gene Expression Patterns Associated with Epstein-Barr Virus Copy Number in Lymphoblastoid Cell Lines. Houldcroft CJ et al. PLoS ONE, 2014. doi: 10.1371/journal.pone.0108384

Disease-associated XMRV sequences are consistent with laboratory contamination. Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft CJ et al. Retrovirology, 2010. doi: 10.1186/1742-4690-7-111

Other publications: 

Rabid about whole lyssa genomes. E Archer, CJ Houldcroft
Nature Reviews Microbiology, 316 2014

Sequencing drug-resistant cytomegalovirus in pediatric patients: toward personalized medicine. C Houldcroft
Future Virology, doi:10.2217/fvl.15.58 2015

Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. CJ Houldcroft, J Breuer
Frontiers in Microbiology 6, 188

Migrating microbes: inferring ancient human migrations from pathogen genomes. Houldcroft CJ, Ramond JB, Rifkin R & Underdown SJ. Annals of Human Biology, 2017. doi: 10.1080/03014460.2017.1325515

Assistant professor in virus genomics
Dr Charlotte   Houldcroft

Contact Details

Takes PhD students
Not available for consultancy