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Vos B, Debouverie L, Doggen K, Delvaux N, Aertgeerts B, De Schreye R, Vaes B. Monitoring COVID-19 in Belgian general practice: A tool for syndromic surveillance based on electronic health records. Eur J Gen Pract 2024; 30:2293699. [PMID: 38186340 PMCID: PMC10776082 DOI: 10.1080/13814788.2023.2293699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND COVID-19 may initially manifest as flu-like symptoms. As such, general practitioners (GPs) will likely to play an important role in monitoring the pandemic through syndromic surveillance. OBJECTIVES To present a COVID-19 syndromic surveillance tool in Belgian general practices. METHODS We performed a nationwide observational prospective study in Belgian general practices. The surveillance tool extracted the daily entries of diagnostic codes for COVID-19 and associated conditions (suspected or confirmed COVID-19, acute respiratory infection and influenza-like illness) from electronic medical records. We calculated the 7-day rolling average for these diagnoses and compared them with data from two other Belgian population-based sources (laboratory-confirmed new COVID-19 cases and hospital admissions for COVID-19), using time series analysis. We also collected data from users and stakeholders about the syndromic surveillance tool and performed a thematic analysis. RESULTS 4773 out of 11,935 practising GPs in Belgium participated in the study. The curve of contacts for suspected COVID-19 followed a similar trend compared with the curves of the official data sources: laboratory-confirmed COVID-19 cases and hospital admissions but with a 10-day delay for the latter. Data were quickly available and useful for decision making, but some technical and methodological components can be improved, such as a greater standardisation between EMR software developers. CONCLUSION The syndromic surveillance tool for COVID-19 in primary care provides rapidly available data useful in all phases of the COVID-19 pandemic to support data-driven decision-making. Potential enhancements were identified for a prospective surveillance tool.
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Affiliation(s)
- Bénédicte Vos
- Health Services Research, Sciensano, Brussels, Belgium
| | | | - Kris Doggen
- Health Services Research, Sciensano, Brussels, Belgium
| | - Nicolas Delvaux
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Bert Aertgeerts
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | | | - Bert Vaes
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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Ares-Blanco S, Guisado-Clavero M, Del Rio LR, Larrondo IG, Fitzgerald L, Murauskienė L, López NP, Perjés Á, Petek D, Petrazzuoli F, Petricek G, Sattler M, Saurek-Aleksandrovska N, Senn O, Seifert B, Serafini A, Sentker T, Ticmane G, Tiili P, Torzsa P, Valtonen K, Vaes B, Vinker S, Adler L, Assenova R, Bakola M, Bayen S, Brutskaya-Stempkovskaya E, Busneag IC, Divjak AĆ, Peña MD, Díaz E, Domeyer PR, Feldmane S, Gjorgjievski D, Gómez-Johansson M, de la Fuente ÁG, Hanževački M, Hoffmann K, Ільков О, Ivanna S, Jandrić-Kočić M, Karathanos VT, Üçüncü EK, Kirkovski A, Knežević S, Korkmaz BÇ, Kostić M, Krztoń-Królewiecka A, Kozlovska L, Nessler K, Gómez-Bravo R, Peña MPA, Lingner H. Primary care indicators for disease burden, monitoring and surveillance of COVID-19 in 31 European countries: Eurodata Study. Eur J Public Health 2024; 34:402-410. [PMID: 38326993 PMCID: PMC10990533 DOI: 10.1093/eurpub/ckad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND During the COVID-19 pandemic, the majority of patients received ambulatory treatment, highlighting the importance of primary health care (PHC). However, there is limited knowledge regarding PHC workload in Europe during this period. The utilization of COVID-19 PHC indicators could facilitate the efficient monitoring and coordination of the pandemic response. The objective of this study is to describe PHC indicators for disease surveillance and monitoring of COVID-19's impact in Europe. METHODS Descriptive, cross-sectional study employing data obtained through a semi-structured ad hoc questionnaire, which was collectively agreed upon by all participants. The study encompasses PHC settings in 31 European countries from March 2020 to August 2021. Key-informants from each country answered the questionnaire. Main outcome: the identification of any indicator used to describe PHC COVID-19 activity. RESULTS Out of the 31 countries surveyed, data on PHC information were obtained from 14. The principal indicators were: total number of cases within PHC (Belarus, Cyprus, Italy, Romania and Spain), number of follow-up cases (Croatia, Cyprus, Finland, Spain and Turkey), GP's COVID-19 tests referrals (Poland), proportion of COVID-19 cases among respiratory illnesses consultations (Norway and France), sick leaves issued by GPs (Romania and Spain) and examination and complementary tests (Cyprus). All COVID-19 cases were attended in PHC in Belarus and Italy. CONCLUSIONS The COVID-19 pandemic exposes a crucial deficiency in preparedness for infectious diseases in European health systems highlighting the inconsistent recording of indicators within PHC organizations. PHC standardized indicators and public data accessibility are urgently needed, conforming the foundation for an effective European-level health services response framework against future pandemics.
