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27. Comparison of Postoperative Pain After the Utilization of Different File Systems in Single Visit Endodontics

Author

Bhardwaj A, Gupta RK, Ates AA, Wahjuningrum DA, Arıcan B, AlOmari T, Luke AM, and Pawar AM

Subjects
postoperative pain, protaper next, randomized clinical trial, root canal treatment, xp-endo shaper, patient satisfaction, Medicine (General), R5-920
Abstract

Anuj Bhardwaj,1,2 Rudra Kumar Gupta,1 Ayfer Atav Ates,3 Dian Agustin Wahjuningrum,2 Burçin Ar&inodot;can,4 Taher AlOmari,5 Alexander Maniangat Luke,6,7 Ajinkya M Pawar2,8 1Department of Conservative Dentistry and Endodontics, College of Dental Science and Hospital, Indore, India; 2Department of Conservative Dentistry, Universitas Airlangga, Surabaya, Indonesia; 3Department of Endodontics, Istinye University, Faculty of Dentistry, Istanbul, Turkey; 4Department of Endodontics, Bahçe&scedil;ehir University, School of Dental Medicine, Istanbul, Turkey; 5Department of Conservative Dentistry, Jordan University of Science and Technology, Al-Ramtha, Jordan; 6Department of Clinical Science, College of Dentistry, Ajman University, Ajman, United Arab Emirates; 7Center of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates; 8Department of Conservative Dentistry and Endodontics, Nair Hospital Dental College, Mumbai, 400008, IndiaCorrespondence: Dian Agustin Wahjuningrum, Department of Conservative Dentistry, Faculty of Dental Medicine, Universitas Airlangga, Surabaya, 60132, Indonesia, Email dian-agustin-w@fkg.unair.ac.id Alexander Maniangat Luke, Department of Clinical Science, College of Dentistry, Ajman University, J1 Building C Block, Al-Jurf 346, Ajman, United Arab Emirates, Email a.luke@ajman.ac.aePurpose: This prospective single-blind, parallel-group, randomized clinical trial was aimed to compare the effect of three different rotary instrumentation systems ProTaper Next (PTN), Self-Adjusting File (SAF) and XP-endo Shaper (XPS) on postoperative pain and analgesic intakes.Patients and Methods: A total of 159 molars diagnosed with symptomatic irreversible pulpitis were randomly divided into three study groups according to the instrumentation techniques: PTN (n = 54), SAF (n = 52), and XPS (n = 53). The preoperative pain scores were taken before the onset of treatment in the groups. After a single appointment for root canal treatment, the patients were asked to rate the level of their pain according to the Visual Analog Scale (VAS) of 100 mm at 6, 24, 48, and 72-hour post-treatment intervals. Ibuprofen was prescribed to be taken while experiencing pain; patients were requested to note the number of pills consumed at intervals after treatment.Results: The patients in SAF and XPS groups had lower mean VAS scores than the PTN group at 24-, 48-, and 72-hour intervals (p < 0.05). The most common analgesic intake was optimally seen in the PTN group at a 6-hour interval. All shaping procedures caused postoperative pain, whose intensity decreased with time.Conclusion: The SAF and XPS groups had a lesser intensity of pain as well as minimum analgesic intakes as compared to the PTN group. All instrumentation systems moderately caused pain, and the PTN group experienced the highest pain among others.Keywords: postoperative pain, ProTaper next, randomized clinical trial, root canal treatment, XP-endo shaper, patient satisfaction

