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Myrga JM, Erpenbeck SP, Watts A, Stencel MG, Staniorski CJ, Patnaik S, Yabes JG, Yu M, Allaway MJ, Gorin MA, Jacobs BL, Davies BJ. Patient Reported Outcomes of Transperineal Prostate Biopsy With Tumescent Local Anesthesia. Urology 2023; 182:33-39. [PMID: 37742847 DOI: 10.1016/j.urology.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/01/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023]
Abstract
OBJECTIVE To report the outcomes of performing transperineal prostate biopsy in the office setting using the novel anesthetic technique of tumescent local anesthesia. We report anxiety, pain, and embarrassment of patients who underwent this procedure compared to patients who underwent a transrectal prostate biopsy using standard local anesthesia. MATERIALS AND METHODS Consecutive patients undergoing either a transperineal prostate biopsy under tumescent local anesthesia or a transrectal prostate biopsy with standard local anesthetic technique were prospectively enrolled. The tumescent technique employed dilute lidocaine solution administered using a self-filling syringe. Patients were asked to rate their pain before, during, and after their procedure using a visual analog scale. Patient anxiety and embarrassment was assessed using the Testing Modalities Index Questionnaire. RESULTS Between April 2021 and June 2022, 430 patients underwent a transperineal prostate biopsy using tumescent local anesthesia and 65 patients underwent a standard transrectal prostate biopsy. Patients who underwent a transperineal biopsy had acceptable but significantly higher pain scores than those who underwent a transrectal prostate biopsy (3.9 vs 1.6, P-value <.01). These scores fell to almost zero immediately following their procedure. Additionally, transperineal biopsy patients were more likely to experience anxiety (71% vs 45%, P < .01) and embarrassment (32% vs 15%, P < .01). CONCLUSION Transperineal biopsy using local tumescent anesthesia is safe and well-tolerated. Despite the benefits, patients undergoing a transperineal prostate biopsy under tumescent anesthesia still experienced worse procedural pain, anxiety, and embarrassment. Additional studies examining other adjunctive interventions to improve patient experience during transperineal prostate biopsy are needed.
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Affiliation(s)
- John M Myrga
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA.
| | | | - Alexander Watts
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | - Michael G Stencel
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | - Christopher J Staniorski
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | - Shyam Patnaik
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | - Jonathan G Yabes
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Michelle Yu
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | | | - Michael A Gorin
- Milton and Carroll Petrie Department of Urology at the Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Bruce L Jacobs
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
| | - Benjamin J Davies
- University of Pittsburgh Medical Center, Division of Health Services Research, Department of Urology, Pittsburgh, PA
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Tahmazian I, Watts A, Chen O, Ferrara HJ, McCrimmon A, Hu B, Chomiak T. A wearable device-enabled therapeutic approach to improve joint attention in autism spectrum disorder: a prospective pilot study. J Neural Transm (Vienna) 2023; 130:1601-1607. [PMID: 37648903 DOI: 10.1007/s00702-023-02683-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023]
Abstract
It has been previously proposed that interventions aimed at integrating and co-activating music processing and motor control systems could have therapeutic potential for priming social skill development in children with autism spectrum disorder (ASD). In this study, we assessed this hypothesis through a wearable sensor platform called Ambulosono ("Ambulo"-walk; "sono"-sound) in which pleasurable children's musical stimuli are contingently linked to effortful motor action (locomotor step size), thus creating a motivational state proposed to be conducive to joint attention (JA) operation. Five participants were recruited from a community-based partner and were assessed by scoring responses following therapist-directed bids for JA. Multiple assessment sessions through a repeated time-series design were conducted to determine baseline and post-intervention scores. The intervention session consisted of approximately 15 min of Ambulosono exposure. Baseline and post-intervention data were aggregated and analyzed using a linear mixed-effect model. The wearable sensor and wireless headphones of the Ambulosono system were tolerated by the participants, and there were no adverse effects associated with the use of the device. We found an increase in the average responses to bids for JA during the Ambulosono intervention phase compared to baseline across participants. This increase did not appear to result from enhanced general arousal. Our pilot data support feasibility and further testing of Ambulosono as a therapeutic aid for integration into community-based ASD programs to augment shared child-therapist social interactions.
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Affiliation(s)
- Isabelle Tahmazian
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada
| | - Alexander Watts
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada
| | - Oswald Chen
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada
| | - Hannah J Ferrara
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada
| | - Adam McCrimmon
- Werklund School of Education, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Bin Hu
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Taylor Chomiak
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 1N4, Canada.
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Colón-González FJ, Gibb R, Khan K, Watts A, Lowe R, Brady OJ. Author Correction: Projecting the future incidence and burden of dengue in Southeast Asia. Nat Commun 2023; 14:6518. [PMID: 37845219 PMCID: PMC10579311 DOI: 10.1038/s41467-023-42378-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Affiliation(s)
- Felipe J Colón-González
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Tyndall Centre for Climate Change Research, School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
- Data for Science and Health, Wellcome Trust, London, NW1 2BE, UK.
| | - Rory Gibb
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Kamran Khan
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, M5S 3H2, Canada
- BlueDot, Toronto, ON, M5J 1A7, Canada
| | - Alexander Watts
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Esri Canada, Toronto, ON, M3C 3R8, Canada
| | - Rachel Lowe
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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Colón-González FJ, Gibb R, Khan K, Watts A, Lowe R, Brady OJ. Projecting the future incidence and burden of dengue in Southeast Asia. Nat Commun 2023; 14:5439. [PMID: 37673859 PMCID: PMC10482941 DOI: 10.1038/s41467-023-41017-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
The recent global expansion of dengue has been facilitated by changes in urbanisation, mobility, and climate. In this work, we project future changes in dengue incidence and case burden to 2099 under the latest climate change scenarios. We fit a statistical model to province-level monthly dengue case counts from eight countries across Southeast Asia, one of the worst affected regions. We project that dengue incidence will peak this century before declining to lower levels with large variations between and within countries. Our findings reveal that northern Thailand and Cambodia will show the biggest decreases and equatorial areas will show the biggest increases. The impact of climate change will be counterbalanced by income growth, with population growth having the biggest influence on increasing burden. These findings can be used for formulating mitigation and adaptation interventions to reduce the immediate growing impact of dengue virus in the region.
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Affiliation(s)
- Felipe J Colón-González
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Tyndall Centre for Climate Change Research, School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
- Data for Science and Health, Wellcome Trust, London, NW1 2BE, UK.
| | - Rory Gibb
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Kamran Khan
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, M5S 3H2, Canada
- BlueDot, Toronto, ON, M5J 1A7, Canada
| | - Alexander Watts
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Esri Canada, Toronto, ON, M3C 3R8, Canada
| | - Rachel Lowe
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre on Climate Change and Planetary Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Barcelona Supercomputing Center (BSC), Barcelona, 08034, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
| | - Oliver J Brady
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
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Condren J, Byrne T, Watts A. Seven years of SimWars - Reflecting on the educational value of competitive simulation training. Ir Med J 2023; 116:821. [PMID: 37606533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
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Smitherman EA, Chahine RA, Beukelman T, Lewandowski LB, Rahman AKMF, Wenderfer SE, Curtis JR, Hersh AO, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar‐Smiley F, Barillas‐Arias L, Basiaga M, Baszis K, Becker M, Bell‐Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang‐Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel‐Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie‐Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui‐Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein‐Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PM, McGuire S, McHale I, McMonagle A, McMullen‐Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O'Brien B, O'Brien T, Okeke O, Oliver M, Olson J, O'Neil K, Onel K, Orandi A, Orlando M, Osei‐Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan‐Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas‐Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth‐Wojcicki E, Rouster – Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert‐Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner‐Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Childhood-Onset Lupus Nephritis in the Childhood Arthritis and Rheumatology Research Alliance Registry: Short-Term Kidney Status and Variation in Care. Arthritis Care Res (Hoboken) 2023; 75:1553-1562. [PMID: 36775844 PMCID: PMC10500561 DOI: 10.1002/acr.25002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/14/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The goal was to characterize short-term kidney status and describe variation in early care utilization in a multicenter cohort of patients with childhood-onset systemic lupus erythematosus (cSLE) and nephritis. METHODS We analyzed previously collected prospective data from North American patients with cSLE with kidney biopsy-proven nephritis enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry from March 2017 through December 2019. We determined the proportion of patients with abnormal kidney status at the most recent registry visit and applied generalized linear mixed models to identify associated factors. We also calculated frequency of medication use, both during induction and ever recorded. RESULTS We identified 222 patients with kidney biopsy-proven nephritis, with 64% class III/IV nephritis on initial biopsy. At the most recent registry visit at median (interquartile range) of 17 (8-29) months from initial kidney biopsy, 58 of 106 patients (55%) with available data had abnormal kidney status. This finding was associated with male sex (odds ratio [OR] 3.88, 95% confidence interval [95% CI] 1.21-12.46) and age at cSLE diagnosis (OR 1.23, 95% CI 1.01-1.49). Patients with class IV nephritis were more likely than class III to receive cyclophosphamide and rituximab during induction. There was substantial variation in mycophenolate, cyclophosphamide, and rituximab ever use patterns across rheumatology centers. CONCLUSION In this cohort with predominately class III/IV nephritis, male sex and older age at cSLE diagnosis were associated with abnormal short-term kidney status. We also observed substantial variation in contemporary medication use for pediatric lupus nephritis between pediatric rheumatology centers. Additional studies are needed to better understand the impact of this variation on long-term kidney outcomes.