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Affiliation(s)
- Sara Ares-Blanco
- Federica Montseny Health Centre, Gerencia Asistencial Atención Primaria, Servicio Madrileño de Salud, Madrid, Spain; Medical Specialties and Public Health, School of Health Sciences, University Rey Juan Carlos, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Marina Guisado-Clavero
- Investigation Support Multidisciplinary Unit for Primary care and Community North Area of Madrid, Gerencia Asistencial Atención Primaria, Servicio Madrileño de Salud, Madrid, Spain
| | - Lourdes Ramos Del Rio
- Federica Montseny Health Centre, Gerencia Asistencial de Atención Primaria, Servicio Madrileño de Salud, Madrid, Spain
| | - Ileana Gefaell Larrondo
- Federica Montseny Health Centre, Gerencia Asistencial de Atención Primaria, Servicio Madrileño de Salud, Madrid, Spain
| | - Louise Fitzgerald
- Member of Irish College of General Practice (MICGP), Member of Royal College of Physician (MRCSI), Dublin, Ireland
| | - Liubovė Murauskienė
- Department of Public Health, Institute of Health Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Naldy Parodi López
- Närhälsan Kungshöjd Health Centre, Gothenburg, Sweden; Department of Pharmacology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ábel Perjés
- Department of Family Medicine at the University of Semmelweis, Budapest, Hungary
| | - Davorina Petek
- Department of Family Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Ferdinando Petrazzuoli
- Department of Clinical Sciences in Malmö, Centre for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Goranka Petricek
- Department of Family Medicine “Andrija Stampar” School of Public Health, School of Medicine, University of Zagreb, Croatia; Health Centre Zagreb West, Croatia
| | | | | | - Oliver Senn
- Institute of Primary Care, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Bohumil Seifert
- Charles University, First Faculty of Medicine, Institute of General Practice, Prague, Czech Republic
| | - Alice Serafini
- Azienda Unità Sanitaria Locale di Modena, Laboratorio EduCare, University of Modena and Reggio Emilia, Modena, Italy
| | - Theresa Sentker
- Center for Public Health and Healthcare, Hannover Medical School, Hannover, Germany
| | - Gunta Ticmane
- Department of Family Medicine at Riga Stradiņš University, Riga, Latvia; Member of the board of the Rural Family Doctors’ Association of Latvia, Latvia
| | - Paula Tiili
- Communicable Diseases and Infection Control Unit, City of Vantaa, Vantaa. University of Helsinki, Helsinki, Finland
| | - Péter Torzsa
- Department of Family Medicine at the University of Semmelweis, Budapest, Hungary
| | - Kirsi Valtonen
- Communicable Diseases and Infection Control Unit, City of Vantaa, Vantaa, Finland
| | - Bert Vaes
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Shlomo Vinker
- Department of Family Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. WONCA Europe President, Israel
| | - Limor Adler
- Department of Family Medicine, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Radost Assenova
- Department Urology and General Practice, Faculty of Medicine, Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Maria Bakola
- Research Unit for General Medicine and Primary Health Care, Faculty of Medicine, School of Health Science, University of Ioannina, Ioannina, Greece
| | - Sabine Bayen
- Department of General Practice, University of Lille, Lille, France
| | | | | | | | - Maryher Delphin Peña
- Department of Geriatric Medicine, Hôpitaux Robert Schuman, Luxembourg, Luxembourg
| | - Esperanza Díaz
