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

Autor: Villabona-Arenas, CJ, Hué, S, Baxter, JAC, Hall, M, Lythgoe, KA, Bradley, J, Atkins, KE

Publikováno v: Villabona-Arenas, C J, Hué, S, Baxter, J A C, Hall, M, Lythgoe, K A, Bradley, J & Atkins, K E 2022, ' Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs ', Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 38, pp. e2210604119 . https://doi.org/10.1073/pnas.2210604119

Inferring the transmission direction between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. Phylogenetic ancestral-state reconstruction approaches infer the transmission dir

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6f91f2bae1c32c668ee58db42ec59c86
https://pubmed.ncbi.nlm.nih.gov/36103580

Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England

Autor: Leclerc, QJ, Fuller, NM, Keogh, RH, Diaz-Ordaz, K, Sekula, R, Semple, MG, Baillie, JK, Openshaw, PJM, Carson, G, Alex, B, Bach, B, Barclay, WS, Bogaert, D, Chand, M, Cooke, GS, Docherty, AB, Dunning, J, da Silva Filipe, A, Fletcher, T, Green, CA, Harrison, EM, Hiscox, JA, Ho, AYW, Horby, PW, Ijaz, S, Khoo, S, Klenerman, P, Law, A, Lim, WS, Mentzer, AJ, Merson, L, Meynert, AM, Noursadeghi, M, Moore, SC, Palmarini, M, Paxton, WA, Pollakis, G, Price, N, Rambaut, A, Robertson, DL, Russell, CD, Sancho-Shimizu, V, Scott, JT, de Silva, T, Sigfrid, L, Solomon, T, Sriskandan, S, Stuart, D, Summers, C, Tedder, RS, Thomson, EC, Thompson, AAR, Thwaites, RS, Turtle, LCW, Zambon, M, Hardwick, H, Donohue, C, Lyons, R, Griffiths, F, Oosthuyzen, W, Norman, L, Pius, R, Drake, TM, Fairfield, CJ, Knight, S, Mclean, KA, Murphy, D, Shaw, CA, Dalton, J, Lee, J, Plotkin, D, Girvan, M, Saviciute, E, Roberts, S, Harrison, J, Marsh, L, Connor, M, Halpin, S, Jackson, C, Gamble, C, Petersen, C, Mullaney, S, Leeming, G, Wham, M, Clohisey, S, Hendry, R, Scott-Brown, J, Greenhalf, W, Shaw, V, McDonald, S, Keating, S, Ahmed, KA, Armstrong, JA, Ashworth, M, Asiimwe, IG, Bakshi, S, Barlow, SL, Booth, L, Brennan, B, Bullock, K, Catterall, BWA, Clark, JJ, Clarke, EA, Cole, S, Cooper, L, Cox, H, Davis, C, Dincarslan, O, Dunn, C, Dyer, P, Elliott, A, Evans, A, Finch, L, Fisher, LWS, Foster, T, Garcia-Dorival, I, Gunning, P, Hartley, C, Ho, A, Jensen, RL, Jones, CB, Jones, TR, Khandaker, S, King, K, Kiy, RT, Koukorava, C, Lake, A, Lant, S, Latawiec, D, Lavelle-Langham, L, Lefteri, D, Lett, L, Livoti, LA, Mancini, M, McEvoy, L, McLauchlan, J, Metelmann, S, Miah, NS, Middleton, J, Mitchell, J, Murphy, EG, Penrice-Randal, R, Pilgrim, J, Prince, T, Reynolds, W, Ridley, PM, Sales, D, Shaw, VE, Shears, RK, Small, B, Subramaniam, KS, Szemiel, A, Taggart, A, Tanianis-Hughes, J, Thomas, J, Trochu, E, van