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Huber C, Watts A, Thomas-Bachli A, McIntyre E, Tuite A, Khan K, Cetron M, Merrill RD. Using spatial and population mobility models to inform outbreak response approaches in the Ebola affected area, Democratic Republic of the Congo, 2018-2020. Spat Spatiotemporal Epidemiol 2023; 44:100558. [PMID: 36707191 PMCID: PMC10864106 DOI: 10.1016/j.sste.2022.100558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 06/22/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
The Democratic Republic of the Congo's (DRC) 10th known Ebola virus disease (EVD) outbreak occurred between August 1, 2018 and June 25, 2020, and was the largest EVD outbreak in the country's history. During this outbreak, the DRC Ministry of Health initiated traveller health screening at points of control (POC, locations not on the border) and points of entry (POE) to minimize disease translocation via ground and air travel. We sought to develop a model-based approach that could be applied in future outbreaks to inform decisions for optimizing POC and POE placement, and allocation of resources more broadly, to mitigate the risk of disease translocation associated with ground-level population mobility. We applied a parameter-free mobility model, the radiation model, to estimate likelihood of ground travel between selected origin locations (including Beni, DRC) and surrounding population centres, based on population size and drive-time. We then performed a road network route analysis and included estimated population movement results to calculate the proportionate volume of travellers who would move along each road segment; this reflects the proportion of travellers that could be screened at a POC or POE. For Beni, the road segments estimated to have the highest proportion of travellers that could be screened were part of routes into Uganda and Rwanda. Conversely, road segments that were part of routes to other population centres within the DRC were estimated to have relatively lower proportions. We observed a posteriori that, in many instances, our results aligned with locations that were selected for actual POC or POE placement through more time-consuming methods. This study has demonstrated that mobility models and simple spatial techniques can help identify potential locations for health screening at newly placed POC or existing POE during public health emergencies based on expected movement patterns. Importantly, we have provided methods to estimate the proportionate volume of travellers that POC or POE screening measures would assess based on their location. This is critical information in outbreak situations when timely decisions must be made to implement public health interventions that reach the most individuals across a network.
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Affiliation(s)
- Carmen Huber
- BlueDot, 207 Queens Quay West #820, Toronto, Ontario, Canada.
| | - Alexander Watts
- BlueDot, 207 Queens Quay West #820, Toronto, Ontario, Canada
| | | | - Elvira McIntyre
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, Georgia, United States of America (USA); Perspecta Inc., 15052 Conference Center Drive, Chantilly, Virginia, United States of America (USA)
| | - Ashleigh Tuite
- BlueDot, 207 Queens Quay West #820, Toronto, Ontario, Canada; Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, Ontario, Canada
| | - Kamran Khan
- BlueDot, 207 Queens Quay West #820, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, 38 Shuter St, Toronto, Ontario, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada
| | - Martin Cetron
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, Georgia, United States of America (USA)
| | - Rebecca D Merrill
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, Georgia, United States of America (USA)
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Hahn T, Daymont C, Beukelman T, Groh B, Hays K, Bingham CA, Scalzi L, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Intraarticular steroids as DMARD-sparing agents for juvenile idiopathic arthritis flares: Analysis of the Childhood Arthritis and Rheumatology Research Alliance Registry. Pediatr Rheumatol Online J 2022; 20:107. [PMID: 36434731 PMCID: PMC9701017 DOI: 10.1186/s12969-022-00770-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Children with juvenile idiopathic arthritis (JIA) who achieve a drug free remission often experience a flare of their disease requiring either intraarticular steroids (IAS) or systemic treatment with disease modifying anti-rheumatic drugs (DMARDs). IAS offer an opportunity to recapture disease control and avoid exposure to side effects from systemic immunosuppression. We examined a cohort of patients treated with IAS after drug free remission and report the probability of restarting systemic treatment within 12 months. METHODS We analyzed a cohort of patients from the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry who received IAS for a flare after a period of drug free remission. Historical factors and clinical characteristics and of the patients including data obtained at the time of treatment were analyzed. RESULTS We identified 46 patients who met the inclusion criteria. Of those with follow up data available 49% had restarted systemic treatment 6 months after IAS injection and 70% had restarted systemic treatment at 12 months. The proportion of patients with prior use of a biologic DMARD was the only factor that differed between patients who restarted systemic treatment those who did not, both at 6 months (79% vs 35%, p < 0.01) and 12 months (81% vs 33%, p < 0.05). CONCLUSION While IAS are an option for all patients who flare after drug free remission, it may not prevent the need to restart systemic treatment. Prior use of a biologic DMARD may predict lack of success for IAS. Those who previously received methotrexate only, on the other hand, are excellent candidates for IAS.
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Affiliation(s)
- Timothy Hahn
- Department of Pediatrics, Penn State Children's Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA, 17033-0855, USA.
| | - Carrie Daymont
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Timothy Beukelman
- grid.265892.20000000106344187Department of Pediatrics, University of Alabama at Birmingham, CPPN G10, 1600 7th Ave South, Birmingham, AL 35233 USA
| | - Brandt Groh
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | | | - Catherine April Bingham
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
| | - Lisabeth Scalzi
- grid.240473.60000 0004 0543 9901Department of Pediatrics, Penn State Children’s Hospital, 500 University Dr, Hershey, 90 Hope Drive, P.O. Box 855, Hershey, PA 17033-0855 USA
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Watts A, Park K, Vohra S, Raj K, Toquica CC, Jalal A, Shah M, Patel KV. Inequalities in accessing quality healthcare, does insurance play a role? retrospective analysis of aortic emergencies from national inpatient sample 2019. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Aortic emergencies, dissection and rupture, are rare but catastrophic entities, with the cornerstone to survival being prompt diagnosis and treatment. Insurance status often limits access to healthcare, and our study aims to determine if it plays a role in the outcomes of aortic emergencies.
Method
A retrospective analysis of the 2019 Nationwide Inpatient Sample was conducted to identify hospitalization (Age ≥18 & non-elective) with aortic dissection and ruptured aortic aneurysms using ICD-10 codes. Discharge-level weight analysis was used to produce a national estimate. Variables were screened with univariate regression, and intermediate and co-linear variables were screened-out before a multivariable regression analysis model was built and performed to calculate the odds ratio.
Results
A total of 19,685 (0.06%) hospitalizations are identified for aortic emergencies (14965 dissections & 4720 ruptured aneurysms). The mean age was 58.56, 62.7% were males, and ethnic distribution was 65.1% white, 19.5% blacks, 7.6% Hispanics, and others.
11.4% of the hospitalizations underwent diagnostic imaging with either CTA/MRA/TEE/Aortography within 24 hours. Hypotension/shock was present in 32% of these hospitalizations and was a risk factor for mortality OR 3.21 (p<0.00), increasing LOS by an average of 5.1 days and resource utilization by 156,000$. Another risk factor for mortality was stroke/TIA (OR-1.76, p<0.00), increasing LOS and resource utilization by 3.1 days and 80,662$, respectively.
3220 hospitalizations (16.4%) did not survive the course, and the mortality rate in uninsured, Medicare, and Medicaid was 17%, 20%,9% compared with 12% in privately insured. On crude analysis, uninsured and medicare patients appeared to have higher odds of mortality [OR 1.50, p<0.04, and OR 1.83 p-value <0.002 respectively], however upon adjusting for confounders, only uninsured patients showed statistically significant difference (OR 2.13, p<0.002). Similar results were corroborated on analyzing hospitalizations for aortic dissection; however, insurance status did not influence mortality in a ruptured aneurysm.
When comparing hospitalization of median household income of ≥79,000$ with household of median income of 59,000–78,999 $, 46,000–58,999 $ and <46,000$ had higher odds of mortality (OR-1.38, p<0.04), (OR-1.44, p<0.02) and (OR-1.44, p<0.03) respectively. Of all the insurance types, a statistically significant difference compared with private insurance, Medicaid on average, had 2.8 more days and incurred an additional 62,912$ in resource utilization (p<0.00).
Conclusion
Inequalities in accessing healthcare, median household income, and insurance status are risk factors for mortality in aortic emergencies. Efforts are needed to bridge the gap in this particular facet of social determinants of health to find a sustainable and equitable solution for quality healthcare for aall regardless of their insurance status.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- A Watts
- Saint Peter's University Hospital , New Brunswick , United States of America
| | - K Park
- Memorial Healthcare System, Internal Medicine , Pembroke Pines , United States of America
| | - S Vohra
- Saint Peter's University Hospital , New Brunswick , United States of America
| | - K Raj
- Saint Peter's University Hospital , New Brunswick , United States of America
| | - C C Toquica
- Saint Peter's University Hospital , New Brunswick , United States of America
| | - A Jalal
- Memorial Healthcare System, Internal Medicine , Pembroke Pines , United States of America
| | - M Shah
- Saint Peter's University Hospital , New Brunswick , United States of America
| | - K V Patel
- Saint Peter's University Hospital , New Brunswick , United States of America