Published
2023

30. Tumor Classification and Segmentation of MR Brain Images

Author

Gupta, Tanvi, Manocha, Pranay, Gandhi, Tapan K., Gupta, RK, and Panigrahi, BK

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The diagnosis and segmentation of tumors using any medical diagnostic tool can be challenging due to the varying nature of this pathology. Magnetic Reso- nance Imaging (MRI) is an established diagnostic tool for various diseases and disorders and plays a major role in clinical neuro-diagnosis. Supplementing this technique with automated classification and segmentation tools is gaining importance, to reduce errors and time needed to make a conclusive diagnosis. In this paper a simple three-step algorithm is proposed; (1) identification of patients that present with tumors, (2) automatic selection of abnormal slices of the patients, and (3) segmentation and detection of the tumor. Features were extracted by using discrete wavelet transform on the normalized images and classified by support vector machine (for step (1)) and random forest (for step (2)). The 400 subjects were divided in a 3:1 ratio between training and test with no overlap. This study is novel in terms of use of data, as it employed the entire T2 weighted slices as a single image for classification and a unique combination of contralateral approach with patch thresholding for segmentation, which does not require a training set or a template as is used by most segmentation studies. Using the proposed method, the tumors were segmented accurately with a classification accuracy of 95% with 100% specificity and 90% sensitivity.

Published
2017

31. Comparison of Bone-Patellar Tendon-Bone Graft, Semitendinosus–Gracilis Graft and Semitendinosus–Gracilis with Preserved Tibial Insertion Graft in Anterior Cruciate Ligament Reconstruction in Sports Persons

Author

Soni A, Gupta RK, Raghav M, Masih GD, and Bansal P

Subjects
cruciate ligament, reconstruction, graft, semitendinosus, gracilis, Orthopedic surgery, RD701-811
Abstract

INTRODUCTION: Bone-patellar tendon-bone (BPTB) and semitendinosus–gracilis (STG) are the commonest grafts used for ACL reconstruction. However even after having been debated for years, there is no consensus about the ideal graft. Moreover, the literature is deficient about STG graft with preserved tibial insertion (STGPI) which preserves the proprioception. Our aim is to compare the outcome of BPTB, free STG and STGPI grafts after ACL reconstruction in professional sports persons. We compared the outcome in terms of mechanical stability, functional outcome, return to sports activity and degenerative changes. MATERIALS AND METHODS: Professional sports persons aged between 16-50 years operated for ACL tear using BPTB, free STG and STGPI grafts with minimum follow-up of two years were identified from hospital records. Patients with associated knee injuries were excluded. Patients, divided in three groups according to graft used, were compared in terms of mechanical stability (arthrometric examination KT-1000 score), functional outcome (Lysholm Score), return to sports activity (Tegner score and difference in thigh circumference) and degenerative changes (KL grading). RESULTS: BPTB graft group was found to be better than free STG and STGPI graft groups in terms of KT-1000 score. There was no statistically significant difference among the groups in terms of Lysholm score, Tegner score, difference in thigh circumference and KL grading. CONCLUSION: BPTB graft is better than free STG and STGPI grafts in terms of knee stability. When compared for patient reported outcome, return to sports activity, osteoarthritic changes and graft failure there is no significant difference among the three types of grafts.

Published
2021
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32. Association Between FeNO, Total Blood IgE, Peripheral Blood Eosinophil and Inflammatory Cytokines in Partly Controlled Asthma

Author

Badar A, Salem AM, Bamosa AO, Qutub HO, Gupta RK, and Siddiqui IA

Subjects
partly controlled asthma, feno, eosinophils, ige, cytokines, Immunologic diseases. Allergy, RC581-607
Abstract