- Pandemic Center, Department of Public Health and Primary Health Care, University of Bergen, Bergen, Norway; Norwegian National Institute of Public Health, Bergen, Norway
| | | | - Sabine Feldmane
- Department of Family Medicine, Rīga Stradins University, Riga, Latvia
| | | | | | | | - Miroslav Hanževački
- Department of Family Medicine “Andrija Stampar” School of Public Health, School of Medicine, University of Zagreb, Croatia; Health Centre Zagreb West, Croatia
| | - Kathryn Hoffmann
- Department of General Practice and Primary Care, Med. University of Vienna, Vienna, Austria
| | - Оксана Ільков
- Department of Family Medicine and Outpatient Care, Medical Faculty 2, Uzhhorod National University, Uzhhorod, Ukraine
| | - Shushman Ivanna
- Department of Family Medicine and Outpatient Care, Medical Faculty 2, Uzhhorod National University, Uzhhorod, Ukraine
| | | | - Vasilis Trifon Karathanos
- Laboratory of Hygiene and Epidemiology, Medical Department, Faculty of Health Sciences, University of Ioannina- Greece; GHS, Larnaca, Cyprus
| | - Erva Kirkoç Üçüncü
- Department of Family Medicine, Prof. Dr Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Aleksandar Kirkovski
- Faculty of Medicine, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | | | | | - Milena Kostić
- Health Center “Dr Đorđe Kovačević”, Lazarevac, Belgrade, Serbia
| | | | - Liga Kozlovska
- Department of Family Medicine of Riga Stradins University, Riga, Latvia; President of the Rural Family Doctors' Association of Latvia
| | - Katarzyna Nessler
- Department of Family Medicine UJCM at Uniwersytet Jagielloński - Collegium Medicum, Kraków, Poland
| | - Raquel Gómez-Bravo
- CHNP, Rehaklinik, Ettelbruck, Luxembourg; Research Group Self-Regulation and Health, Institute for Health and Behaviour, Department of Behavioural and Cognitive Sciences, Faculty of Humanities, Education, and Social Sciences, Luxembourg University, Luxembourg, Luxembourg
| | - María Pilar Astier Peña
- Technical Advisor for Quality and Safety, Territorial Healthcare Quality Unit, Territorial Healthcare Direction of Camp de Tarragona, Healthcare Institut of Catalonia, Health Departament, Generalitat de Catalunya GIBA-IIS-Aragón, Catalunya, Spain; Chair of Patient Safety Working Party of semFYC (Spanish Society for Family and Community Medicine) and Quality and Safety in Family Medicine of WONCA World (Global Family Doctors), Board Member of WONCA World and SECA (Spanish Society for Healthcare Quality), Spain
| | - Heidrun Lingner
- Center for Public Health and Healthcare, Hannover Medical School, Hannover, Germany
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Rodríguez JP, Eguíluz VM. Coupling between infectious diseases leads to synchronization of their dynamics. CHAOS (WOODBURY, N.Y.) 2023; 33:021103. [PMID: 36859206 DOI: 10.1063/5.0137380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Interactions between different diseases may change their dynamics. Thus, these interactions represent a source of uncertainty in the modeling of empirical data when the symptoms of both infections are hard to distinguish. We recall previously proposed models of interacting infections, generalizing them to non-symmetric scenarios, showing that both cooperative and competitive interactions lead to synchronization of the maximum fraction of infected individuals in their dynamics. We exemplify this framework with a model coupling the dynamics of COVID-19 and seasonal influenza, simulating cooperation, competition, and asymmetric interactions. We find that the coupling synchronizes both infections, with a stronger influence on the dynamics of influenza.