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Lai S, Bogoch II, Ruktanonchai NW, Watts A, Lu X, Yang W, Yu H, Khan K, Tatem AJ. Assessing spread risk of COVID-19 within and beyond China in early 2020. Data Science and Management 2022. [PMCID: PMC9411104 DOI: 10.1016/j.dsm.2022.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Soulsby WD, Balmuri N, Cooley V, Gerber LM, Lawson E, Goodman S, Onel K, Mehta B, Abel N, Abulaban K, Adams A, Adams M, Agbayani R, Aiello J, Akoghlanian S, Alejandro C, Allenspach E, Alperin R, Alpizar M, Amarilyo G, Ambler W, Anderson E, Ardoin S, Armendariz S, Baker E, Balboni I, Balevic S, Ballenger L, Ballinger S, Balmuri N, Barbar-Smiley F, Barillas-Arias L, Basiaga M, Baszis K, Becker M, Bell-Brunson H, Beltz E, Benham H, Benseler S, Bernal W, Beukelman T, Bigley T, Binstadt B, Black C, Blakley M, Bohnsack J, Boland J, Boneparth A, Bowman S, Bracaglia C, Brooks E, Brothers M, Brown A, Brunner H, Buckley M, Buckley M, Bukulmez H, Bullock D, Cameron B, Canna S, Cannon L, Carper P, Cartwright V, Cassidy E, Cerracchio L, Chalom E, Chang J, Chang-Hoftman A, Chauhan V, Chira P, Chinn T, Chundru K, Clairman H, Co D, Confair A, Conlon H, Connor R, Cooper A, Cooper J, Cooper S, Correll C, Corvalan R, Costanzo D, Cron R, Curiel-Duran L, Curington T, Curry M, Dalrymple A, Davis A, Davis C, Davis C, Davis T, De Benedetti F, De Ranieri D, Dean J, Dedeoglu F, DeGuzman M, Delnay N, Dempsey V, DeSantis E, Dickson T, Dingle J, Donaldson B, Dorsey E, Dover S, Dowling J, Drew J, Driest K, Du Q, Duarte K, Durkee D, Duverger E, Dvergsten J, Eberhard A, Eckert M, Ede K, Edelheit B, Edens C, Edens C, Edgerly Y, Elder M, Ervin B, Fadrhonc S, Failing C, Fair D, Falcon M, Favier L, Federici S, Feldman B, Fennell J, Ferguson I, Ferguson P, Ferreira B, Ferrucho R, Fields K, Finkel T, Fitzgerald M, Fleming C, Flynn O, Fogel L, Fox E, Fox M, Franco L, Freeman M, Fritz K, Froese S, Fuhlbrigge R, Fuller J, George N, Gerhold K, Gerstbacher D, Gilbert M, Gillispie-Taylor M, Giverc E, Godiwala C, Goh I, Goheer H, Goldsmith D, Gotschlich E, Gotte A, Gottlieb B, Gracia C, Graham T, Grevich S, Griffin T, Griswold J, Grom A, Guevara M, Guittar P, Guzman M, Hager M, Hahn T, Halyabar O, Hammelev E, Hance M, Hanson A, Harel L, Haro S, Harris J, Harry O, Hartigan E, Hausmann J, Hay A, Hayward K, Heiart J, Hekl K, Henderson L, Henrickson M, Hersh A, Hickey K, Hill P, Hillyer S, Hiraki L, Hiskey M, Hobday P, Hoffart C, Holland M, Hollander M, Hong S, Horwitz M, Hsu J, Huber A, Huggins J, Hui-Yuen J, Hung C, Huntington J, Huttenlocher A, Ibarra M, Imundo L, Inman C, Insalaco A, Jackson A, Jackson S, James K, Janow G, Jaquith J, Jared S, Johnson N, Jones J, Jones J, Jones J, Jones K, Jones S, Joshi S, Jung L, Justice C, Justiniano A, Karan N, Kaufman K, Kemp A, Kessler E, Khalsa U, Kienzle B, Kim S, Kimura Y, Kingsbury D, Kitcharoensakkul M, Klausmeier T, Klein K, Klein-Gitelman M, Kompelien B, Kosikowski A, Kovalick L, Kracker J, Kramer S, Kremer C, Lai J, Lam J, Lang B, Lapidus S, Lapin B, Lasky A, Latham D, Lawson E, Laxer R, Lee P, Lee P, Lee T, Lentini L, Lerman M, Levy D, Li S, Lieberman S, Lim L, Lin C, Ling N, Lingis M, Lo M, Lovell D, Lowman D, Luca N, Lvovich S, Madison C, Madison J, Manzoni SM, Malla B, Maller J, Malloy M, Mannion M, Manos C, Marques L, Martyniuk A, Mason T, Mathus S, McAllister L, McCarthy K, McConnell K, McCormick E, McCurdy D, Stokes PMC, McGuire S, McHale I, McMonagle A, McMullen-Jackson C, Meidan E, Mellins E, Mendoza E, Mercado R, Merritt A, Michalowski L, Miettunen P, Miller M, Milojevic D, Mirizio E, Misajon E, Mitchell M, Modica R, Mohan S, Moore K, Moorthy L, Morgan S, Dewitt EM, Moss C, Moussa T, Mruk V, Murphy A, Muscal E, Nadler R, Nahal B, Nanda K, Nasah N, Nassi L, Nativ S, Natter M, Neely J, Nelson B, Newhall L, Ng L, Nicholas J, Nicolai R, Nigrovic P, Nocton J, Nolan B, Oberle E, Obispo B, O’Brien B, O’Brien T, Okeke O, Oliver M, Olson J, O’Neil K, Onel K, Orandi A, Orlando M, Osei-Onomah S, Oz R, Pagano E, Paller A, Pan N, Panupattanapong S, Pardeo M, Paredes J, Parsons A, Patel J, Pentakota K, Pepmueller P, Pfeiffer T, Phillippi K, Marafon DP, Phillippi K, Ponder L, Pooni R, Prahalad S, Pratt S, Protopapas S, Puplava B, Quach J, Quinlan-Waters M, Rabinovich C, Radhakrishna S, Rafko J, Raisian J, Rakestraw A, Ramirez C, Ramsay E, Ramsey S, Randell R, Reed A, Reed A, Reed A, Reid H, Remmel K, Repp A, Reyes A, Richmond A, Riebschleger M, Ringold S, Riordan M, Riskalla M, Ritter M, Rivas-Chacon R, Robinson A, Rodela E, Rodriquez M, Rojas K, Ronis T, Rosenkranz M, Rosolowski B, Rothermel H, Rothman D, Roth-Wojcicki E, Rouster-Stevens K, Rubinstein T, Ruth N, Saad N, Sabbagh S, Sacco E, Sadun R, Sandborg C, Sanni A, Santiago L, Sarkissian A, Savani S, Scalzi L, Schanberg L, Scharnhorst S, Schikler K, Schlefman A, Schmeling H, Schmidt K, Schmitt E, Schneider R, Schollaert-Fitch K, Schulert G, Seay T, Seper C, Shalen J, Sheets R, Shelly A, Shenoi S, Shergill K, Shirley J, Shishov M, Shivers C, Silverman E, Singer N, Sivaraman V, Sletten J, Smith A, Smith C, Smith J, Smith J, Smitherman E, Soep J, Son M, Spence S, Spiegel L, Spitznagle J, Sran R, Srinivasalu H, Stapp H, Steigerwald K, Rakovchik YS, Stern S, Stevens A, Stevens B, Stevenson R, Stewart K, Stingl C, Stokes J, Stoll M, Stringer E, Sule S, Sumner J, Sundel R, Sutter M, Syed R, Syverson G, Szymanski A, Taber S, Tal R, Tambralli A, Taneja A, Tanner T, Tapani S, Tarshish G, Tarvin S, Tate L, Taxter A, Taylor J, Terry M, Tesher M, Thatayatikom A, Thomas B, Tiffany K, Ting T, Tipp A, Toib D, Torok K, Toruner C, Tory H, Toth M, Tse S, Tubwell V, Twilt M, Uriguen S, Valcarcel T, Van Mater H, Vannoy L, Varghese C, Vasquez N, Vazzana K, Vehe R, Veiga K, Velez J, Verbsky J, Vilar G, Volpe N, von Scheven E, Vora S, Wagner J, Wagner-Weiner L, Wahezi D, Waite H, Walker J, Walters H, Muskardin TW, Waqar L, Waterfield M, Watson M, Watts A, Weiser P, Weiss J, Weiss P, Wershba E, White A, Williams C, Wise A, Woo J, Woolnough L, Wright T, Wu E, Yalcindag A, Yee M, Yen E, Yeung R, Yomogida K, Yu Q, Zapata R, Zartoshti A, Zeft A, Zeft R, Zhang Y, Zhao Y, Zhu A, Zic C. Social determinants of health influence disease activity and functional disability in Polyarticular Juvenile Idiopathic Arthritis. Pediatr Rheumatol Online J 2022; 20:18. [PMID: 35255941 PMCID: PMC8903717 DOI: 10.1186/s12969-022-00676-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Social determinants of health (SDH) greatly influence outcomes during the first year of treatment in rheumatoid arthritis, a disease similar to polyarticular juvenile idiopathic arthritis (pJIA). We investigated the correlation of community poverty level and other SDH with the persistence of moderate to severe disease activity and functional disability over the first year of treatment in pJIA patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance Registry. METHODS In this cohort study, unadjusted and adjusted generalized linear mixed effects models analyzed the effect of community poverty and other SDH on disease activity, using the clinical Juvenile Arthritis Disease Activity Score-10, and disability, using the Child Health Assessment Questionnaire, measured at baseline, 6, and 12 months. RESULTS One thousand six hundred eighty-four patients were identified. High community poverty (≥20% living below the federal poverty level) was associated with increased odds of functional disability (OR 1.82, 95% CI 1.28-2.60) but was not statistically significant after adjustment (aOR 1.23, 95% CI 0.81-1.86) and was not associated with increased disease activity. Non-white race/ethnicity was associated with higher disease activity (aOR 2.48, 95% CI: 1.41-4.36). Lower self-reported household income was associated with higher disease activity and persistent functional disability. Public insurance (aOR 1.56, 95% CI 1.06-2.29) and low family education (aOR 1.89, 95% CI 1.14-3.12) was associated with persistent functional disability. CONCLUSION High community poverty level was associated with persistent functional disability in unadjusted analysis but not with persistent moderate to high disease activity. Race/ethnicity and other SDH were associated with persistent disease activity and functional disability.
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Affiliation(s)
- William Daniel Soulsby
- University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA, 94158, USA.
| | - Nayimisha Balmuri
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Victoria Cooley
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Linda M. Gerber
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Erica Lawson
- grid.266102.10000 0001 2297 6811University of California, San Francisco, 550 16th Street, 4th Floor, Box #0632, San Francisco, CA 94158 USA
| | - Susan Goodman
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Karen Onel
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
| | - Bella Mehta
- grid.239915.50000 0001 2285 8823Hospital for Special Surgery, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA
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Donnachie D, Yim G, Watts A. 130 Paediatric Hand Fractures Requiring Surgery – the Results of a Bespoke Hand Surgery Service. Br J Surg 2022. [DOI: 10.1093/bjs/znac039.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
To evaluate the management of The Royal Devon and Exeter Hospital (RD&E) bespoke hand surgery service on paediatric closed hand fractures. In particular, an assessment against The British Society for Surgery of the Hand (BSSH) closed fracture standards on treatment timelines and national guidance compliance.
Method
A retrospective review of all paediatric patients requiring plastic surgery seen at the RD&E plastics trauma clinic from 1st Nov 2020 to 28th Feb 2021 was performed. This was compared to two previous audit cycles completed during winter 2019 and summer 2020. Health informatics was collated via our IT department and thoroughly reviewed using departmental notes. Exclusion criteria included: all non-fracture injuries, patients > 18 years old and open fractures.
Results
In winter 2020–21 all patients were referred the same day of injury and 92% were seen by a Plastic Surgeon within 24 hours of injury. This was an improvement from the mean time from referral to clinic of 5 days in winter 2019 and 1.33 days in summer 2020 respectively. 85% of cases are now operated within 48 hours of review and 92% of cases were operated within 72 hours of the decision to operate where conservative management had failed.
Conclusions
The introduction of a ‘rapid-access’ musculoskeletal unit with early senior review and a dedicated theatre has created ‘gold-standard’ compliance with national standards for the operative management of closed paediatric fractures. We should continue to focus on improving and increasing capacity of this service as it has likely improved both the patient journey and outcomes.
