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1.
Virus Evolution ; 8(veac080), 2022.
Article in English | CAB Abstracts | ID: covidwho-2051563

ABSTRACT

The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK and the imposition of new restrictions, in particular, the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages that preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically infected individual. We conclude that the latter provides the best explanation of the observed behaviour and dynamics of the variant, although the individual need not be immunocompromised, as persistently infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs and find that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations and a lack of the rapid evolutionary rate on its ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms), it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.

2.
HemaSphere ; 6:1985-1987, 2022.
Article in English | EMBASE | ID: covidwho-2032163

ABSTRACT

Background: Ibrutinib (IBR) is an oral covalent Bruton tyrosine kinase inhibitor (BTKi), licensed for treatment of relapsed or refractory mantle cell lymphoma (MCL). Under NHS interim Covid-19 agreements in England, IBR with or without rituximab (R) was approved for the frontline treatment for MCL patients (pts) as a safer alternative to conventional immunochemotherapy. Although recent phase 2 studies have reported high response rates in low-risk patients for this combination in the frontline setting, randomised phase 3 and real-world data are currently lacking. Aims: To describe the real-world response rates (overall response rate (ORR), complete response (CR) rate) and toxicity profile of IBR +/-R in adult patients with previously untreated MCL. Methods: Following institutional approval, adults commencing IBR +/-R for untreated MCL under interim Covid-19 arrangements were prospectively identified by contributing centres. Hospital records were interrogated for demographic, pathology, response, toxicity and survival data. ORR/CR were assessed per local investigator according to the Lugano criteria using CT and/or PET-CT. Results: Data were available for 66 pts (72.7% male, median age 71 years, range 41-89). Baseline demographic and clinical features are summarised in Table 1. 23/66 pts (34.8%) had high-risk disease (defined as presence of TP53 mutation/deletion, blastoid or pleomorphic variant MCL, or Ki67%/MiB-1 ≥30%). IBR starting dose was 560mg in 56/62 pts (90%) and was given with R in 22/64 pts (34%). At a median follow up of 8.7 months (m) (range 0-18.6), pts had received a median of 7 cycles of IBR. 19/60 pts (32%) required a dose reduction or delay in IBR treatment. New atrial fibrillation and grade ≥3 any-cause toxicity occurred in 3/59 pts (5.8%) and 8/57 (14.0%) respectively. For the whole population and high-risk pts only, ORR was 74.4% and 64.7% respectively (p=0.2379), with a median time to response of 3.8m, coinciding with the first response assessment scan. Seven pts (16.7%), of whom 2 had highrisk disease, attained CR at a median of 6.0m. ORR for pts receiving vs not receiving R were 84.2% and 66.7% respectively (p=0.1904). IBR was discontinued in 20/61 pts (32.8%) at a median time to discontinuation of 4.1m, due to progressive disease (PD, 19.7%), toxicity (4.9%), death (3.3%;1 pt each of Covid-19 and E. coli infection), pt choice (3.3%) and other unspecified reasons (1.6%). 15/66 pts (22.7%) overall and 7/23 (30.4%) with high-risk disease progressed on IBR at a median time to PD of 4.0m. No pts underwent autologous stem cell transplantation consolidation during the study period. 12/57 pts (21.1%) received second line treatment (R-chemotherapy n=7, Nordic MCL protocol n=2, VR-CAP n=2, pirtobrutinib n=1). Response to second line treatment was CR in 4/11 pts, PD in 7/11. Of the 2 Nordic-treated patients, 1 had CR after cycle 2 and 1 PD. Fourteen pts (21.2%) died during the follow up period, due to MCL (n=11), Covid-19 (n=2) and congestive cardiac failure (n=1). Overall survival was lower for patients with high-risk disease (HR 0.55, p=0.038). Image: Summary/Conclusion: In this real-world UK cohort of pts receiving first-line IBR +/-R for MCL, including older and high-risk pts, we report high ORR rates in a similar range to the phase II Geltamo IMCL-2015 study of combination IBR-R in an exclusively low-risk population. Documented CR rates were lower, possibly reflecting a low usage of rituximab in the Covid-19 pandemic as well as CT assessment of response. Treatment was generally well tolerated, with low rates of toxicityrelated treatment discontinuation. The study is ongoing.

