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


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

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

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

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

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

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: 2019
Publisher: medRxiv
DOI: 10.1101/19013524

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