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Affiliation(s)
- Jorge P Rodríguez
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), CSIC-UIB, 07190 Esporles, Spain
| | - Víctor M Eguíluz
- Instituto de Física Interdisciplinar y Sistemas Complejos (IFISC), CSIC-UIB, 07122 Palma de Mallorca, Spain
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4
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Cong S, Wang C, Wei T, Xie Z, Huang Y, Tan J, Chen A, Ma F, Zheng L. Human metapneumovirus in hospitalized children with acute respiratory tract infections in Beijing, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105386. [PMID: 36372116 DOI: 10.1016/j.meegid.2022.105386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND This study aims to described the epidemiology and genotypic diversity of Human metapneumovirus (HMPV) and the impact of SARS-CoV-2 on the prevalence of HMPV in hospitalized children with Acute respiratory tract infections (ARTIs) in Beijing, China. METHODS From April 2018 to March 2019 and from September 2020 to August 2021, nasopharyngeal aspirates (NPAs) from hospitalized children with ARTIs in Beijing were collected and subjected to real-time polymerase chain reaction tests for HMPV. Then genotyping, detection of 15 common respiratory viruses and clinical characteristics were analyzed on HMPV positive samples. RESULTS 7.9% (124/1572) enrolled pediatric patients were identified as having HMPV infection, and the majority of children under the age of 5 (78.2%, 92/124), From April 2018 to March 2019. The detection rate of HMPV in spring and winter is significantly higher than that in summer and autumn. The co-infection rate were 37.1% (46/124), the most common co-infected virus were parainfluenza virus type 3 (HPIV-3). The main diagnosis of HMPV infection was pneumonia (92.7%,115/124), most patient have cough and fever. Of 78 HMPV-positive specimens, A2b (82.1%,64/78) were the main epidemic subtypes. Hospitalized children with HMPV genotype A infection had a higher viral load compared to genotype B. During the COVID-19 outbreak, Among 232 samples, only 4 cases were HMPV-positive. After statistical test, the detection rate of HMPV during the COVID-19 pandemic has decreased significantly compared with that before the epidemic (p = 0.001). CONCLUSIONS HMPV is an important cause of ARTIs in children under 5 years old. The epidemic peak is generally in winter and spring, and the A2b subtype is the most common. However, under the prevention and control of the COVID-19 pandemic, the HMPV infection of hospitalized children with ARTIs has decreased significantly.
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Affiliation(s)
- Shanshan Cong
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Tianli Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhiping Xie
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yiman Huang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jingjing Tan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Department of Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Aijun Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Fenlian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
| | - Lishu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
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5
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The Authors' Reply. Eur J Epidemiol 2022; 37:1085-1086. [PMID: 36287341 PMCID: PMC9607751 DOI: 10.1007/s10654-022-00927-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022]
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6
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Influenza mortality in French regions after the Hong Kong flu pandemic. DEMOGRAPHIC RESEARCH 2022. [DOI: 10.4054/demres.2022.47.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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7
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Wang H, Zheng Y, de Jonge MI, Wang R, Verhagen LM, Chen Y, Li L, Xu Z, Wang W. Lockdown measures during the COVID-19 pandemic strongly impacted the circulation of respiratory pathogens in Southern China. Sci Rep 2022; 12:16926. [PMID: 36209167 PMCID: PMC9547377 DOI: 10.1038/s41598-022-21430-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/29/2022] Open
Abstract
A range of public health measures have been implemented to suppress local transmission of coronavirus disease 2019 (COVID-19) in Shenzhen. We examined the effect of these measures on the prevalence of respiratory pathogens in children. Clinical and respiratory pathogen data were collected for routine care from hospitalized children with acute respiratory infections in Shenzhen Children's Hospital from July 2018 to January 2022. Nasopharyngeal swabs were collected and respiratory pathogens were detected using standardized clinical diagnostics as part of routine care. Data were analyzed to describe the effects of COVID-19 prevention procedures on other common pathogens. A total of 56,325 children under 14 years of age were hospitalized with an acute respiratory infection during the study period, 33,909 were tested from July 2018 to January 2020 (pre-lockdown), 1168 from February 2020 to May 2020 (lockdown) and 21,248 from July 2020 to January 2022 (post-lockdown). We observed a 37.3% decline of routine care in respiratory infection associated hospital admission in the 19 months' post-lockdown vs. the 19 months' pre-lockdown. There were 99.4%, 16.0% and 1.26% reductions measured for Mycoplasma pneumoniae, influenza virus A and adenovirus, respectively. However, a 118.7% and 75.8% rise was found for respiratory syncytial virus (RSV) and human para-influenza virus (HPIV) during the 19 months' post-lockdown in comparison to the pre-pandemic period. The detection of RSV especially increased in toddlers after the lockdown. Lockdown measures during the COVID-19 pandemic led to a significant reduction of Mycoplasma pneumoniae, influenza virus A and adenovirus infection. In contrast, RSV and HPIV infection increased.