3.
International Journal of Mental Health Nursing ; 31:28-29, 2022.
Article in English | Web of Science | ID: covidwho-2030760
4.
Multiple Sclerosis Journal ; 28(1_SUPPL):82-83, 2022.
Article in English | Web of Science | ID: covidwho-1866147
5.
McCrone, J. T.; Hill, V.; Bajaj, S.; Pena, R. E.; Lambert, B. C.; Inward, R.; Bhatt, S.; Volz, E.; Ruis, C.; Dellicour, S.; Baele, G.; Zarebski, A. E.; Sadilek, A.; Wu, N.; Schneider, A.; Ji, X.; Raghwani, J.; Jackson, B.; Colquhoun, R.; O'Toole, Á, Peacock, T. P.; Twohig, K.; Thelwall, S.; Dabrera, G.; Myers, R.; Faria, N. R.; Huber, C.; Bogoch, I. I.; Khan, K.; du Plessis, L.; Barrett, J. C.; Aanensen, D. M.; Barclay, W. S.; Chand, M.; Connor, T.; Loman, N. J.; Suchard, M. A.; Pybus, O. G.; Rambaut, A.; Kraemer, M. U. G.; Robson, S. C.; Connor, T. R.; Loman, N. J.; Golubchik, T.; Martinez Nunez, R. T.; Bonsall, D.; Rambaut, A.; Snell, L. B.; Livett, R.; Ludden, C.; Corden, S.; Nastouli, E.; Nebbia, G.; Johnston, I.; Lythgoe, K.; Estee Torok, M.; Goodfellow, I. G.; Prieto, J. A.; Saeed, K.; Jackson, D. K.; Houlihan, C.; Frampton, D.; Hamilton, W. L.; Witney, A. A.; Bucca, G.; Pope, C. F.; Moore, C.; Thomson, E. C.; Harrison, E. M.; Smith, C. P.; Rogan, F.; Beckwith, S. M.; Murray, A.; Singleton, D.; Eastick, K.; Sheridan, L. A.; Randell, P.; Jackson, L. M.; Ariani, C. V.; Gonçalves, S.; Fairley, D. J.; Loose, M. W.; Watkins, J.; Moses, S.; Nicholls, S.; Bull, M.; Amato, R.; Smith, D. L.; Aanensen, D. M.; Barrett, J. C.; Aggarwal, D.; Shepherd, J. G.; Curran, M. D.; Parmar, S.; Parker, M. D.; Williams, C.; Glaysher, S.; Underwood, A. P.; Bashton, M.; Pacchiarini, N.; Loveson, K. F.; Byott, M.; Carabelli, A. M.; Templeton, K. E.; de Silva, T. I.; Wang, D.; Langford, C. F.; Sillitoe, J.; Gunson, R. N.; Cottrell, S.; O'Grady, J.; Kwiatkowski, D.; Lillie, P. J.; Cortes, N.; Moore, N.; Thomas, C.; Burns, P. J.; Mahungu, T. W.; Liggett, S.; Beckett, A. H.; Holden, M. T. G.; Levett, L. J.; Osman, H.; Hassan-Ibrahim, M. O.; Simpson, D. A.; Chand, M.; Gupta, R. K.; Darby, A. C.; Paterson, S.; Pybus, O. G.; Volz, E. M.; de Angelis, D.; Robertson, D. L.; Page, A. J.; Martincorena, I.; Aigrain, L.; Bassett, A. R.; Wong, N.; Taha, Y.; Erkiert, M. J.; Spencer Chapman, M. H.; Dewar, R.; McHugh, M. P.; Mookerjee, S.; Aplin, S.; Harvey, M.; Sass, T.; Umpleby, H.; Wheeler, H.; McKenna, J. P.; Warne, B.; Taylor, J. F.; Chaudhry, Y.; Izuagbe, R.; Jahun, A. S.; Young, G. R.; McMurray, C.; McCann, C. M.; Nelson, A.; Elliott, S.; Lowe, H.; Price, A.; Crown, M. R.; Rey, S.; Roy, S.; Temperton, B.; Shaaban, S.; Hesketh, A. R.; Laing, K. G.; Monahan, I. M.; Heaney, J.; Pelosi, E.; Silviera, S.; Wilson-Davies, E.; Fryer, H.; Adams, H.; du Plessis, L.; Johnson, R.; Harvey, W. T.; Hughes, J.; Orton, R. J.; Spurgin, L. G.; Bourgeois, Y.; Ruis, C.; O'Toole, Á, Gourtovaia, M.; Sanderson, T.; Fraser, C.; Edgeworth, J.; Breuer, J.; Michell, S. L.; Todd, J. A.; John, M.; Buck, D.; Gajee, K.; Kay, G. L.; Peacock, S. J.; Heyburn, D.; Kitchman, K.; McNally, A.; Pritchard, D. T.; Dervisevic, S.; Muir, P.; Robinson, E.; Vipond, B. B.; Ramadan, N. A.; Jeanes, C.; Weldon, D.; Catalan, J.; Jones, N.; da Silva