HIV-1 acquisition and the future of prevention strategies: deciphering the eclipse phase through modelling and phylogenetics

Informations projet

HIV ECLIPSE

N° de convention de subvention: 757688

DOI

10.3030/757688

Projet clôturé

Date de signature de la CE 16 Janvier 2018

Date de début 1 Mars 2018

Date de fin 31 Janvier 2026

Financé au titre de

• EXCELLENT SCIENCE - European Research Council (ERC)

Coût total

€ 1 340 388,00

Contribution de l’UE

€ 1 340 388,00

Coordonné par

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Publications

Peer reviewed articles (15)

Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis

Auteurs: James Baxter, Sarah Langhorne, Ting Shi, Damien C Tully, Ch Julián Villabona-Arenas, Stéphane Hué, Jan Albert, Andrew Leigh Brown, Katherine E Atkins
Publié dans: Lancet Microbe, 2023, ISSN 2666-5247
Éditeur: Elsevier
DOI: 10.1016/s2666-5247(22)00327-5

Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Auteurs: Benjamin B. Lindsey, Ch. Julián Villabona-Arenas, Finlay Campbell, Alexander J. Keeley, Matthew D. Parker, Dhruv R. Shah, Helena Parsons, Peijun Zhang, Nishchay Kakkar, Marta Gallis, Benjamin H. Foulkes, Paige Wolverson, Stavroula F. Louka, Stella Christou, Amy State, Katie Johnson, Mohammad Raza, Sharon Hsu, Thibaut Jombart, Anne Cori, Sheffield COVID-19 Genomics Group, The COVID-19 Genomics UK
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-28681-2

Reconciling founder variant multiplicity of HIV-1 infection with the rate of CD4 ⁺ decline

Auteurs: James Baxter, Ch. Julián Villabona-Arenas, Robin N. Thompson, Stéphane Hué, Roland R. Regoes, Roger D. Kouyos, Huldrych F. Günthard, Jan Albert, Andrew Leigh Brown, Katherine E. Atkins
Publié dans: Journal of The Royal Society Interface, Numéro 21, 2024, ISSN 1742-5689
Éditeur: The Royal Society
DOI: 10.1098/rsif.2024.0255

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

Auteurs: Davies, Nicholas G.; Abbott, Sam; Barnard, Rosanna C.; Jarvis, Christopher I.; Kucharski, Adam J.; Munday, James D.; Pearson, Carl A. B.; Russell, Timothy W.; Tully, Damien C.; Washburne, Alex D.; Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry L. M.; van Zandvoort, Kevin; Silverman, Justin D.; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M.; Funk, Sebastian; Jit, Mark; Atkins, Katheri
Publié dans: Science, Numéro 10, 2021, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1101/2020.12.24.20248822

Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan

Auteurs: Akira Endo, Mitsuo Uchida ,Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, and Sebastian Funk
Publié dans: Proceedings of the National Academy of Sciences, 2021, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2112605118

Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia

Auteurs: Cinthy Jimenez-Silva, Ricardo Rivero, Jordan Douglas, Remco Bouckaert, Ch. Julian Villabona-Arenas, Katherine E. Atkins, Bertha Gastelbondo, Alfonso Calderon, Camilo Guzman, Daniel Echeverri-De la Hoz, Marina Muñoz, Nathalia Ballesteros, Sergio Castañeda, Luz H. Patiño, Angie Ramirez, Nicolas Luna, Alberto Paniz-Mondolfi, Hector Serrano-Coll, Juan David Ramirez, Salim Mattar, Alexei J. Drummond
Publié dans: Communications Medicine, Numéro 3, 2023, ISSN 2730-664X
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/s43856-023-00328-3

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

Auteurs: Ch. Julián Villabona-Arenas, Matthew Hall, Katrina A. Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins
Publié dans: Science, Numéro 369/6499, 2020, Page(s) 103-108, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.aba5443

Using machine learning and big data to explore the drug resistance landscape in HIV

Auteurs: Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, null null
Publié dans: PLOS Computational Biology, Numéro 17, 2024, Page(s) e1008873, ISSN 1553-7358
Éditeur: Public Library of Science (PLoS)
DOI: 10.1371/journal.pcbi.1008873

Global, regional, and national estimates of the population at increased risk of severe COVID-19 due to underlying health conditions in 2020: a modelling study

Auteurs: Andrew Clark, Mark Jit, Charlotte Warren-Gash, Bruce Guthrie, Harry H X Wang, Stewart W Mercer, Colin Sanderson, Martin McKee, Christopher Troeger, Kanyin L Ong, Francesco Checchi, Pablo Perel, Sarah Joseph, Hamish P Gibbs, Amitava Banerjee, Rosalind M Eggo, Emily S Nightingale, Kathleen O'Reilly, Thibaut Jombart, W John Edmunds, Alicia Rosello, Fiona Yueqian Sun, Katherine E Atkins, Nikos I Bosse
Publié dans: The Lancet Global Health, Numéro 8/8, 2020, Page(s) e1003-e1017, ISSN 2214-109X
Éditeur: Elsevier BV
DOI: 10.1016/s2214-109x(20)30264-3