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Affiliation(s)
- Heping Wang
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yuejie Zheng
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China
| | - Marien I. de Jonge
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rongjun Wang
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China
| | - Lilly M. Verhagen
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.461578.9Department of Pediatric Infectious Diseases and Immunology, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yunsheng Chen
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China
| | - Li Li
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China
| | - Zhi Xu
- grid.459830.3Ningbo Health Gene Technologies Co., Ltd, Ningbo, Zhejiang China
| | - Wenjian Wang
- grid.452787.b0000 0004 1806 5224Shenzhen Children’s Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038 Guangdong China
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Cobb NL, Collier S, Attia EF, Augusto O, West TE, Wagenaar BH. Global influenza surveillance systems to detect the spread of influenza-negative influenza-like illness during the COVID-19 pandemic: Time series outlier analyses from 2015-2020. PLoS Med 2022; 19:e1004035. [PMID: 35852993 PMCID: PMC9295997 DOI: 10.1371/journal.pmed.1004035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Surveillance systems are important in detecting changes in disease patterns and can act as early warning systems for emerging disease outbreaks. We hypothesized that analysis of data from existing global influenza surveillance networks early in the COVID-19 pandemic could identify outliers in influenza-negative influenza-like illness (ILI). We used data-driven methods to detect outliers in ILI that preceded the first reported peaks of COVID-19. METHODS AND FINDINGS We used data from the World Health Organization's Global Influenza Surveillance and Response System to evaluate time series outliers in influenza-negative ILI. Using automated autoregressive integrated moving average (ARIMA) time series outlier detection models and baseline influenza-negative ILI training data from 2015-2019, we analyzed 8,792 country-weeks across 28 countries to identify the first week in 2020 with a positive outlier in influenza-negative ILI. We present the difference in weeks between identified outliers and the first reported COVID-19 peaks in these 28 countries with high levels of data completeness for influenza surveillance data and the highest number of reported COVID-19 cases globally in 2020. To account for missing data, we also performed a sensitivity analysis using linear interpolation for missing observations of influenza-negative ILI. In 16 of the 28 countries (57%) included in this study, we identified positive outliers in cases of influenza-negative ILI that predated the first reported COVID-19 peak in each country; the average lag between the first positive ILI outlier and the reported COVID-19 peak was 13.3 weeks (standard deviation 6.8). In our primary analysis, the earliest outliers occurred during the week of January 13, 2020, in Peru, the Philippines, Poland, and Spain. Using linear interpolation for missing data, the earliest outliers were detected during the weeks beginning December 30, 2019, and January 20, 2020, in Poland and Peru, respectively. This contrasts with the reported COVID-19 peaks, which occurred on April 6 in Poland and June 1 in Peru. In many low- and middle-income countries in particular, the lag between detected outliers and COVID-19 peaks exceeded 12 weeks. These outliers may represent undetected spread of SARS-CoV-2, although a limitation of this study is that we could not evaluate SARS-CoV-2 positivity. CONCLUSIONS Using an automated system of influenza-negative ILI outlier monitoring may have informed countries of the spread of COVID-19 more than 13 weeks before the first reported COVID-19 peaks. This proof-of-concept paper suggests that a system of influenza-negative ILI outlier monitoring could have informed national and global responses to SARS-CoV-2 during the rapid spread of this novel pathogen in early 2020.