Filipe, A.; Williams, C.; Fuchs, M.; Miskelly, J.; Jeffries, A. R.; Oliver, K.; Park, N. R.; Ash, A.; Koshy, C.; Barrow, M.; Buchan, S. L.; Mantzouratou, A.; Clark, G.; Holmes, C. W.; Campbell, S.; Davis, T.; Tan, N. K.; Brown, J. R.; Harris, K. A.; Kidd, S. P.; Grant, P. R.; Xu-McCrae, L.; Cox, A.; Madona, P.; Pond, M.; Randell, P. A.; Withell, K. T.; Williams, C.; Graham, C.; Denton-Smith, R.; Swindells, E.; Turnbull, R.; Sloan, T. J.; Bosworth, A.; Hutchings, S.; Pymont, H. M.; Casey, A.; Ratcliffe, L.; Jones, C. R.; Knight, B. A.; Haque, T.; Hart, J.; Irish-Tavares, D.; Witele, E.; Mower, C.; Watson, L. K.; Collins, J.; Eltringham, G.; Crudgington, D.; Macklin, B.; Iturriza-Gomara, M.; Lucaci, A. O.; McClure, P. C.; Carlile, M.; Holmes, N.; Moore, C.; Storey, N.; Rooke, S.; Yebra, G.; Craine, N.; Perry, M.; Alikhan, N. F.; Bridgett, S.; Cook, K. F.; Fearn, C.; Goudarzi, S.; Lyons, R. A.; Williams, T.; Haldenby, S. T.; Durham, J.; Leonard, S.; Davies, R. M.; Batra, R.; Blane, B.; Spyer, M. J.; Smith, P.; Yavus, M.; Williams, R. J.; Mahanama, A. I. K.; Samaraweera, B.; Girgis, S. T.; Hansford, S. E.; Green, A.; Beaver, C.; Bellis, K. L.; Dorman, M. J.; 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, M. L.; Stockton, J.; Henderson, J. H.; Hollis, A.; Stanley, W.; Yew, W. C.; Myers, R.; Thornton, A.; Adams, A.; Annett, T.; Asad, H.; Birchley, A.; Coombes, J.; Evans, J. M.; 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, A. J.; Williams, C. A.; Kermack, L. M.; Foulkes, B. H.; Gallis, M.; Hornsby, H. R.; Louka, S. F.; Pohare, M.; Wolverson, P.; Zhang, P.; MacIntyre-Cockett, G.; Trebes, A.; Moll, R. J.; Ferguson, L.; Goldstein, E. J.; Maclean, A.; Tomb, R.; Starinskij, I.; Thomson, L.; Southgate, J.; Kraemer, M. U. G.; Raghwani, J.; Zarebski, A. E.; Boyd, O.; Geidelberg, L.; Illingworth, C. J.; Jackson, C.; Pascall, D.; Vattipally, S.; Freeman, T. M.; Hsu, S. N.; Lindsey, B. B.; James, K.; Lewis, K.; Tonkin-Hill, G.; Tovar-Corona, J. M.; Cox, M.; Abudahab, K.; Menegazzo, M.; Taylor, B. E. W.; Yeats, C. A.; Mukaddas, A.; Wright, D. W.; de Oliveira Martins, L.; Colquhoun, R.; Hill, V.; Jackson, B.; McCrone, J. T.; Medd, N.; Scher, E.; Keatley, J. P.; Curran, T.; Morgan, S.; Maxwell, P.; Smith, K.; Eldirdiri, S.; Kenyon, A.; Holmes, A. H.; Price, J. R.; Wyatt, T.; Mather, A. E.; Skvortsov, T.; Hartley, J. A.; Guest, M.; Kitchen, C.; Merrick, I.; Munn, R.; Bertolusso, B.; Lynch, J.; Vernet, G.; Kirk, S.; Wastnedge, E.; Stanley, R.; Idle, G.; Bradley, D. T.; Poyner, J.; Mori, M.; Jones, O.; Wright, V.; Brooks, E.; Churcher, C. M.; Fragakis, M.; Galai, K.; Jermy, A.; Judges, S.; McManus, G. M.; Smith, K. S.; Westwick, E.; Attwood, S. W.; 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, V. M.; Howson-Wells, H. C.; Joseph, A.; Khakh, M.; Lister, M. M.; Bird, P. W.; Fallon, K.; Helmer, T.; McMurray, C. L.; Odedra, M.; Shaw, J.; Tang, J. W.; Willford, N. J.; Blakey, V.; Raviprakash, V.; Sheriff, N.; Williams, L. A.; Feltwell, T.; Bedford, L.; Cargill, J. S.; Hughes, W.; Moore, J.; Stonehouse, S.; Atkinson, L.; Lee, J. C. D.; Shah, D.; Alcolea-Medina, 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, S. S. Y.; George, R. P.; Machin, N. W.; 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.; et al..
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326827