Tonder, L, Wilcock, E, Zhang, JE, Adeniji, K, Agranoff, D, Agwuh, K, Ail, D, Alegria, A, Angus, B, Ashish, A, Atkinson, D, Bari, S, Barlow, G, Barnass, S, Barrett, N, Bassford, C, Baxter, D, Beadsworth, M, Bernatoniene, J, Berridge, J, Best, N, Bothma, P, Brealey, D, Brittain-Long, R, Bulteel, N, Burden, T, Burtenshaw, A, Caruth, V, Chadwick, D, Chambler, D, Chee, N, Child, J, Chukkambotla, S, Clark, T, Collini, P, Cosgrove, C, Cupitt, J, Cutino-Moguel, M-T, Dark, P, Dawson, C, Dervisevic, S, Donnison, P, Douthwaite, S, DuRand, I, Dushianthan, A, Dyer, T, Evans, C, Eziefula, C, Fegan, C, Finn, A, Fullerton, D, Garg, S, Garg, A, Gkrania-Klotsas, E, Godden, J, Goldsmith, A, Graham, C, Hardy, E, Hartshorn, S, Harvey, D, Havalda, P, Hawcutt, DB, Hobrok, M, Hodgson, L, Hormis, A, Jacobs, M, Jain, S, Jennings, P, Kaliappan, A, Kasipandian, V, Kegg, S, Kelsey, M, Kendall, J, Kerrison, C, Kerslake, I, Koch, O, Koduri, G, Koshy, G, Laha, S, Laird, S, Larkin, S, Leiner, T, Lillie, P, Limb, J, Linnett, V, Little, J, MacMahon, M, MacNaughton, E, Mankregod, R, Masson, H, Matovu, E, McCullough, K, McEwen, R, Meda, M, Mills, G, Minton, J, Mirfenderesky, M, Mohandas, K, Mok, Q, Moon, J, Moore, E, Morgan, P, Morris, C, Mortimore, K, Moses, S, Mpenge, M, Mulla, R, Murphy, M, Nagel, M, Nagarajan, T, Nelson, M, Otahal, I, Pais, M, Panchatsharam, S, Paraiso, H, Patel, B, Pattison, N, Pepperell, J, Peters, M, Phull, M, Pintus, S, Pooni, JS, Post, F, Price, D, Prout, R, Rae, N, Reschreiter, H, Reynolds, T, Richardson, N, Roberts, M, Roberts, D, Rose, A, Rousseau, G, Ryan, B, Saluja, T, Shah, A, Shanmuga, P, Sharma, A, Shawcross, A, Sizer, J, Shankar-Hari, M, Smith, R, Snelson, C, Spittle, N, Staines, N, Stambach, T, Stewart, R, Subudhi, P, Szakmany, T, Tatham, K, Thompson, C, Thompson, R, Tridente, A, Tupper-Carey, D, Twagira, M, Ustianowski, A, Vallotton, N, Vincent-Smith, L, Visuvanathan, S, Vuylsteke, A, Waddy, S, Wake, R, Walden, A, Welters, I, Whitehouse, T, Whittaker, P, Whittington, A, Wijesinghe, M, Williams, M, Wilson, L, Wilson, S, Winchester, S, Wiselka, M, Wolverson, A, Wooton, DG, Workman, A, Yates, B, Young, P, Quaife, M, Jarvis, CI, Meakin, SR, Quilty, BJ, Prem, K, Villabona-Arenas, CJ, Sun, FY, Abbas, K, Auzenbergs, M, Gimma, A, Tully, DC, Sherratt, K, Rosello, A, Davies, NG, Liu, Y, Lowe, R, Gibbs, HP, Waterlow, NR, Edmunds, WJ, Simons, D, Medley, G, Munday, JD, Flasche, S, Sandmann, FG, Showering, A, Eggo, RM, Chan, Y-WD, Pearson, CAB, Kucharski, AJ, Foss, AM, Russell, TW, Bosse, NI, Jit, M, Abbott, S, Williams, J, Endo, A, Clifford, S, Gore-Langton, GR, Klepac, P, Brady, O, Hellewell, J, Funk, S, van Zandvoort, K, Barnard, RC, Nightingale, ES, Jombart, T, Atkins, KE, Procter, SR, Knight, GM

Background\ud \ud Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient’s “bed pathway” - the sequence of transfers of indi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=core_ac_uk__::80a6045569c4f0ca7375cbb7bbd8c05b

