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

Información del proyecto

HIV ECLIPSE

Identificador del acuerdo de subvención: 757688

DOI

10.3030/757688

Proyecto cerrado

Fecha de la firma de la CE 16 Enero 2018

Fecha de inicio 1 Marzo 2018

Fecha de finalización 31 Enero 2026

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 340 388,00

Aportación de la UE

€ 1 340 388,00

Coordinado por

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (15)

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

Autores: James Baxter, Sarah Langhorne, Ting Shi, Damien C Tully, Ch Julián Villabona-Arenas, Stéphane Hué, Jan Albert, Andrew Leigh Brown, Katherine E Atkins
Publicado en: Lancet Microbe, 2023, ISSN 2666-5247
Editor: 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

Autores: 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
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-28681-2

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

Autores: 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
Publicado en: Journal of The Royal Society Interface, Edición 21, 2024, ISSN 1742-5689
Editor: 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

Autores: 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
Publicado en: Science, Edición 10, 2021, ISSN 0036-8075
Editor: 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

Autores: Akira Endo, Mitsuo Uchida ,Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, and Sebastian Funk
Publicado en: Proceedings of the National Academy of Sciences, 2021, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: Communications Medicine, Edición 3, 2023, ISSN 2730-664X
Editor: 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

Autores: Ch. Julián Villabona-Arenas, Matthew Hall, Katrina A. Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins
Publicado en: Science, Edición 369/6499, 2020, Página(s) 103-108, ISSN 0036-8075
Editor: 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

Autores: Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, null null
Publicado en: PLOS Computational Biology, Edición 17, 2024, Página(s) e1008873, ISSN 1553-7358
Editor: 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

Autores: 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
Publicado en: The Lancet Global Health, Edición 8/8, 2020, Página(s) e1003-e1017, ISSN 2214-109X
Editor: Elsevier BV
DOI: 10.1016/s2214-109x(20)30264-3

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Autores: 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
Publicado en: Emerging Infectious Diseases, Edición 26, 2024, Página(s) 2854-2862, ISSN 1080-6040
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 14, 2025, Página(s) 1673, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081673

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

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

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

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

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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 1, 2022, ISSN 0027-8424
Editor: 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

Autores: 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
Publicado en: Nature Communications, 2021, ISSN 2041-1723
Editor: 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

Autores: Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall
Publicado en: medRxiv, 2026
Editor: openRxiv
DOI: 10.1101/2024.08.01.606208

AtkinsGroup/TransmissionPairs: v1.0

Autores: Ch. Julian Villabona Arenas, Katherine Atkins, Stephen Gaffney
Publicado en: 2020
Editor: Zenodo
DOI: 10.5281/zenodo.3819343

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

Autores: Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE.
Publicado en: medRxiv, 2019
Editor: 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

Autores: Katherine E. Atkins, Tibor Antal, Robin N. Thompson, Katrina Lythgoe, Roland Regoes, Stéphane Hué, Ch. Julián Villabona-Arenas
Publicado en: medRxiv, 2026
Editor: openRxiv
DOI: 10.64898/2026.03.20.26348904