ABSTRACT

The Delta variant of concern of SARS-CoV-2 has spread globally causing large outbreaks and resurgences of COVID-19 cases1-3. The emergence of Delta in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions4,5. Here we analyse 52,992 Delta genomes from England in combination with 93,649 global genomes to reconstruct the emergence of Delta, and quantify its introduction to and regional dissemination across England, in the context of changing travel and social restrictions. Through analysis of human movement, contact tracing, and virus genomic data, we find that the focus of geographic expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced >1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers from India reduced onward transmission from importations;however the transmission chains that later dominated the Delta wave in England had been already seeded before restrictions were introduced. In England, increasing inter-regional travel drove Delta's nationwide dissemination, with some cities receiving >2,000 observable lineage introductions from other regions. Subsequently, increased levels of local population mixing, not the number of importations, was associated with faster relative growth of Delta. Among US states, we find that regions that previously experienced large waves also had faster Delta growth rates, and a model including interactions between immunity and human behaviour could accurately predict the rise of Delta there. Delta's invasion dynamics depended on fine scale spatial heterogeneity in immunity and contact patterns and our findings will inform optimal spatial interventions to reduce transmission of current and future VOCs such as Omicron.

6.
Robson, S. C.; Connor, T. R.; Loman, N. J.; Golubchik, T.; Nunez, R. T. M.; Bonsall, D.; Rambaut, A.; Snell, L. B.; Livett, R.; Ludden, C.; Corden, S.; Nastouli, E.; Nebbia, G.; Johnston, I.; Lythgoe, K.; Torok, M. E.; Goodfellow, I. G.; Prieto, J. A.; Saeed, K.; Jackson, D. K.; Houlihan, C.; Frampton, D.; Hamilton, W. L.; Witney, A. A.; Bucca, G.; Pope, C. F.; Moore, C.; Thomson, E. C.; Harrison, E. M.; Smith, C. P.; Rogan, F.; Beckwith, S. M.; Murray, A.; Singleton, D.; Eastick, K.; Sheridan, L. A.; Randell, P.; Jackson, L. M.; Ariani, C. V.; Gonçalves, S.; Fairley, D. J.; Loose, M. W.; Watkins, J.; Moses, S.; Nicholls, S.; Bull, M.; Amato, R.; Smith, D. L.; Aanensen, D. M.; Barrett, J. C.; Aggarwal, D.; Shepherd, J. G.; Curran, M. D.; Parmar, S.; Parker, M. D.; Williams, C.; Glaysher, S.; Underwood, A. P.; Bashton, M.; Loveson, K. F.; Byott, M.; Pacchiarini, N.; Carabelli, A. M.; Templeton, K. E.; de Silva, T. I.; Wang, D.; Langford, C. F.; Sillitoe, J.; Gunson, R. N.; Cottrell, S.; O'Grady, J.; Kwiatkowski, D.; Lillie, P. J.; Cortes, N.; Moore, N.; Thomas, C.; Burns, P. J.; Mahungu, T. W.; Liggett, S.; Beckett, A. H.; Holden, M. T. G.; Levett, L. J.; Osman, H.; Hassan-Ibrahim, M. O.; Simpson, D. A.; Chand, M.; Gupta, R. K.; Darby, A. C.; Paterson, S.; Pybus, O. G.; Volz, E. M.; de Angelis, D.; Robertson, D. L.; Page, A. J.; Martincorena, I.; Aigrain, L.; Bassett, A. R.; Wong, N.; Taha, Y.; Erkiert, M. J.; Chapman, M. H. S.; Dewar, R.; McHugh, M. P.; Mookerjee, S.; Aplin, S.; Harvey, M.; Sass, T.; Umpleby, H.; Wheeler, H.; McKenna, J. P.; Warne, B.; Taylor, J. F.; Chaudhry, Y.; Izuagbe, R.; Jahun, A. S.; Young, G. R.; McMurray, C.; McCann, C. M.; Nelson, A.; Elliott, S.; Lowe, H.; Price, A.; Crown, M. R.; Rey, S.; Roy, S.; Temperton, B.; Shaaban, S.; Hesketh, A. R.; Laing, K. G.; Monahan, I. M.; Heaney, J.; Pelosi, E.; Silviera, S.; Wilson-Davies, E.; Adams, H.; du Plessis, L.; Johnson, R.; Harvey, W. T.; Hughes, J.; Orton, R. J.; Spurgin, L. G.; Bourgeois, Y.; Ruis, C.; O'Toole, Á, Gourtovaia, M.; Sanderson, T.; Fraser, C.; Edgeworth, J.; Breuer, J.; Michell, S. L.; Todd, J. A.; John, M.; Buck, D.; Gajee, K.; Kay, G. L.; Peacock, S. J.; Heyburn, D.; Kitchman, K.; McNally, A.; Pritchard, D. T.; Dervisevic, S.; Muir, P.; Robinson, E.; Vipond, B. B.; Ramadan, N. A.; Jeanes, C.; Weldon, D.; Catalan, J.; Jones, N.; da