215 results on '"Nastouli, E"'
Search Results
2. Laboratory biomarkers associated with COVID-19 severity and management
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Keddie, S., Ziff, O., Chou, M.K.L., Taylor, R.L., Heslegrave, A., Garr, E., Lakdawala, N., Church, A., Ludwig, D., Manson, J., Scully, M., Nastouli, E., Chapman, M.D., Hart, M., and Lunn, M.P.
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- 2020
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3. Lateral flow test engineering and lessons learned from COVID-19
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Budd J, Miller BS, Weckman NE, Cherkaoui D, Huang D, Decruz AT, Fongwen N, Han G, Broto M, Estcourt CS, Gibbs J, Pillay D, Sonnenberg P, Meurant R, Thomas MR, Keegan N, Stevens MM, Nastouli E, Topol EJ, Johnson AM, Shahmanesh M, Ozcan A, Collins JJ, Suarez MF, Rodriguez B, Peeling RW, McKendry RA
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- 2023
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4. Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study
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Stirrup, O, Blackstone, J, Mapp, F, MacNeil, A, Panca, M, Holmes, A, Machin, N, Shin, GY, Mahungu, T, Saeed, K, Saluja, T, Taha, Y, Mahida, N, Pope, C, Chawla, A, Cutino-Moguel, M-T, Tamuri, A, Williams, R, Darby, A, Robertson, DL, Flaviani, F, Nastouli, E, Robson, S, Smith, D, Laing, K, Monahan, I, Kele, B, Haldenby, S, George, R, Bashton, M, Witney, AA, Byott, M, Coll, F, Chapman, M, Peacock, SJ, COG‐UK HOCI Investigators, COVID‐19 Genomics UK (COG‐UK) Consortium, Hughes, J, Nebbia, G, Partridge, DG, Parker, M, Price, JR, Peters, C, Roy, S, Snell, LB, de Silva, TI, Thomson, E, Flowers, P, Copas, A, and Breuer, J
- Abstract
Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (
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- 2022
5. Paediatric European Network for Treatment of AIDS (PENTA) guidelines for treatment of paediatric HIV‐1 infection 2015: optimizing health in preparation for adult life
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Bamford, A, Turkova, A, Lyall, H, Foster, C, Klein, N, Bastiaans, D, Burger, D, Bernadi, S, Butler, K, Chiappini, E, Clayden, P, Della Negra, M, Giacomet, V, Giaquinto, C, Gibb, D, Galli, L, Hainaut, M, Koros, M, Marques, L, Nastouli, E, Niehues, T, Noguera‐Julian, A, Rojo, P, Rudin, C, Scherpbier, HJ, Tudor‐Williams, G, and Welch, SB
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- 2018
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6. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2
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Eales, O, Page, AJ, de Oliveira Martins, L, Wang, H, Bodinier, B, Haw, D, Jonnerby, J, Atchison, C, Robson, SC, Connor, TR, Loman, NJ, Golubchik, T, Nunez, RTM, Bonsall, D, Rambaut, A, Snell, LB, Livett, R, Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Johnston, I, Lythgoe, K, Torok, ME, Goodfellow, IG, Prieto, JA, Saeed, K, Jackson, DK, Houlihan, C, Frampton, D, Hamilton, WL, Witney, AA, Bucca, G, Pope, CF, Moore, C, Thomson, EC, Harrison, EM, Smith, CP, Rogan, F, Beckwith, SM, Murray, A, Singleton, D, Eastick, K, Sheridan, LA, Randell, P, Jackson, LM, Ariani, CV, Gonçalves, S, Fairley, DJ, Loose, MW, Watkins, J, Moses, S, Nicholls, S, Bull, M, Amato, R, Smith, DL, Aanensen, DM, Barrett, JC, Aggarwal, D, Shepherd, JG, Curran, MD, Parmar, S, Parker, MD, Williams, C, Glaysher, S, Underwood, AP, Bashton, M, Pacchiarini, N, Loveson, KF, Byott, M, Carabelli, AM, Templeton, KE, de Silva, TI, Wang, D, Langford, CF, Sillitoe, J, Gunson, RN, Cottrell, S, O’Grady, J, Kwiatkowski, D, Lillie, PJ, Cortes, N, Moore, N, Thomas, C, Burns, PJ, Mahungu, TW, Liggett, S, Beckett, AH, Holden, MTG, Levett, LJ, Osman, H, Hassan-Ibrahim, MO, Simpson, DA, Chand, M, Gupta, RK, Darby, AC, Paterson, S, Pybus, OG, Volz, EM, de Angelis, D, Robertson, DL, Martincorena, I, Aigrain, L, Bassett, AR, Wong, N, Taha, Y, Erkiert, MJ, Chapman, MHS, Dewar, R, McHugh, MP, Mookerjee, S, Aplin, S, Harvey, M, Sass, T, Umpleby, H, Wheeler, H, McKenna, JP, Warne, B, Taylor, JF, Chaudhry, Y, Izuagbe, R, Jahun, AS, Young, GR, McMurray, C, McCann, CM, Nelson, A, Elliott, S, Lowe, H, Price, A, Crown, MR, Rey, S, Roy, S, Temperton, B, Shaaban, S, Hesketh, AR, Laing, KG, Monahan, IM, Heaney, J, Pelosi, E, Silviera, S, Wilson-Davies, E, Fryer, H, Adams, H, du Plessis, L, Johnson, R, Harvey, WT, Hughes, J, Orton, RJ, Spurgin, LG, Bourgeois, Y, Ruis, C, O’Toole, Á, Gourtovaia, M, Sanderson, T, Fraser, C, Edgeworth, J, Breuer, J, Michell, SL, Todd, JA, John, M, Buck, D, Gajee, K, Kay, GL, Peacock, SJ, Heyburn, D, Kitchman, K, McNally, A, Pritchard, DT, Dervisevic, S, Muir, P, Robinson, E, Vipond, BB, Ramadan, NA, Jeanes, C, Weldon, D, Catalan, J, Jones, N, da Silva Filipe, A, Fuchs, M, Miskelly, J, Jeffries, AR, Oliver, K, Park, NR, Ash, A, Koshy, C, Barrow, M, Buchan, SL, Mantzouratou, A, Clark, G, Holmes, CW, Campbell, S, Davis, T, Tan, NK, Brown, JR, Harris, KA, Kidd, SP, Grant, PR, Xu-McCrae, L, Cox, A, Madona, P, Pond, M, Randell, PA, Withell, KT, Graham, C, Denton-Smith, R, Swindells, E, Turnbull, R, Sloan, TJ, Bosworth, A, Hutchings, S, Pymont, HM, Casey, A, Ratcliffe, L, Jones, CR, Knight, BA, Haque, T, Hart, J, Irish-Tavares, D, Witele, E, Mower, C, Watson, LK, Collins, J, Eltringham, G, Crudgington, D, Macklin, B, Iturriza-Gomara, M, Lucaci, AO, McClure, PC, Carlile, M, Holmes, N, Storey, N, Rooke, S, Yebra, G, Craine, N, Perry, M, Alikhan, N - F, Bridgett, S, Cook, KF, Fearn, C, Goudarzi, S, Lyons, RA, Williams, T, Haldenby, ST, Durham, J, Leonard, S, Davies, RM, Batra, R, Blane, B, Spyer, MJ, Smith, P, Yavus, M, Williams, RJ, Mahanama, AIK, Samaraweera, B, Girgis, ST, Hansford, SE, Green, A, Beaver, C, Bellis, KL, Dorman, MJ, Kay, S, Prestwood, L, Rajatileka, S, Quick, J, Poplawski, R, Reynolds, N, Mack, A, Morriss, A, Whalley, T, Patel, B, Georgana, I, Hosmillo, M, Pinckert, ML, Stockton, J, Henderson, JH, Hollis, A, Stanley, W, Yew, WC, Myers, R, Thornton, A, Adams, A, Annett, T, Asad, H, Birchley, A, Coombes, J, Evans, JM, Fina, L, Gatica-Wilcox, B, Gilbert, L, Graham, L, Hey, J, Hilvers, E, Jones, S, Jones, H, Kumziene-Summerhayes, S, McKerr, C, Powell, J, Pugh, G, Taylor, S, Trotter, AJ, Williams, CA, Kermack, LM, Foulkes, BH, Gallis, M, Hornsby, HR, Louka, SF, Pohare, M, Wolverson, P, Zhang, P, MacIntyre-Cockett, G, Trebes, A, Moll, RJ, Ferguson, L, Goldstein, EJ, Maclean, A, Tomb, R, Starinskij, I, Thomson, L, Southgate, J, Kraemer, MUG, Raghwani, J, Zarebski, AE, Boyd, O, Geidelberg, L, Illingworth, CJ, Jackson, C, Pascall, D, Vattipally, S, Freeman, TM, Hsu, SN, Lindsey, BB, James, K, Lewis, K, Tonkin-Hill, G, Tovar-Corona, JM, Cox, MG, Abudahab, K, Menegazzo, M, MEng, BEWT, Yeats, CA, Mukaddas, A, Wright, DW, Colquhoun, R, Hill, V, Jackson, B, McCrone, JT, Medd, N, Scher, E, Keatley, J - P, Curran, T, Morgan, S, Maxwell, P, Smith, K, Eldirdiri, S, Kenyon, A, Holmes, AH, Price, JR, Wyatt, T, Mather, AE, Skvortsov, T, Hartley, JA, Guest, M, Kitchen, C, Merrick, I, Munn, R, Bertolusso, B, Lynch, J, Vernet, G, Kirk, S, Wastnedge, E, Stanley, R, Idle, G, Bradley, DT, Poyner, J, Mori, M, Jones, O, Wright, V, Brooks, E, Churcher, CM, Fragakis, M, Galai, K, Jermy, A, Judges, S, McManus, GM, Smith, KS, Westwick, E, Attwood, SW, Bolt, F, Davies, A, De Lacy, E, Downing, F, Edwards, S, Meadows, L, Jeremiah, S, Smith, N, Foulser, L, Charalampous, T, Patel, A, Berry, L, Boswell, T, Fleming, VM, Howson-Wells, HC, Joseph, A, Khakh, M, Lister, MM, Bird, PW, Fallon, K, Helmer, T, McMurray, CL, Odedra, M, Shaw, J, Tang, JW, Willford, NJ, Blakey, V, Raviprakash, V, Sheriff, N, Williams, L - A, Feltwell, T, Bedford, L, Cargill, JS, Hughes, W, Moore, J, Stonehouse, S, Atkinson, L, Lee, JCD, Shah, D, Alcolea-Medina, A, Ohemeng-Kumi, N, Ramble, J, Sehmi, J, Williams, R, Chatterton, W, Pusok, M, Everson, W, Castigador, A, Macnaughton, E, Bouzidi, KE, Lampejo, T, Sudhanva, M, Breen, C, Sluga, G, Ahmad, SSY, George, RP, Machin, NW, Binns, D, James, V, Blacow, R, Coupland, L, Smith, L, Barton, E, Padgett, D, Scott, G, Cross, A, Mirfenderesky, M, Greenaway, J, Cole, K, Clarke, P, Duckworth, N, Walsh, S, Bicknell, K, Impey, R, Wyllie, S, Hopes, R, Bishop, C, Chalker, V, Harrison, I, Gifford, L, Molnar, Z, Auckland, C, Evans, C, Johnson, K, Partridge, DG, Raza, M, Baker, P, Bonner, S, Essex, S, Murray, LJ, Lawton, AI, Burton-Fanning, S, Payne, BAI, Waugh, S, Gomes, AN, Kimuli, M, Murray, DR, Ashfield, P, Dobie, D, Ashford, F, Best, A, Crawford, L, Cumley, N, Mayhew, M, Megram, O, Mirza, J, Moles-Garcia, E, Percival, B, Driscoll, M, Ensell, L, Lowe, HL, Maftei, L, Mondani, M, Chaloner, NJ, Cogger, BJ, Easton, LJ, Huckson, H, Lewis, J, Lowdon, S, Malone, CS, Munemo, F, Mutingwende, M, Nicodemi, R, Podplomyk, O, Somassa, T, Beggs, A, Richter, A, Cormie, C, Dias, J, Forrest, S, Higginson, EE, Maes, M, Young, J, Davidson, RK, Jackson, KA, Turtle, L, Keeley, AJ, Ball, J, Byaruhanga, T, Chappell, JG, Dey, J, Hill, JD, Park, EJ, Fanaie, A, Hilson, RA, Yaze, G, Lo, S, Afifi, S, Beer, R, Maksimovic, J, McCluggage, K, Spellman, K, Bresner, C, Fuller, W, Marchbank, A, Workman, T, Shelest, E, Debebe, J, Sang, F, Zamudio, ME, Francois, S, Gutierrez, B, Vasylyeva, TI, Flaviani, F, Ragonnet-Cronin, M, Smollett, KL, Broos, A, Mair, D, Nichols, J, Nomikou, K, Tong, L, Tsatsani, I, O’Brien, PS, Rushton, S, Sanderson, R, Perkins, J, Cotton, S, Gallagher, A, Allara, E, Pearson, C, Bibby, D, Dabrera, G, Ellaby, N, Gallagher, E, Hubb, J, Lackenby, A, Lee, D, Manesis, N, Mbisa, T, Platt, S, Twohig, KA, Morgan, M, Aydin, A, Baker, DJ, Foster-Nyarko, E, Prosolek, SJ, Rudder, S, Baxter, C, Carvalho, SF, Lavin, D, Mariappan, A, Radulescu, C, Singh, A, Tang, M, Morcrette, H, Bayzid, N, Cotic, M, Balcazar, CE, Gallagher, MD, Maloney, D, Stanton, TD, Williamson, KA, Manley, R, Michelsen, ML, Sambles, CM, Studholme, DJ, Warwick-Dugdale, J, Eccles, R, Gemmell, M, Gregory, R, Hughes, M, Nelson, C, Rainbow, L, Vamos, EE, Webster, HJ, Whitehead, M, Wierzbicki, C, Angyal, A, Green, LR, Whiteley, M, Betteridge, E, Bronner, IF, Farr, BW, Goodwin, S, Lensing, SV, McCarthy, SA, Quail, MA, Rajan, D, Redshaw, NM, Scott, C, Shirley, L, Thurston, SAJ, Rowe, W, Gaskin, A, Le-Viet, T, Bonfield, J, Liddle, J, Whitwham, A, Ashby, D, Barclay, W, Taylor, G, Cooke, G, Ward, H, Darzi, A, Riley, S, Chadeau-Hyam, M, Donnelly, CA, Elliott, P, The COVID-19 Genomics UK (COG-UK) Consortium, Department of Health, Imperial College Healthcare NHS Trust- BRC Funding, Medical Research Council (MRC), Cancer Research UK, Commission of the European Communities, Wellcome Trust, National Institute for Health Research, and Imperial College Healthcare NHS Trust: Research Capability Funding (RCF)
- Subjects
Delta variant ,Science & Technology ,SARS-CoV-2 ,COVID-19 ,1103 Clinical Sciences ,C500 ,Microbiology ,Genetic diversity ,B900 ,Infectious Diseases ,England ,COVID-19 Genomics UK (COG-UK) Consortium ,1108 Medical Microbiology ,Mutation ,Humans ,Transmission advantage ,Life Sciences & Biomedicine ,Phylogeny ,0605 Microbiology - Abstract
Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. Methods We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September–27 September 2021) and 15 (19 October–5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. Results We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8–23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. Conclusions As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
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- 2022
7. Vessel wall magnetic resonance and arterial spin labelling imaging in the management of presumed inflammatory intracranial arterial vasculopathy
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Benjamin, L A, primary, Lim, E, additional, Sokolska, M, additional, Markus, J, additional, Zaletel, T, additional, Aggarwal, V, additional, Luder, R, additional, Sanchez, E, additional, Brown, K, additional, Sofat, R, additional, Singh, A, additional, Houlihan, C, additional, Nastouli, E, additional, Losseff, N, additional, Werring, D J, additional, Brown, M M, additional, Mason, J C, additional, Simister, R J, additional, and Jäger, H R, additional
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- 2022
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8. Antenatal Seroprevalence of Zika and Chikungunya Viruses, Kingston Metropolitan Area, Jamaica, 2017-2019
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Anzinger, JJ, Mears, CD, Ades, AE, Francis, K, Phillips, Y, Leys, YE, Spyer, MJ, Brown, D, de Filippis, AMB, Nastouli, E, Byrne, T, Bailey, H, Palmer, P, Bryan, L, Webster-Kerr, K, Giaquinto, C, Thorne, C, Christie, CDC, Brown, B, Campbell, L, Gordon-Strachan, G, Grindley, M, Kamicka, D, Kelly, C, Lindo, J, Mitchell, P, Morgan, O, Onyonyor, A, Pierre, R, Rousseau, A, Scott, S, Anzinger, JJ, Mears, CD, Ades, AE, Francis, K, Phillips, Y, Leys, YE, Spyer, MJ, Brown, D, de Filippis, AMB, Nastouli, E, Byrne, T, Bailey, H, Palmer, P, Bryan, L, Webster-Kerr, K, Giaquinto, C, Thorne, C, Christie, CDC, Brown, B, Campbell, L, Gordon-Strachan, G, Grindley, M, Kamicka, D, Kelly, C, Lindo, J, Mitchell, P, Morgan, O, Onyonyor, A, Pierre, R, Rousseau, A, and Scott, S
- Abstract
To determine the extent of exposure to Zika virus (ZIKV) and chikungunya virus (CHIKV) in Jamaica, we collected serum from 584 pregnant women during 2017-2019. We found that 15.6% had antibodies against ZIKV and 83.6% against CHIKV. These results indicate potential recirculation of ZIKV but not CHIKV in the near future.
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- 2022
9. Cohort Profile: The Hepatitis C Virus (HCV) Research UK Clinical Database and Biobank
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McLauchlan, J, Innes, H, Dillon, J F, Foster, G, Holtham, E, McDonald, S, Wilkes, B, Hutchinson, S J, Irving, W L, Agarwal, K, Aldersley, M, Ala, A, Alexander, G, Aspinall, R, Barclay, S, Barnes, E, Bansal, S, Bassendine, M, Benselin, J, Brown, A, Butterworth, J, Ch’ng, C, Cooke, G, Corless, L, Cramp, M, Datta, S, Davison, S, Dillon, J, Forton, D, Foster, G, Foxton, M, Fraser, A, Gelson, W, Gera, A, Geretti, A M, Goldberg, D, Gorard, D, Gordon, F, Gore, C, Harris, H, Hayes, P, Heydtmann, M, Higham, A, Holtham, E, Hubscher, Hutchinson, S, Irving, W L, Jenkins, N, Kelly, D, Kennedy, N, Khakoo, S, Knowles, J, Langford, A, Lawson, A, Leen, C, Loganathan, S, McDonald, S E, McLauchlan, J, McPherson, S, Mills, P, Moreea, S, Mutimer, D, Nastouli, E, Neal, K, Patel, A, Priest, M, Prince, M, Quinlan, P, Reddy, Y, Richardson, P, Rosenberg, W, Ryder, S, Shields, P, Shorrock, C, Singhal, S, Sreedharan, A, Srirajaskanthan, R, Stone, B, Thursz, M, Tudor-Williams, G, Ustianowski, A, Verma, S, Wilkes, B, and Wiselka, M
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- 2017
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10. Quantitation of hepatitis delta virus using a single-step internally controlled real-time RT-qPCR and a full-length genomic RNA calibration standard
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Ferns, R.B., Nastouli, E., and Garson, J.A.
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- 2012
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11. Genomic reconstruction of the SARS-CoV-2 epidemic in England
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Vöhringer, HS, Sanderson, T, Sinnott, M, De Maio, N, Nguyen, T, Goater, R, Schwach, F, Harrison, I, Hellewell, J, Ariani, CV, Gonçalves, S, Jackson, DK, Johnston, I, Jung, AW, Saint, C, Sillitoe, J, Suciu, M, Goldman, N, Panovska-Griffiths, J, Abnizova, I, Aigrain, L, Alderton, A, Ali, M, Allen, L, Amato, R, Anderson, R, Ariani, C, Austin-Guest, S, Bala, S, Barrett, J, Bassett, A, Battleday, K, Beal, J, Beale, M, Beaver, C, Bellany, S, Bellerby, T, Bellis, K, Berger, D, Berriman, M, Betteridge, E, Bevan, P, Binley, S, Bishop, J, Blackburn, K, Bonfield, J, Boughton, N, Bowker, S, Brendler-Spaeth, T, Bronner, I, Brooklyn, T, Buddenborg, SK, Bush, R, Caetano, C, Cagan, A, Carter, N, Cartwright, J, Monteiro, TC, Chapman, L, Chillingworth, T-J, Clapham, P, Clark, R, Clarke, A, Clarke, C, Cole, D, Cook, E, Coppola, M, Cornell, L, Cornwell, C, Corton, C, Crackett, A, Cranage, A, Craven, H, Craw, S, Crawford, M, Cutts, T, Dabrowska, M, Davies, M, Davies, R, Dawson, J, Day, C, Densem, A, Dibling, T, Dockree, C, Dodd, D, Dogga, S, Dorman, M, Dougan, G, Dougherty, M, Dove, A, Drummond, L, Drury, E, Dudek, M, Durham, J, Durrant, L, Easthope, E, Eckert, S, Ellis, P, Farr, B, Fenton, M, Ferrero, M, Flack, N, Fordham, H, Forsythe, G, Foulser, L, Francis, M, Fraser, A, Freeman, A, Galvin, A, Garcia-Casado, M, Gedny, A, Girgis, S, Glover, J, Goncalves, S, Goodwin, S, Gould, O, Gourtovaia, M, Gray, A, Gray, E, Griffiths, C, Gu, Y, Guerin, F, Hamilton, W, Hanks, H, Harrison, E, Harrott, A, Harry, E, Harvison, J, Heath, P, Hernandez-Koutoucheva, A, Hobbs, R, Holland, D, Holmes, S, Hornett, G, Hough, N, Huckle, L, Hughes-Hallet, L, Hunter, A, Inglis, S, Iqbal, S, Jackson, A, Jackson, D, James, K, Jamrozy, D, Verdejo, CJ, Jones, M, Kallepally, K, Kane, L, Kay, K, Kay, S, Keatley, J, Keith, A, King, A, Kitchin, L, Kleanthous, M, Klimekova, M, Korlevic, P, Krasheninnkova, K, Lane, G, Langford, C, Laverack, A, Law, K, Lawniczak, M, Lensing, S, Leonard, S, Letchford, L, Lewis, K, Lewis-Wade, A, Liddle, J, Lin, Q, Lindsay, S, Linsdell, S, Livett, R, Lo, S, Long, R, Lovell, J, Ludden, C, Mack, J, Maddison, M, Makunin, A, Mamun, I, Mansfield, J, Marriott, N, Martin, M, Mayho, M, McCarthy, S, McClintock, J, McGuigan, S, McHugh, S, McMinn, L, Meadows, C, Mobley, E, Moll, R, Morra, M, Morrow, L, Murie, K, Nash, S, Nathwani, C, Naydenova, P, Neaverson, A, Nelson, R, Nerou, E, Nicholson, J, Nimz, T, Noell, GG, O’Meara, S, Ohan, V, Oliver, K, Olney, C, Ormond, D, Oszlanczi, A, Palmer, S, Pang, YF, Pardubska, B, Park, N, Parmar, A, Patel, G, Patel, M, Payne, M, Peacock, S, Petersen, A, Plowman, D, Preston, T, Prestwood, L, Puethe, C, Quail, M, Rajan, D, Rajatileka, S, Rance, R, Rawlings, S, Redshaw, N, Reynolds, J, Reynolds, M, Rice, S, Richardson, M, Roberts, C, Robinson, K, Robinson, M, Robinson, D, Rogers, H, Rojo, EM, Roopra, D, Rose, M, Rudd, L, Sadri, R, Salmon, N, Saul, D, Scott, C, Seekings, P, Shirley, L, Simms, A, Sivadasan, S, Siwek, B, Sizer, D, Skeldon, K, Skelton, J, Slater-Tunstill, J, Sloper, L, Smerdon, N, Smith, C, Smith, J, Smith, K, Smith, M, Smith, S, Smith, T, Sneade, L, Soria, CD, Sousa, C, Souster, E, Sparkes, A, Spencer-Chapman, M, Squares, J, Stanley, R, Steed, C, Stickland, T, Still, I, Stratton, MR, Strickland, M, Swann, A, Swiatkowska, A, Sycamore, N, Swift, E, Symons, E, Szluha, S, Taluy, E, Tao, N, Taylor, K, Taylor, S, Thompson, S, Thompson, M, Thomson, M, Thomson, N, Thurston, S, Tonkin-Hill, G, Toombs, D, Topping, B, Tovar-Corona, J, Ungureanu, D, Uphill, J, Urbanova, J, Van