Divergent HIV-1 strains (CRF92_C2U and CRF93_cpx) co-circulating in the Democratic Republic of the Congo: Phylogenetic insights on the early evolutionary history of subtype C

Autor: Villabona Arenas, CJ, Vidal, N, Ahuka Mundeke, S, Muwonga, J, Serrano, L, Muyembe, JJ, Boillot, F, Delaporte, E, Peeters, M

Molecular epidemiological studies revealed that the epicenter of the HIV pandemic was Kinshasa, the capital city of the Democratic Republic of the Congo (DRC) in Central Africa. All known subtypes and numerous complex recombinant strains co-circulate

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=core_ac_uk__::ab6b40d15b89b0fd0de8bb3fc65c0381

Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia.

Autor: Jimenez-Silva C; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand. cjim882@aucklanduni.ac.nz.; School of Biological Sciences, University of Auckland, Auckland, New Zealand. cjim882@aucklanduni.ac.nz., Rivero R; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia. ricardoriveroh@correo.unicordoba.edu.co.; Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA. ricardoriveroh@correo.unicordoba.edu.co., Douglas J; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; Department of Physics, University of Auckland, Auckland, New Zealand., Bouckaert R; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; School of Computer Science, University of Auckland, Auckland, New Zealand., Villabona-Arenas CJ; Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK., Atkins KE; Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.; Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK., Gastelbondo B; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.; Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia.; Grupo de Salud Pública y Auditoría en Salud, Corporación Universitaria del Caribe- CECAR, Sincelejo, Colombia., Calderon A; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia., Guzman C; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.; Grupo de Investigación, Evaluación y Desarrollo de Farmacos y Afines - IDEFARMA, Universidad de Córdoba, Montería, Colombia., Echeverri-De la Hoz D; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia., Muñoz M; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Ballesteros N; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Castañeda S; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Patiño LH; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Ramirez A; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Luna N; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia., Paniz-Mondolfi A; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA., Serrano-Coll H; Instituto Colombiano de Medicina Tropical-Universidad CES, Medellín, Colombia., Ramirez JD; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia. juan.ramirezgonzalez@mountsinai.org.; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA. juan.ramirezgonzalez@mountsinai.org., Mattar S; Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia. smattar@correo.unicordoba.edu.co., Drummond AJ; Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.; School of Biological Sciences, University of Auckland, Auckland, New Zealand.; School of Computer Science, University of Auckland, Auckland, New Zealand.

Publikováno v: Communications medicine [Commun Med (Lond)] 2023 Jul 13; Vol. 3 (1), pp. 97. Date of Electronic Publication: 2023 Jul 13.

Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Autor: Lindsey BB; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Villabona-Arenas CJ; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK., Campbell F; Health Emergencies Programme, World Health Organization, Geneva, Switzerland., Keeley AJ; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Parker MD; Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, UK.; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK.; The Department of Neuroscience/Neuroscience Institute, The University of Sheffield, Sheffield, UK., Shah DR; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Parsons H; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Zhang P; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Kakkar N; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Gallis M; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Foulkes BH; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Wolverson P; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Louka SF; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., Christou S; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK., State A; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Johnson K; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Raza M; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Hsu S; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK., Jombart T; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK., Cori A; MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK., Evans CM; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Partridge DG; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK., Atkins KE; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK. Katherine.Atkins@ed.ac.uk.; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK. Katherine.Atkins@ed.ac.uk.; Usher Institute, The University of Edinburgh, Edinburgh, UK. Katherine.Atkins@ed.ac.uk., Hué S; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK. Stephane.Hue@lshtm.ac.uk.; Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK. Stephane.Hue@lshtm.ac.uk., de Silva TI; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK. t.desilva@sheffield.ac.uk.; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK. t.desilva@sheffield.ac.uk.; MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia. t.desilva@sheffield.ac.uk.

Publikováno v: Nature communications [Nat Commun] 2022 Feb 17; Vol. 13 (1), pp. 1013. Date of Electronic Publication: 2022 Feb 17.