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Publications

Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.

Zhao L. et al, (2025), PLoS pathogens, 21

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

Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods.

Cahuantzi R. et al, (2024), Proceedings of the National Academy of Sciences of the United States of America, 121

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

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

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

Lythgoe KA. et al, (2023), Proceedings. Biological sciences, 290

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)

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. 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)

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