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Affiliation(s)
- Natalie L. Cobb
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Sigrid Collier
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, United States of America
| | - Engi F. Attia
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Orvalho Augusto
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - T. Eoin West
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Bradley H. Wagenaar
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
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9
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Glatman-Freedman A, Gur-Arie L, Sefty H, Kaufman Z, Bromberg M, Dichtiar R, Rosenberg A, Pando R, Nemet I, Kliker L, Mendelson E, Keinan-Boker L, Zuckerman NS, Mandelboim M. The impact of SARS-CoV-2 on respiratory syndromic and sentinel surveillance in Israel, 2020: a new perspective on established systems. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022; 27. [PMID: 35451365 PMCID: PMC9027148 DOI: 10.2807/1560-7917.es.2022.27.16.2100457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background The COVID-19 pandemic presented new challenges for the existing respiratory surveillance systems, and adaptations were implemented. Systematic assessment of the syndromic and sentinel surveillance platforms during the pandemic is essential for understanding the value of each platform in the context of an emerging pathogen with rapid global spread. Aim We aimed to evaluate systematically the performance of various respiratory syndromic surveillance platforms and the sentinel surveillance system in Israel from 1 January to 31 December 2020. Methods We compared the 2020 syndromic surveillance trends to those of the previous 3 years, using Poisson regression adjusted for overdispersion. To assess the performance of the sentinel clinic system as compared with the national SARS-CoV-2 repository, a cubic spline with 7 knots and 95% confidence intervals were applied to the sentinel network's weekly percentage of positive SARS-CoV-2 cases. Results Syndromic surveillance trends changed substantially during 2020, with a statistically significant reduction in the rates of visits to physicians and emergency departments to below previous years' levels. Morbidity patterns of the syndromic surveillance platforms were inconsistent with the progress of the pandemic, while the sentinel surveillance platform was found to reflect the national circulation of SARS-CoV-2 in the population. Conclusion Our findings reveal the robustness of the sentinel clinics platform for the surveillance of the main respiratory viruses during the pandemic and possibly beyond. The robustness of the sentinel clinics platform during 2020 supports its use in locations with insufficient resources for widespread testing of respiratory viruses.
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Affiliation(s)
- Aharona Glatman-Freedman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lea Gur-Arie
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Hanna Sefty
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Zalman Kaufman
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Michal Bromberg
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rita Dichtiar
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Alina Rosenberg
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Rakefet Pando
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Ital Nemet
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Limor Kliker
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Ella Mendelson
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Lital Keinan-Boker
- The Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel.,School of Public Health, University of Haifa, Israel
| | - Neta S Zuckerman
- The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Michal Mandelboim
- Department of Epidemiology and Preventive Medicine, School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Central Virology Laboratory, Israel Ministry of Health, Tel Hashomer, Ramat Gan, Israel
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- The Israeli Respiratory Viruses Surveillance Network (IRVSN) members are listed under Acknowledgements
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10
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Huang QM, Song WQ, Liang F, Ye BL, Li ZH, Zhang XR, Zhong WF, Zhang PD, Liu D, Shen D, Chen PL, Liu Q, Yang X, Mao C. Non-Pharmaceutical Interventions Implemented to Control the COVID-19 Were Associated With Reduction of Influenza Incidence. Front Public Health 2022; 10:773271. [PMID: 35252083 PMCID: PMC8894245 DOI: 10.3389/fpubh.2022.773271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Non-pharmaceutical interventions were implemented in most countries to reduce the transmission of COVID-19. We aimed to describe the incidence of influenza in four countries in the 2019–2020 season and examined the effect of these non-pharmaceutical interventions on the incidence of influenza. Methods We used the network surveillance data from 2015 to 2020 to estimate the percentage increase in influenza cases to explore the effect of non-pharmaceutical interventions implemented to control the COVID-19 on the incidence of influenza in China, the United States, Japan, and Singapore. Results We found that the incidence of influenza has been almost zero and reached a persistent near-zero level for a continuous period of six months since epidemiologic week 14 of 2020 in the four countries. Influenza incidence decreased by 77.71% and 60.50% in the early days of COVID-19 in the 2019–2020 season compared to the same period in preceding years in Japan and Singapore, respectively. Furthermore, influenza incidence decreased by 60.50–99.48% during the period of compulsory interventions in the 2019–2020 season compared to the same period in preceding years in the four countries. Conclusion These findings suggest that the application of non-pharmaceutical interventions, even everyday preventive action, was associated with a reduction of influenza incidence, which highlights that more traditional public health interventions need to be reasserted and universalized to reduce influenza incidence.
