Publications

An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.

Gonçalves BP. et al, (2022), eLife, 11

The value of open-source clinical science in pandemic response: lessons from ISARIC

Abbas A. et al, (2021), The Lancet Infectious Diseases, 21, 1623 - 1624

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Abdukahil SA. et al, (2021), Infection, 49, 889 - 905

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

Hinch R. et al, (2021), PLOS Computational Biology, 17, e1009146 - e1009146

USING PHYLOGENETICS TO INFER HIV-1 TRANSMISSION DIRECTION BETWEEN KNOWN TRANSMISSION PAIRS

Villabona-Arenas CJ. et al, (2021)

SARS-CoV-2 within-host diversity and transmission

Lythgoe KA. et al, (2021), Science, 372

A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings

Bonsall D. et al, (2020), Journal of Clinical Microbiology, 58

ISARIC COVID-19 Clinical Data Report: Final report January 2020 – January 2023

Baillie JK. et al, (2020)

Number of HIV-1 founder variants is determined by the recency of the source partner infection

Villabona-Arenas CJ. et al, (2020), Science, 369, 103 - 108

Within-host genomics of SARS-CoV-2

Lythgoe KA. et al, (2020)

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda

Ratmann O. et al, (2020), The Lancet HIV, 7, e173 - e183

Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052

Zhang Y. et al, (2020), Clinical Infectious Diseases

HIV-1 founder variant multiplicity is determined by the infection stage of the source partner

Villabona-Arenas CJ. et al, (2019)

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

Hall MD. et al, (2019), eLife, 8

Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort

Rose R. et al, (2019), The Journal of Infectious Diseases, 220, 1406 - 1413

Oral abstracts of the 10th IAS Conference on HIV Science, 21-24 July 2019, Mexico City, Mexico.

(2019), Journal of the International AIDS Society, 22 Suppl 5

Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.

Hall MD. and Colijn C., (2019), Molecular biology and evolution, 36, 1333 - 1343

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Ratmann O. et al, (2019), Nature Communications, 10

The evolution of subtype B HIV-1 tat in the Netherlands during 1985–2012

van der Kuyl AC. et al, (2018), Virus Research, 250, 51 - 64

PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity

Wymant C. et al, (2018), Molecular Biology and Evolution, 35, 719 - 733

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

Wymant C. et al, (2018), Virus Evolution, 4

High prevalence fishing communities are not a major source of new HIV infections to the inland populations in Rakai District, Uganda: implications for geo-spatially targeted HIV prevention interventions

Ratmann O. et al, (2018), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 21, 70 - 71

HIV genotyping and phylogenetics in the HPTN 071 (PopART) study: validation of a high-throughput sequencing assay for viral load quantification, genotyping, resistance testing and high-resolution transmission networking

Bonsall D. et al, (2018), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 21, 58 - 59

Correction: Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

Blanquart F. et al, (2017), PLOS Biology, 15, e1002608 - e1002608

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

Blanquart F. et al, (2017), PLOS Biology, 15, e2001855 - e2001855

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

Ratmann O. et al, (2017), Molecular Biology and Evolution, 34, 185 - 203

Phylogenetics between and within hosts along the genome reveals transmission, dual infections, recombination and contamination

Wymant CM. et al, (2017), JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 20, 101 - 102

Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting.

Bourhy H. et al, (2016), PLoS pathogens, 12

Erratum to: Patients’, clinicians’ and the research communities’ priorities for treatment research: there is an important mismatch

Crowe S. et al, (2015), Research Involvement and Engagement, 1

Patients’, clinicians’ and the research communities’ priorities for treatment research: there is an important mismatch

Crowe S. et al, (2015), Research Involvement and Engagement, 1

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Publications