Dr Samantha Lycett
Senior Lecturer / Group Leader - Pathogen Phylodynamics
Contact details
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. Now since February 2019 I am a Group Leader in Pathogen Phylodynamics at the Roslin Institute, Infection and Immunity Division 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 now 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. I apply machine learning techniques and Bayesian phylogenetics to investigate cross species transmissions, host adaptations, epistatic interactions, phylodynamics and phylogeography. I'm currently developing fast computational methods and simulation tools to infer transmission patterns of livestock pathogens including Avian and Swine Influenza, Bovine TB and Bovine Viral Diarrhoea, and now since I'm also applying this to 2020 SARS-CoV-2.Current project grants
2021-2024: EEID-BBSRC “US-UK-China Collab: Predictive phylogenetics for evolutionary and transmission dynamics of newly emerging avian influenza viruses”, £1.3M (UK, Co-I)
2021-2024: 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 May-Oct: Chief Scientist Office “Tracking the rise and fall of Scottish SARS-CoV-2 / COVID-19 using virus sequences”, £62k (PI)
2020-2025: EU Horizon 2020 “VEO: Versatile Emerging Infectious Disease Observatory”(University of Edinburgh Co-I)
2019-2023: BBSRC-NSF-EEID “Drivers of diversity and transmission of co-circulating viral lineages in host meta-populations”, £499k (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)
2017-2022: BBSRC Strategic Programme Roslin Institute “Control of Infectious Diseases” (Co-I)
2016-2021: Scottish Government, “Centre of Expertise on Animal Disease Outbreaks” (EPIC III), £1.75M to Roslin (Co-I)
Past project grants
2014-2019: Chancellor’s Fellowship from University of Edinburgh
-
Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography
(18 pages)
In:
Pathogens, vol. 12, pp. 1-18
DOI: https://doi.org/10.3390/pathogens12050740
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Unraveling the epidemiology of Mycobacterium bovis using whole-genome sequencing combined with environmental and demographic data
(16 pages)
In:
Frontiers in Veterinary Science, vol. 10, pp. 1-16
DOI: https://doi.org/10.3389/fvets.2023.1086001
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Novel clade 2.3.4.4b H5N1 avian influenza virus reassortants identified from migratory birds in China: posing risks to birds and public health
In:
Emerging Infectious Diseases, vol. 29
DOI: https://doi.org/10.3201/eid2906.221723
Research output: Contribution to Journal › Article (E-pub ahead of print) -
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis
(19 pages)
In:
PLoS ONE, vol. 18, pp. 1-19
DOI: https://doi.org/10.1371/journal.pone.0284187
Research output: Contribution to Journal › Article (Published) -
Effect of neonatal immunoglobulin status on the outcomes of spring-born suckler calves
In:
Veterinary Record, vol. 192
DOI: https://doi.org/10.1002/vetr.2587
Research output: Contribution to Journal › Article (Published) -
Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock: Evolutionary history of bovine Staphylococcus aureus
(11 pages)
In:
Proceedings of the National Academy of Sciences (PNAS), vol. 119, pp. 1-11
DOI: https://doi.org/10.1073/pnas.2211217119
Research output: Contribution to Journal › Article (E-pub ahead of print) -
West Nile Virus spread in Europe - phylogeographic pattern analysis and key drivers
DOI: https://doi.org/10.1101/2022.11.10.515886
Research output: › Preprint (Published) -
Ecological and evolutionary dynamics of multi-strain RNA viruses
In:
Nature Ecology & Evolution, vol. 6, pp. 1414-1422
DOI: https://doi.org/10.1038/s41559-022-01860-6
Research output: Contribution to Journal › Article (Published) -
No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo: Tiled amplicon sequencing with improved assembly of African Swine Fever Virus
(35 pages)
DOI: https://doi.org/10.1101/2021.12.01.470769
Research output: › Preprint (E-pub ahead of print) -
Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands
In:
Nature Communications
DOI: https://doi.org/10.1038/s41467-021-27096-9
Research output: Contribution to Journal › Article (Published)