Prof Samantha Lycett (MA DIC PhD MRes MIET MInstP CPhys MRSB)

Personal Chair in Pathogen Phylodynamics

Address

Street

The Roslin Institute
Easter Bush Campus
Midlothian

City
Post code
EH25 9RG

Availability

  • Willingness to take Ph.D. students: Please see links on Roslin webpage for latest available projects

Background

Originally trained in physics, I received my bachelors degree from the University of Cambridge and PhD in semiconductor quantum physics from Imperial College London. Subsequently I worked in radar signal and image processing R & D for nearly 10 years, but then converted to Life Sciences by doing a research masters in Bioinformatics at Newcastle University. I joined the Institute of Evolutionary Biology, University of Edinburgh, as a Computational Biologist to study Influenza and HIV in Professor Andrew Leigh Brown’s group 2007-2013, and Professor Andrew Rambaut’s group in 2010-2013. In 2013-2014 I worked in Professor Rowland Kao’s group in the Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow on molecular epidemiology in livestock. In October 2014 I joined the Roslin Institute, University of Edinburgh, as a Chancellor’s Fellow to develop computational techniques for utilising sequence data to investigate pathogen evolution and transmission patterns. From 2019-2024 I was a Group Leader in Pathogen Phylodynamics at the Roslin Institute, and now since August 2024 I am a Professor in Pathogen Phylodynamics and have research programmes in viral and bacterial evolution and epidemiology.

Area of Expertise

Research expertise: Analysis and modelling of virus spread and evolution, phylodynamics.  Pathogens including - Influenza Virus, Porcine reproductive and respiratory syndrome virus, Bovine Viral Diahorrea Virus, Foot-and-Mouth Disease Virus, Bovine Tuberculosis, Staphylococcus aureus; and since 2020 SARS-CoV-2 (Coronaviruses)

Qualifications

2006 Master of Research, Newcastle University MRes in Bioinformatics

1993 Doctor of Philosophy (PhD), Imperial College of Science, Technology and Medicine, University of London Optical Properties of Compositionally Varying Quantum Wells and Dots

1990 Bachelor of Arts, University of Cambridge Physics and Theoretical Physics, Natural Science Tripos

Research summary

Pathogen Phylodynamics - evolution and epidemiology of viruses and bacteria using bayesian and machine learning methods.

Current research interests

I am interested in the evolution and epidemiology of viruses and bacteria, and my research makes use of the large quantity of pathogen sequence data now available. Pathogen sequences accumulate mutations over time, and this information can be used to infer transmission patterns. In my group, we develop and use advanced computational, Bayesian, machine learning, bioinformatic and phylogenetic / phylodynamic modelling techniques to investigate cross species transmissions, host adaptations, epistatic interactions and factors for disease spread. Current active research projects in several pathogens including avian influenza viruses and other fast evolving animal and zoonotic RNA viruses, DNA viruses, outbreaks and epidemic spread, effect of escape mutations, evolution of virulence and new variants, and predictability in host populations.

Current project grants

2023-2028: BBSRC Institute Strategic Programme: Prevention & Control of Infectious Diseases; Co-I (20%) – Theme Lead for Epidemiology (£10M).

2022-2025: Scottish Government, Centre of Expertise on Animal Disease Outbreaks: EPIC-IV, Co-I (20%) – Co-lead for Early Warning Challenge (£2M to Roslin-GAAFS)

2024-2025: NERC ECOFLU : Understanding the ecology of Highly Pathogenic Avian Influenza in wild bird populations [NE/Y001591/1] (£988k, Co-I)

2023-2025: BBSRC FLU-Trailmap Consortium (1): “Transmission and risk of avian influenza: learning more to advance preparedness”. [BB/Y007298/1] (£3.2M total, Co-I)

2024-2025: MRC Flu-TrailMap-One Health Consortium (2) [MR/Y03368X/1] (£3.2M total, Co-I)

2021-2025: EEID-BBSRC “US-UK-China Collab: Predictive phylogenetics for evolutionary and transmission dynamics of newly emerging avian influenza viruses”, £1.3M (UK, Co-I)

2021-2025: EEID-BBSRC “US-UK Collab: Combined influence of imperfect vaccines, host genetics, and non-genetic drivers on virus transmission and virulence evolution”, £1.7M (UK, Co-I)

2020-2025: EU Horizon 2020 “VEO: Versatile Emerging Infectious Disease Observatory”(University of Edinburgh Co-I)

2019-2024: BBSRC-NSF-EEID “Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations”, £499k (PI)

Past project grants

2022-2023: BBSRC Rapid response “Understanding animal health threats from emerging H5 high pathogenicity avian influenza viruses” Co-I (5%); FluMap consortium (£1M to Roslin).

2022-2023: CSO HIPS/21/21/ Spatial and network analysis of SARS-CoV-2 sequences to inform COVID-19 control in Scotland, 18 month with Public Health Scotland; Co-I (10%)

2022-2023: CSO HIPS/21/63 Using national whole-genome sequence data to inform epidemiological models of COVID-19 variant emergence and outbreak risks in Scotland, 12 month with Public Health Scotland and University of Glasgow; Co-I (10%)

2017-2022: BBSRC Strategic Programme Roslin Institute “Control of Infectious Diseases” (Co-I)

2016-2022: Scottish Government, “Centre of Expertise on Animal Disease Outbreaks” (EPIC III), £1.75M to Roslin (Co-I)

2020 May-Oct: Chief Scientist Office “Tracking the rise and fall of Scottish SARS-CoV-2 / COVID-19 using virus sequences”, £62k (PI)

2018-2021: BBSRC-Newton “A strategic approach to identifying and combating porcine reproductive and respiratory syndrome virus outbreaks and other porcine viral diseases”, £968k (Co-I)

2017-2020: Bilateral BBSRC-SFI: “Tackling a multi-host pathogen problem - phylodynamic analyses of the epidemiology of M. bovis in Britain and Ireland”, £550k (Co-I)

2014-2019: Chancellor’s Fellowship from University of Edinburgh