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Affiliation(s)
- D. Donnachie
- Royal Devon & Exeter NHS Trust, Exeter, United Kingdom
| | - G. Yim
- Royal Devon & Exeter NHS Trust, Exeter, United Kingdom
| | - A. Watts
- Royal Devon & Exeter NHS Trust, Exeter, United Kingdom
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13
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Bodner K, Rauen Firkowski C, Bennett JR, Brookson C, Dietze M, Green S, Hughes J, Kerr J, Kunegel‐Lion M, Leroux SJ, McIntire E, Molnár PK, Simpkins C, Tekwa E, Watts A, Fortin M. Bridging the divide between ecological forecasts and environmental decision making. Ecosphere 2021. [DOI: 10.1002/ecs2.3869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Korryn Bodner
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Ontario Canada
| | - Carina Rauen Firkowski
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Cole Brookson
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Michael Dietze
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - Stephanie Green
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Josie Hughes
- National Wildlife Research Centre Environment and Climate Change Canada Ottawa Ontario Canada
| | - Jeremy Kerr
- Department of Biology University of Ottawa Ottawa Ontario Canada
| | - Mélodie Kunegel‐Lion
- Canadian Forest Service Northern Forestry Centre Natural Resources Canada Edmonton Alberta Canada
| | - Shawn J. Leroux
- Department of Biology Memorial University of Newfoundland St. John’s Newfoundland Canada
| | - Eliot McIntire
- Canadian Forest Service Pacific Forestry Centre Natural Resources Canada Victoria British Columbia Canada
- Faculty of Forestry Forest Resources Management University of British Columbia Vancouver British Columbia Canada
| | - Péter K. Molnár
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Ontario Canada
| | - Craig Simpkins
- School of Environment University of Auckland Auckland New Zealand
- Department of Biology Wilfrid Laurier University Waterloo Ontario Canada
- Department of Ecological Modelling Georg‐August University of Goettingen Goettingen Germany
| | - Edward Tekwa
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
| | | | - Marie‐Josée Fortin
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
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14
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Yoon J, Sayan M, Wang S, Watts A, Greener A, Kelly M, Word N. Effect of Hydrogel Rectal Spacer on Intrafraction Prostate Motion During Radiotherapy of Prostate Cancer Patients. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Dbeis R, Yim G, Watts A. 1018 Did COVID Compromise the Care of Closed Paediatric Hand Fractures? Br J Surg 2021. [DOI: 10.1093/bjs/znab259.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Aim
To assess the effect of a ‘rapid-access’ musculoskeletal unit, established in March 2020, as part of the Royal Devon & Exeter hospital COVID response, with direct assessment of hand trauma by the Plastic Surgery department staff, on treatment timelines and national guidance compliance for closed paediatric hand fractures.
Method
This was a retrospective review from 1st January to 31st December 2019 and a prospective study from the 1st April to 15th June 2020. The retrospective cases were collated by health informatics. The prospective data was recorded on the department’s database. Exclusion criteria: nail bed injuries with tuft fractures, ligament injuries only, open fractures and patients aged 18 at time of surgery.
Results
In 2019 the majority (73%) of patients (n = 26) were referred within 48hrs but waited a median of 5 days to be seen in clinic by a hand surgeon resulting in significant delays in treatment. After service reconfiguration in 2020, all patients (n = 6) were operated on within 72 hours of the decision to operate - mean time to surgery 1.5 days (range 0-3 days). The mean time from referral to clinic was 1.33 days (range 0-6 days). 4 patients were operated on within 7 days of injury. Of the 2 patients operated on > 7 days, 1 was referred 32 days post injury and 1 failed conservative management.
Conclusions
The introduction of a ‘rapid-access’ musculoskeletal unit with early senior review and a dedicated theatre has created ‘gold-standard’ compliance with national standards for the operative management of closed paediatric fractures.
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Affiliation(s)
- R Dbeis
- Aberdeen Royal Infirmary, Aberdeen, United Kingdom
- Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - G Yim
- Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - A Watts
- Royal Devon & Exeter Hospital, Exeter, United Kingdom
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16
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Watts A, Watkinson W, Shaw D. 89 Do Corticosteroid and Local Anaesthetic Hip Injections Administered Proximal or Distal to The Zona Orbicularis Have an Effect on Patient Satisfaction? Br J Surg 2021. [DOI: 10.1093/bjs/znab259.967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
Pubofemoral and ischiofemoral ligaments blend to make zona orbicularis. Zonaorbicularis has been suggested to force fluid from peripheral compartment to central compartment in unidirectional flow. This study aims to assess whether injection of corticosteroid with local anaesthetic injected either proximal or distal to the zona orbicularis has effect on patient satisfaction.
Method
This retrospective study investigated consecutive patients undergoing ultrasound guided hip injections at a single centre in the UK between November 2018 and March 2019. Patients were identified using IMPAX© picture archiving and communications system. Radiographs were assessed to see if radiopaque dye and therefore corticosteroid and local anaesthetic had been injected proximal or distal to the zona orbicularis. Clinic letters were accessed on the electronic patient record and we recorded whether patients had pain relief at 24 hours and 2 weeks following hip injection.
Results
133 Patients were identified during the study period, of which 40 were included. At 24 hours post-injection 72% of patients were satisfied and 28% were unsatisfied, for which there was 76% and 70% satisfaction for proximal and distal injections respectively (p = 0.63). At 2 weeks post-injection 45% of patients were satisfied and 55% of patients unsatisfied, for which there was 47% and 44% satisfaction for proximal and distal injections respectively (p = 0.9).
Conclusions
Overall patient satisfaction is high following hip corticosteroid and local anaesthetic injection. No difference was found between injections proximal and distal to the zona orbicularis. Further research is needed to quantify the association between proximal and distal injections.
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Affiliation(s)
- A Watts
- Bradford Royal Infirmary, Bradford, United Kingdom
| | - W Watkinson
- Bradford Royal Infirmary, Bradford, United Kingdom
| | - D Shaw
- Bradford Royal Infirmary, Bradford, United Kingdom
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17
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Dudas G, Hong SL, Potter BI, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, Fuh-Neba T, Vickos U, Ulrich M, Leendertz FH, Khan K, Huber C, Watts A, Olendraitė I, Snijder J, Wijnant KN, Bonvin AMJJ, Martres P, Behillil S, Ayouba A, Maidadi MF, Djomsi DM, Godwe C, Butel C, Šimaitis A, Gabrielaitė M, Katėnaitė M, Norvilas R, Raugaitė L, Koyaweda GW, Kandou JK, Jonikas R, Nasvytienė I, Žemeckienė Ž, Gečys D, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Alzbutas G, Aziza AA, Lusamaki EK, Cigolo JCM, Mawete FM, Lofiko EL, Kingebeni PM, Tamfum JJM, Belizaire MRD, Essomba RG, Assoumou MCO, Mboringong AB, Dieng AB, Juozapaitė D, Hosch S, Obama J, Ayekaba MO, Naumovas D, Pautienius A, Rafaï CD, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Lesauskaitė V, Žemaitis L, Griškevičius L, Baele G. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nat Commun 2021; 12:5769. [PMID: 34599175 PMCID: PMC8486757 DOI: 10.1038/s41467-021-26055-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
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Affiliation(s)
- Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Barney I Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
- Viral Evolution, Robert Koch Institute, 13353, Berlin, Germany
| | - Frédéric S Niatou-Singa
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Thais B Tombolomako
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Terence Fuh-Neba
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Ulrich Vickos
- Infectious and Tropical Diseases Unit, Department of medicine, Amitié Hospital, Bangui, Central African Republic
- Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Kamran Khan
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | | | | | - Ingrida Olendraitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kim N Wijnant
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Pascale Martres
- Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
| | - Sylvie Behillil
- Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Ahidjo Ayouba
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Martin Foudi Maidadi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Dowbiss Meta Djomsi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Celestin Godwe
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Aistis Šimaitis
- The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
| | | | - Monika Katėnaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Rimvydas Norvilas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Ligita Raugaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Giscard Wilfried Koyaweda
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Jephté Kaleb Kandou
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Rimvydas Jonikas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Inga Nasvytienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Živilė Žemeckienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Dovydas Gečys
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kamilė Tamušauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Milda Norkienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Emilija Vasiliūnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Danguolė Žiogienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marius Šukys
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mantas Šarauskas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Gediminas Alzbutas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Adrienne Amuri Aziza
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Claude Makangara Cigolo
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Francisca Muyembe Mawete
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Emmanuel Lokilo Lofiko
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
| | - Placide Mbala Kingebeni
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | | | - René Ghislain Essomba
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marie Claire Okomo Assoumou
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Alle Baba Dieng
- World Health Organization, Cameroon Office, Yaoundé, Cameroon
| | - Dovilė Juozapaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Justino Obama
- Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
| | | | - Daniel Naumovas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Clotaire Donatien Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Astra Vitkauskienė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rasa Ugenskienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alma Gedvilaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Čereškevičius
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lukas Žemaitis
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Laimonas Griškevičius
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
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18
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell 2021; 184:4939-4952.e15. [PMID: 34508652 PMCID: PMC8313480 DOI: 10.1016/j.cell.2021.07.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
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Affiliation(s)
- Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allison R Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John A Vanchiere
- Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA
| | | | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maximilian Marshall
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Amy K Feehan
- Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Rona S Scott
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Arnaud C Drouin
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kaylynn J Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Sarah Topol
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura Nicholson
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | | | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada
| | - Dahlene N Fusco
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.
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20
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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21
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Aurell J, Gullett B, Holder A, Kiros F, Mitchell W, Watts A, Ottmar R. Wildland Fire Emission Sampling at Fishlake National Forest, Utah Using an Unmanned Aircraft System. Atmos Environ (1994) 2021; 247:118193. [PMID: 34335074 PMCID: PMC8318188 DOI: 10.1016/j.atmosenv.2021.118193] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Emissions from a stand replacement prescribed burn were sampled using an unmanned aircraft system (UAS, or "drone") in Fishlake National Forest, Utah, U.S.A. Sixteen flights over three days in June 2019 provided emission factors for a broad range of compounds including carbon monoxide (CO), carbon dioxide (CO2), nitric oxide (NO), nitrogen oxide (NO2), particulate matter < 2.5 microns in diameter (PM2.5), volatile organic compounds (VOCs) including carbonyls, black carbon, and elemental/organic carbon. To our knowledge, this is the first UAS-based emission sampling for a fire of this magnitude, including both slash pile and crown fires resulting in wildfire-like conditions. The burns consisted of drip torch ignitions as well as ground-mobile and aerial helicopter ignitions of large stands comprising over 1,000 ha, allowing for comparison of same-species emission factors burned under different conditions. The use of a UAS for emission sampling minimizes risk to personnel and equipment, allowing flexibility in sampling location and ensuring capture of representative, fresh smoke constituents. PM2.5 emission factors varied 5-fold and, like most pollutants, varied inversely with combustion efficiency resulting in lower emission factors from the slash piles than the crown fires.