Ahmed Badar,1 Ayad Mohammed Salem,1 Abdullah Omar Bamosa,1 Hatem Othman Qutub,2 Rakesh Kumar Gupta,2 Intisar Ahmad Siddiqui3 1Department of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia; 2Department of Internal Medicine, College of Medicine & King Fahd Hospital of the University, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia; 3Department of Dental Education, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi ArabiaCorrespondence: Abdullah Omar BamosaDepartment of Physiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi ArabiaEmail ayadsalem@iau.edu.saBackground: Fractional exhaled nitric oxide (FeNO) is a convenient to use biomarker of airway inflammation. However, the mutual relationship between FeNO, peripheral blood eosinophil, total immunoglobulin E (IgE) and inflammatory cytokines showed some controversy.Objective: This study was carried out to determine the accuracy of peripheral blood eosinophil and total IgE to detect eosinophilic airway inflammation as determined by two FeNO cutoff points. The correlation between FeNO, peripheral blood eosinophil, total IgE and certain inflammatory cytokines was also examined.Methods: Seventy-six patients with partly controlled asthma performed the following tests on the same day: FeNO, pulmonary function tests (PFTs), peripheral blood eosinophils, total IgE, and inflammatory cytokine assay. The correlation between these markers was investigated and the diagnostic accuracy of peripheral blood eosinophils and total IgE to identify eosinophilic asthma phenotype was calculated using receiver operating characteristics area under the curve (ROC AUC).Results: FeNO was positively correlated with percentage of blood eosinophils (r=0.276, p=0.017) and total blood IgE (r=0.3647; p=0.0013). No relationship between FeNO and serum inflammatory cytokines was detected. AUC of blood eosinophils and total IgE were 57% and 64% at FeNO ≥ 25 ppb and were 67% and 64% at FeNO > 50, respectively. The higher predictive ability was detected at FeNO > 50 ppb where the best cutoff point for blood eosinophil % was ≥ 4.0% (sensitivity 66.7%, specificity 60.0%) and the best cutoff point for total IgE was ≥ 350 (sensitivity 66.7%, specificity 63.6%).Conclusion: In patients with partly controlled asthma, peripheral blood eosinophil and total IgE showed equal useful accuracy in predicting eosinophilic airways. However, higher predictive values were reported at FeNO level > 50 ppb. FeNO was positively correlated with peripheral blood eosinophil, total IgE but not with any of the studied cytokines.Keywords: partly controlled asthma, FeNO, eosinophils, IgE, cytokines

Published
2020

33. Cubitus Valgus with Tardy Ulnar Nerve Palsy – Functional Outcome of Milch Osteotomy without Anterior Transposition of Ulnar Nerve

Author

Gupta RK, Khiyani R, Majumdar KP, and Potalia R

Subjects
non-union, lateral condyle humerus, cubitus valgus, deformity, milch osteotomy, Orthopedic surgery, RD701-811
Abstract

INTRODUCTION: To assess the results of Milch osteotomy in terms of deformity correction and functional outcome in the absence of ulnar nerve transposition. MATERIALS AND METHODS: Nine patients with cubitus valgus deformity greater than 20° with tardy ulnar nerve palsy (TUNP) operated between 2012 and 2017 were evaluated. Correction by Milch osteotomy and fixation was done in each case, without osteosynthesis of the non-union lateral condyle humerus or transposition of the ulnar nerve. At one year post-operatively, carrying angle, elbow function (Mayo Elbow Performance Score) and ulnar nerve symptoms were assessed. RESULTS: The mean carrying angle pre-operatively was 30.8° on the affected side which improved to a mean of 8.3° postoperatively with an average correction of 22.5°. The mean elbow flexion pre-operatively was 129.4° which improved to 133.3° post-operatively. The mean preoperative MEP score was 76.7 which improved to a mean of 92.2 post-operatively (p < 0.01). TUNP recovered completely in all the patients. CONCLUSION: Milch osteotomy is an effective procedure for cubitus valgus deformity correction and its associated tardy ulnar nerve palsy without a decrease in elbow ROM. Correction of even severe valgus deformities without concurrent anterior transposition of the ulnar nerve is likely to improve ulnar nerve symptoms.