Vuuren, PJ, Vancollie, V, Voak, P, Walker, D, Walker, M, Waller, M, Ward, G, Weatherhogg, C, Webb, N, Weldon, D, Wells, A, Wells, E, Westwood, L, Whipp, T, Whiteley, T, Whitton, G, Whitwham, A, Widaa, S, Williams, M, Wilson, M, Wright, S, Robson, SC, Connor, TR, Loman, NJ, Golubchik, T, Martinez Nunez, RT, Bonsall, D, Rambaut, A, Snell, LB, Corden, S, Nastouli, E, Nebbia, G, Lythgoe, K, Torok, ME, Goodfellow, IG, Prieto, JA, Saeed, K, Houlihan, C, Frampton, D, Hamilton, WL, Witney, AA, Bucca, G, Pope, CF, Moore, C, Thomson, EC, Harrison, EM, Smith, CP, Rogan, F, Beckwith, SM, Murray, A, Singleton, D, Eastick, K, Sheridan, LA, Randell, P, Jackson, LM, Fairley, DJ, Loose, MW, Watkins, J, Moses, S, Nicholls, S, Bull, M, Smith, DL, Aanensen, DM, Aggarwal, D, Shepherd, JG, Curran, MD, Parmar, S, Parker, MD, Williams, C, Glaysher, S, Underwood, AP, Bashton, M, Pacchiarini, N, Loveson, KF, Byott, M, Carabelli, AM, Templeton, KE, de Silva, TI, Wang, D, Langford, CF, Gunson, RN, Cottrell, S, O’Grady, J, Kwiatkowski, D, Lillie, PJ, Cortes, N, Moore, N, Thomas, C, Burns, PJ, Mahungu, TW, Liggett, S, Beckett, AH, Holden, MTG, Levett, LJ, Osman, H, Hassan-Ibrahim, MO, Simpson, DA, Chand, M, Gupta, RK, Darby, AC, Paterson, S, Pybus, OG, Volz, EM, de Angelis, D, Robertson, DL, Page, AJ, Bassett, AR, Wong, N, Taha, Y, Erkiert, MJ, Spencer Chapman, MH, Dewar, R, McHugh, MP, Mookerjee, S, Aplin, S, Harvey, M, Sass, T, Umpleby, H, Wheeler, H, McKenna, JP, Warne, B, Taylor, JF, Chaudhry, Y, Izuagbe, R, Jahun, AS, Young, GR, McMurray, C, McCann, CM, Nelson, A, Elliott, S, Lowe, H, Price, A, Crown, MR, Rey, S, Roy, S, Temperton, B, Shaaban, S, Hesketh, AR, Laing, KG, Monahan, IM, Heaney, J, Pelosi, E, Silviera, S, Wilson-Davies, E, Fryer, H, Adams, H, du Plessis, L, Johnson, R, Harvey, WT, Hughes, J, Orton, RJ, Spurgin, LG, Bourgeois, Y, Ruis, C, O’Toole, Á, Fraser, C, Edgeworth, J, Breuer, J, Michell, SL, Todd, JA, John, M, Buck, D, Gajee, K, Kay, GL, Peacock, SJ, Heyburn, D, Kitchman, K, McNally, A, Pritchard, DT, Dervisevic, S, Muir, P, Robinson, E, Vipond, BB, Ramadan, NA, Jeanes, C, Catalan, J, Jones, N, da Silva Filipe, A, Fuchs, M, Miskelly, J, Jeffries, AR, Park, NR, Ash, A, Koshy, C, Barrow, M, Buchan, SL, Mantzouratou, A, Clark, G, Holmes, CW, Campbell, S, Davis, T, Tan, NK, Brown, JR, Harris, KA, Kidd, SP, Grant, PR, Xu-McCrae, L, Cox, A, Madona, P, Pond, M, Randell, PA, Withell, KT, Graham, C, Denton-Smith, R, Swindells, E, Turnbull, R, Sloan, TJ, Bosworth, A, Hutchings, S, Pymont, HM, Casey, A, Ratcliffe, L, Jones, CR, Knight, BA, Haque, T, Hart, J, Irish-Tavares, D, Witele, E, Mower, C, Watson, LK, Collins, J, Eltringham, G, Crudgington, D, Macklin, B, Iturriza-Gomara, M, Lucaci, AO, McClure, PC, Carlile, M, Holmes, N, Storey, N, Rooke, S, Yebra, G, Craine, N, Perry, M, Alikhan, N-F, Bridgett, S, Cook, KF, Fearn, C, Goudarzi, S, Lyons, RA, Williams, T, Haldenby, ST, Davies, RM, Batra, R, Blane, B, Spyer, MJ, Smith, P, Yavus, M, Williams, RJ, Mahanama, AIK, Samaraweera, B, Girgis, ST, Hansford, SE, Green, A, Bellis, KL, Dorman, MJ, Quick, J, Poplawski, R, Reynolds, N, Mack, A, Morriss, A, Whalley, T, Patel, B, Georgana, I, Hosmillo, M, Pinckert, ML, Stockton, J, Henderson, JH, Hollis, A, Stanley, W, Yew, WC, Myers, R, Thornton, A, Adams, A, Annett, T, Asad, H, Birchley, A, Coombes, J, Evans, JM, Fina, L, Gatica-Wilcox, B, Gilbert, L, Graham, L, Hey, J, Hilvers, E, Jones, S, Jones, H, Kumziene-Summerhayes, S, McKerr, C, Powell, J, Pugh, G, Trotter, AJ, Williams, CA, Kermack, LM, Foulkes, BH, Gallis, M, Hornsby, HR, Louka, SF, Pohare, M, Wolverson, P, Zhang, P, MacIntyre-Cockett, G, Trebes, A, Moll, RJ, Ferguson, L, Goldstein, EJ, Maclean, A, Tomb, R, Starinskij, I, Thomson, L, Southgate, J, Kraemer, MUG, Raghwani, J, Zarebski, AE, Boyd, O, Geidelberg, L, Illingworth, CJ, Jackson, C, Pascall, D, Vattipally, S, Freeman, TM, Hsu, SN, Lindsey, BB, Tovar-Corona, JM, Cox, M, Abudahab, K, Menegazzo, M, Taylor, BEW, Yeats, CA, Mukaddas, A, Wright, DW, de Oliveira Martins, L, Colquhoun, R, Hill, V, Jackson, B, McCrone, JT, Medd, N, Scher, E, Keatley, J-P, Curran, T, Morgan, S, Maxwell, P, Eldirdiri, S, Kenyon, A, Holmes, AH, Price, JR, Wyatt, T, Mather, AE, Skvortsov, T, Hartley, JA, Guest, M, Kitchen, C, Merrick, I, Munn, R, Bertolusso, B, Lynch, J, Vernet, G, Kirk, S, Wastnedge, E, Idle, G, Bradley, DT, Poyner, J, Mori, M, Jones, O, Wright, V, Brooks, E, Churcher, CM, Fragakis, M, Galai, K, Jermy, A, Judges, S, McManus, GM, Smith, KS, Westwick, E, Attwood, SW, Bolt, F, Davies, A, De Lacy, E, Downing, F, Edwards, S, Meadows, L, Jeremiah, S, Smith, N, Charalampous, T, Patel, A, Berry, L, Boswell, T, Fleming, VM, Howson-Wells, HC, Joseph, A, Khakh, M, Lister, MM, Bird, PW, Fallon, K, Helmer, T, McMurray, CL, Odedra, M, Shaw, J, Tang, JW, Willford, NJ, Blakey, V, Raviprakash, V, Sheriff, N, Williams, L-A, Feltwell, T, Bedford, L, Cargill, JS, Hughes, W, Moore, J, Stonehouse, S, Atkinson, L, Lee, JCD, Shah, D, Alcolea, A, Ohemeng-Kumi, N, Ramble, J, Sehmi, J, Williams, R, Chatterton, W, Pusok, M, Everson, W, Castigador, A, Macnaughton, E, El Bouzidi, K, Lampejo, T, Sudhanva, M, Breen, C, Sluga, G, Ahmad, SSY, George, RP, Machin, NW, Binns, D, James, V, Blacow, R, Coupland, L, Smith, L, Barton, E, Padgett, D, Scott, G, Cross, A, Mirfenderesky, M, Greenaway, J, Cole, K, Clarke, P, Duckworth, N, Walsh, S, Bicknell, K, Impey, R, Wyllie, S, Hopes, R, Bishop, C, Chalker, V, Gifford, L, Molnar, Z, Auckland, C, Evans, C, Johnson, K, Partridge, DG, Raza, M, Baker, P, Bonner, S, Essex, S, Murray, LJ, Lawton, AI, Burton-Fanning, S, Payne, BAI, Waugh, S, Gomes, AN, Kimuli, M, Murray, DR, Ashfield, P, Dobie, D, Ashford, F, Best, A, Crawford, L, Cumley, N, Mayhew, M, Megram, O, Mirza, J, Moles-Garcia, E, Percival, B, Ensell, L, Lowe, HL, Maftei, L, Mondani, M, Chaloner, NJ, Cogger, BJ, Easton, LJ, Huckson, H, Lewis, J, Lowdon, S, Malone, CS, Munemo, F, Mutingwende, M, Nicodemi, R, Podplomyk, O, Somassa, T, Beggs, A, Richter, A, Cormie, C, Dias, J, Forrest, S, Higginson, EE, Maes, M, Young, J, Davidson, RK, Jackson, KA, Turtle, L, Keeley, AJ, Ball, J, Byaruhanga, T, Chappell, JG, Dey, J, Hill, JD, Park, EJ, Fanaie, A, Hilson, RA, Yaze, G, Afifi, S, Beer, R, Maksimovic, J, Masters, KM, Spellman, K, Bresner, C, Fuller, W, Marchbank, A, Workman, T, Shelest, E, Debebe, J, Sang, F, Zamudio, ME, Francois, S, Gutierrez, B, Vasylyeva, TI, Flaviani, F, Ragonnet-Cronin, M, Smollett, KL, Broos, A, Mair, D, Nichols, J, Nomikou, K, Tong, L, Tsatsani, I, O’Brien, S, Rushton, S, Sanderson, R, Perkins, J, Cotton, S, Gallagher, A, Allara, E, Pearson, C, Bibby, D, Dabrera, G, Ellaby, N, Gallagher, E, Hubb, J, Lackenby, A, Lee, D, Manesis, N, Mbisa, T, Platt, S, Twohig, KA, Morgan, M, Aydin, A, Baker, DJ, Foster-Nyarko, E, Prosolek, SJ, Rudder, S, Baxter, C, Carvalho, SF, Lavin, D, Mariappan, A, Radulescu, C, Singh, A, Tang, M, Morcrette, H, Bayzid, N, Cotic, M, Balcazar, CE, Gallagher, MD, Maloney, D, Stanton, TD, Williamson, KA, Manley, R, Michelsen, ML, Sambles, CM, Studholme, DJ, Warwick-Dugdale, J, Eccles, R, Gemmell, M, Gregory, R, Hughes, M, Nelson, C, Rainbow, L, Vamos, EE, Webster, HJ, Whitehead, M, Wierzbicki, C, Angyal, A, Green, LR, Whiteley, M, Bronner, IF, Farr, BW, Lensing, SV, McCarthy, SA, Quail, MA, Redshaw, NM, Thurston, SAJ, Rowe, W, Gaskin, A, Le-Viet, T, Birney, E, Volz, E, Funk, S, Martincorena, I, Barrett, JC, and Gerstung, M
- Abstract
The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.
