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DeWitt ME, Wierzba TF. Automatic case cluster detection using hospital electronic health record data. Biol Methods Protoc 2023; 8:bpad004. [PMID: 37016667 PMCID: PMC10067150 DOI: 10.1093/biomethods/bpad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/05/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Case detection through contact tracing is a key intervention during an infectious disease outbreak. However, contact tracing is an intensive process where a given contact tracer must locate not only confirmed cases but also identify and interview known contacts. Often these data are manually recorded. During emerging outbreaks, the number of contacts could expand rapidly and beyond this, when focused on individual transmission chains, larger patterns may not be identified. Understanding if particular cases can be clustered and linked to a common source can help to prioritize contact tracing effects and understand underlying risk factors for large spreading events. Electronic health records systems are used by the vast majority of private healthcare systems across the USA, providing a potential way to automatically detect outbreaks and connect cases through already collected data. In this analysis, we propose an algorithm to identify case clusters within a community during an infectious disease outbreak using Bayesian probabilistic case linking and explore how this approach could supplement outbreak responses; especially when human contact tracing resources are limited.
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Affiliation(s)
- Michael E DeWitt
- Department of Internal Medicine, Section on Infectious Disease, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Thomas F Wierzba
- Department of Internal Medicine, Section on Infectious Disease, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
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Zhang HP, Sun YL, Wang YF, Yazici D, Azkur D, Ogulur I, Azkur AK, Yang ZW, Chen XX, Zhang AZ, Hu JQ, Liu GH, Akdis M, Akdis CA, Gao YD. Recent developments in the immunopathology of COVID-19. Allergy 2023; 78:369-388. [PMID: 36420736 PMCID: PMC10108124 DOI: 10.1111/all.15593] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
There has been an important change in the clinical characteristics and immune profile of Coronavirus disease 2019 (COVID-19) patients during the pandemic thanks to the extensive vaccination programs. Here, we highlight recent studies on COVID-19, from the clinical and immunological characteristics to the protective and risk factors for severity and mortality of COVID-19. The efficacy of the COVID-19 vaccines and potential allergic reactions after administration are also discussed. The occurrence of new variants of concerns such as Omicron BA.2, BA.4, and BA.5 and the global administration of COVID-19 vaccines have changed the clinical scenario of COVID-19. Multisystem inflammatory syndrome in children (MIS-C) may cause severe and heterogeneous disease but with a lower mortality rate. Perturbations in immunity of T cells, B cells, and mast cells, as well as autoantibodies and metabolic reprogramming may contribute to the long-term symptoms of COVID-19. There is conflicting evidence about whether atopic diseases, such as allergic asthma and rhinitis, are associated with a lower susceptibility and better outcomes of COVID-19. At the beginning of pandemic, the European Academy of Allergy and Clinical Immunology (EAACI) developed guidelines that provided timely information for the management of allergic diseases and preventive measures to reduce transmission in the allergic clinics. The global distribution of COVID-19 vaccines and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with reduced pathogenic potential dramatically decreased the morbidity, severity, and mortality of COVID-19. Nevertheless, breakthrough infection remains a challenge for disease control. Hypersensitivity reactions (HSR) to COVID-19 vaccines are low compared to other vaccines, and these were addressed in EAACI statements that provided indications for the management of allergic reactions, including anaphylaxis to COVID-19 vaccines. We have gained a depth knowledge and experience in the over 2 years since the start of the pandemic, and yet a full eradication of SARS-CoV-2 is not on the horizon. Novel strategies are warranted to prevent severe disease in high-risk groups, the development of MIS-C and long COVID-19.