Published
2020
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35. Regulation of Early Adipose Commitment by Zfp521

Author

Kajimura, Shingo, Kang, S, Akerblad, P, Kiviranta, R, Gupta, RK, Griffin, MJ, Min, J, Baron, R, and Rosen, ED

Abstract

While there has been significant progress in determining the transcriptional cascade involved in terminal adipocyte differentiation, less is known about early events leading to lineage commitment and cell fate choice. It has been recently discovered that z

Published
2012

38. Predicted effects of the introduction of long-acting injectable cabotegravir pre-exposure prophylaxis in sub-Saharan Africa: a modelling study

Author

Smith, J, Bansi-Matharu, L, Cambiano, V, Dimitrov, D, Bershteyn, A, Van de Vijver, D, Kripke, K, Revill, P, Boily, M-C, Meyer-Rath, G, Taramusi, I, Lundgren, JD, Van Oosterhout, JJ, Kuritzkes, D, Schaefer, R, Siedner, MJ, Schapiro, J, Delany-Moretlwe, S, Landovitz, RJ, Flexner, C, Jordan, M, Venter, F, Radebe, M, Ripin, D, Jenkins, S, Resar, D, Amole, C, Shahmanesh, M, Gupta, RK, Raizes, E, Johnson, C, Inzaule, S, Shafer, R, Warren, M, Stansfield, S, Paredes, R, Phillips, AN, HIV Modelling Consortium, and Virology

Subjects
Infectious Diseases, SDG 3 - Good Health and Well-being, Epidemiology, Virology, Immunology
Abstract

Background: Long-acting injectable cabotegravir pre-exposure prophylaxis (PrEP) is recommended by WHO as an additional option for HIV prevention in sub-Saharan Africa, but there is concern that its introduction could lead to an increase in integrase-inhibitor resistance undermining treatment programmes that rely on dolutegravir. We aimed to project the health benefits and risks of cabotegravir-PrEP introduction in settings in sub-Saharan Africa. Methods: With HIV Synthesis, an individual-based HIV model, we simulated 1000 setting-scenarios reflecting both variability and uncertainty about HIV epidemics in sub-Saharan Africa and compared outcomes for each with and without cabotegravir-PrEP introduction. PrEP use is assumed to be risk-informed and to be used only in 3-month periods (the time step for the model) when having condomless sex. We consider three groups at risk of integrase-inhibitor resistance emergence: people who start cabotegravir-PrEP after (unknowingly) being infected with HIV, those who seroconvert while on PrEP, and those with HIV who have residual cabotegravir drugs concentrations during the early tail period after recently stopping PrEP. We projected the outcomes of policies of cabotegravir-PrEP introduction and of no introduction in 2022 across 50 years. In 50% of setting-scenarios we considered that more sensitive nucleic-acid-based HIV diagnostic testing (NAT), rather than regular antibody-based HIV rapid testing, might be used to reduce resistance risk. For cost-effectiveness analysis we assumed in our base case a cost of cabotegravir-PrEP drug to be similar to oral PrEP, resulting in a total annual cost of USD$144 per year ($114 per year and $264 per year considered in sensitivity analyses), a cost-effectiveness threshold of $500 per disability-adjusted life years averted, and a discount rate of 3% per year. Findings: Reflecting our assumptions on the appeal of cabotegravir-PrEP, its introduction is predicted to lead to a substantial increase in PrEP use with approximately 2·6% of the adult population (and 46% of those with a current indication for PrEP) receiving PrEP compared with 1·5% (28%) without cabotegravir-PrEP introduction across 20 years. As a result, HIV incidence is expected to be lower by 29% (90% range across setting-scenarios 6–52%) across the same period compared with no introduction of cabotegravir-PrEP. In people initiating antiretroviral therapy, the proportion with integrase-inhibitor resistance after 20 years is projected to be 1·7% (0–6·4%) without cabotegravir-PrEP introduction but 13·1% (4·1–30·9%) with. Cabotegravir-PrEP introduction is predicted to lower the proportion of all people on antiretroviral therapy with viral loads less than 1000 copies per mL by 0·9% (–2·5% to 0·3%) at 20 years. For an adult population of 10 million an overall decrease in number of AIDS deaths of about 4540 per year (–13 000 to –300) across 50 years is predicted, with little discernible benefit with NAT when compared with standard antibody-based rapid testing. AIDS deaths are predicted to be averted with cabotegravir-PrEP introduction in 99% of setting-scenarios. Across the 50-year time horizon, overall HIV programme costs are predicted to be similar regardless of whether cabotegravir-PrEP is introduced (total mean discounted annual HIV programme costs per year across 50 years is $151·3 million vs $150·7 million), assuming the use of standard antibody testing. With antibody-based rapid HIV testing, the introduction of cabotegravir-PrEP is predicted to be cost-effective under an assumed threshold of $500 per disability-adjusted life year averted in 82% of setting-scenarios at the cost of $144 per year, in 52% at $264, and in 87% at $114. Interpretation: Despite leading to increases in integrase-inhibitor drug resistance, cabotegravir-PrEP introduction is likely to reduce AIDS deaths in addition to HIV incidence. Long-acting cabotegravir-PrEP is predicted to be cost-effective if delivered at similar cost to oral PrEP with antibody-based rapid HIV testing. Funding: Bill & Melinda Gates Foundation, National Institute of Allergy and Infectious Diseases of the National Institutes of Health.