- Published
- 2021
12. Serological profile of first SARS-CoV-2 reinfection cases detected within the SIREN study
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Atti, A., primary, Ferrari, M., additional, Castillo-Olivares, J., additional, Monk, E.J.M., additional, Gopal, R., additional, Patel, M., additional, Hoschler, K., additional, Cole, M.J., additional, Semper, A., additional, Hewson, J., additional, Otter, A.D., additional, Foulkes, S., additional, Islam, J., additional, Mirfenderesky, M., additional, Jain, S., additional, Murira, J., additional, Favager, C., additional, Nastouli, E., additional, Chand, M.A., additional, Brown, C.S., additional, Heeney, J.L., additional, Brooks, T., additional, Hall, V.J., additional, Hopkins, S., additional, and Zambon, M., additional
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- 2022
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13. Sustained HIV-1 remission following CCR5D32/D32 allogeneic haematopoietic stem cell transplantation
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Gupta, R, Abduljawad, S, McCoy, L, Peppa, D, Salgado, M, Martinez-Picado, J, Wensing, A, Nijhuis, M, Mok, HP, Nastouli, E, Pace, M, Frater, J, Waters, L, Edwards, S, Lever, A, Gabriel, I, and Olivarria, E
- Published
- 2020
14. Evidence for HIV-1 cure after CCR5 Delta 32/Delta 32 allogeneic haemopoietic stem-cell transplantation 30 months post analytical treatment interruption: a case report
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Gupta, RK, Peppa, D, Hill, AL, Galvez, C, Salgado, M, Pace, M, McCoy, LE, Griffith, SA, Thornhill, J, Alrubayyi, A, Huyveneers, LEP, Nastouli, E, Grant, P, Edwards, SG, Innes, AJ, Frater, J, Nijhuis, M, Wensing, AMJ, Martinez-Picado, J, and Olavarria, E
- Abstract
Background The London patient (participant 36 in the IciStem cohort) underwent allogeneic stem-cell transplantation with cells that did not express CCR5 (CCR5 Delta 32/Delta 32); remission was reported at 18 months after analytical treatment interruption (ATI). Here, we present longer term data for this patient (up to 30 months after ATI), including sampling from diverse HIV-1 reservoir sites. Methods We used ultrasensitive viral load assays of plasma, semen, and cerebrospinal fluid (CSF) samples to detect HIV-1 RNA. In gut biopsy samples and lymph-node tissue, cell-copy number and total HIV-1 DNA levels were quantified in multiple replicates, using droplet digital PCR (ddPCR) and quantitative real-time PCR. We also analysed the presence of intact proviral DNA using multiplex ddPCR targeting the packaging signal (psi) and envelope (env). We did intracellular cytokine staining to measure HIV-1-specific T-cell responses. We used low-sensitive and low-avidity antibody assays to measure the humoral response to HIV-1. We predicted the probability of rebound using a mathematical model and inference approach. Findings HIV-1 viral load in plasma remained undetectable in the London patient up to 30 months (last tested on March 4, 2020), using an assay with a detection limit of 1 copy per mL. The patient's CD4 count was 430 cells per mu L (23.5% of total T cells) at 28 months. A very low-level positive signal for HIV-1 DNA was recorded in peripheral CD4 memory cells at 28 months. The viral load in semen was undetectable in both plasma (lower limit of detection [LLD]
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- 2020
15. The size of HIV reservoir is associated with telomere shortening and immunosenescence in early ART-treated HIV-infected children
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De Rossi, A, Dalzini, A, Ballin, G, Dominguez-Rodriguez, S, Conejo, Pr, Foster, C, Palma, P, Sessa, L, Nastouli, E, Pahwa, S, Rossi, P, and Giaquinto, C
- Published
- 2020
16. The impact of Spike mutations on SARS-CoV-2 neutralization
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Rees-Spear, C, primary, Muir, L, additional, Griffith, SA, additional, Heaney, J, additional, Aldon, Y, additional, Snitselaar, JL, additional, Thomas, P, additional, Graham, C, additional, Seow, J, additional, Lee, N, additional, Rosa, A, additional, Roustan, C, additional, Houlihan, CF, additional, Sanders, RW, additional, Gupta, R, additional, Cherepanov, P, additional, Stauss, H, additional, Nastouli, E, additional, Doores, KJ, additional, van Gils, MJ, additional, and McCoy, LE, additional
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- 2021
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17. Review of the pregnancy and neonatal outcomes of HIV positive pregnant women booked in a tertiary centre: EP1.342
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Lee, P, Dominguez Hernandez, J, Nayar, B, Harding, S, Roedling, S, Whitten, S M, and Nastouli, E
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- 2013
18. Identification of longitudinal vaginal septum in labour: have we missed the diagnosis and what is the best mode of delivery?: EP1.349
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Kalumbi, C, Ajayi, S, Gupta, S, and Nastouli, E
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- 2013
19. Laboratory biomarkers associated with COVID-19 severity and management
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Keddie, S, primary, Ziff, O, additional, Chou, MKL, additional, Taylor, RL, additional, Heslegrave, A, additional, Garr, E, additional, Lakdawala, N, additional, Church, A, additional, Ludwig, D, additional, Manson, J, additional, Scully, M, additional, Nastouli, E, additional, Chapman, MD, additional, Hart, M, additional, and Lunn, MP, additional
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- 2020
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20. Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples
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Papadakis, G., primary, Pantazis, A. K., additional, Fikas, N., additional, Chatziioannidou, S., additional, Tsiakalou, V., additional, Michaelidou, K., additional, Pogka, V., additional, Megariti, M., additional, Vardaki, M., additional, Giarentis, K., additional, Heaney, J., additional, Nastouli, E., additional, Karamitros, T., additional, Mentis, A., additional, Zafiropoulos, A., additional, Sourvinos, G., additional, Agelaki, S., additional, and Gizeli, E., additional
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- 2020
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21. PD-1+ CD4 T cells are associated with HIV reservoir size and impaired function of T follicular helper cells in children and young adults on long-term viral control
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Rinaldi, S., primary, Dinh, V., additional, Pallikkuth, S., additional, De Armas, L., additional, Pahwa, R., additional, Cotugno, N., additional, Nastouli, E., additional, Foster, C., additional, Palma, P., additional, and Pahwa, S., additional
- Published
- 2019
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22. An integrated national scale SARS-CoV-2 genomic surveillance network
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Aanensen, DM, Abudahab, K, Adams, A, Afifi, S, Alam, MT, Alderton, A, Alikhan, N-F, Allan, J, Almsaud, M, Alrezaihi, A, Alruwaili, M, Amato, R, Andersson, M, Angyal, A, Aranday-Cortes, E, Ariani, C, Armstrong, SD, Asamaphan, P, Attwood, S, Aydin, A, Badhan, A, Baker, D, Baker, P, Balcazar, CE, Ball, J, Barton, AE, Bashton, M, Baxter, L, Beale, M, Beaver, C, Beckett, A, Beer, R, Beggs, A, Bell, A, Bellis, KL, Bentley, EG, Berriman, M, Betteridge, E, Bibby, D, Bicknell, K, Birchley, A, Black, G, Blane, B, Bloomfield, S, Bolt, F, Bonsall, DG, Bosworth, A, Bourgeois, Y, Boyd, O, Bradshaw, D, Breuer, J, Bridgewater, H, Brooks, T, Broos, A, Brown, JR, Brown, RL, Brunker, K, Bucca, G, Buck, D, Bull, M, Butcher, E, Caddy, SL, Caller, LG, Cambell, S, Carlile, M, Carmichael, S, Carrilero, L, Castellano, S, Chaloner, J, Chand, M, Chapman, MR, Chappell, J, Charles, I, Chauhan, AJ, Chawla, A, Cheng, E, Churcher, CM, Clark, G, Clark, JJ, Collins, J, Colquhoun, R, Connor, TR, Constantinidou, C, Coombes, J, Corden, S, Cottrell, S, Cowell, A, Curran, MD, Curran, T, Dabrera, G, Danesh, J, Darby, AC, De Cesare, M, Martins, LDO, De Silva, TI, Debebe, B, Dervisevic, S, Dewar, RA, Dia, M, Dorman, M, Dougan, G, Dover, L, Downing, F, Drury, E, Du Plessis, L, Dyal, PL, Eccles, R, Edwards, S, Ellaby, N, Elliott, S, Eltringham, G, Elumogo, N, Essex, S, Evans, CM, Evans, J, Nascimento, FF, Fairley, DJ, Farr, B, Feltwell, T, Ferguson, N, Filipe, ADS, Findlay, J, Forrest, LM, Forrest, S, Foulser, L, Francois, S, Fraser, C, Frost, L, Gallagher, E, Gallagher, MD, Garcia-Dorival, I, Gaskin, A, Gatica-Wilcox, B, Gavriil, A, Geidelberg, L, Gemmell, M, Gerada, A, Gifford, L, Gilbert, L, Gilmore, P, Gilroy, R, Girgis, S, Glaysher, S, Golubchik, T, Goncalves, S, Goodfellow, I, Goodwin, S, Graham, C, Graham, L, Grammatopoulos, D, Green, A, Green, LR, Greenaway, J, Gregory, R, Groves, DC, Groves, N, Guest, M, Gunson, R, Haldenby, S, Hall, G, Hamilton, WL, Han, X, Harris, KA, Harrison, EM, Hartley, C, Herrera, C, Hesketh, A, Heyburn, D, Hill, V, Hiscox, JA, Holden, M, Holmes, A, Holmes, N, Holt, GS, Hopes, R, Hosmillo, M, Houldcroft, CJ, Howson-Wells, H, Hubb, J, Hughe, J, Hughes, M, Hutchings, S, Impey, R, Iturriza-Gomara, M, Jackson, A, Jackson, B, Jackson, DK, Jahun, AS, James, K, Jamrozy, D, Jeffries, A, Jesudason, N, John, M, Johnson, J, Johnson, KJ, Johnson, N, Johnston, I, Jones, B, Jones, R, Jones, S, Jorgensen, D, Kane, L, Kay, GL, Kay, S, Keatley, J-P, Keeley, AJ, Khakh, M, Khokhar, FA, Kitchen, C, Knight, B, Kolyva, A, Kraemer, M, Kristiansen, M, Kumziene-Summerhayes, S, Kwiatkowski, D, Lackenby, A, Langford, C, Lawniczak, M, Thanh, L-V, Lee, D, Letchford, L, Li, K, Li, L, Liggett, S, Lindsey, BB, Livett, R, Lloyd, A, Lo, S, Lockhart, M, Loh, J, Loman, NJ, Loose, M, Lucaci, A, Ludden, C, Luu, L, Lyons, RA, MacIntyre-Cockett, G, MacLean, A, Mair, D, Maksimovic, J, Manley, R, Manso, C, Manson, J, Martincorena, I, Masoli, J, Mather, AE, Mbisa, T, McCluggage, K, McClure, P, McCrone, JT, McDonald, S, McHugh, MP, McKenna, JM, McMinn, L, McMurray, C, Meadows, L, Menegazzo, M, Meredith, LW, Merrick, I, Mestek-Boukhibar, L, Miah, S, Michell, S, Michelsen, ML, Molnar, Z, Moore, C, Moore, N, Morgan, M, Morgan, S, Muddyman, D, Muir, DA, Muir, P, Myers, R, Nastouli, E, Naydenova, P, Nelson, A, Nelson, C, Nelson, R, Nicholls, S, Nichols, J, Niebel, M, Niola, P, Nomikou, K, O'Grady, J, O'Toole, AN, O'Toole, E, Olateju, C, Orton, RJ, Osman, H, Ott, S, Pacchiarini, N, Padgett, D, Page, AJ, Palmer, S, Panchbhaya, YN, Pandey, S, Park, N, Parker, MD, Parkhill, J, Parr, YA, Parsons, PJ, Partridge, DG, Patel, M, Patterson, S, Payne, B, Peacock, SJ, Penrice-Randal, R, Perry, M, Platt, S, Poplawski, R, Prakash, R, Prestwood, L, Price, A, Price, JR, Puethe, C, Pybus, O, Pymont, H, Quail, M, Quick, J, Raghwani, J, Ragonnet-Cronin, M, Rahman, S, Rainbow, L, Rajatileka, S, Rambaut, A, Ramsay, M, Randell, PA, Randle, NP, Raviprakash, V, Raza, M, Silva, PR, Rey, S, Richter, A, Robertson, DL, Robinson, TI, Robson, SC, Rooke, S, Rowan, A, Rowe, W, Roy, S, Rudder, S, Ruis, C, Sang, F, Scarlett, G, Schaefer, U, Scott, C, Scott, G, Sethi, D, Shaaban, S, Shah, R, Sharma, P, Shawli, GT, Shepherd, J, Sherriff, N, Shirley, L, Sillitoe, J, Simpson, DA, Singer, JB, Siveroni, I, Smith, C, Smith, CP, Smith, DL, Smith, N, Smith, W, Smith-Palmer, A, Smollett, K, Southgate, J, Spellman, K, Spencer-Chapman, M, Sridhar, S, Stanley, R, Stark, R, Stewart, JP, Stockton, J, Stuart, C, Studholme, D, Swainston, N, Swindells, E, Taha, Y, Tariq, MA, Taylor, B, Taylor, GP, Taylor, S, Taylor-Joyce, G, Tedim, AP, Temperton, B, Templeton, KE, Thomson, EC, Thomson, NM, Thornton, A, Thurston, S, Todd, J, Tong, L, Tonkin-Hill, G, Torok, ME, Trebes, A, Trotter, AJ, Tsoleridis, T, Tucker, RM, Tutill, HJ, Underwood, A, Unnikrishnan, M, Vamos, E, Vasylyeva, T, Vattipally, S, Victoria, A, Vipond, B, Volz, EM, Wain, J, Wang, D, Warwick-Dugdale, J, Wastnedge, E, Watkins, J, Watts, J, Webber, M, Weeks, S, Weldon, D, Whitehead, M, Williams, CA, Williams, C, Williams, D, Williams, R, Williams, TC, Wise, E, Wright, V, Wyles, MD, Wyllie, S, Yakovleva, A, Yasir, M, Yeats, C, Yew, WC, Young, GR, Yu, X, and Zarebski, A
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Microbiology (medical) ,Scale (ratio) ,SARS-CoV-2 ,viruses ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,COVID-19 ,COVID-19 Genomics UK (COG-UK) consortiumcontact@cogconsortium.uk ,C500 ,Genome, Viral ,Genomics ,Biology ,C700 ,Microbiology ,Article ,Infectious Diseases ,Virology ,Humans ,Cartography - Abstract
The Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (COG-UK) was launched in March, 2020, with £20 million support from UK Research and Innovation, the UK Department of Health and Social Care, and Wellcome Trust. The goal of this consortium is to sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for up to 230 000 patients, health-care workers, and other essential workers in the UK with COVID-19, which will help to enable the tracking of SARS-CoV-2 transmission, identify viral mutations, and integrate with health data to assess how the viral genome interacts with cofactors and consequences of COVID-19.