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Affiliation(s)
- J. Aurell
- University of Dayton Research Institute, 300 College Park, Dayton, OH 45469, USA
| | - B. Gullett
- U.S. Environmental Protection Agency, Office of Research and Development, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
- Corresponding author : phone (+1-919) 541-1534; fax (+1-919) 541-0554
| | - A. Holder
- U.S. Environmental Protection Agency, Office of Research and Development, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - F. Kiros
- University of Dayton Research Institute, 300 College Park, Dayton, OH 45469, USA
| | - W. Mitchell
- U.S. Environmental Protection Agency, Office of Research and Development, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - A. Watts
- Desert Research Institute, 2215 Raggio Parkway, Reno, NV 89512, USA
| | - R. Ottmar
- U.S. Forest Service, Pacific Wildland Forest Service Laboratory, 400 North 34 Street, Seattle, WA 98103, USA
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22
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du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole Á, Nicholls SM, Parag KV, Scher E, Vasylyeva TI, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG. Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science 2021; 371:708-712. [PMID: 33419936 PMCID: PMC7877493 DOI: 10.1126/science.abf2946] [Citation(s) in RCA: 234] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.
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Affiliation(s)
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- School of Biological and Environmental Sciences, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Jordan Ashworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Thomas R Connor
- School of Biosciences, Cardiff University, Cardiff, UK
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Samuel M Nicholls
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Kris V Parag
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Emily Scher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Erik M Volz
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
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23
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Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Dudas G, Snyder DJ, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem A, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. medRxiv 2021. [PMID: 33564781 PMCID: PMC7872376 DOI: 10.1101/2021.02.05.21251235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras and that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate COVID-19 epidemics on a local and regional scale.
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24
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Poterek ML, Kraemer MUG, Watts A, Khan K, Perkins TA. Air Passenger Travel and International Surveillance Data Predict Spatiotemporal Variation in Measles Importations to the United States. Pathogens 2021; 10:155. [PMID: 33546131 PMCID: PMC7913265 DOI: 10.3390/pathogens10020155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/30/2021] [Accepted: 01/30/2021] [Indexed: 11/17/2022] Open
Abstract
Measles incidence in the United States has grown dramatically, as vaccination rates are declining and transmission internationally is on the rise. Because imported cases are necessary drivers of outbreaks in non-endemic settings, predicting measles outbreaks in the US depends on predicting imported cases. To assess the predictability of imported measles cases, we performed a regression of imported measles cases in the US against an inflow variable that combines air travel data with international measles surveillance data. To understand the contribution of each data type to these predictions, we repeated the regression analysis with alternative versions of the inflow variable that replaced each data type with averaged values and with versions of the inflow variable that used modeled inputs. We assessed the performance of these regression models using correlation, coverage probability, and area under the curve statistics, including with resampling and cross-validation. Our regression model had good predictive ability with respect to the presence or absence of imported cases in a given state in a given year (area under the curve of the receiver operating characteristic curve (AUC) = 0.78) and the magnitude of imported cases (Pearson correlation = 0.84). By comparing alternative versions of the inflow variable averaging over different inputs, we found that both air travel data and international surveillance data contribute to the model's ability to predict numbers of imported cases and individually contribute to its ability to predict the presence or absence of imported cases. Predicted sources of imported measles cases varied considerably across years and US states, depending on which countries had high measles activity in a given year. Our results emphasize the importance of the relationship between global connectedness and the spread of measles. This study provides a framework for predicting and understanding imported case dynamics that could inform future studies and outbreak prevention efforts.
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Affiliation(s)
- Marya L. Poterek
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (A.W.); (K.K.)
- BlueDot, Toronto, ON M5J 1A7, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (A.W.); (K.K.)
- BlueDot, Toronto, ON M5J 1A7, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - T. Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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25
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Huber C, Watts A, Grills A, Yong JHE, Morrison S, Bowden S, Tuite A, Nelson B, Cetron M, Khan K. Modelling airport catchment areas to anticipate the spread of infectious diseases across land and air travel. Spat Spatiotemporal Epidemiol 2021; 36:100380. [PMID: 33509428 PMCID: PMC10413988 DOI: 10.1016/j.sste.2020.100380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/06/2020] [Accepted: 10/23/2020] [Indexed: 11/23/2022]
Abstract
Air travel is an increasingly important conduit for the worldwide spread of infectious diseases. However, methods to identify which airports an individual may use to initiate travel, or where an individual may travel to upon arrival at an airport is not well studied. This knowledge gap can be addressed by estimating airport catchment areas: the geographic extent from which the airport derives most of its patronage. While airport catchment areas can provide a simple decision-support tool to help delineate the spatial extent of infectious disease spread at a local scale, observed data for airport catchment areas are rarely made publicly available. Therefore, we evaluated a probabilistic choice behavior model, the Huff model, as a potential methodology to estimate airport catchment areas in the United States in data-limited scenarios. We explored the impact of varying input parameters to the Huff model on estimated airport catchment areas: distance decay exponent, distance cut-off, and measures of airport attractiveness. We compared Huff model catchment area patterns for Miami International Airport (MIA) and Harrisburg International Airport (MDT). We specifically compared our model output to observed data sampled for MDT to align model parameters with an established, observed catchment area. Airport catchment areas derived using the Huff model were highly sensitive to changes in model parameters. We observed that a distance decay exponent of 2 and a distance cut-off of 500 km represented the most realistic spatial extent and heterogeneity of the MIA catchment area. When these parameters were applied to MDT, the Huff model produced similar spatial patterns to the observed MDT catchment area. Finally, our evaluation of airport attractiveness showed that travel volume to the specific international destinations of interest for infectious disease importation risks (i.e., Brazil) had little impact on the predicted choice of airport when compared to all international travel. Our work is a proof of concept for use of the Huff model to estimate airport catchment areas as a generalizable decision-support tool in data-limited scenarios. While our work represents an initial examination of the Huff model as a method to approximate airport catchment areas, an essential next step is to conduct a quantitative calibration and validation of the model based on multiple airports, possibly leveraging local human mobility data such as call detail records or online social network data collected from mobile devices. Ultimately, we demonstrate how the Huff model could be potentially helpful to improve the precision of early warning systems that anticipate infectious disease spread, or to incorporate when local public health decision makers need to identify where to mobilize screening infrastructure or containment strategies at a local level.
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Affiliation(s)
- Carmen Huber
- BlueDot, 207 Queens Quay West #801b, Toronto, Ontario, Canada.
| | - Alexander Watts
- BlueDot, 207 Queens Quay West #801b, Toronto, Ontario, Canada
| | - Ardath Grills
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA, United States of America (USA)
| | | | - Stephanie Morrison
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA, United States of America (USA); Eagle Medical Services, LLC, 1826 Loop 1604 W, Suite 336-D, San Antonio, TX, United States of America (USA)
| | - Sarah Bowden
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA, United States of America (USA); Eagle Medical Services, LLC, 1826 Loop 1604 W, Suite 336-D, San Antonio, TX, United States of America (USA)
| | - Ashleigh Tuite
- BlueDot, 207 Queens Quay West #801b, Toronto, Ontario, Canada
| | - Bradley Nelson
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA, United States of America (USA)
| | - Martin Cetron
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, 1600 Clifton Road, Atlanta, GA, United States of America (USA)
| | - Kamran Khan
- BlueDot, 207 Queens Quay West #801b, Toronto, Ontario, Canada; Department of Medicine, Division of Infectious Diseases, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, 38 Shuter St, Toronto, Ontario, Canada
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26
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Menkir TF, Chin T, Hay JA, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina MJ, Lipsitch M, Niehus R. Estimating internationally imported cases during the early COVID-19 pandemic. Nat Commun 2021. [PMID: 33436574 DOI: 10.1101/2020.03.23.20038331v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing imports from other cities. We provide a method, combining daily COVID-19 prevalence and flight passenger volume, to estimate importations from 18 Chinese cities to 43 international destinations, including 26 in Africa. Global case importations from China in early January came primarily from Wuhan, but the inferred source shifted to other cities in mid-February, especially for importations to African destinations. We estimate that 10.4 (6.2 - 27.1) COVID-19 cases were imported to these African destinations, which exhibited marked variation in their magnitude and main sources of importation. We estimate that 90% of imported cases arrived between 17 January and 7 February, prior to the first case detections. Our results highlight the dynamic role of source locations, which can help focus surveillance and response efforts.
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Affiliation(s)
- Tigist F Menkir
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Taylor Chin
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - James A Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Erik D Surface
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Pablo M De Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Kamran Khan
- BlueDot, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Ada W C Yan
- Section of Immunology of Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael J Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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27
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Menkir TF, Chin T, Hay JA, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina MJ, Lipsitch M, Niehus R. Estimating internationally imported cases during the early COVID-19 pandemic. Nat Commun 2021; 12:311. [PMID: 33436574 PMCID: PMC7804934 DOI: 10.1038/s41467-020-20219-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023] Open
Abstract
Early in the COVID-19 pandemic, predictions of international outbreaks were largely based on imported cases from Wuhan, China, potentially missing imports from other cities. We provide a method, combining daily COVID-19 prevalence and flight passenger volume, to estimate importations from 18 Chinese cities to 43 international destinations, including 26 in Africa. Global case importations from China in early January came primarily from Wuhan, but the inferred source shifted to other cities in mid-February, especially for importations to African destinations. We estimate that 10.4 (6.2 - 27.1) COVID-19 cases were imported to these African destinations, which exhibited marked variation in their magnitude and main sources of importation. We estimate that 90% of imported cases arrived between 17 January and 7 February, prior to the first case detections. Our results highlight the dynamic role of source locations, which can help focus surveillance and response efforts.
