Overview
I'm currently a PhD student within the Microbiomes, Microbes and Informatics (MMI) research unit in the School of Biosciences.
My doctoral research is focused on Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), where I'm studying how its genome has changed during the course of the pandemic (evolution) and whether there are particular changes within the replication proteins that facilitate this. I'm also analysing viral genomic data (COG-UK and GISAID) and clinical patient data (SAIL) using machine learning techniques to determine whether certain mutations within the SARS-CoV-2 genome result in more severe disease (virulence). I'm also looking to identify whether certain clinical and individual factors relating to the patient (e.g. age, co-morbidities, socio-economic status) can also predict the outcome of individuals infected with SARS-CoV-2 and thus the severity of COVID-19 on case-by-case basis.
I have previous experience in both academic and clinical settings. From 2016-2020 I trained and worked from Public Health Wales as a Biomedical Scientist where I have developed, validated and deployed diagnostic services within the fields of bacteriology and virology. In 2020 I was a key member PHWs national response to the SARS-CoV-2 emergency and assisted in deploying the national testing effort. Prior to this, I worked within the field of sexually transmitted infections and antimicrobial resistance and was responsible for validating and operating the national Mycoplasma Genitalium testing service for Wales.
I am keen to engage the public in science, particularly in microbiology. Along with academics from Cardiff Metropolitan University I've ran several public engagement "tents". In 2016 we were residents within Einsteins Garden at Green Man Festival (Brecon Beacons) where the public were invited into our "Micrographia" lab to look at pollen and insects under the microscope. Following this we were invited to brin the tent to How The Light Gets In Festival (Hay-on-Wye). Since 2018 I have been active in running the science programme at Between The Trees Festival (Candleston) where we host an array of engaging scientific talks and activities over a weekend in Merthyr Mawr Nature Reserve.
Publication
2023
- Mack, A. H., Menzies, G., Southgate, A., Jones, D. D., Connor, T. R. and Leitner, T. 2023. A proofreading mutation with an allosteric effect allows a cluster of SARS-CoV-2 viruses to rapidly evolve. Molecular Biology and Evolution 40(10), article number: msad209. (10.1093/molbev/msad209)
- Pasqualetto, G. et al. 2023. CryoEM structure and Alphafold molecular modelling of a novel molluscan hemocyanin. PLoS ONE 18(6), article number: e0287294. (10.1371/journal.pone.0287294)
- Cotton, S. et al. 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135, pp. 28-36. (10.1016/j.jhin.2023.02.010)
2022
- Willett, B. J. et al. 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7, pp. 1161-1179. (10.1038/s41564-022-01143-7)
- Eales, O. et al. 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22(1), article number: 647. (10.1186/s12879-022-07628-4)
- Nickbakhsh, S. et al. 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12(1), article number: 11735. (10.1038/s41598-022-15661-1)
- Kläser, K. et al. 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12(1), article number: 10904. (10.1038/s41598-022-14016-0)
2021
- Boostrom, I. et al. 2021. Evaluation of the MYCOPLASMA IST3 urogenital mycoplasma assay in an international multicentre trial. Journal of Antimicrobial Chemotherapy 76(12), pp. 3175-3182. (10.1093/jac/dkab320)
Articles
- Mack, A. H., Menzies, G., Southgate, A., Jones, D. D., Connor, T. R. and Leitner, T. 2023. A proofreading mutation with an allosteric effect allows a cluster of SARS-CoV-2 viruses to rapidly evolve. Molecular Biology and Evolution 40(10), article number: msad209. (10.1093/molbev/msad209)
- Pasqualetto, G. et al. 2023. CryoEM structure and Alphafold molecular modelling of a novel molluscan hemocyanin. PLoS ONE 18(6), article number: e0287294. (10.1371/journal.pone.0287294)
- Cotton, S. et al. 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135, pp. 28-36. (10.1016/j.jhin.2023.02.010)
- Willett, B. J. et al. 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7, pp. 1161-1179. (10.1038/s41564-022-01143-7)
- Eales, O. et al. 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22(1), article number: 647. (10.1186/s12879-022-07628-4)
- Nickbakhsh, S. et al. 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12(1), article number: 11735. (10.1038/s41598-022-15661-1)
- Kläser, K. et al. 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12(1), article number: 10904. (10.1038/s41598-022-14016-0)
- Boostrom, I. et al. 2021. Evaluation of the MYCOPLASMA IST3 urogenital mycoplasma assay in an international multicentre trial. Journal of Antimicrobial Chemotherapy 76(12), pp. 3175-3182. (10.1093/jac/dkab320)
Research
- Infectious disease epidemiology
- Pathogen evolution
- Host/pathogen interactions
- Drivers of genetic variation within pathogens
- Pathogen replication systems and proofreading
- Antimicrobial resistance
- Computational methodologies
- Machine learning
- Novel diagnostic methodologies
- Next generation sequencing
- Phylogenetics