Published
2023

41. Cold atoms in space: community workshop summary and proposed road-map

Author

Alonso, I, Alpigiani, C, Altschul, B, Araújo, H, Arduini, G, Arlt, J, Badurina, L, Balaž, A, Bandarupally, S, Barish, BC, Barone, M, Barsanti, M, Bass, S, Bassi, A, Battelier, B, Baynham, CFA, Beaufils, Q, Belić, A, Bergé, J, Bernabeu, J, Bertoldi, A, Bingham, R, Bize, S, Blas, D, Bongs, K, Bouyer, P, Braitenberg, C, Brand, C, Braxmaier, C, Bresson, A, Buchmueller, O, Budker, D, Bugalho, L, Burdin, S, Cacciapuoti, L, Callegari, S, Calmet, X, Calonico, D, Canuel, B, Caramete, LI, Carraz, O, Cassettari, D, Chakraborty, P, Chattopadhyay, S, Chauhan, U, Chen, X, Chen, YA, Chiofalo, ML, Coleman, J, Corgier, R, Cotter, JP, Michael Cruise, A, Cui, Y, Davies, G, De Roeck, A, Demarteau, M, Derevianko, A, Di Clemente, M, Djordjevic, GS, Donadi, S, Doré, O, Dornan, P, Doser, M, Drougakis, G, Dunningham, J, Easo, S, Eby, J, Elertas, G, Ellis, J, Evans, D, Examilioti, P, Fadeev, P, Fanì, M, Fassi, F, Fattori, M, Fedderke, MA, Felea, D, Feng, CH, Ferreras, J, Flack, R, Flambaum, VV, Forsberg, R, Fromhold, M, Gaaloul, N, Garraway, BM, Georgousi, M, Geraci, A, Gibble, K, Gibson, V, Gill, P, Giudice, GF, Goldwin, J, Gould, O, Grachov, O, Graham, PW, Grasso, D, Griffin, PF, Guerlin, C, Gündoğan, M, Gupta, RK, and Apollo - University of Cambridge Repository

Subjects
5102 Atomic, Molecular and Optical Physics, Review, 51 Physical Sciences, 5108 Quantum Physics
Abstract

We summarise the discussions at a virtual Community Workshop on Cold Atoms in Space concerning the status of cold atom technologies, the prospective scientific and societal opportunities offered by their deployment in space, and the developments needed before cold atoms could be operated in space. The cold atom technologies discussed include atomic clocks, quantum gravimeters and accelerometers, and atom interferometers. Prospective applications include metrology, geodesy and measurement of terrestrial mass change due to, e.g., climate change, and fundamental science experiments such as tests of the equivalence principle, searches for dark matter, measurements of gravitational waves and tests of quantum mechanics. We review the current status of cold atom technologies and outline the requirements for their space qualification, including the development paths and the corresponding technical milestones, and identifying possible pathfinder missions to pave the way for missions to exploit the full potential of cold atoms in space. Finally, we present a first draft of a possible road-map for achieving these goals, that we propose for discussion by the interested cold atom, Earth Observation, fundamental physics and other prospective scientific user communities, together with the European Space Agency (ESA) and national space and research funding agencies.

