Katie Atkins (BSc MSc PhD)
Chancellor's Fellow & Reader
- Usher Institute
- College of Medicine and Veterinary Medicine
Contact details
Address
- Street
-
Usher Institute - University of Edinburgh
MacKenzie House
30 West Richmond Street - City
- Post code
- EH8 9DX
Background
I work on Evolutionary Epidemiology. My work focuses on understanding the dynamics of infectious disease through modelling and phylogenetics.
My ERC Starting Grant uses quantitative tools to understand HIV infection immediately after exposure. Our recent work published in Science found that more genetic variants are transmitted during the early stages of infection. Ongoing work is trying to understand why some routes of transmission are incredibly permissive to HIV infection despite showing similar genetic bottlenecks as those less permissive, and whether this can be explained by events happening in the first week after exposure. We integrate mathematical modelling with phylogenetics to understand processes that cannot be monitored directly.
My work funded by the Wellcome Trust is understanding how drug resistant bacteria are transmitted between people, and how this is affected by vaccines. Specifically, we are modelling a cluster randomised trial for pneumococcal conjugate vaccine in Vietnam. For this, we are using mathematical modelling tools in addition to phylogenetic analysis
Qualifications
BSc (Mathematics), MSc (Mathematical Biology), PhD (Biological Sciences)
Postgraduate teaching
Course Director of Infectious Disease Epidemiology, a core module on the MSc Epidemiology
Open to PhD supervision enquiries?
Yes
Areas of interest for supervision
PhD Supervisor on
- Precision Medicine Programme (MRC)
- Hosts, Pathogens, and Global Health (Wellcome)
- Edinburgh Clinical Academical Track (Wellcome)
-
Vaccination of older adults against RSV: the final pieces of the puzzle
In:
Clinical Infectious Diseases
DOI: https://doi.org/10.1093/cid/ciad162
Research output: Contribution to Journal › Article (E-pub ahead of print) -
Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis
In:
The Lancet Microbe, vol. 4, pp. e102-e112
DOI: https://doi.org/10.1016/S2666-5247(22)00327-5
Research output: Contribution to Journal › Article (Published) -
Optimal Respiratory Syncytial Virus intervention programmes using Nirsevimab in England and Wales
(7 pages)
In:
Vaccine, vol. 40, pp. 7151-7157
DOI: https://doi.org/10.1016/j.vaccine.2022.10.041
Research output: Contribution to Journal › Article (Published) -
Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs
In:
Proceedings of the National Academy of Sciences (PNAS), vol. 119, pp. e2210604119
DOI: https://doi.org/10.1073/pnas.2210604119
Research output: Contribution to Journal › Article (Published) -
Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools
In:
Proceedings of the National Academy of Sciences (PNAS), vol. 119, pp. e2203019119
DOI: https://doi.org/10.1073/pnas.2203019119
Research output: Contribution to Journal › Article (Published) -
Detection of HIV-1 transmission clusters from dried blood spots within a universal test-and-treat trial in East Africa
(18 pages)
In:
Viruses, vol. 14
DOI: https://doi.org/10.3390/v14081673
Research output: Contribution to Journal › Article (Published) -
Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa
In:
Viruses, vol. 14
DOI: https://doi.org/10.3390/v14081673
Research output: Contribution to Journal › Article (Published) -
The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020
In:
BMC Infectious Diseases, vol. 22
DOI: https://doi.org/10.1186/s12879-022-07490-4
Research output: Contribution to Journal › Article (Published) -
SCoVMod - a spatially explicit mobility and deprivation adjusted model of first wave COVID-19 transmission dynamics
In:
Wellcome Open Research , vol. 7, pp. 1-20
DOI: https://doi.org/10.12688/wellcomeopenres.17716.1
Research output: Contribution to Journal › Article (Published) -
Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK
In:
Scientific Reports, vol. 12
DOI: https://doi.org/10.1038/s41598-022-12517-6
Research output: Contribution to Journal › Article (Published) -
The impact of COVID-19 vaccination in prisons in England and Wales: a metapopulation model
In:
BMC Public Health, vol. 22
DOI: https://doi.org/10.1186/s12889-022-13219-4
Research output: Contribution to Journal › Article (Published) -
Measuring the effects of COVID-19-related disruption on dengue transmission in southeast Asia and Latin America: a statistical modelling study
(11 pages)
In:
The Lancet Infectious Diseases, vol. 22, pp. 657-667
DOI: https://doi.org/10.1016/S1473-3099(22)00025-1
Research output: Contribution to Journal › Article (Published) -
Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events
In:
Nature Communications, vol. 13
DOI: https://doi.org/10.1038/s41467-022-29522-y
Research output: Contribution to Journal › Article (Published) -
Changes in social contacts in England during the COVID-19 pandemic between March 2020 and March 2021 as measured by the CoMix survey: A repeated cross-sectional study
In:
PLoS Medicine, vol. 19
DOI: https://doi.org/10.1371/journal.pmed.1003907
Research output: Contribution to Journal › Article (Published) -
Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level
In:
BMC Medicine, vol. 20
DOI: https://doi.org/10.1186/s12916-022-02271-x
Research output: Contribution to Journal › Article (Published)
PhD students
- Dr Germander Soothill (ECAT Wellcome)
- Yicong Liu (Chancellor's Fellowship personal award)
- James Baxter (MRC Precision Medicine)
- Emma Pujol-Hodge (HPGH, Wellcome)
Postdocs
- Julián Villabona-Arenas (ERC, LSHTM)
- Hannah Lepper (Wellcome)
Rotation students
- Olivia Fleming (HPGH)