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- 2020
23. Increasing incidence of acute hepatitis C in individuals diagnosed with primary HIV in the United Kingdom
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Fox, Julie, Nastouli, E, Thomson, E, Muir, D, McClure, Myra, Weber, Jonathan, and Fidler, Sarah
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- 2008
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24. Associations between baseline characteristics, CD4 cell count response and virological failure on first-line efavirenz
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Stirrup, OT, Sabin, CA, Phillips, AN, Williams, I, Churchill, D, Tostevin, A, Hill, T, Dunn, DT, Asboe, D, Pozniak, A, Cane, P, Chadwick, D, Clark, D, Collins, S, Delpech, V, Douthwaite, S, Dunn, D, Fearnhill, E, Porter, K, Stirrup, O, Fraser, C, Geretti, AM, Gunson, R, Hale, A, Hue, S, Lazarus, L, Leigh-Brown, A, Mbisa, T, Mackie, N, Orkin, C, Nastouli, E, Pillay, D, Phillips, A, Sabin, C, Smit, E, Templeton, K, Tilston, P, Volz, E, Zhang, H, Fairbrother, K, Dawkins, J, O'Shea, S, Mullen, J, Cox, A, Tandy, R, Fawcett, T, Hopkins, M, Booth, C, Garcia-Diaz, A, Renwick, L, Schmid, ML, Payne, B, Hubb, J, Dustan, S, Kirk, S, Bradley-Stewart, A, Ainsworth, J, Allan, S, Anderson, J, Babiker, A, Gazzard, B, Gilson, R, Compels, M, Hay, P, Johnson, M, Jose, S, Kegg, S, Leen, C, Martin, F, Mital, D, Nelson, M, Palfreeman, A, Post, F, Pritchard, J, Schwenk, A, Tariq, A, Trevelion, R, Ustianowski, A, Walsh, J, Thornton, A, Huntington, S, Glabay, A, Shidfar, S, Lynch, J, Hand, J, De Souza, C, Perry, N, Tilbury, S, Youssef, E, Mabika, T, Mandalia, S, Munshi, S, Adefisan, A, Taylor, C, Gleisner, Z, Ibrahim, F, Campbell, L, Baillie, K, Brima, N, Miller, S, Wood, C, Youle, M, Lampe, F, Smith, C, Tsintas, R, Chaloner, C, Hutchinson, S, Winston, A, Weber, J, Ramzan, F, Carder, M, Wilson, A, Morris, S, Gompels, M, Lewszuk, A, Faleye, A, Ogunbiyi, V, Mitchell, S, Kemble, C, Russell-Sharpe, S, Gravely, J, Harte, A, Spencer, H, Jones, R, Cumming, S, Atkinson, C, Edgell, V, Allen, J, Murphy, C, and Gunder, I
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NNRTI ,viral suppression ,Science & Technology ,drug resistance ,MUTATIONS ,Immunology ,antiretroviral therapy ,MODELS ,viral failure ,HIV ,HIV-1 DRUG-RESISTANCE ,TIME ,INDIVIDUALS ,Infectious Diseases ,ADHERENCE ,NRTI ,Virology ,INFECTION ,UK ,COMBINATION ANTIRETROVIRAL THERAPY ,UK HIV Drug Resistance Database and the UK Collaborative HIV Cohort ,Life Sciences & Biomedicine ,ART ,SUPPRESSION - Abstract
Objectives The aim of this study was to investigate associations between baseline characteristics and CD4 cell count response on first-line antiretroviral therapy and risk of virological failure (VF) with or without drug resistance. Methods We conducted an analysis of UK Collaborative HIV Cohort data linked to the UK HIV Drug Resistance Database. Inclusion criteria were viral sequence showing no resistance prior to initiation of first-line efavirenz + tenofovir disoproxil fumarate + emtricitabine and virological suppression within 6 months. Outcomes of VF (≥200 copies/mL) with or without drug resistance were assessed using a competing risks approach fitted jointly with a model for CD4 cell count recovery. Hazard ratios for each VF outcome were estimated for baseline CD4 cell count and viral load and characteristics of CD4 cell count response using latent variables on a standard normal scale. Results A total of 3640 people were included with 338 VF events; corresponding viral sequences were available in 134 with ≥1 resistance mutation in 36. VF with resistance was associated with lower baseline CD4 (0.30, 0.09–0.62), lower CD4 recovery (0.04, 0.00–0.17) and higher CD4 variability (4.40, 1.22–12.68). A different pattern of associations was observed for VF without resistance, but the strength of these results was less consistent across sensitivity analyses. Cumulative incidence of VF with resistance was estimated to be
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- 2019
25. Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014)
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Blackburn, RM, Frampton, D, Smith, CM, Fragaszy, EB, Watson, SJ, Ferns, RB, Binter, S, Coen, PG, Grant, P, Shallcross, LJ, Kozlakidis, Z, Pillay, D, Kellam, P, Hue, S, Nastouli, E, Hayward, AC, Kinghorn, J, Wurie, F, Rahman, S, Johnson, A, Dunn, D, Leigh-Brown, A, Morris, S, Irving, W, Clark, D, Zambon, M, De, S, Pillay, T, Freeman, S, Kidd, M, Gothard, P, Miller, R, and Brealey, D
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Male ,Pediatrics ,Epidemiology ,Cross-sectional study ,HEMAGGLUTININ ,030312 virology ,molecular epidemiology ,law.invention ,law ,London ,Cluster Analysis ,Child ,0303 health sciences ,Middle Aged ,Orthomyxoviridae ,Hospitals ,3. Good health ,H1N1 VIRUS ,Transmission (mechanics) ,Infectious Diseases ,INFECTIONS ,Child, Preschool ,ICONIC group ,RNA, Viral ,Female ,Original Article ,influenza ,Life Sciences & Biomedicine ,OUTBREAKS ,Pulmonary and Respiratory Medicine ,Adult ,medicine.medical_specialty ,Adolescent ,Genome, Viral ,Biology ,SEASONAL INFLUENZA ,DNA sequencing ,1117 Public Health and Health Services ,03 medical and health sciences ,Young Adult ,Virology ,Influenza, Human ,medicine ,Humans ,human ,Illumina dye sequencing ,Aged ,Retrospective Studies ,Infection Control ,Science & Technology ,Molecular epidemiology ,Nosocomial transmission ,Public Health, Environmental and Occupational Health ,Outbreak ,Influenza a ,1103 Clinical Sciences ,Sequence Analysis, DNA ,Original Articles ,cross infection ,Cross-Sectional Studies ,disease outbreaks - Abstract
BACKGROUND The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains. OBJECTIVES We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely‐collected data. METHODS All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space‐time links and assessed genetic relatedness. RESULTS We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space‐time links with other cases in the same cluster. Genetic distances between pairs of cases with space‐time links were lower than for pairs without spatial links (P < .001). CONCLUSIONS Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.
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- 2019
26. HIV-1 remission following CCR5 Delta 32/Delta 32 haematopoietic stem-cell transplantation
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Gupta, RK, Abdul-Jawad, S, Mccoy, LE, Mok, HP, Peppa, D, Salgado, M, Martinez-Picado, J, Nijhuis, M, Wensing, AMJ, Lee, H, Grant, P, Nastouli, E, Lambert, J, Pace, M, Salasc, F, Monit, C, Innes, AJ, Muir, L, Waters, L, Frater, J, Lever, AML, Edwards, SG, Gabriel, IH, and Olavarria, E
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A cure for HIV-1 remains unattainable as only one case has been reported, a decade ago(1,2). The individual-who is known as the 'Berlin patient'-underwent two allogeneic haematopoietic stem-cell transplantation (HSCT) procedures using a donor with a homozygous mutation in the HIV coreceptor CCR5 (CCR5 Delta 32/Delta 32) to treat his acute myeloid leukaemia. Total body irradiation was given with each HSCT. Notably, it is unclear which treatment or patient parameters contributed to this case of long-term HIV remission. Here we show that HIV-1 remission may be possible with a less aggressive and toxic approach. An adult infected with HIV-1 underwent allogeneic HSCT for Hodgkin's lymphoma using cells from a CCR5 Delta 32/Delta 32 donor. He experienced mild gut graft-versus-host disease. Antiretroviral therapy was interrupted 16 months after transplantation. HIV-1 remission has been maintained over a further 18 months. Plasma HIV-1 RNA has been undetectable at less than one copy per millilitre along with undetectable HIV-1 DNA in peripheral CD4 T lymphocytes. Quantitative viral outgrowth assays from peripheral CD4 T lymphocytes show no reactivatable virus using a total of 24 million resting CD4 T cells. CCR5-tropic, but not CXCR4-tropic, viruses were identified in HIV-1 DNA from CD4 T cells of the patient before the transplant. CD4 T cells isolated from peripheral blood after transplantation did not express CCR5 and were susceptible only to CXCR4-tropic virus ex vivo. HIV-1 Gag-specific CD4 and CD8 T cell responses were lost after transplantation, whereas cytomegalovirus-specific responses were detectable. Similarly, HIV-1-specific antibodies and avidities fell to levels comparable to those in the Berlin patient following transplantation. Although at 18 months after the interruption of treatment it is premature to conclude that this patient has been cured, these data suggest that a single allogeneic HSCT with homozygous CCR5 Delta 32 donor cells may be sufficient to achieve HIV-1 remission with reduced intensity conditioning and no irradiation, and the findings provide further support for the development of HIV-1 remission strategies based on preventing CCR5 expression.