Published
2022
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44. 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

Author

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.

Published
2022

45. Procalcitonin is not a reliable biomarker of bacterial coinfection in people with coronavirus disease 2019 undergoing microbiological investigation at the time of hospital admission

Author

Relph, KA, Russell, CD, Fairfield, CJ, Turtle, L, de Silva, TI, Siggins, MK, Drake, TM, Thwaites, RS, Abrams, S, Moore, SC, Hardwick, HE, Oosthuyzen, W, Harrison, EM, Docherty, AB, Openshaw, PJM, Baillie, JK, Semple, MG, Ho, A, Carson, G, Alex, B, Bach, B, Barclay, WS, Bogaert, D, Chand, M, Cooke, GS, Dunning, J, Filipe, ADS, Fletcher, T, Green, CA, Hiscox, JA, Ho, AYW, Horby, PW, Ijaz, S, Khoo, S, Klenerman, P, Law, A, Lim, WS, Mentzer, AJ, Merson, L, Meynert, AM, Noursadeghi, M, Palmarini, M, Paxton, WA, Pollakis, G, Price, N, Rambaut, A, Robertson, DL, Sancho-Shimizu, V, Scott, JT, de Silva, T, Sigfrid, L, Solomon, T, Sriskandan, S, Stuart, D, Summers, C, Tedder, RS, Thomson, EC, Roger Thompson, AA, Turtle, LCW, Gupta, RK, Zambon, M, Hardwick, H, Donohue, C, Lyons, R, Griffiths, F, Norman, L, Pius, R, Knight, SR, Mclean, KA, Murphy, D, Shaw, CA, Dalton, J, Girvan, M, Saviciute, E, Roberts, S, Harrison, J, Marsh, L, Connor, M, Halpin, S, Jackson, C, Gamble, C, Leeming, G, Wham, M, Clohisey, S, Hendry, R, Scott-Brown, J, Greenhalf, W, Shaw, V, McDonald, S, Keating, S, Ahmed, KA, Armstrong, JA, Ashworth, M, Asiimwe, IG, Bakshi, S, Barlow, SL, Booth, L, Brennan, B, Bullock, K, Catterall, BWA, Clark, JJ, Clarke, EA, Cole, S, Cooper, L, Cox, H, Davis, C, Dincarslan, O, Dunn, C, Dyer, P, Elliott, A, Evans, A, Finch, L, Fisher, LWS, Foster, T, Garcia-Dorival, I, Gunning, P, Hartley, C, Jensen, RL, Jones, CB, Jones, TR, Khandaker, S, King, K, Kiy, RT, Koukorava, C, Lake, A, Lant, S, Latawiec, D, Lavelle-Langham, L, Lefteri, D, Lett, L, Livoti, LA, Mancini, M, McEvoy, L, McLauchlan, J, Metelmann, S, Miah, NS, Middleton, J, Mitchell, J, Murphy, EG, Penrice-Randal, R, Pilgrim, J, Prince, T, Reynolds, W, Matthew Ridley, P, Sales, D, Shaw, VE, Shears, RK, Small, B, Subramaniam, KS, Szemiel, A, Taggart, A, Tanianis-Hughes, J, Thomas, J, Trochu, E, van Tonder, L, Wilcock, E, Eunice Zhang, J, Flaherty, L, Maziere, N, Cass, E, Doce