Publications

Reconstructing the first COVID-19 pandemic wave with minimal data in England.

Chen S. et al, (2025), Epidemics, 50

Improving the representativeness of UK’s national COVID-19 Infection Survey through spatio-temporal regression and post-stratification

Pouwels KB. et al, (2024), Nature Communications, 15

Prevalence of persistent SARS-CoV-2 in a large community surveillance study.

Ghafari M. et al, (2024), Nature

Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population

Wei J. et al, (2024), Nature Communications, 15

The social role of defective viral genomes in chronic viral infections: a commentary on Leeks et al. 2023.

Zhao L. and Lythgoe KA., (2023), Journal of evolutionary biology, 36, 1577 - 1581

Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey

Lythgoe KA. et al, (2023), Proceedings of the Royal Society B: Biological Sciences, 290

Directional predictions of HIV transmission with optimised genomics in cohorts of serodiscordant couples

Zhao L. et al, (2023)

Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer HR. et al, (2023), PLoS pathogens, 19

Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias.

Fryer HR. et al, (2023), PLoS pathogens, 19

The evolution of SARS-CoV-2.

Markov PV. et al, (2023), Nature reviews. Microbiology, 21, 361 - 379

COVID-19 vaccination, risk-compensatory behaviours, and contacts in the UK

Buckell J. et al, (2023), Scientific Reports, 13

Protection against SARS-CoV-2 Omicron BA.4/5 variant following booster vaccination or breakthrough infection in the UK

Wei J. et al, (2023), Nature Communications, 14

High number of SARS-CoV-2 persistent infections uncovered through genetic analysis of samples from a large community-based surveillance study

Ghafari M. et al, (2023)

Reconstructing the first COVID-19 pandemic wave with minimal data in the UK

Chen S. et al, (2023)

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias

Fryer HR. et al, (2022)

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Nickbakhsh S. et al, (2022), Scientific Reports, 12

The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Zhao L. et al, (2022), Proceedings of the Royal Society B: Biological Sciences, 289

Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs

Villabona-Arenas CJ. et al, (2022), Proceedings of the National Academy of Sciences, 119

Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods

Cahuantzi R. et al, (2022)

EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

Overton CE. et al, (2022), PLOS Computational Biology, 18, e1010406 - e1010406

Omicron-associated changes in SARS-CoV-2 symptoms in the United Kingdom

Vihta1 KD. et al, (2022), Clinical Infectious Diseases

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Willett BJ. et al, (2022), Nature Microbiology, 7, 1161 - 1179

Recurrent SARS-CoV-2 mutations in immunodeficient patients.

Wilkinson SAJ. et al, (2022), Virus evolution, 8

Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021.

Smallman-Raynor MR. et al, (2022), Epidemiology and infection, 150

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.

Vöhringer HS. et al, (2022), Nature, 606

Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer

Wright DW. et al, (2022), Virus Evolution

Lineage replacement and evolution captured by three years of the United Kingdom Covid Infection Survey

Lythgoe K. et al, (2022)

Genomic reconstruction of the SARS-CoV-2 epidemic in England.

Vöhringer HS. et al, (2021), Nature, 600, 506 - 511

Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics

Dyson L. et al, (2021)

Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein

Golubchik T. et al, (2021)

OpenABM-Covid19 - an agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

Hinch R. et al, (2020)

Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa

Downs LO. et al, (2020), Wellcome Open Research, 5, 113 - 113

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Publications