Silva Filipe, A.; Williams, C.; Fuchs, M.; Miskelly, J.; Jeffries, A. R.; Oliver, K.; Park, N. R.; Ash, A.; Koshy, C.; Barrow, M.; Buchan, S. L.; Mantzouratou, A.; Clark, G.; Holmes, C. W.; Campbell, S.; Davis, T.; Tan, N. K.; Brown, J. R.; Harris, K. A.; Kidd, S. P.; Grant, P. R.; Xu-McCrae, L.; Cox, A.; Madona, P.; Pond, M.; Randell, P. A.; Withell, K. T.; Williams, C.; Graham, C.; Denton-Smith, R.; Swindells, E.; Turnbull, R.; Sloan, T. J.; Bosworth, A.; Hutchings, S.; Pymont, H. M.; Casey, A.; Ratcliffe, L.; Jones, C. R.; Knight, B. A.; Haque, T.; Hart, J.; Irish-Tavares, D.; Witele, E.; Mower, C.; Watson, L. K.; Collins, J.; Eltringham, G.; Crudgington, D.; Macklin, B.; Iturriza-Gomara, M.; Lucaci, A. O.; McClure, P. C.; Carlile, M.; Holmes, N.; Moore, C.; Storey, N.; Rooke, S.; Yebra, G.; Craine, N.; Perry, M.; Fearn, N. C.; Goudarzi, S.; Lyons, R. A.; Williams, T.; Haldenby, S. T.; Durham, J.; Leonard, S.; Davies, R. M.; Batra, R.; Blane, B.; Spyer, M. J.; Smith, P.; Yavus, M.; Williams, R. J.; Mahanama, A. I. K.; Samaraweera, B.; Girgis, S. T.; Hansford, S. E.; Green, A.; Beaver, C.; Bellis, K. L.; Dorman, M. J.; 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, M. L.; Stockton, J.; Henderson, J. H.; Hollis, A.; Stanley, W.; Yew, W. C.; Myers, R.; Thornton, A.; Adams, A.; Annett, T.; Asad, H.; Birchley, A.; Coombes, J.; Evans, J. M.; 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, A. J.; Williams, C. A.; Kermack, L. M.; Foulkes, B. H.; Gallis, M.; Hornsby, H. R.; Louka, S. F.; Pohare, M.; Wolverson, P.; Zhang, P.; MacIntyre-Cockett, G.; Trebes, A.; Moll, R. J.; Ferguson, L.; Goldstein, E. J.; Maclean, A.; Tomb, R.; Starinskij, I.; Thomson, L.; Southgate, J.; Kraemer, M. U. G.; Raghwani, J.; Zarebski, A. E.; Boyd, O.; Geidelberg, L.; Illingworth, C. J.; Jackson, C.; Pascall, D.; Vattipally, S.; Freeman, T. M.; Hsu, S. N.; Lindsey, B. B.; James, K.; Lewis, K.; Tonkin-Hill, G.; Tovar-Corona, J. M.; Cox, M.; Abudahab, K.; Menegazzo, M.; Taylor, B. E. W.; Yeats, C. A.; Mukaddas, A.; Wright, D. W.; de Oliveira Martins, L.; Colquhoun, R.; Hill, V.; Jackson, B.; McCrone, J. T.; Medd, N.; Scher, E.; Keatley, J. P.; Curran, T.; Morgan, S.; Maxwell, P.; Smith, K.; Eldirdiri, S.; Kenyon, A.; Holmes, A. H.; Price, J. R.; Wyatt, T.; Mather, A. E.; Skvortsov, T.; Hartley, J. A.; Guest, M.; Kitchen, C.; Merrick, I.; Munn, R.; Bertolusso, B.; Lynch, J.; Vernet, G.; Kirk, S.; Wastnedge, E.; Stanley, R.; Idle, G.; Bradley, D. T.; Poyner, J.; Mori, M.; Jones, O.; Wright, V.; Brooks, E.; Churcher, C. M.; Fragakis, M.; Galai, K.; Jermy, A.; Judges, S.; McManus, G. M.; Smith, K. S.; Westwick, E.; Attwood, S. W.; 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, V. M.; Howson-Wells, H. C.; Joseph, A.; Khakh, M.; Lister, M. M.; Bird, P. W.; Fallon, K.; Helmer, T.; McMurray, C. L.; Odedra, M.; Shaw, J.; Tang, J. W.; Willford, N. J.; Blakey, V.; Raviprakash, V.; Sheriff, N.; Williams, L. A.; Feltwell, T.; Bedford, L.; Cargill, J. S.; Hughes, W.; Moore, J.; Stonehouse, S.; Atkinson, L.; Lee, J. C. D.; 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, K. El, Lampejo, T.; Sudhanva, M.; Breen, C.; Sluga, G.; Ahmad, S. S. Y.; George, R. P.; Machin, N. W.; 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, D. G.; Raza, M.; Baker, P.; Bonner, S.; Essex, S.; Murray, L. J.; Lawton, A. I.; Burton-Fanning, S.; Payne, B. A. I.; Waugh, S.; Gomes, A. N.; Kimuli, M.; Murray, D. R.; 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, H. L.; Maftei, L.; Mondani, M.; Chaloner, N. J.; Cogger, B. J.; Easton, L. J.; Huckson, H.; Lewis, J.; Lowdon, S.; Malone, C. S.; Munemo, F.; Mutingwende, M.; et al..
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326811