Carracedo, A, Carlucci, N, Holmes, A, Massey, H, Murphy, L, Wrobel, N, McCafferty, S, Morrice, K, MacLean, A, Adeniji, K, Agranoff, D, Agwuh, K, Ail, D, Aldera, EL, Alegria, A, Angus, B, Ashish, A, Atkinson, D, Bari, S, Barlow, G, Barnass, S, Barrett, N, Bassford, C, Basude, S, Baxter, D, Beadsworth, M, Bernatoniene, J, Berridge, J, Best, N, Bothma, P, Chadwick, D, Brittain-Long, R, Bulteel, N, Burden, T, Burtenshaw, A, Caruth, V, Chambler, D, Chee, N, Child, J, Chukkambotla, S, Clark, T, Collini, P, Cosgrove, C, Cupitt, J, Cutino-Moguel, M-T, Dark, P, Dawson, C, Dervisevic, S, Donnison, P, Douthwaite, S, DuRand, I, Dushianthan, A, Dyer, T, Evans, C, Eziefula, C, Fegan, C, Finn, A, Fullerton, D, Garg, S, Garg, A, Gkrania-Klotsas, E, Godden, J, Goldsmith, A, Graham, C, Hardy, E, Hartshorn, S, Harvey, D, Havalda, P, Hawcutt, DB, Hobrok, M, Hodgson, L, Hormis, A, Jacobs, M, Jain, S, Jennings, P, Kaliappan, A, Kasipandian, V, Kegg, S, Kelsey, M, Kendall, J, Kerrison, C, Kerslake, I, Koch, O, Koduri, G, Koshy, G, Laha, S, Laird, S, Larkin, S, Leiner, T, Lillie, P, Limb, J, Linnett, V, Little, J, Lyttle, M, MacMahon, M, MacNaughton, E, Mankregod, R, Masson, H, Matovu, E, McCullough, K, McEwen, R, Meda, M, Mills, G, Minton, J, Mirfenderesky, M, Mohandas, K, Mok, Q, Moon, J, Moore, E, Morgan, P, Morris, C, Mortimore, K, Moses, S, Mpenge, M, Mulla, R, Murphy, M, Nagel, M, Nagarajan, T, Nelson, M, O’Shea, MK, Otahal, I, Ostermann, M, Pais, M, Panchatsharam, S, Papakonstantinou, D, Paraiso, H, Patel, B, Pattison, N, Pepperell, J, Peters, M, Phull, M, Pintus, S, Pooni, JS, Post, F, Price, D, Prout, R, Rae, N, Reschreiter, H, Reynolds, T, Richardson, N, Roberts, M, Roberts, D, Rose, A, Rousseau, G, Ryan, B, Saluja, T, Shah, A, Shanmuga, P, Sharma, A, Shawcross, A, Sizer, J, Shankar-Hari, M, Smith, R, Snelson, C, Spittle, N, Staines, N, Stambach, T, Stewart, R, Subudhi, P, Szakmany, T, Tatham, K, Thompson, C, Thompson, R, Tridente, A, Tupper-Carey, D, Twagira, M, Ustianowski, A, Vallotton, N, Vincent-Smith, L, Visuvanathan, S, Vuylsteke, A, Waddy, S, Wake, R, Walden, A, Welters, I, Whitehouse, T, Whittaker, P, Whittington, A, Papineni, P, Wijesinghe, M, Williams, M, Wilson, L, Winchester, S, Wiselka, M, Wolverson, A, Wootton, DG, Workman, A, Yates, B, and Young, P

Abstract

Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory and Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although procalcitonin was higher in bacterial coinfection, this was neither clinically significant (median [IQR], 0.33 [0.11–1.70] ng/mL vs 0.24 [0.10–0.90] ng/mL) nor diagnostically useful (area under the receiver operating characteristic curve, 0.56 [95% confidence interval, .51–.60]).

Published
2022

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