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- 2019
27. Virological outcomes of boosted protease inhibitor-based first-line ART in subjects harbouring thymidine analogue-associated mutations as the sole form of transmitted drug resistance
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Geretti, AM, White, E, Orkin, C, Tostevin, A, Tilston, P, Chadwick, D, Leen, C, Sabin, C, Dunn, DT, Asboe, D, Pozniak, A, Cane, P, Churchill, D, Clark, D, Collins, S, Delpech, V, Douthwaite, S, Dunn, D, Fearnhill, E, Porter, K, Stirrup, O, Fraser, C, Gunson, R, Hale, A, Hue, S, Lazarus, L, Leigh-Brown, A, Mbisa, T, Mackie, N, Nastouli, E, Pillay, D, Phillips, A, Smit, E, Templeton, K, Volz, E, Williams, I, Zhang, H, Dawkins, J, O'Shea, S, Mullen, J, Cox, A, Tandy, R, Fawcett, T, Hopkins, M, Booth, C, Garcia-Diaz, A, Renwick, L, Schmid, ML, Payne, B, Hubb, J, Dustan, S, Kirk, S, Bradley-Stewart, A, Ainsworth, J, Allan, S, Anderson, J, Babiker, A, Gazzard, B, Gilson, R, Gompels, M, Hay, P, Hill, T, Johnson, M, Jose, S, Kegg, S, Martin, F, Mital, D, Nelson, M, Palfreeman, A, Post, F, Pritchard, J, Sabin, CA, Schwenk, A, Tariq, A, Trevelion, R, Ustianowski, A, Walsh, J, Thornton, A, Huntington, S, Glabay, A, Shidfar, S, Lynch, J, Hand, J, De Souza, C, Perry, N, Tilbury, S, Youssef, E, Mabika, T, Mandalia, S, Munshi, S, Adefisan, A, Taylor, C, Gleisner, Z, Ibrahim, F, Campbell, L, Baillie, K, Brima, N, Miller, S, Wood, C, Youle, M, Lampe, F, Smith, C, Tsintas, R, Chaloner, C, Hutchinson, S, Winston, A, Weber, J, Ramzan, F, Carder, M, Wilson, A, Morris, S, Lewszuk, A, Faleye, A, Ogunbiyi, V, Mitchell, S, Kemble, C, Russell-Sharpe, S, Gravely, J, Harte, A, Spencer, H, Jones, R, Cumming, S, Atkinson, C, Edgell, V, Allen, J, Murphy, C, and Gunder, I
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0301 basic medicine ,Oncology ,Male ,HIV Infections ,Drug resistance ,Kaplan-Meier Estimate ,chemistry.chemical_compound ,0302 clinical medicine ,1108 Medical Microbiology ,Abacavir ,Antiretroviral Therapy, Highly Active ,INFECTION ,Pharmacology (medical) ,Pharmacology & Pharmacy ,030212 general & internal medicine ,Original Research ,Proteolytic enzymes ,Lamivudine ,virus diseases ,Viral Load ,Prognosis ,ANTIRETROVIRAL TREATMENT ,Infectious Diseases ,Treatment Outcome ,Cohort ,RNA, Viral ,Female ,1115 Pharmacology and Pharmaceutical Sciences ,UK HIV Drug Resistance Database and UK CHIC Study ,Life Sciences & Biomedicine ,Viral load ,0605 Microbiology ,medicine.drug ,Microbiology (medical) ,Adult ,medicine.medical_specialty ,Efavirenz ,Genotype ,TRANSMISSION ,Anti-HIV Agents ,030106 microbiology ,REGIMENS ,Emtricitabine ,Microbiology ,03 medical and health sciences ,Internal medicine ,Drug Resistance, Viral ,medicine ,Humans ,Protease Inhibitors ,Alleles ,Pharmacology ,Science & Technology ,TREATMENT-NAIVE PATIENTS ,business.industry ,HIV ,INDIVIDUALS ,chemistry ,Amino Acid Substitution ,Mutation ,HIV-1 ,business - Abstract
Objectives: In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data.Methods: We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of ≥1 TAM as the sole form of transmitted drug resistance.Results: Participants with ≥1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5 years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88-2.51; P Conclusions: In this cohort, patients harbouring ≥1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.
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- 2018
28. Development of the R263K Mutation to Dolutegravir in an HIV-1 Subtype D Virus Harboring 3 Class-Drug Resistance
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Ahmed, N, Flavell, S, Ferns, B, Frampton, D, Edwards, S G, Miller, R F, Grant, P, Nastouli, E, and Gupta, R K
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ID Cases ,resistance ,ARVs ,HIV ,adolescents ,dolutegravir - Abstract
Dolutegravir (DTG), a second-generation integrase strand-transfer inhibitor (INSTI), is equivalent or superior to current non-nucleotide reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and first-generation INSTI-based antiretroviral regimens (ARVs). It has the potential to make big improvements in HIV control globally and within patients. This is perhaps the most “precious” HIV drug available. The integrase mutation R263K has been observed in tissue culture experiments and in patients treated with dolutegravir monotherapy in clinical trials. Globally, adherence and monitoring may be less than optimal and therefore DTG resistance more common. This is particularly important in low–middle-income countries, where patients may remain on failing regimens for longer periods of time and accumulate drug resistance. Data on this mutation in non–subtype B infections do not exist. We describe the first report of the R263K integrase mutation in a dolutegravir-exposed subtype D–infected individual with vertically acquired HIV. We have used deep sequencing of longitudinal samples to highlight the change in resistance over time while on a failing regimen. The case highlights that poorly adherent patients should not be offered dolutegravir even as part of a combination regimen and that protease inhibitors should be used preferentially.
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- 2018
29. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis:Results from the ICONIC project
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Yebra, G, Frampton, D, Cassarino, TG, Raffle, J, Hubb, J, Ferns, RB, Waters, L, Tong, CYW, Kozlakidis, Z, Hayward, A, Kellam, P, Pillay, D, Clark, D, Nastouli, E, and Brown, AJL
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Adult ,Male ,NON-B SUBTYPES ,General Science & Technology ,ICONIC Consortium ,Genome, Viral ,London ,MD Multidisciplinary ,Journal Article ,Humans ,COHORT ,TYPE-1 ,Phylogeny ,DRUG-RESISTANCE ,Recombination, Genetic ,Science & Technology ,COMPLEX ,IDENTIFICATION ,SPAIN ,Middle Aged ,Multidisciplinary Sciences ,RECOMBINANT FORM ,RELIABILITY ,HIV-1 ,Science & Technology - Other Topics ,GENETIC DIVERSITY ,Female - Abstract
BACKGROUND & METHODS: The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker.RESULTS: The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset.CONCLUSIONS: The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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- 2018
30. Near full-length genomic sequencing and molecular analysis of HIV-infected individuals in a network-based intervention (TRIP) in Athens, Greece: evidence that transmissions occur more frequently from those with high HIV-RNA
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Kostaki, E.-G. Frampton, D. Paraskevis, D. Pantavou, K. Ferns, B. Raffle, J. Grant, P. Kozlakidis, Z. Hadjikou, A. Pavlitina, E. Williams, L.D. Hatzakis, A. Friedman, S.R. Nastouli, E. Nikolopoulos, G.K.
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virus diseases - Abstract
Background: TRIP (Transmission Reduction Intervention Project) was a network-based, contact tracing approach to locate and link to care, mostly people who inject drugs (PWID) with recent HIV infection.Objective: We investigated whether sequences from HIV-infected participants with high viral load cluster together more frequently than what is expected by chance. Methods: Paired end reads were generated for 104 samples using Illumina MiSeq next-generation sequencing. Results: 63 sequences belonged to previously identified local transmission networks of PWID (LTNs) of an HIV outbreak in Athens, Greece. For two HIV-RNA cut-offs (105 and 106 IU/mL), HIV transmissions were more likely between PWID with similar levels of HIV-RNA (p106 IU/mL were clustered in 5 pairs. For 4 of these clusters (80%), there was in each one of them at least one sequence from a recently HIV-infected PWID. Conclusion: We showed that transmissions are more likely among PWID with high viremia. © 2018 Bentham Science Publishers.
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- 2018
31. Weekends-off efavirenz-based antiretroviral therapy in HIV-infected children, adolescents and young adults (BREATHER): Extended follow-up results of a randomised, open-label, non-inferiority trial
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Turkova, A, Moore, Cl, Butler, K, Compagnucci, A, Saidi, Y, Musiime, V, Nanduudu, A, Kaudha, E, Cressey, Tr, Chalermpantmetagul, S, Scott, K, Harper, L, Montero, S, Riault, Y, Bunupuradah, T, Volokha, A, Flynn, Pm, Bologna, R, Ramos Amador JT, Welch, Sb, Nastouli, E, Klein, N, Giaquinto, C, Ford, D, Babiker, A, Gibb, Dm, and Brather Penta 16 Trial Group
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Cyclopropanes ,RNA viruses ,Male ,Genetics and Molecular Biology (all) ,Pulmonology ,HIV Infections ,Pathology and Laboratory Medicine ,Toxicology ,Adolescents ,Biochemistry ,Families ,Immunodeficiency Viruses ,Medicine and Health Sciences ,Public and Occupational Health ,Child ,Children ,Viral Load ,Vaccination and Immunization ,Adolescent ,Benzoxazines ,Drug Administration Schedule ,Female ,Follow-Up Studies ,HIV-1 ,Humans ,Reverse Transcriptase Inhibitors ,Treatment Outcome ,Young Adult ,Biochemistry, Genetics and Molecular Biology (all) ,Agricultural and Biological Sciences (all) ,Medical Microbiology ,Research Design ,Alkynes ,Viral Pathogens ,Viruses ,Medicine ,Pathogens ,Research Article ,Clinical Research Design ,Science ,Immunology ,Antiretroviral Therapy ,Research and Analysis Methods ,Microbiology ,Antiviral Therapy ,Virology ,Retroviruses ,Microbial Pathogens ,Toxicity ,Lentivirus ,Organisms ,Biology and Life Sciences ,HIV ,Age Groups ,People and Places ,Respiratory Infections ,Population Groupings ,Preventive Medicine ,Adverse Events ,Viral Transmission and Infection - Abstract
BackgroundWeekends off antiretroviral therapy (ART) may help engage HIV-1-infected young people facing lifelong treatment. BREATHER showed short cycle therapy (SCT; 5 days on, 2 days off ART) was non-inferior to continuous therapy (CT) over 48 weeks. Planned follow-up was extended to 144 weeks, maintaining original randomisation.MethodsBREATHER was an open-label, non-inferiority trial. Participants aged 8-24yrs with virological suppression on efavirenz-based first-line ART were randomised 1:1, stratified by age and African/non-African sites, to remain on CT or change to SCT. The Kaplan-Meier method was used to estimate the proportion of participants with viral rebound (confirmed VL≥50 copies/mL) under intent-to-treat at 48 weeks (primary outcome), and in extended follow-up at 96, 144, and 192 weeks. SCT participants returned to CT following viral rebound, 3 VL blips or discontinuation of efavirenz.FindingsOf 199 participants (99 SCT, 100 CT), 97 per arm consented to extended follow-up. Median follow-up was 185.3 weeks (IQR 160.9-216.1). 69 (70%) SCT participants remained on SCT at last follow-up. 105 (53%) were male, baseline median age 14 years (IQR 12-18), median CD4 count 735 cells/μL (IQR 576-968). 16 SCT and 16 CT participants had confirmed VL≥50 copies/mL by the end of extended follow-up (HR 1.00, 95% CI 0.50-2.00). Estimated difference in percentage with viral rebound (SCT minus CT) by week 144 was 1.9% (90% CI -6.6-10.4; p = 0.72) and was similar in a per-protocol analysis. There were no significant differences between arms in proportions of participants with grade 3/4 adverse events (18 SCT vs 16 CT participants; p = 0.71) or ART-related adverse events (10 vs 12; p = 0.82). 20 versus 8 serious adverse events (SAEs) were reported in 16 SCT versus 4 CT participants, respectively (p = 0.005 comparing proportions between groups; incidence rate ratio 2.49, 95%CI 0.71-8.66, p = 0.15). 75% of SAEs (15 SCT, 6 CT) were hospitalisations for a wide range of conditions. 3 SCT and 6 CT participants switched to second-line ART following viral failure (p = 0.50).ConclusionsSustainable non-inferiority of virological suppression in young people was shown for SCT versus CT over median 3.6 years. Standard-dose efavirenz-based SCT is a viable option for virologically suppressed HIV-1 infected young people on first-line ART with 3-monthly VL monitoring.Trial registrationEudraCT 2009-012947-40 ISRCTN 97755073 ClinicalTrials.gov NCT01641016.
