Publications by authors named "Katrina Lythgoe"

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Attenuation of HIV severity by slightly deleterious mutations can explain the long-term trajectory of virulence evolution.
Harriet Longley, Christophe Fraser, Chris Wymant, Katrina Lythgoe

PLoS Comput Biol· December 2025

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SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.
Mahan Ghafari, Steven A Kemp, Matthew Hall, Joseph Clarke, Luca Ferretti, Katrina Lythgoe

Lancet Microbe· September 2025

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Within-host bacterial evolution and the emergence of pathogenicity.
Gerry Tonkin-Hill, Christopher Ruis, Stephen D Bentley, Katrina A Lythgoe, Josephine M Bryant

Nat Microbiol· August 2025

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Estimates of HIV-1 within-host recombination rates across the whole genome.
Harriet Longley, David Bonsall, Joshua Herbeck, George MacIntyre-Cockett, Sandra E Chaudron, Katrina Lythgoe

Virus Evol· July 2025

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Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.
Lele Zhao, Matthew Hall, Prahalad Giridhar, Mahan Ghafari, Steven Kemp, Katrina Lythgoe

PLoS Pathog· April 2025

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Reconstructing the first COVID-19 pandemic wave with minimal data in England.
Siyu Chen, Jennifer A Flegg, Katrina A Lythgoe, Lisa J White

Epidemics· March 2025

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Epidemiological and phylogenetic analyses of public SARS-CoV-2 data from Malawi.
Mwandida Kamba Afuleni, Roberto Cahuantzi, Katrina A Lythgoe, Atupele Ngina Mulaga, Ian Hall

PLOS Glob Public Health· March 2025

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Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods.
Roberto Cahuantzi, Katrina A Lythgoe, Ian Hall, Lorenzo Pellis, Thomas House

Proc Natl Acad Sci U S A· March 2024

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Prevalence of persistent SARS-CoV-2 in a large community surveillance study.
Mahan Ghafari, Matthew Hall, Tanya Golubchik, Daniel Ayoubkhani, Thomas House, Katrina Lythgoe

Nature· February 2024

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The social role of defective viral genomes in chronic viral infections: a commentary on Leeks et al. 2023.
Lele Zhao, Katrina A Lythgoe

J Evol Biol· November 2023

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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.
Helen R Fryer, Tanya Golubchik, Matthew Hall, Christophe Fraser, Robert Hinch, Katrina A Lythgoe

PLoS Pathog· October 2023

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Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey.
Katrina A Lythgoe, Tanya Golubchik, Matthew Hall, Thomas House, Roberto Cahuantzi

Proc Biol Sci· October 2023

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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.
Helen R Fryer, Tanya Golubchik, Matthew Hall, Christophe Fraser, Robert Hinch, Katrina A Lythgoe

PLoS Pathog· August 2023

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The evolution of SARS-CoV-2.
Peter V Markov, Mahan Ghafari, Martin Beer, Katrina Lythgoe, Peter Simmonds

Nat Rev Microbiol· June 2023

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The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA.
Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe

Proc Biol Sci· November 2022

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EpiBeds: Data informed modelling of the COVID-19 hospital burden in England.
Christopher E Overton, Lorenzo Pellis, Helena B Stage, Francesca Scarabel, Joshua Burton, Katrina A Lythgoe

PLoS Comput Biol· September 2022

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Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs.
Christian Julian Villabona-Arenas, Stéphane Hué, James A C Baxter, Matthew Hall, Katrina A Lythgoe

Proc Natl Acad Sci U S A· September 2022

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Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.
Baisheng Li, Aiping Deng, Kuibiao Li, Yao Hu, Zhencui Li, Katrina A Lythgoe

Nat Commun· January 2022

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Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics.
Louise Dyson, Edward M Hill, Sam Moore, Jacob Curran-Sebastian, Michael J Tildesley, Katrina A Lythgoe

Nat Commun· September 2021

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Challenges in control of COVID-19: short doubling time and long delay to effect of interventions.
Lorenzo Pellis, Francesca Scarabel, Helena B Stage, Christopher E Overton, Lauren H K Chappell, Katrina A Lythgoe

Philos Trans R Soc Lond B Biol Sci· July 2021

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OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing.
Robert Hinch, William J M Probert, Anel Nurtay, Michelle Kendall, Chris Wymant, Katrina Lythgoe

PLoS Comput Biol· July 2021

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SARS-CoV-2 within-host diversity and transmission.
Katrina A Lythgoe, Matthew Hall, Luca Ferretti, Mariateresa de Cesare, George MacIntyre-Cockett

Science· April 2021

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Time to evaluate COVID-19 contact-tracing apps.
Vittoria Colizza, Eva Grill, Rafael Mikolajczyk, Ciro Cattuto, Adam Kucharski, Katrina Lythgoe

Nat Med· March 2021

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Estimating hepatitis B virus cccDNA persistence in chronic infection.
Katrina A Lythgoe, Sheila F Lumley, Lorenzo Pellis, Jane A McKeating, Philippa C Matthews

Virus Evol· January 2021

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Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa.
Louise O Downs, Sabeehah Vawda, Phillip Armand Bester, Katrina A Lythgoe, Tingyan Wang

Wellcome Open Res· October 2020

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