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

Informacje na temat projektu

HIV ECLIPSE

Identyfikator umowy o grant: 757688

DOI

10.3030/757688

Projekt został zamknięty

Data podpisania przez KE 16 Stycznia 2018

Data rozpoczęcia 1 Marca 2018

Data zakończenia 31 Stycznia 2026

Finansowanie w ramach

• EXCELLENT SCIENCE - European Research Council (ERC)

Koszt całkowity

€ 1 340 388,00

Wkład UE

€ 1 340 388,00

Koordynowany przez

THE UNIVERSITY OF EDINBURGH
United Kingdom

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Publikacje

Peer reviewed articles (15)

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

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

Autorzy: 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
Opublikowane w: Nature Communications, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-28681-2

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

Autorzy: 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
Opublikowane w: Journal of The Royal Society Interface, Numer 21, 2024, ISSN 1742-5689
Wydawca: 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

Autorzy: 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
Opublikowane w: Science, Numer 10, 2021, ISSN 0036-8075
Wydawca: 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

Autorzy: Akira Endo, Mitsuo Uchida ,Naoki Hayashi, Yang Liu, Katherine E. Atkins, Adam J. Kucharski, and Sebastian Funk
Opublikowane w: Proceedings of the National Academy of Sciences, 2021, ISSN 0027-8424
Wydawca: 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

Autorzy: 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
Opublikowane w: Communications Medicine, Numer 3, 2023, ISSN 2730-664X
Wydawca: 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

Autorzy: Ch. Julián Villabona-Arenas, Matthew Hall, Katrina A. Lythgoe, Stephen G. Gaffney, Roland R. Regoes, Stéphane Hué, Katherine E. Atkins
Opublikowane w: Science, Numer 369/6499, 2020, Strona(/y) 103-108, ISSN 0036-8075
Wydawca: 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

Autorzy: Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, null null
Opublikowane w: PLOS Computational Biology, Numer 17, 2024, Strona(/y) e1008873, ISSN 1553-7358
Wydawca: 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

Autorzy: 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
Opublikowane w: The Lancet Global Health, Numer 8/8, 2020, Strona(/y) e1003-e1017, ISSN 2214-109X
Wydawca: Elsevier BV
DOI: 10.1016/s2214-109x(20)30264-3

Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia

Autorzy: 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
Opublikowane w: Emerging Infectious Diseases, Numer 26, 2024, Strona(/y) 2854-2862, ISSN 1080-6040
Wydawca: 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

Autorzy: 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
Opublikowane w: Viruses, Numer 14, 2025, Strona(/y) 1673, ISSN 1999-4915
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14081673

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

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

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

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

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

Autorzy: 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
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 1, 2022, ISSN 0027-8424
Wydawca: 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

Autorzy: 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
Opublikowane w: Nature Communications, 2021, ISSN 2041-1723
Wydawca: 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

Autorzy: Luca Ferretti, Tanya Golubchik, Francesco Di Lauro, Mahan Ghafari, Julian Villabona-Arenas, Katherine E. Atkins, Christophe Fraser, Matthew Hall
Opublikowane w: medRxiv, 2026
Wydawca: openRxiv
DOI: 10.1101/2024.08.01.606208

AtkinsGroup/TransmissionPairs: v1.0

Autorzy: Ch. Julian Villabona Arenas, Katherine Atkins, Stephen Gaffney
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3819343

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

Autorzy: Villabona-Arenas CJ, Hall M, Lythgoe KA, Gaffney SG, Regoes RR, Hué S, Atkins KE.
Opublikowane w: medRxiv, 2019
Wydawca: 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

Autorzy: Katherine E. Atkins, Tibor Antal, Robin N. Thompson, Katrina Lythgoe, Roland Regoes, Stéphane Hué, Ch. Julián Villabona-Arenas
Opublikowane w: medRxiv, 2026
Wydawca: openRxiv
DOI: 10.64898/2026.03.20.26348904