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- 2018
32. What we know and what we don't know about perinatal Zika virus infection: a systematic review
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Soriano-Arandes A, Rivero-Calle I, Nastouli E, Espiau M, Frick MA, Alarcon A, and Martinón-Torres F
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teratogen ,maternal-fetal infection transmission ,Zika virus ,Arbovirus infection - Abstract
Zika virus (ZIKV) infection has caused the most challenging worldwide infectious epidemic outbreak in recent months. ZIKV causes microcephaly and other congenital malformations. There is a need to perform updated systematic reviews on ZIKV infection periodically because this epidemic is bringing up new evidence with extraordinary speed. Areas covered: Evidence related to ZIKV infection in the gestational, perinatal, and early infant periods covering epidemiology, virology, pathogenesis, risk factors, time of infection during pregnancy, newborn symptoms, treatment, and vaccines. To this end, a search was performed using terms ['Zika'] AND ['Perinatal Infection'] OR ['Congenital Infection'] in the PubMed® international electronic database. Out of a total of 1,538 articles published until 30 November 2017, we finally assessed 106 articles articles that were relevant to the research areas included in this study. Expert commentary: ZIKV is a new teratogenic/neurotropic virus affecting fetuses. Many challenges are still far from being solved regarding the epidemiology, case definition, clinical and laboratory diagnosis, and preventive measures. An approach using 'omics' and new biomarkers for diagnosis, and a ZIKV-vaccine for treatment, might finally give us the tools to solve these challenges.
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- 2018
33. The CARMA study – children on early suppressive therapy: total HIV-1 DNA quantitation 12 years post ART initiation
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Foster, C., primary, Dominguez, S., additional, Tagarro, A., additional, Nastouli, E., additional, Palma, P., additional, Gkouleli, R., additional, Heaney, J., additional, Giaquinto, C., additional, Rossi, P., additional, and Rojo, P., additional
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- 2019
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34. A High HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project
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Yebra, G, Frampton, D, Cassarino, TG, Raffle, J, Hubb, J, Ferns, B, Kozlakidis, Z, Hayward, A, Kellam, P, Pillay, D, Clark, D, Nastouli, E, Leigh Brown, A, and On behalf of the ICONIC consortium
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on behalf of the ICONIC consortium - Abstract
Background & Methods The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef ) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospital and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. Results The pipeline generated sequences of at least 1Kb of length (median=7.4Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n=149, 40.8%) and C (n=77, 21.1%) and the circulating recombinant form CRF02_AG (n=32, 8.8%). We found 14 different CRFs (n=66, 18.1%) and multiple URFs (n=32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. Conclusions The initial analysis of genome sequences detected substantial hidden variability in the London HIV epidemic. Analysing full genome sequences, as opposed to only PR+RT, identified previously undetected recombinants. It provided a more reliable description of CRFs (that would be otherwise misclassified) and transmission clusters.
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- 2017
35. Report from the First EPIICAL (Early-treated Perinatally HIV-infected Individuals: Improving Children's Actual Life with Novel Immunotherapeutic Strategies) General Assembly meeting, 9–11 November 2017, Rome, Italy
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Zangari, P., primary, Palma, P., additional, Cotugno, N., additional, Rojo, P., additional, Tagarro, A., additional, Pepponi, I., additional, De Rossi, A., additional, Kuhn, L., additional, Pahwa, S., additional, Cameron, M., additional, Nastouli, E., additional, Watters, S., additional, Marceline, A.G., additional, McCoy, L.E., additional, Persaud, D., additional, Violari, A., additional, Chan, M., additional, Babiker, A.G., additional, Foster, C., additional, Ananworanich, J., additional, Giaquinto, C., additional, and Rossi, P., additional
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- 2018
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36. Neurocognition and quality of life after reinitiating antiretroviral therapy in children randomized to planned treatment interruption
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Ananworanich, J, Melvin, D, Amador, Jt, Childs, T, Medin, G, Boscolo, V, Compagnucci, A, Kanjanavanit, S, Montero, S, Gibb, Dm, PENTA 11 Study Group including Aboulker, J, Babiker, A, Belfrage, E, Bernardi, S, Bologna, R, Burger, D, Butler, K, Castelli Gattinara, G, Castro, H, Clayden, P, Cressey, T, Darbyshire, Jh, Debré, M, de Groot, R, della Negra, M, di Biagio, A, De Rossi, A, Duicelescu, D, Faye, A, Giaquinto, C, Giacomet, V, Grosch Wörner, I, Hainault, M, Klein, N, Lallemant, M, Levy, J, Lyall, H, Marczynska, M, Marques, L, Mardarescu, M, Mellado Peña MJ, Nadal, D, Nastouli, E, Naver, L, Niehues, T, Peckham, C, Pillay, D, Popieska, J, Ramos Amador JT, Rojo Conejo, P, Rosado, L, Rosso, R, Rudin, C, Scherpbier, Hj, Sharland, M, Stevanovic, M, Thorne, C, Tovo, Pier Angelo, Tudor Williams, G, Turkova, A, Valerius, N, Volokha, A, Walker, As, Welch, S, Wintergerst, U, Aboulker, Jp, Burger, Dm, Green, H, Harper, L, Mofenson, L, Moye, J, Saïdi, Y, Cressey, Tr, Jacqz Aigrain, E, Khoo, S, Regazzi, M, Tréluyer, Jm, Ngo Giang Huong, N, Muñoz Fernandez MA, Hill, C, Lepage, P, Pozniak, A, Vella, S, Chêne, G, Vesikari, T, Hadjou, G, Léonardo, S, Riault, Y, Bleier, J, Buck, L, Duong, T, Farrelly, L, Forcat, S, Harrison, L, Horton, J, Johnson, D, Taylor, C, Chalermpantmetagul, S, Peongjakta, R, Khamjakkaew, W, Than in at, K, Chailert, S, Jourdain, G, Le Coeur, S, Floret, D, Costanzo, P, Le Thi TT, Monpoux, F, Mellul, S, Caranta, I, Boudjoudi, N, Firtion, G, Denon, M, Charlemaine, E, Picard, F, Hellier, E, Heuninck, C, Damond, F, Alexandre, G, Tricoire, J, Antras, M, Lachendowier, C, Nicot, F, Krivine, A, Rivaux, D, Notheis, G, Strotmann, G, Schlieben, S, Rampon, O, Zanchetta, M, Ginocchio, F, Viscoli, C, Martino, A, Pontrelli, G, Baldassar, S, Concato, C, Mazza, A, Rossetti, G, Dobosz, S, Oldakowska, A, Popielska, J, Kaflik, M, Stanczak, J, Stanczack, G, Dyda, T, Kruk, M, González Tomé MI, Delgado García, R, Fernandez Gonzalez MT, Mellado Peña, M, Martín Fontelos, P, Garcia Mellado MI, Medina, Af, Ascencion, B, Garcia Bermejo, I, Navarro Gomez DM, Saavedra, J, Prieto, C, Jimenez, Jl, Garcia Torre, A, de José Gómez MI, García Rodriguez MC, Moreno Pérez, D, Núñez Cuadros, E, Asensi Botet, F, Otero Reigada, C, Pérez Tamarit MD, Vilalta, R, Molina Moreno JM, Rainer, T, Schupbach, J, Rutishauser, M, Bunupuradah, T, Butterworth, O, Phasomsap, C, Prasitsuebsai, W, Chuanjaroen, T, Jupimai, T, Ubolyam, S, Phanuphak, P, Puthanakit, T, Pancharoen, C, Mai, C, Namwong, T, Punsakoon, W, Payakachat, S, Chutima, D, Raksasang, M, Foster, C, Hamadache, D, Campbell, S, Newbould, C, Monrose, C, Abdulla, A, Walley, A, Patel, D, Kaye, S, Seery, P, Rankin, A, Wildfire, A, Novelli, V, Shingadia, D, Moshal, K, Flynn, J, Clapson, M, Allen, A, Spencer, L, Rackstraw, C, Ward, B, Parkes, K, Depala, M, Jacobsen, M, Poulsom, H, Barkley, L, Miah, J, Lurie, P, Keane, C, Mcmaster, P, Phipps, M, Orendi, J, Farmer, C, Liebeschuetz, S, Sodeinde, O, Wong, S, Bostock, V, Heath, Y, Scott, S, Gandhi, K, Lewis, P, Daglish, J, Miles, K, Summerhill, L, Subramaniam, B, Weiner, L, Famiglietti, M, Rana, S, Yu, P, Roa, J, Puga, A, Haerry, A., AII - Amsterdam institute for Infection and Immunity, Paediatric Infectious Diseases / Rheumatology / Immunology, and Global Health
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0301 basic medicine ,Male ,Pediatrics ,medicine.medical_specialty ,antiretroviral therapy ,children ,HIV ,neurocognition ,neurodevelopment ,quality of life ,treatment interruption ,Immunology and Allergy ,Immunology ,Infectious Diseases ,Adolescent ,lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4] ,Antiretroviral Therapy ,HIV Infections ,Standard score ,03 medical and health sciences ,0302 clinical medicine ,Cognition ,Acquired immunodeficiency syndrome (AIDS) ,Antiretroviral Therapy, Highly Active ,Memory span ,Medicine ,Humans ,Highly Active ,030212 general & internal medicine ,Child ,Wechsler Intelligence Scale for Children ,business.industry ,Wechsler Adult Intelligence Scale ,medicine.disease ,030112 virology ,lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4] ,Treatment Outcome ,Anti-Retroviral Agents ,Test score ,Mann–Whitney U test ,Quality of Life ,Female ,business ,Neurocognitive - Abstract
Item does not contain fulltext OBJECTIVE: Understanding the effects of antiretroviral treatment (ART) interruption on neurocognition and quality of life (QoL) are important for managing unplanned interruptions and planned interruptions in HIV cure research. DESIGN: Children previously randomized to continuous (continuous ART, n = 41) vs. planned treatment interruption (PTI, n = 47) in the Pediatric European Network for Treatment of AIDS (PENTA) 11 study were enrolled. At study end, PTI children resumed ART. At 1 and 2 years following study end, children were assessed by the coding, symbol search and digit span subtests of Wechsler Intelligence Scale for Children (6-16 years old) or Wechsler Adult Intelligence Scale (>/=17 years old) and by Pediatrics QoL questionnaires for physical and psychological QoL. Transformed scaled scores for neurocognition and mean standardized scores for QoL were compared between arms by t-test and Mann-Whitney U test, respectively. Scores indicating clinical concern were compared (
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- 2016
37. Weekends-off efavirenz-based antiretroviral therapy in HIV-infected children, adolescents, and young adults (BREATHER): a randomised, open-label, non-inferiority, phase 2/3 trial
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Butler, K, Turkova, A, Inshaw, J, Compagnucci, A, Kenny, J, Saidi, Y, Musiime, V, Nanduudu, A, Cressey, Tm, Chalermpantmetagul, Ks, Harper, L, Montero, S, Riault, Y, Bunupuradah, T, Volokha, A, Flynn, Pm, Bologna, R, Kizito, H, Ramos, Jt, Nastouli, E, Klein, N, Giaquinto, Carlo, Ford, D, Babiker, A, Gibb, Dm, and on behalf of the BREATHER trial team
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Infectious Diseases ,Epidemiology ,Immunology ,Virology - Published
- 2016
38. Caring for a patient with rabies: implications of the Milwaukee protocol for infection control and public health measures
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Lampejo, T., primary, Bruce, M., additional, Teall, A., additional, Dall'Antonia, M., additional, Crawley-Boevey, E., additional, Grant, P., additional, Polhill, S., additional, Pillay, D., additional, Brown, D., additional, Brown, M., additional, and Nastouli, E., additional
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- 2017
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39. The EPIICAL project: an emerging global collaboration to investigate\ud immunotherapeutic strategies in HIV-infected children
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Palma, P., Foster, C., Zangari, P., Yates, A., Cotugno, N., Klein, N., Luzuriaga, K., Pahwa, S., Nastouli, E., Gibb, D.M., Borkowsky, W., Bernardi, S., Calvez, V., Manno, E., Mora, Nadia, Compagnucci, A., Wahren, B., Muñoz-Fernández, M.Á., De Rossi, A., Ananworanich, J., Pillay, D., Giaquinto, C., and Rossi, P.
