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

Informazioni relative al progetto

HIV ECLIPSE

ID dell’accordo di sovvenzione: 757688

DOI

10.3030/757688

Progetto chiuso

Data della firma CE 16 Gennaio 2018

Data di avvio 1 Marzo 2018

Data di completamento 31 Gennaio 2026

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 340 388,00

Contributo UE

€ 1 340 388,00

Coordinato da

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (15)

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

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

Autori: 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
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-28681-2

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

Autori: 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
Pubblicato in: Journal of The Royal Society Interface, Numero 21, 2024, ISSN 1742-5689
Editore: 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

Autori: 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
Pubblicato in: Science, Numero 10, 2021, ISSN 0036-8075
Editore: 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

Autori: Akira Endo, Mitsuo Uchida ,Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, and Sebastian Funk
Pubblicato in: Proceedings of the National Academy of Sciences, 2021, ISSN 0027-8424
Editore: 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

Autori: 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
Pubblicato in: Communications Medicine, Numero 3, 2023, ISSN 2730-664X
Editore: 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

Autori: Ch. Julián Villabona-Arenas, Matthew Hall, Katrina A. Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins
Pubblicato in: Science, Numero 369/6499, 2020, Pagina/e 103-108, ISSN 0036-8075
Editore: 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

Autori: Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, null null
Pubblicato in: PLOS Computational Biology, Numero 17, 2024, Pagina/e e1008873, ISSN 1553-7358
Editore: 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

Autori: 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
Pubblicato in: The Lancet Global Health, Numero 8/8, 2020, Pagina/e e1003-e1017, ISSN 2214-109X
Editore: Elsevier BV
DOI: 10.1016/s2214-109x(20)30264-3

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Autori: 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
Pubblicato in: Emerging Infectious Diseases, Numero 26, 2024, Pagina/e 2854-2862, ISSN 1080-6040
Editore: 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

Autori: 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
Pubblicato in: Viruses, Numero 14, 2025, Pagina/e 1673, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081673

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

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

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

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

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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 1, 2022, ISSN 0027-8424
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, 2021, ISSN 2041-1723
Editore: 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

Autori: Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall
Pubblicato in: medRxiv, 2026
Editore: openRxiv
DOI: 10.1101/2024.08.01.606208

AtkinsGroup/TransmissionPairs: v1.0

Autori: Ch. Julian Villabona Arenas, Katherine Atkins, Stephen Gaffney
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3819343

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

Autori: Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE.
Pubblicato in: medRxiv, 2019
Editore: 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

Autori: Katherine E. Atkins, Tibor Antal, Robin N. Thompson, Katrina Lythgoe, Roland Regoes, Stéphane Hué, Ch. Julián Villabona-Arenas
Pubblicato in: medRxiv, 2026
Editore: openRxiv
DOI: 10.64898/2026.03.20.26348904