ABSTRACT

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

7.
Journal of biomolecular techniques : JBT ; 32(3):180-185, 2021.
Article in English | EuropePMC | ID: covidwho-1619311

ABSTRACT

Frequent and accessible testing is a critical tool to contain the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To develop low-cost rapid tests, many researchers have used reverse transcription loop-mediated isothermal amplification (RT-LAMP) with fluorescent readout. Fluorescent LAMP-based assays can be performed using cost-effective, portable, isothermal instruments that are simpler to use and more rugged than polymerase chain reaction (PCR) instruments. However, false-positive results due to nonspecific priming and amplification have been reported for a number of LAMP-based assays. In this report, we implemented a RT-LAMP assay for SARS-CoV-2 on a portable isothermal fluorimeter and a traditional thermocycler;nonspecific amplification was not observed using the thermocycler but did occur frequently with the isothermal fluorimeter. We explored 4 strategies to optimize the SARS-CoV-2 RT-LAMP assay for use with an isothermal fluorimeter and found that overlaying the reaction with mineral oil and including the enzyme Tte UvrD helicase in the reaction eliminated the problem. We anticipate these results and strategies will be relevant for use with a wide range of portable isothermal instruments.

12.
American Journal of Respiratory and Critical Care Medicine ; 203(9):2, 2021.
Article in English | Web of Science | ID: covidwho-1407481
13.
Journal of General Internal Medicine ; 36(SUPPL 1):S359-S359, 2021.
Article in English | Web of Science | ID: covidwho-1349049
14.
Journal of Burn Care and Research ; 42(SUPPL 1):S164, 2021.
Article in English | EMBASE | ID: covidwho-1288073

ABSTRACT

Introduction: 2020 brought numerous challenges for burn survivors and their families. This project assessed the impact of two major global / national phenomena, specifically the impact of a) COVID-19 and b) local / community / national actions around racism and policing on child and youth burn survivors and their families. Methods: Our burn camp program moved to a virtual format for 2020. Campers (ages 8-18) and their caregivers / parents completed questionnaires about their year, rating and specifying the personal impacts of these phenomena. They rated how their year has been overall and selected 'what has helped you get through tough times'. 47 campers and 47 caregivers / parents participated. Results: Impact of COVID-19 The majority of youth rated the impact of COVID-19 as 'somewhat' to 'highly' (78%), while the majority of caregivers rated 'somewhat' (64%). Campers and caregivers identified the following impacts most often and to similar degrees: Online school/virtual learning, Friends/Social, Sports/Activities, Quarantine, Isolation, Worries, Quality time with family. Caregivers also highlighted: Getting creative at home and Uncertainties. Impact of local / community / national actions around racism and policing on you and your family The majority of campers and caregivers rated the impact as 'Somewhat', 'Very Little' or 'Not Impacted' (86%), although participants rating higher impact also provided moving personal experiences. What has helped you get through tough times this year Over 85% of campers and caregivers / parents rated their year overall as 'OK' or 'Pretty Good'. Campers and caregivers endorsed Family, Friends, Faith, and What I learned recovering from my burn injury as factors helping them get through tough times. Conclusions: Children, youth, and families who have experienced a burn injury report both negative and positive impacts from the global and national phenomena of COVID-19 and local / community / national actions around racism and policing. Not all youth and families are equally impacted. Family and friends were the greatest sources of support during tough times. One burn survivor family indicated that what they learned recovering from burn injury has helped them through this challenging year-'I have learned to just adapt and change because anything can happen at any point.' Most burn survivors and their families indicate the year has been 'OK' or 'pretty good'. Connection through burn camp provided the opportunity to share the impacts, but also the strengths and resiliencies in our burn community.

15.
American Journal of Respiratory and Critical Care Medicine ; 203(9), 2021.
Article in English | EMBASE | ID: covidwho-1277797

ABSTRACT

RATIONALE: Although lung cancer screening (LCS) uptake has increased to 5-16% nationally, screening initiation and adherence rates are threatened by the ongoing COVID-19 pandemic. Consistent with guidelines from a CHEST expert panel, our LCS program deferred new and annual low-dose CT (LDCT) screens during the pandemic's spring surge. Upon resuming screening, we pivoted to shared decision-making (SDM) via telemedicine. We characterized how these changes in screening implementation impacted our LCS volume and adherence. METHODS: We measured LCS patient- and LDCT scan-related volumes through our centralized program during pre-COVID (2019), deferral (March 18-May 18, 2020), and follow-up (May 18-November 18, 2020) to measure 3 outcomes: 1). Monthly volume of LDCTs in 2020 compared to 2019, 2). LDCT completion rate for SDM via telemedicine during the follow-up period, and 3). Adherence rates among patients due for LDCT during the deferral period and returned in the subsequent 6 months, compared to adherence among pre-COVID LCS patients. Adherence was defined as a subsequent CT within 11-18 months of a Lung-RADS 1 or 2 result, 4-8 months for Lung-RADS 3, and 2.5-4.5 months for Lung-RADS 4 patients recommended for 3-month follow-up. RESULTS: Monthly scan volume in our LCS program decreased during the COVID-19 first wave but increased following resumption of screening, and by August, the number of LDCTs exceeded 2019 (Figure). The number of patients screened between May-November 2020 and May-November 2019 was comparable (491 and 505 patients, respectively). However, the frequency of patients returning for follow-up was higher in 2020 compared with 2019 (62.1% vs. 46.3%). Following implementation of telemedicine, the screening completion rate decreased during May-November 2020, with 88.6% of patients (435/491) completing SDM but not LDCT, compared with 100% between May-November 2019. During the deferral period March-May 2020, 124 patients were due for a follow-up scan, and 54 (43.5%) received their scan within the study period. In comparison, 60.3% due for follow-up during the same period in 2019 completed their scan. CONCLUSIONS: Maintaining screening adherence has become a focus for many LCS programs. We observed that following the spring surge of the COVID-19 pandemic, the frequency of returning patients was greater than that of new patients initiating screening. Conducting SDM via telemedicine may introduce a barrier to LCS completion. Adherence rates decreased from 2019, with the lowest rates among Lung-RADS 3 patients due for a 6-month follow-up. Additional research should test LCS implementation strategies to improve adherence during the COVID-19 pandemic.

