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

Project Information

HIV ECLIPSE

Grant agreement ID: 757688

DOI

10.3030/757688

Project closed

EC signature date 16 January 2018

Start date 1 March 2018

End date 31 January 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 340 388,00

EU contribution

€ 1 340 388,00

Coordinated by

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from 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

Author(s): James Baxter, Sarah Langhorne, Ting Shi, Damien C Tully, Ch Julián Villabona-Arenas, Stéphane Hué, Jan Albert, Andrew Leigh Brown, Katherine E Atkins
Published in: Lancet Microbe, 2023, ISSN 2666-5247
Publisher: 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

Author(s): 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
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-28681-2

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

Author(s): 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
Published in: Journal of The Royal Society Interface, Issue 21, 2024, ISSN 1742-5689
Publisher: 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

Author(s): 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
Published in: Science, Issue 10, 2021, ISSN 0036-8075
Publisher: 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

Author(s): Akira Endo, Mitsuo Uchida ,Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, and Sebastian Funk
Published in: Proceedings of the National Academy of Sciences, 2021, ISSN 0027-8424
Publisher: 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

Author(s): 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
Published in: Communications Medicine, Issue 3, 2023, ISSN 2730-664X
Publisher: 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

Author(s): Ch. Julián Villabona-Arenas, Matthew Hall, Katrina A. Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins
Published in: Science, Issue 369/6499, 2020, Page(s) 103-108, ISSN 0036-8075
Publisher: 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

Author(s): Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, null null
Published in: PLOS Computational Biology, Issue 17, 2024, Page(s) e1008873, ISSN 1553-7358
Publisher: 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

Author(s): 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
Published in: The Lancet Global Health, Issue 8/8, 2020, Page(s) e1003-e1017, ISSN 2214-109X
Publisher: Elsevier BV
DOI: 10.1016/s2214-109x(20)30264-3

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Author(s): 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
Published in: Emerging Infectious Diseases, Issue 26, 2024, Page(s) 2854-2862, ISSN 1080-6040
Publisher: 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

Author(s): 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
Published in: Viruses, Issue 14, 2025, Page(s) 1673, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081673

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

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

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

Author(s): Christian Julian Villabona-Arenas; Stéphane Hué; James A. C. Baxter; Matthew Hall; Katrina A. Lythgoe; John Bradley; Katherine E. Atkins
Published in: Proceedings of the National Academy of Sciences, Issue 1, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2210604119

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

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 1, 2022, ISSN 0027-8424
Publisher: 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

Author(s): 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
Published in: Nature Communications, 2021, ISSN 2041-1723
Publisher: 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

Author(s): Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall
Published in: medRxiv, 2026
Publisher: openRxiv
DOI: 10.1101/2024.08.01.606208

AtkinsGroup/TransmissionPairs: v1.0

Author(s): Ch. Julian Villabona Arenas, Katherine Atkins, Stephen Gaffney
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3819343

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

Author(s): Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE.
Published in: medRxiv, 2019
Publisher: 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

Author(s): Katherine E. Atkins, Tibor Antal, Robin N. Thompson, Katrina Lythgoe, Roland Regoes, Stéphane Hué, Ch. Julián Villabona-Arenas
Published in: medRxiv, 2026
Publisher: openRxiv
DOI: 10.64898/2026.03.20.26348904