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Affiliation(s)
- Tigist F Menkir
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Taylor Chin
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - James A Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Erik D Surface
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Pablo M De Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | | | - Kamran Khan
- BlueDot, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada
| | | | - Ada W C Yan
- Section of Immunology of Infection, Department of Infectious Disease, Imperial College London, London, UK
| | - Michael J Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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28
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Watts A, Au NH, Thomas-Bachli A, Forsyth J, Mayah O, Popescu S, Bogoch II. Potential for inter-state spread of Covid-19 from Arizona, USA: analysis of mobile device location and commercial flight data. J Travel Med 2020; 27:5895365. [PMID: 32822473 PMCID: PMC7499632 DOI: 10.1093/jtm/taaa136] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 01/24/2023]
Abstract
A significant rise of SARS-CoV-2 transmission in Arizona in June 2020 prompted the need to evaluate potential dispersion to other regions in the United States. We evaluate the potential for domestic dissemination of SARS-CoV-2 from Arizona using mobile device-location and scheduled flights data.
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Affiliation(s)
- Alexander Watts
- BlueDot, Toronto M5J 1A7, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto M5B 1T8, Canada
| | | | - Andrea Thomas-Bachli
- BlueDot, Toronto M5J 1A7, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto M5B 1T8, Canada
| | | | | | - Saskia Popescu
- Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto M5G 2C4, Canada.,Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto M5G 2C4, Canada
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29
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Menkir TF, Chin T, Hay J, Surface ED, De Salazar PM, Buckee CO, Watts A, Khan K, Sherbo R, Yan AWC, Mina M, Lipsitch M, Niehus R. Estimating internationally imported cases during the early COVID-19 pandemic. medRxiv 2020:2020.03.23.20038331. [PMID: 32511613 PMCID: PMC7276040 DOI: 10.1101/2020.03.23.20038331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Early in the COVID-19 pandemic, when cases were predominantly reported in the city of Wuhan, China, local outbreaks in Europe, North America, and Asia were largely predicted from imported cases on flights from Wuhan, potentially missing imports from other key source cities. Here, we account for importations from Wuhan and from other cities in China, combining COVID-19 prevalence estimates in 18 Chinese cities with estimates of flight passenger volume to predict for each day between early December 2019 to late February 2020 the number of cases exported from China. We predict that the main source of global case importation in early January was Wuhan, but due to the Wuhan lockdown and the rapid spread of the virus, the main source of case importation from mid February became Chinese cities outside of Wuhan. For destinations in Africa in particular, non-Wuhan cities were an important source of case imports (1 case from those cities for each case from Wuhan, range of model scenarios: 0.1-9.8). Our model predicts that 18.4 (8.5 - 100) COVID-19 cases were imported to 26 destination countries in Africa, with most of them (90%) predicted to have arrived between 7th January (±10 days) and 5th February (±3 days), and all of them predicted prior to the first case detections. We finally observed marked heterogeneities in expected imported cases across those locations. Our estimates shed light on shifting sources and local risks of case importation which can help focus surveillance efforts and guide public health policy during the final stages of the pandemic. We further provide a time window for the seeding of local epidemics in African locations, a key parameter for estimating expected outbreak size and burden on local health care systems and societies, that has yet to be defined in these locations.
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Affiliation(s)
- Tigist F. Menkir
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Taylor Chin
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - James Hay
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Erik D. Surface
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Pablo M. De Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | | | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada
- BlueDot, Toronto, Canada
| | | | - Ada W. C. Yan
- Section of Immunology of Infection, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Michael Mina
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
| | - Rene Niehus
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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30
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Tuite AR, Bogoch II, Sherbo R, Watts A, Fisman D, Khan K. Estimation of Coronavirus Disease 2019 (COVID-19) Burden and Potential for International Dissemination of Infection From Iran. Ann Intern Med 2020. [PMID: 32176272 DOI: 10.1101/2020.02.24.20027375v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Affiliation(s)
| | - Isaac I Bogoch
- University of Toronto and University Health Network, Toronto, Ontario, Canada (I.I.B.)
| | - Ryan Sherbo
- St. Michael's Hospital and BlueDot, Toronto, Ontario, Canada (R.S., A.W.)
| | - Alexander Watts
- St. Michael's Hospital and BlueDot, Toronto, Ontario, Canada (R.S., A.W.)
| | - David Fisman
- University of Toronto, Toronto, Ontario, Canada (A.R.T., D.F.)
| | - Kamran Khan
- University of Toronto, St. Michael's Hospital, and BlueDot, Toronto, Ontario, Canada (K.K.)
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31
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Tuite AR, Bogoch II, Sherbo R, Watts A, Fisman D, Khan K. Estimation of Coronavirus Disease 2019 (COVID-19) Burden and Potential for International Dissemination of Infection From Iran. Ann Intern Med 2020; 172:699-701. [PMID: 32176272 PMCID: PMC7081176 DOI: 10.7326/m20-0696] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
| | - Isaac I Bogoch
- University of Toronto and University Health Network, Toronto, Ontario, Canada (I.I.B.)
| | - Ryan Sherbo
- St. Michael's Hospital and BlueDot, Toronto, Ontario, Canada (R.S., A.W.)
| | - Alexander Watts
- St. Michael's Hospital and BlueDot, Toronto, Ontario, Canada (R.S., A.W.)
| | - David Fisman
- University of Toronto, Toronto, Ontario, Canada (A.R.T., D.F.)
| | - Kamran Khan
- University of Toronto, St. Michael's Hospital, and BlueDot, Toronto, Ontario, Canada (K.K.)
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32
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Candido DDS, Watts A, Abade L, Kraemer MUG, Pybus OG, Croda J, de Oliveira W, Khan K, Sabino EC, Faria NR. Routes for COVID-19 importation in Brazil. J Travel Med 2020; 27:5809508. [PMID: 32211799 PMCID: PMC7184379 DOI: 10.1093/jtm/taaa042] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 11/15/2022]
Abstract
The global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization. As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.
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Affiliation(s)
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Leandro Abade
- Department of Zoology, University of Oxford, Oxford, UK
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.,Harvard Medical School, Harvard University, Boston, MA, USA.,Computational Epidemiology Group, Boston Children's Hospital, Boston, MA, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.,Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK
| | - Julio Croda
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil.,Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados Mato Grosso do Sul, Brazil.,Fundação Oswaldo Cruz Campo Grande, Campo Grande, Brazil
| | - Wanderson de Oliveira
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Brazil
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.,Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ester C Sabino
- Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK.,Instituto de Medicina Tropical, University of São Paulo, São Paulo, Brazil.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London
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33
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Bogoch II, Watts A, Thomas-Bachli A, Huber C, Kraemer MUG, Khan K. Pneumonia of unknown aetiology in Wuhan, China: potential for international spread via commercial air travel. J Travel Med 2020. [PMID: 31943059 DOI: 10.1093/jtm/taaa1008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
There is currently an outbreak of pneumonia of unknown aetiology in Wuhan, China. Although there are still several unanswered questions about this infection, we evaluate the potential for international dissemination of this disease via commercial air travel should the outbreak continue.
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Affiliation(s)
- Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Andrea Thomas-Bachli
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Carmen Huber
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
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34
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Bogoch II, Watts A, Thomas-Bachli A, Huber C, Kraemer MUG, Khan K. Pneumonia of unknown aetiology in Wuhan, China: potential for international spread via commercial air travel. J Travel Med 2020; 27:5704418. [PMID: 31943059 PMCID: PMC7107534 DOI: 10.1093/jtm/taaa008] [Citation(s) in RCA: 403] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/04/2022]
Abstract
There is currently an outbreak of pneumonia of unknown aetiology in Wuhan, China. Although there are still several unanswered questions about this infection, we evaluate the potential for international dissemination of this disease via commercial air travel should the outbreak continue.
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Affiliation(s)
- Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada.,Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,BlueDot, Toronto, Canada
| | - Andrea Thomas-Bachli
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,BlueDot, Toronto, Canada
| | - Carmen Huber
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,BlueDot, Toronto, Canada
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,BlueDot, Toronto, Canada
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35
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Bogoch II, Watts A, Thomas-Bachli A, Huber C, Kraemer MUG, Khan K. Potential for global spread of a novel coronavirus from China. J Travel Med 2020; 27:5716260. [PMID: 31985790 PMCID: PMC7074660 DOI: 10.1093/jtm/taaa011] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 11/17/2022]
Abstract
An epidemic of a novel coronavirus emerged from Wuhan, China, in late December 2019 and has since spread to several large Chinese cities. Should a scenario arise where this coronavirus spreads more broadly across China, we evaluate how patterns of international disease transmission could change.
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Affiliation(s)
- Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Ontario, Canada
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
| | - Andrea Thomas-Bachli
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
| | - Carmen Huber
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK.,Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,BlueDot, Toronto, Ontario, Canada
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36
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Lai S, Bogoch II, Ruktanonchai NW, Watts A, Lu X, Yang W, Yu H, Khan K, Tatem AJ. Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study. medRxiv 2020:2020.02.04.20020479. [PMID: 32511631 PMCID: PMC7276059 DOI: 10.1101/2020.02.04.20020479] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background A novel coronavirus (2019-nCoV) emerged in Wuhan City, China, at the end of 2019 and has caused an outbreak of human-to-human transmission with a Public Health Emergency of International Concern declared by the World Health Organization on January 30, 2020. Aim We aimed to estimate the potential risk and geographic range of Wuhan novel coronavirus (2019-nCoV) spread within and beyond China from January through to April, 2020. Methods A series of domestic and international travel network-based connectivity and risk analyses were performed, by using de-identified and aggregated mobile phone data, air passenger itinerary data, and case reports. Results The cordon sanitaire of Wuhan is likely to have occurred during the latter stages of peak population numbers leaving the city before Lunar New Year (LNY), with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% UI: 478 - 1349) had 2019-nCoV infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to Wuhan's lockdown. The majority of these cities were in Asia, but major hubs in Europe, the US and Australia were also prominent, with strong correlation seen between predicted importation risks and reported cases. Because significant spread has already occurred, a large number of airline travellers (3.3 million under the scenario of 75% travel reduction from normal volumes) may be required to be screened at origin high-risk cities in China and destinations across the globe for the following three months of February to April, 2020 to effectively limit spread beyond its current extent. Conclusion Further spread of 2019-nCoV within China and international exportation is likely to occur. All countries, especially vulnerable regions, should be prepared for efforts to contain the 2019-nCoV infection.