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Auteurs: Katherine Laiton-Donato, Christian Julián Villabona-Arenas, José A. Usme-Ciro, Carlos Franco-Muñoz, Diego A. Álvarez-Díaz, Liz Stephany Villabona-Arenas, Susy Echeverría-Londoño, Zulma M. Cucunubá, Nicolás D. Franco-Sierra, Astrid C. Flórez, Carolina Ferro, Nadim J. Ajami, Diana Marcela Walteros, Franklin Prieto, Carlos Andrés Durán, Martha Lucia Ospina-Martínez, Marcela Mercado-Reyes
Publié dans: Emerging Infectious Diseases, Numéro 26, 2024, Page(s) 2854-2862, ISSN 1080-6040
Éditeur: US National Center for Infectious Diseases
DOI: 10.3201/eid2612.202969

Detection of HIV-1 Transmission Clusters from Dried Blood Spots within a Universal Test-and-Treat Trial in East Africa

Auteurs: Emma Pujol-Hodge, Jesus Salazar-Gonzalez, Deogratius Ssemwanga, Edwin Charlebois, James Ayieko, Heather Grant, Teri Liegler, Katherine Atkins, Pontiano Kaleebu, Moses Kamya, Maya Petersen, Diane Havlir, Andrew Leigh Brown
Publié dans: Viruses, Numéro 14, 2025, Page(s) 1673, ISSN 1999-4915
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081673

Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreaks

Auteurs: 28. ENDO, A. ; CMMID COVID-19 Working Group,; LECLERC, QJ. ; KNIGHT, GM. ; MEDLEY, GF. ; ATKINS, KE. ; FUNK, S. ; KUCHARSKI, AJ
Publié dans: Wellcome Open Research, 2021, ISSN 2398-502X
Éditeur: Wellcome Trust
DOI: 10.12688/wellcomeopenres.16344.3

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

Auteurs: Christian Julian Villabona-Arenas; Stéphane Hué; James A. C. Baxter; Matthew Hall; Katrina A. Lythgoe; John Bradley; Katherine E. Atkins
Publié dans: Proceedings of the National Academy of Sciences, Numéro 1, 2022, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2210604119

Simulating respiratory disease transmission within and between classrooms to assess pandemic management strategies at schools

Auteurs: Endo, Akira; Uchida, Mitsuo; Liu, Yang; Atkins, Katherine E.; Kucharski, Adam J.; Funk, Sebastian; Abbas, Kaja; van Zandvoort, Kevin; Bosse, Nikos I; Waterlow, Naomi R; Tully, Damien C; Meakin, Sophie R; Quaife, Matthew; Russell, Timothy W; Jit, Mark; Foss, Anna M; Rosello, Alicia; Quilty, Billy J; Prem, Kiesha; Knight, Gwenan M; Abbott, Sam; Klepac, Petra; Brady, Oliver; Pearson, Carl A B; Medley
Publié dans: Proceedings of the National Academy of Sciences, Numéro 1, 2022, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2203019119

Implications of the school-household network structure on SARS-CoV-2 transmission under school reopening strategies in England

Auteurs: James D. Munday, Katharine Sherratt, Sophie Meakin, Akira Endo, Carl A. B. Pearson, Joel Hellewell, Sam Abbott, Nikos I. Bosse, CMMID COVID-19 Working Group, Katherine E. Atkins, Jacco Wallinga, W. John Edmunds, Albert Jan van Hoek, Sebastian Funk
Publié dans: Nature Communications, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-22213-0

Other (4)

Biased estimates of phylogenetic branch lengths resulting from the discretised Gamma model of site rate heterogeneity

Auteurs: Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall
Publié dans: medRxiv, 2026
Éditeur: openRxiv
DOI: 10.1101/2024.08.01.606208

AtkinsGroup/TransmissionPairs: v1.0

Auteurs: Ch. Julian Villabona Arenas, Katherine Atkins, Stephen Gaffney
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3819343

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

Auteurs: Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE.
Publié dans: medRxiv, 2019
Éditeur: medRxiv
DOI: 10.1101/19013524

Accounting for barriers to HIV infection in the recipient partner reveals frequent transient infections and explains transmission risk under viral suppression

Auteurs: Katherine E. Atkins, Tibor Antal, Robin N. Thompson, Katrina Lythgoe, Roland Regoes, Stéphane Hué, Ch. Julián Villabona-Arenas
Publié dans: medRxiv, 2026
Éditeur: openRxiv
DOI: 10.64898/2026.03.20.26348904