16.
American Journal of Respiratory and Critical Care Medicine ; 203(9), 2021.
Article in English | EMBASE | ID: covidwho-1277135

ABSTRACT

Background: ARICA (AdheRence to Inhaled Corticosteroids in Asthma) is a comprehensive inhaled corticosteroid (ICS) adherence intervention designed to remediate each patient's unique reason for not taking their ICS as prescribed. Objective: The primary objective was to evaluate the feasibility and acceptability of implementing ARICA in a health system. Methods: 29 Black adults who self-reported ICS nonadherence, had uncontrolled persistent asthma, and a Duke Primary Care provider visit within the past 3 years were randomly assigned to intervention (N=15) or control (N=14) in a waitlist randomized controlled pilot trial. Participants were assigned to 1-3 ARICA components based on adherence barriers selected by participants;including, an asthma selfmanagement program, financial assistance referral program, and/or objective feedback on asthma control. All participants received weekly texts and emails dispelling asthma myths. Activities were delivered virtually due to COVID-19. Primary outcomes were feasibility (e.g., process outcomes) and acceptability (e.g., patient exit interviews) measured at 12 weeks. Secondary asthma (e.g., ACT) and adherence outcomes (e.g., DOSEnonadherence) were measured. Results: Most participants were female (N=27, 93%), nonsmokers (N=26, 70%), poorly controlled with ACT <15 (N=14, 48%), and mean age 49.8. Most (N=14, 93%) completed all assigned intervention components and reported mean 4.8 of 5 on Weiner feasibility, acceptability, and appropriateness of intervention. The intervention group had a greater and statistically significant improvement in ACT (Δ-3.5, CI 6.0,0.96) and Marks AQLQ (Δ 11.5, CI 5.5,17.4) when compared to changes in the control ACT (Δ-2.5, CI-5.2,0.05) and Marks AQLQ (Δ5.7, CI-1.3,12.8), respectively. The improvement in ACT in the intervention group was clinically significant. The intervention group also reported a greater and statistically significant decrease in degree of nonadherence (DOSE Δ 0.74, CI 0.2,1.3) than control (DOSE Δ 0.36, CI-0.04,0.75) and a greater decrease in the number of adherence barriers identified in the intervention group (Δ 2.1, CI 1.2,3.0) versus control group (Δ1.6, CI 0.3,3.0). The study was not powered to assess a statistically significant change between groups. Conclusion: The implementation of ARICA in a cohort of Black adults was feasibly deployed in a health system and acceptable to participants. There was a trend in improvement in asthma control and asthma quality of life and a decrease in nonadherence and barriers to adherence.

17.
American Journal of Respiratory and Critical Care Medicine ; 203(9), 2021.
Article in English | EMBASE | ID: covidwho-1277038

ABSTRACT

RATIONALE: During the COVID-19 pandemic's spring surge, many lung cancer screening (LCS) programs delayed scans. Upon resuming screening, programs pivoted to telemedicine for shared decision-making (SDM) to minimize COVID transmission risks. This can lead to a cascade of alterations in LCS implementation, exacerbating disparities in screening. We hypothesize these changes have altered the sociodemographic characteristics of our LCS population. METHODS: At our institution in Philadelphia, LCS was deferred beginning March 18, 2020. We analyzed data from patients living in Philadelphia undergoing LCS through our centralized program upon resumption of screening on May 18 and the subsequent 6 months. Patient-level sociodemographic characteristics were compared with a “Pre-COVID” cohort screened May-November 2019. Geospatial analysis was performed for neighborhood-level internet access among patients receiving SDM inperson vs. telemedicine. RESULTS: The 408 patients screened after program reopening had a mean age of 64.2±5.8 years, 246 patients (60.3%) were female, 204 (50.1%) were White and 196 (48.2%) were Black/African-American. Over half were current smokers (n=224, 54.9%), and 172 patients (42.2%) had COPD. Compared with the Pre-COVID cohort, the Post-reopening cohort had no statistically significant differences in age, sex, race, smoking status or intensity, BMI, COPD, personal or family history of lung cancer, or insurance status. Education was significantly different between the two groups, with the Post-reopening cohort comprised of a lower percentage of patients with <HS education (16.9% vs. 11.3%), a greater frequency of patients with a HS diploma (42.6% vs. 46.1%), and fewer patients with education beyond HS (39.2% vs. 35.2%) (p<0.001). There was no significant difference in mean PLCOm2012 lung cancer risk (6.5±5.6% vs. 6.4±5.7%) or frequency of positive screens (≥Lung-RADS 3;8.9% vs. 8.4%). After excluding follow-up patients, education remained the only significant difference between groups. Analysis of neighborhood-level household internet access revealed no difference in the number of patients from census tracts with the lowest availability of household internet. Among the 15 census tracts with the greatest loss of patients from Pre-COVID to Postreopening, only 26.7% were in the highest quartile of internet deficit. CONCLUSIONS: LCS disparities can include disproportionate underscreening of individuals who are Black/African-American, live in rural areas, or have low socioeconomic status. Despite significant changes to our LCS program's workflow, the only significant difference between our Pre-COVID and Post-reopening cohorts was education level. Future research should be directed toward developing strategies to support LCS-eligible patients with low levels of education in the era of telemedicine.