- Abstract
The EPIICAL (Early-treated Perinatally HIV-infected Individuals: Improving Children’s Actual Life with Novel Immunotherapeutic Strategies) project arises from the firm belief that perinatally infected children treated with suppressive antiretroviral therapy (ART) from early infancy represent the optimal population model in which to study novel immunotherapeutic strategies aimed at achieving ART-free remission. This is because HIV-infected infants treated within 2–3 months of life have a much reduced viral reservoir size, and rarely show HIV-specific immunity but preserve normal immune development. The goal of EPIICAL is the establishment of an international collaboration to develop a predictive platform using this model to select promising HIV therapeutic vaccine candidates, leading to prioritisation or deprioritisation of novel immunotherapeutic strategies. To establish this platform, the EPIICAL Consortium aims to: develop predictive models of virological and immunological dynamics associated with response to early ART and to treatment interruption using available data from existing cohorts/studies of early-treated perinatally HIV-infected children; optimise methodologies to better characterise immunological, virological and genomic correlates/profiles associated with viral control; test novel immunotherapeutic strategies using in vivo proof-of-concept (PoC) studies with the aim of inducing virological, immunological and transcriptomic correlates/profiles equivalent to those defined by the predictive model. This approach will strengthen the capacity for discovery, development and initial testing of new therapeutic vaccine strategies through the integrated efforts of leading international scientific groups, with the aim of improving the health of HIV-infected individuals.
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- 2015
40. HIV-1 Drug Resistance and Second-Line Treatment in Children Randomized to Switch at Low Versus Higher RNA Thresholds
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Harrison, L., Melvin, A., Fiscus, S., Saidi, Y., Nastouli, E., Harper, L., Compagnucci, A., Babiker, A., McKinney, R., Gibb, D., Tudor-Williams, G., Burger, D.M., et al., Harrison, L., Melvin, A., Fiscus, S., Saidi, Y., Nastouli, E., Harper, L., Compagnucci, A., Babiker, A., McKinney, R., Gibb, D., Tudor-Williams, G., Burger, D.M., and et al.
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Item does not contain fulltext, BACKGROUND: The PENPACT-1 trial compared virologic thresholds to determine when to switch to second-line antiretroviral therapy (ART). Using PENPACT-1 data, we aimed to describe HIV-1 drug resistance accumulation on first-line ART by virologic threshold. METHODS: PENPACT-1 had a 2 x 2 factorial design, randomizing HIV-infected children to start protease inhibitor (PI) versus nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART, and switch at a 1000 copies/mL versus 30,000 copies/mL threshold. Switch criteria were not achieving the threshold by week 24, confirmed rebound above the threshold thereafter, or Center for Disease Control and Prevention stage C event. Resistance tests were performed on samples >/=1000 copies/mL before switch, resuppression, and at 4-years/trial end. RESULTS: Sixty-seven children started PI-based ART and were randomized to switch at 1000 copies/mL (PI-1000), 64 PIs and 30,000 copies/mL (PI-30,000), 67 NNRTIs and 1000 copies/mL (NNRTI-1000), and 65 NNRTI and 30,000 copies/mL (NNRTI-30,000). Ninety-four (36%) children reached the 1000 copies/mL switch criteria during 5-year follow-up. In 30,000 copies/mL threshold arms, median time from 1000 to 30,000 copies/mL switch criteria was 58 (PI) versus 80 (NNRTI) weeks (P = 0.81). In NNRTI-30,000, more nucleoside reverse transcriptase inhibitor (NRTI) resistance mutations accumulated than other groups. NNRTI mutations were selected before switching at 1000 copies/mL (23% NNRTI-1000, 27% NNRTI-30,000). Sixty-two children started abacavir + lamivudine, 166 lamivudine + zidovudine or stavudine, and 35 other NRTIs. The abacavir + lamivudine group acquired fewest NRTI mutations. Of 60 switched to second-line, 79% PI-1000, 63% PI-30,000, 64% NNRTI-1000, and 100% NNRTI-30,000 were <400 copies/mL 24 weeks later. CONCLUSIONS: Children on first-line NNRTI-based ART who were randomized to switch at a higher virologic threshold developed the most resistance, yet resuppressed on second-line. An abacavi
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- 2015
41. P0478 : NKG2D-dependent cross-talk between NK cells and CD4 T cells in chronic hepatitis B
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Huang, W.-C., primary, Peppa, D., additional, Easom, N., additional, Tang, X.-Z., additional, Singh, H., additional, Fusai, G., additional, Rosenberg, W., additional, Ghosh, I., additional, Gilson, R., additional, Nastouli, E., additional, Gill, U., additional, Kennedy, P., additional, Chang, C.-W., additional, Trowsdale, J., additional, Toubert, A., additional, and Maini, M.K., additional
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- 2015
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42. Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017.
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Harvala, H., Frampton, D., Grant, P., Raffle, J., Ferns, R. B., Kozlakidis, Z., Kellam, P., Pillay, D., Hayward, A., and Nastouli, E.
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- 2017
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43. Pooled Specimens for HIV RNA Monitoring: Cheaper, but Is It Reliable?
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El Bouzidi, K., primary, Grant, P., additional, Edwards, S., additional, Benn, P., additional, Pillay, D., additional, Waters, L., additional, and Nastouli, E., additional
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- 2014
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44. PWE-140 Comparison Of 4 Serum Markers Panels of Fibrosis in Chc: Variants of the Hyaluronic Acid (HA) Assay Significantly Affect Their Diagnostic Performance: Abstract PWE-140 Table
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Tanwar, S, primary, Trembling, P M, additional, Hogan, B, additional, Ellis, E L, additional, Parkes, J, additional, Grant, P, additional, Nastouli, E, additional, Schuppan, D, additional, and Rosenberg, W M, additional
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- 2013
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45. PWE-138 Treatment Of Patients with Chronic Hepatitis C Genotype 1 and Advanced Fibrosis with Protease Inhibitors- Il28B Discordance Results in Early Viral Decline but Late Relapse: Abstract PWE-138 Table
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Tanwar, S, primary, Trembling, P M, additional, Hogan, B J, additional, Catt, J, additional, Glasgow, S, additional, Glover, N, additional, Ju, M, additional, Hains, M, additional, Moore, M T, additional, Velazquez, C, additional, Conibear, T, additional, Labbett, W, additional, Irish, D, additional, Macartney, M, additional, Haque, T, additional, Nastouli, E, additional, Smith, B, additional, Smith, P, additional, Suri, D, additional, Oben, J A, additional, Jacobs, M G, additional, Dusheiko, G M, additional, and Rosenberg, W M, additional
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- 2013
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46. 1224 TIMING AND CHARACTERISTICS OF DRUG RESISTANCE MUTATIONS (DRMS) IN CHRONIC HEPATITIS C PATIENTS DURING AND AFTER TREATMENT WITH PROTEASE INHIBITOR THERAPY AT A SINGLE CENTRE
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Velazquez, C., primary, Macartney, M., additional, Irish, D., additional, Tanwar, S., additional, Trembling, P., additional, Hogan, B., additional, Catt, J., additional, Glasgow, S., additional, Ju, M., additional, Moore, M.T., additional, Hains, M., additional, Smith, B., additional, Suri, D., additional, Jacobs, M.G., additional, Oben, J., additional, Smith, P., additional, Booth, C., additional, Bridge, S., additional, Garcia, A., additional, McCormick, A., additional, Nastouli, E., additional, Dusheiko, G.M., additional, Rosenberg, W., additional, and Haque, T., additional
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- 2013
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47. Erratum to “Quantitation of hepatitis delta virus using a single-step internally controlled real-time RT-qPCR and a full-length genomic RNA calibration standard” [J. Virol. Methods 179 (January (1)) (2012) 189–194]
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Ferns, R.B., primary, Nastouli, E., additional, and Garson, J.A., additional
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- 2013
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48. Development of the R263K Mutation to Dolutegravir in an HIV-1 Subtype D Virus Harboring 3 Class-Drug Resistance.
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Ahmed, N, Flavell, S, Ferns, B, Frampton, D, Edwards, S G, Miller, R F, Grant, P, Nastouli, E, and Gupta, R K
- Abstract
Dolutegravir (DTG), a second-generation integrase strand-transfer inhibitor (INSTI), is equivalent or superior to current non-nucleotide reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and first-generation INSTI-based antiretroviral regimens (ARVs). It has the potential to make big improvements in HIV control globally and within patients. This is perhaps the most "precious" HIV drug available. The integrase mutation R263K has been observed in tissue culture experiments and in patients treated with dolutegravir monotherapy in clinical trials. Globally, adherence and monitoring may be less than optimal and therefore DTG resistance more common. This is particularly important in low–middle-income countries, where patients may remain on failing regimens for longer periods of time and accumulate drug resistance. Data on this mutation in non–subtype B infections do not exist. We describe the first report of the R263K integrase mutation in a dolutegravir-exposed subtype D–infected individual with vertically acquired HIV. We have used deep sequencing of longitudinal samples to highlight the change in resistance over time while on a failing regimen. The case highlights that poorly adherent patients should not be offered dolutegravir even as part of a combination regimen and that protease inhibitors should be used preferentially. [ABSTRACT FROM AUTHOR]
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- 2019
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49. Report from the First EPIICAL (Early-treated Perinatally HIV-infected Individuals: Improving Children's Actual Life with Novel Immunotherapeutic Strategies) General Assembly meeting, 9-11 November 2017, Rome, Italy
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Zangari P, Paolo Palma, Cotugno N, Rojo P, Tagarro A, Pepponi I, De Rossi A, Kuhn L, Pahwa S, Cameron M, Nastouli E, Watters S, Ag, Marceline, Le, Mccoy, and Rossi P
50. The EPIICAL project: an emerging global collaboration to investigate immunotherapeutic strategies in HIV-infected children
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Paolo Palma, Foster C, Rojo P, Zangari P, Yates A, Cotugno N, Klein N, Luzuriaga K, Pahwa S, Nastouli E, Dm, Gibb, Borkowsky W, Bernardi S, Calvez V, Manno E, Mora N, Compagnucci A, Wahren B, Muñoz-Fernández M, and De Rossi A
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