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Affiliation(s)
- Shengjie Lai
- WorldPop, School of Geography and Environmental Science, University of Southampton, UK
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Isaac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Nick W Ruktanonchai
- WorldPop, School of Geography and Environmental Science, University of Southampton, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- Bluedot, Toronto, Canada
| | - Xin Lu
- College of Systems Engineering, National University of Defense Technology, Changsha, China
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Weizhong Yang
- Chinese Academy of Medical Sciences & Peking Union Medical College
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- Bluedot, Toronto, Canada
| | - Andrew J Tatem
- WorldPop, School of Geography and Environmental Science, University of Southampton, UK
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37
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Kain D, Findlater A, Lightfoot D, Maxim T, Kraemer MUG, Brady OJ, Watts A, Khan K, Bogoch II. Factors Affecting Pre-Travel Health Seeking Behaviour and Adherence to Pre-Travel Health Advice: A Systematic Review. J Travel Med 2019; 26:5549355. [PMID: 31407776 DOI: 10.1093/jtm/taz059] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Recent years have seen unprecedented growth in international travel. Travellers are at high risk for acquiring infections while abroad and potentially bringing these infections back to their home country. There are many ways to mitigate this risk by seeking pre-travel advice (PTA), including receiving recommended vaccinations and chemoprophylaxis, however many travellers do not seek or adhere to PTA. We conducted a systematic review to further understand PTA-seeking behaviour with an ultimate aim to implement interventions that improve adherence to PTA and reduce morbidity and mortality in travellers. METHODS We conducted a systematic review of published medical literature selecting studies that examined reasons for not seeking PTA and non-adherence to PTA over the last ten years. 4484 articles were screened of which 56 studies met our search criteria after full text review. RESULTS The major reason for not seeking or non-adherence to PTA was perceived low risk of infection while travelling. Side effects played a significant role for lack of adherence specific to malaria prophylaxis. CONCLUSIONS These data may help clinicians and public health providers to better understand reasons for non-adherence to PTA and target interventions to improve travellers understanding of potential and modifiable risks. Additionally, we discuss specific recommendations to increase public health education that may enable travellers to seek PTA.
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Affiliation(s)
- Dylan Kain
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Aidan Findlater
- Department of Medicine, McMaster University, Hamilton, Canada
| | | | - Timea Maxim
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | | | - Oliver J Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada.,Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada.,Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
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38
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Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic. Cell 2019; 178:1057-1071.e11. [PMID: 31442400 PMCID: PMC6716374 DOI: 10.1016/j.cell.2019.07.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/15/2019] [Accepted: 07/12/2019] [Indexed: 12/21/2022]
Abstract
The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Zika cases to identify transmission not captured by reporting. We uncovered an unreported outbreak in Cuba during 2017, a year after peak transmission in neighboring islands. By sequencing Zika virus, we show that the establishment of the virus was delayed by a year and that the ensuing outbreak was sparked by long-lived lineages of Zika virus from other Caribbean islands. Our data suggest that, although mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, such measures need to be maintained to be effective. Our study highlights how Zika virus may still be "silently" spreading and provides a framework for understanding outbreak dynamics. VIDEO ABSTRACT.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Sharada Saraf
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Amanda L Tan
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA; Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Rachel J Oidtman
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA; Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Glenn Oliveira
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Aaron Hentoff
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Deepit Bhatia
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA
| | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA
| | - Vanessa Landis
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA
| | - Ian Stryker
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Marshall R Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Edgar W Kopp
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Andrew C Cannons
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Lea Heberlein-Larson
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA
| | - Stephen White
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, FL 33125, USA
| | - Leah D Gillis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, FL 33125, USA
| | - Michael J Ricciardi
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jaclyn Kwal
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Paola K Lichtenberger
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Diogo M Magnani
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA; Section of Infectious Diseases, Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - Lauren M Gardner
- School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Department of Civil Engineering, Johns Hopkins University, Baltimore, MD 21287, USA
| | - T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8, Canada
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA
| | - Sharon Isern
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA
| | - Scott F Michael
- Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA.
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.
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Kraemer MUG, Brady OJ, Watts A, German M, Hay SI, Khan K, Bogoch II. Zika virus transmission in Angola and the potential for further spread to other African settings. Trans R Soc Trop Med Hyg 2019; 111:527-529. [PMID: 29394415 PMCID: PMC5914323 DOI: 10.1093/trstmh/try001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
Abstract
Background Cases of Zika virus were recently detected in Luanda, Angola, a major travel hub in Africa. The risk of Zika virus transmission throughout the continent from Angola is evaluated. Methods Travel volumes were assessed using monthly passenger-level flight data from Luanda to all locations throughout Africa. Travel data was superimposed onto seasonal environmental suitability maps that predict the potential for subsequent Zika virus transmission. Results and Conclusions Windhoek, Maputo, Durban and Kinshasa have the greatest potential for Zika virus introduction and transmission during the southern hemisphere summer months, and Nairobi during the northern hemisphere summer months.
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Affiliation(s)
- Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, United Kingdom.,Harvard Medical School, Boston.,Boston Children's Hospital Informatics Program, Boston, United States
| | - Oliver J Brady
- Centre for the Mathematical Modeling of Infectious Diseases, London School of Hygiene and Tropical Medicine, University of London, United Kingdom
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Matthew German
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto
| | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto.,Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
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40
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Bogoch II, Maxim T, Acosta H, Bhatia D, Chen S, Huber C, Janes A, Yong JHE, Thomas A, Kraemer MUG, Watts A, Khan K. Potential plague exportation from Madagascar via international air travel. Lancet Infect Dis 2019; 18:247-248. [PMID: 29485085 DOI: 10.1016/s1473-3099(18)30077-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/09/2018] [Accepted: 01/09/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada; Division of Internal Medicine and Division of Infectious Diseases, University Health Network, Toronto General Hospital, Toronto, ON M5G 2C4, Canada.
| | - Timea Maxim
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Hernan Acosta
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Deepit Bhatia
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Shirley Chen
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Carmen Huber
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Andrew Janes
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Jean H E Yong
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Andrea Thomas
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Moritz U G Kraemer
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA; Department of Zoology, University of Oxford, Oxford, UK
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
| | - Kamran Khan
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada; Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, ON, Canada
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41
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Laffer A, Bevan A, Watts A. SEDENTARY BEHAVIOR AND COGNITION IN COGNITIVELY INTACT OLDER ADULTS. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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42
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Losinski G, Hicks H, Watts A. BENEFIT OF LIGHT PHYSICAL ACTIVITY ON EXECUTIVE FUNCTION FOR INDIVIDUALS WITH ALZHEIMER’S DISEASE. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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43
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Watts A, Michaelis E, Swerdlow R. TOMM40 ‘523 GENE ASSOCIATED WITH COGNITIVE PERFORMANCE AND DECLINE AMONG NON-APOE E4 CARRIERS. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.1581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - R Swerdlow
- University of Kansas Alzheimer’s Disease Center
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44
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Foster JD, Tou S, Curtis NJ, Smart NJ, Acheson A, Maxwell-Armstrong C, Watts A, Singh B, Francis NK. Closure of the perineal defect after abdominoperineal excision for rectal adenocarcinoma - ACPGBI Position Statement. Colorectal Dis 2018; 20 Suppl 5:5-23. [PMID: 30182511 DOI: 10.1111/codi.14348] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 07/16/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Perineal wound morbidity is common following abdominoperineal excision of the rectum (APE). There is no consensus on the optimum perineal reconstruction method after APE, and in particular 'extra-levator APE' (ELAPE). METHODS A systematic review of the PubMed, Embase and Cochrane databases was performed. This position statement formulated clinical questions and graded the evidence to make recommendations. RESULTS Perineal wound complications may be higher following ELAPE compared to 'conventional APE (cAPE)' however there is insufficient evidence to recommend cAPE over ELAPE with regards to the impact upon perineal wound healing. The majority of cAPE studies have used primary closure with varying complication rates reported. Where concerns regarding perineal wound healing exist, myocutaneous flap closure may be considered as an alternative method. There is minimal available evidence on perineal mesh reconstruction following cAPE. Primary closure, mesh use and myocutaneous flap reconstruction following ELAPE has been reported although variations in definitions and low-quality of available evidence limit comparison. There is insufficient evidence to recommend one particular method of perineal closure after ELAPE. Primary perineal closure is likely to have a higher risk of perineal herniation. Myocutaneous flaps and biological mesh have been effectively used in ELAPE closure. There is insufficient evidence to support one particular type of flap or mesh. Perineal wound complication rates are significantly increased when neo-adjuvant radiotherapy is delivered, regardless of surgical technique. There is no evidence that laparoscopy reduces APE perineal wound complications. CONCLUSION This position statement updates clinicians on current evidence around perineal closure after APE surgery.
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Affiliation(s)
- J D Foster
- Department of General Surgery, Poole Hospital NHS Foundation Trust, Poole, Dorset, UK
| | - S Tou
- Department of General Surgery, Royal Derby Hospital, Derby, UK
| | - N J Curtis
- Department of General Surgery, Yeovil District Hospital NHS Foundation Trust, Yeovil, Somerset, UK.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - N J Smart
- Department of Surgery, Royal Devon and Exeter Hospital, Exeter, UK
| | - A Acheson
- Department of Colorectal Surgery, Nottingham University Hospital, Nottingham, UK
| | - C Maxwell-Armstrong
- Department of Colorectal Surgery, Nottingham University Hospital, Nottingham, UK
| | - A Watts
- Department of Surgery, Royal Devon and Exeter Hospital, Exeter, UK
| | - B Singh
- Department of General Surgery, Leicester General Hospital, Leicester, UK
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45
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Chomiak T, Watts A, Burt J, Camicioli R, Tan SN, McKeown MJ, Hu B. Differentiating cognitive or motor dimensions associated with the perception of fall-related self-efficacy in Parkinson's disease. NPJ Parkinsons Dis 2018; 4:26. [PMID: 30155514 PMCID: PMC6102294 DOI: 10.1038/s41531-018-0059-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 05/28/2018] [Accepted: 06/07/2018] [Indexed: 12/18/2022] Open
Abstract
In Parkinson's disease (PD), concurrent declines in cognitive and motor domain function can severely limit an individual's ability to conduct daily tasks. Current diagnostic methods, however, lack precision in differentiating domain-specific contributions of cognitive or motor impairments based on a patients' clinical manifestation. Fear of falling (FOF) is a common clinical manifestation among the elderly, in which both cognitive and motor impairments can lead to significant barriers to a patients' physical and social activities. The present study evaluated whether a set of analytical and machine-learning approaches could be used to help delineate boundary conditions and separate cognitive and motor contributions to a patient's own perception of self-efficacy and FOF. Cognitive and motor clinical scores, in conjunction with FOF, were collected from 57 Parkinson's patients during a multi-center rehabilitation intervention trial. Statistical methodology was used to extract a subset of uncorrelated cognitive and motor components associated with cognitive and motor predictors, which were then used to independently identify and visualize cognitive and motor dimensions associated with FOF. We found that a central cognitive process, extracted from tests of executive, attentional, and visuoperceptive function, was a unique and significant independent cognitive predictor of FOF in PD. In addition, we provide evidence that the approaches described here may be used to computationally discern specific types of FOF based on separable cognitive or motor models. Our results are consistent with a contemporary model that the deterioration of a central cognitive mechanism that modulates self-efficacy also plays a critical role in FOF in PD.