18.
Open Forum Infectious Diseases ; 7(SUPPL 1):S251, 2020.
Article in English | EMBASE | ID: covidwho-1185729

ABSTRACT

Background: Acute kidney injury (AKI) is a complication that has been described among severely ill patients with COVID-19 and may be more common in those with underlying chronic kidney disease (CKD). Some patients with AKI require renal replacement therapy (RRT), including continuous RRT (CRRT). During the COVID-19 pandemic, some US areas experienced CRRT supply shortages. We sought to describe the percent of hospitalized COVID-19 patients who developed AKI or needed RRT to inform patient care and resource planning. Methods: We searched for studies in the literature and public health investigations that described CKD, AKI, and/or RRT in COVID-19 patients from January 2020 onward. Studies were excluded if no CKD, AKI, or RRT information was provided. We abstracted counts of hospitalized COVID-19 patients, including those admitted to intensive care units (ICU) who developed AKI, underwent RRT, and/or had CKD. Data were pooled across cohorts by geographic region with available data (US, China, or United Kingdom [UK]). We compared proportions using Chi-square tests. Results: A total of 311 studies were identified;23 studies (US n=11;China n=11;UK n=1) that described kidney disease and/or kidney-related outcomes in hospitalized COVID-19 patients were included. Underlying CKD prevalence was higher in US cohorts (10.3%) compared with China (2.5%) or UK (1.5%) (p< 0.0001). AKI was markedly higher among hospitalized (31.3% vs. 6.4%;p < 0 .001) and ICU patients (55.4% vs. 18.2%;p< 0.0001) in the US compared to China. The percent of ICU patients requiring RRT in the US (16.8%) was significantly different from that reported in China (12.5%) and the UK (23.9%) (p< 0.0001). Limitations include differences in CKD and RRT definitions across studies. Conclusion: AKI is a frequent outcome among US COVID-19 patients, affecting almost one third of hospitalized and more than half of ICU patients. AKI was reported more frequently in the US than China. The percent of ICU patients who received RRT was higher in the US and UK than in China. Understanding the occurrence of kidney-related outcomes among patients with COVID-19 including the impact of underlying CKD and regional practice variations is essential for healthcare systems to successfully plan for RRT needs during the pandemic.

19.
Journal of Change Management ; 2020.
Article in English | Scopus | ID: covidwho-1042643

ABSTRACT

A major assumption for both leadership researchers and practitioners is that the relationship between leaders and followers is the pivotal concern for leadership. Viewing leadership through the lens of responsibility, however, changes the pivotal relationship substantially. The principal relationship concern becomes the relationship between leaders and their stakeholders. To better understand this relationship the article seeks to explore the question: Leadership for what purpose? The article offers an initial answer to this question by looking at the responsibilities of those who lead in the corporate world. In particular, we argue that leaders need to give primary attention to what they seek to achieve, why, for whom, and where. In this way the article seeks to (re)centre the concerns of leadership scholarship to address the challenges and responsibilities of those who seek to lead. The article offers an inter-disciplinary theory rooted in an inter-complementary perspective on capitalism, purpose and responsibility that enables organizational leaders to understand how the fiduciary duty of generating value for shareholders can be aligned with other stakeholder interests including employees, communities, societies, the environment and indeed humanity. This theory we describe as the ‘The theory of Good Dividends’. MAD statement: This article seeks to Make a Difference (MAD) through challenging how we consider leadership in order to address the perfect storm of societal challenges that threaten humanity. In the recent past, our most pressing challenge was Climate Change;but this has been overshadowed by Covid 19. And this too will be overshadowed by other more compelling challenges. Corporate leadership has the power and influence to address and tackle these challenges. The article argues that leadership scholars need to fundamentally shift our focus away from the leader-follower relationship that has traditionally dominated our field of inquiry to the leader-stakeholder relationship. © 2021 Informa UK Limited, trading as Taylor & Francis Group.

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