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Affiliation(s)
- Huan-Ping Zhang
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuan-Li Sun
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan-Fen Wang
- Department of Pediatrics, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Duygu Yazici
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Dilek Azkur
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Ismail Ogulur
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ahmet Kursat Azkur
- Department of Virology, Faculty of Veterinary Medicine, University of Kirikkale, Kirikkale, Turkey
| | - Zhao-Wei Yang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Xue Chen
- Department of Allergology, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Ai-Zhi Zhang
- Intensive Care Unit, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jia-Qian Hu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guang-Hui Liu
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ya-Dong Gao
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan, China
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Brüssow H. COVID-19: Omicron - the latest, the least virulent, but probably not the last variant of concern of SARS-CoV-2. Microb Biotechnol 2022; 15:1927-1939. [PMID: 35443078 PMCID: PMC9111164 DOI: 10.1111/1751-7915.14064] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 01/10/2023] Open
Abstract
The Omicron variant rapidly became the dominant SARS-CoV-2 strain in South Africa and elsewhere. This review explores whether this rise was due to an increased transmission of the variant or its escape from population immunity by an extensively mutated spike protein. The mutations affected the structure of the spike protein leading to the loss of neutralization by most, but not all, therapeutic monoclonal antibodies. Omicron also shows substantial immune escape from serum antibodies in convalescent patients and vaccinees. A booster immunization increased, however, the titre and breadth of antiviral antibody response. The cellular immune response against Omicron was largely preserved explaining a satisfying protection of boosted vaccinees against severe infections. Clinicians observed less severe infection with Omicron, but other scientists warned that this must not necessarily reflect less intrinsic virulence. However, in animal experiments with mice and hamsters, Omicron infections also displayed a lesser virulence than previous VOCs and lung functions were less compromised. Cell biologists demonstrated that Omicron differs from Delta by preferring the endocytic pathway for cell entry over fusion with the plasma membrane which might explain Omicron's distinct replication along the respiratory tract compared with Delta. Omicron represents a distinct evolutionary lineage that deviated from the mainstream of evolving SARS-CoV-2 already in mid-2020 raising questions about where it circulated before getting widespread in December 2021. The role of Omicron for the future trajectory of the COVID-19 pandemic is discussed.
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Affiliation(s)
- Harald Brüssow
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenLeuvenBelgium
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Elliott P, Eales O, Steyn N, Tang D, Bodinier B, Wang H, Elliott J, Whitaker M, Atchison C, Diggle PJ, Page AJ, Trotter AJ, Ashby D, Barclay W, Taylor G, Ward H, Darzi A, Cooke GS, Donnelly CA, Chadeau-Hyam M. Twin peaks: The Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England. Science 2022; 376:eabq4411. [PMID: 35608440 PMCID: PMC9161371 DOI: 10.1126/science.abq4411] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/20/2022] [Indexed: 12/11/2022]
Abstract
Rapid transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has led to record-breaking incidence rates around the world. The Real-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using reverse transcription polymerase chain reaction (RT-PCR) results from self-administered throat and nose swabs from randomly selected participants aged 5 years and older approximately monthly from May 2020 to March 2022. Weighted prevalence in March 2022 was the highest recorded in REACT-1 at 6.37% (N = 109,181), with the Omicron BA.2 variant largely replacing the BA.1 variant. Prevalence was increasing overall, with the greatest increase in those aged 65 to 74 years and 75 years and older. This was associated with increased hospitalizations and deaths, but at much lower levels than in previous waves against a backdrop of high levels of vaccination.
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Affiliation(s)
- Paul Elliott
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Health Data Research (HDR) UK, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
| | - Oliver Eales
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Nicholas Steyn
- Department of Statistics, University of Oxford, Oxford, UK
- Department of Mathematics, Imperial College London, London, UK
| | - David Tang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Barbara Bodinier
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Haowei Wang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Joshua Elliott
- Imperial College Healthcare NHS Trust, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Matthew Whitaker
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christina Atchison
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Peter J. Diggle
- CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, Lancaster, UK
| | | | | | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Department of Infectious Disease, Imperial College London, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- MRC Centre for Global infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation, Imperial College London, London, UK
| | - Graham S. Cooke
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christl A. Donnelly
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Marc Chadeau-Hyam
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
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