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Affiliation(s)
- Taylor Chomiak
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Alexander Watts
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
| | - Jacqueline Burt
- Department of Medicine, Division of Neurology, Clinical Sciences Building, University of Alberta, Edmonton, AB T6G 2R7 Canada
| | - Richard Camicioli
- Department of Medicine, Division of Neurology, Clinical Sciences Building, University of Alberta, Edmonton, AB T6G 2R7 Canada
| | - Sun Nee Tan
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Martin J. McKeown
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Bin Hu
- Division of Translational Neuroscience, Department of Clinical Neurosciences, Hotchkiss Brain Institute, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1 Canada
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46
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Brent SE, Watts A, Cetron M, German M, Kraemer MUG, Bogoch II, Brady OJ, Hay SI, Creatore MI, Khan K. International travel between global urban centres vulnerable to yellow fever transmission. Bull World Health Organ 2018; 96:343-354B. [PMID: 29875519 PMCID: PMC5985425 DOI: 10.2471/blt.17.205658] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/27/2018] [Accepted: 03/06/2018] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE To examine the potential for international travel to spread yellow fever virus to cities around the world. METHODS We obtained data on the international flight itineraries of travellers who departed yellow fever-endemic areas of the world in 2016 for cities either where yellow fever was endemic or which were suitable for viral transmission. Using a global ecological model of dengue virus transmission, we predicted the suitability of cities in non-endemic areas for yellow fever transmission. We obtained information on national entry requirements for yellow fever vaccination at travellers' destination cities. FINDINGS In 2016, 45.2 million international air travellers departed from yellow fever-endemic areas of the world. Of 11.7 million travellers with destinations in 472 cities where yellow fever was not endemic but which were suitable for virus transmission, 7.7 million (65.7%) were not required to provide proof of vaccination upon arrival. Brazil, China, India, Mexico, Peru and the United States of America had the highest volumes of travellers arriving from yellow fever-endemic areas and the largest populations living in cities suitable for yellow fever transmission. CONCLUSION Each year millions of travellers depart from yellow fever-endemic areas of the world for cities in non-endemic areas that appear suitable for viral transmission without having to provide proof of vaccination. Rapid global changes in human mobility and urbanization make it vital for countries to re-examine their vaccination policies and practices to prevent urban yellow fever epidemics.
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Affiliation(s)
- Shannon E Brent
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario, M5B 1W8, Canada
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario, M5B 1W8, Canada
| | - Martin Cetron
- Division of Global Migration and Quarantine, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, United States of America (USA)
| | - Matthew German
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario, M5B 1W8, Canada
| | - Moritz UG Kraemer
- Computational Epidemiology Laboratory, Boston Children’s Hospital, Boston, USA
| | - Isaac I Bogoch
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Oliver J Brady
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, England
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA
| | - Maria I Creatore
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario, M5B 1W8, Canada
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Abstract
AIM To determine the impact of sodium molybdate treatment, given weekly, on concentrations of Cu in liver, activity of liver enzymes, and weight gain over 4 weeks, in yearling bulls with elevated concentrations of Cu in liver. METHODS The study was carried on two commercial grazing farms in the Otago region of New Zealand in yearling Friesian bulls (n=150 on Farm A and n=49 on Farm B) with mean concentration of Cu in liver >3,000 µmol/kg fresh weight. On Day 0, all animals were weighed and half were systematically allocated to treatment with sodium molybdate (3 mg/kg liveweight on Farm A and 7 mg/kg liveweight on Farm B); the remainder received no treatment (Control). Sodium molybdate was given as a drench weekly for 4 weeks and all animals were weighed again on Day 28. Ten animals on each farm (five from each treatment group) were systematically selected for blood sampling and liver biopsies on Days 0 and 28. Samples were analysed for concentrations of Cu in plasma, vitamin B12 in serum, activities of γ-glutamyl transferase, aspartate aminotransferase and glutamate dehydrogenase in serum, and concentrations of Cu and vitamin B12 in liver. Separate multivariable linear models were used to compare the change in outcome variables between Days 0 and 28 between bulls that had been drenched with sodium molybdate or not. RESULTS On Farm A, mean concentrations of Cu in liver on Day 28, as a percentage of concentrations on Day 0, for the control group was 55 (95% CI=40-73)% and for the treatment group was 73 (95% CI=43-111)%. On Farm B, the equivalent mean for the control group was 75 (95% CI=42-131)% and for the treatment group was 85 (95% CI=38-134)%. The multivariable linear models indicated that the changes in concentrations of Cu in liver, activities of liver enzymes and weight gain between Days 0 and 28 did not differ between the bulls treated or not with sodium molybdate (p>0.18). CONCLUSIONS AND CLINICAL RELEVANCE Treatment with sodium molybdate in one bolus at weekly intervals for 4 weeks did not affect concentrations of Cu in liver, activity of liver enzymes or weight gain in animals with high concentrations of Cu liver on two farms.
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Affiliation(s)
- E L Cuttance
- a VetEnt Research , 49 Benson Road, Te Awamutu , New Zealand
| | - R A Laven
- b School of Veterinary Science , Massey University , Palmerston North , 4410 , New Zealand
| | - A Watts
- c VetEnt Ranfurly , Stuart Road, Ranfurly , New Zealand
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Tuite AR, Thomas-Bachli A, Acosta H, Bhatia D, Huber C, Petrasek K, Watts A, Yong JHE, Bogoch II, Khan K. Infectious disease implications of large-scale migration of Venezuelan nationals. J Travel Med 2018; 25:5091517. [PMID: 30192972 PMCID: PMC6142906 DOI: 10.1093/jtm/tay077] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/21/2018] [Accepted: 09/04/2018] [Indexed: 01/20/2023]
Abstract
Background The ongoing economic and political crisis in Venezuela has resulted in a collapse of the healthcare system and the re-emergence of previously controlled or eliminated infectious diseases. There has also been an exodus of Venezuelan international migrants in response to the crisis. We sought to describe the infectious disease risks faced by Venezuelan nationals and assess the international mobility patterns of the migrant population. Methods We synthesized data on recent infectious disease events in Venezuela and among international migrants from Venezuela, as well as on current country of residence among the migrant population. We used passenger-level itinerary data from the International Air Transport Association to evaluate trends in outbound air travel from Venezuela over time. We used two parameter-free mobility models, the radiation and impedance models, to estimate the expected population flows from Venezuelan cities to other major Latin American and Caribbean cities. Results Outbreaks of measles, diphtheria and malaria have been reported across Venezuela and other diseases, such as HIV and tuberculosis, are resurgent. Changes in migration in response to the crisis are apparent, with an increase in Venezuelan nationals living abroad, despite an overall decline in the number of outbound air passengers. The two models predicted different mobility patterns, but both highlighted the importance of Colombian cities as destinations for migrants and also showed that some migrants are expected to travel large distances. Despite the large distances that migrants may travel internationally, outbreaks associated with Venezuelan migrants have occurred primarily in countries proximate to Venezuela. Conclusions Understanding where international migrants are relocating is critical, given the association between human mobility and the spread of infectious diseases. In data-limited situations, simple models can be useful for providing insights into population mobility and may help identify areas likely to receive a large number of migrants.
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Affiliation(s)
- Ashleigh R Tuite
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Andrea Thomas-Bachli
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Hernan Acosta
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Deepit Bhatia
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Carmen Huber
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Kieran Petrasek
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Jean H E Yong
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Canada
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49
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Jones CS, Nowers J, Smart NJ, Coelho J, Watts A, Daniels IR. Pelvic floor reconstruction with bilateral gracilis flaps following extralevator abdominoperineal excision - a video vignette. Colorectal Dis 2017; 19:1120-1121. [PMID: 29053218 DOI: 10.1111/codi.13933] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 09/12/2017] [Indexed: 02/08/2023]
Affiliation(s)
- C S Jones
- University of Exeter Medical School, Exeter, UK
| | - J Nowers
- Exeter Surgical Health Services Research Unit (HESRU), Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - N J Smart
- Exeter Surgical Health Services Research Unit (HESRU), Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - J Coelho
- Plastic and Reconstructive Surgery Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - A Watts
- Plastic and Reconstructive Surgery Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - I R Daniels
- Exeter Surgical Health Services Research Unit (HESRU), Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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Laffer A, Sandoval R, Blocker E, Vidoni E, Watts A, Burns J, Sullivan D. ASSESSMENT OF HEALTH-PROMOTING BEHAVIORS BEFORE AND AFTER AN ALZHEIMER’S PREVENTION PROGRAM. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- A. Laffer
- University of Kansas, Lawrence, Kansas,
| | - R. Sandoval
- University of Kansas Medical Center, Fairway, Kansas
| | - E. Blocker
- University of Kansas Medical Center, Fairway, Kansas
| | - E. Vidoni
- University of Kansas Medical Center, Fairway, Kansas
| | - A. Watts
- University of Kansas, Lawrence, Kansas,
| | - J. Burns
- University of Kansas Medical Center, Fairway, Kansas
| | - D.K. Sullivan
- University of Kansas Medical Center, Fairway, Kansas
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