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Affiliation(s)
- Qing-Mei Huang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- Longgang Center for Disease Control and Prevention in Shenzhen, Shenzhen, China
| | - Wei-Qi Song
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fen Liang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Bi-Li Ye
- Longgang Center for Disease Control and Prevention in Shenzhen, Shenzhen, China
| | - Zhi-Hao Li
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xi-Ru Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wen-Fang Zhong
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Pei-Dong Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Dan Liu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Dong Shen
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Pei-Liang Chen
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qu Liu
- Longgang Center for Disease Control and Prevention in Shenzhen, Shenzhen, China
- Qu Liu
| | - Xingfen Yang
- Food Safety and Health Research Center, School of Public Health, Southern Medical University, Guangzhou, China
- Xingfen Yang
| | - Chen Mao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
- *Correspondence: Chen Mao
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11
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Lukowsky LR, Der-Martirosian C, Steers WN, Kamble KS, Dobalian A. Using an Administrative and Clinical Database to Determine the Early Spread of COVID-19 at the US Department of Veterans Affairs during the Beginning of the 2019–2020 Flu Season: A Retrospective Longitudinal Study. Viruses 2022; 14:v14020200. [PMID: 35215795 PMCID: PMC8879908 DOI: 10.3390/v14020200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Background. Previous studies examining the early spread of COVID-19 have used influenza-like illnesses (ILIs) to determine the early spread of COVID-19. We used COVID-19 case definition to identify COVID-like symptoms (CLS) independently of other influenza-like illnesses (ILIs). Methods. Using data from Emergency Department (ED) visits at VA Medical Centers in CA, TX, and FL, we compared weekly rates of CLS, ILIs, and non-influenza ILIs encounters during five consecutive flu seasons (2015–2020) and estimated the risk of developing each illness during the first 23 weeks of the 2019–2020 season compared to previous seasons. Results. Patients with CLS were significantly more likely to visit the ED during the first 23 weeks of the 2019–2020 compared to prior seasons, while ED visits for influenza and non-influenza ILIs did not differ substantially. Adjusted CLS risk was significantly lower for all seasons relative to the 2019–2020 season: RR15–16 = 0.72, 0.75, 0.72; RR16–17 = 0.81, 0.77, 0.79; RR17–18 = 0.80, 0.89, 0.83; RR18–19 = 0.82, 0.96, 0.81, in CA, TX, and FL, respectively. Conclusions. The observed increase in ED visits for CLS indicates the likely spread of COVID-19 in the US earlier than previously reported. VA data could potentially help identify emerging infectious diseases and supplement existing syndromic surveillance systems.
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Affiliation(s)
- Lilia R. Lukowsky
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
- Correspondence:
| | - Claudia Der-Martirosian
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
| | - William Neil Steers
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
- Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Kiran S. Kamble
- School of Public Health, University of Memphis, Memphis, TN 38152, USA;
| | - Aram Dobalian
- Veteran Emergency Management Evaluation Center (VEMEC), US Department of Veterans Affairs, North Hills, CA 91343, USA; (C.D.-M.); (W.N.S.); (A.D.)
- School of Public Health, University of Memphis, Memphis, TN 38152, USA;
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12
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Rezel‐Potts E, Douiri A, Chowienczyk PJ, Gulliford MC. Antihypertensive medications and COVID-19 diagnosis and mortality: Population-based case-control analysis in the United Kingdom. Br J Clin Pharmacol 2021; 87:4598-4607. [PMID: 33908074 PMCID: PMC8239680 DOI: 10.1111/bcp.14873] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/15/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022] Open
Abstract
AIMS Antihypertensive drugs have been implicated in coronavirus disease 2019 (COVID-19) susceptibility and severity, but estimated associations may be susceptible to bias. We aimed to evaluate antihypertensive medications and COVID-19 diagnosis and mortality, accounting for healthcare-seeking behaviour. METHODS A population-based case-control study was conducted including 16 866 COVID-19 cases and 70 137 matched controls from the UK Clinical Practice Research Datalink. We evaluated all-cause mortality among COVID-19 cases. Exposures were angiotensin-converting enzyme inhibitors (ACEIs), angiotensin receptor blockers (ARBs), beta-blockers (B), calcium-channel blockers (C), thiazide diuretics (D) and other antihypertensive drugs (O). Analyses were adjusted for covariates and consultation frequency. RESULTS ACEIs were associated with lower odds of COVID-19 diagnosis (adjusted odds ratio [AOR] 0.82, 95% confidence interval [CI] 0.77-0.88) as were ARBs (AOR 0.87, 95% CI 0.80-0.95) with little attenuation from adjustment for consultation frequency. C and D were also associated with lower odds of COVID-19 diagnosis. Increased odds of COVID-19 for B (AOR 1.19, 95% CI 1.12-1.26) were attenuated after adjustment for consultation frequency (AOR 1.01, 95% CI 0.95-1.08). Patients treated with ACEIs or ARBs had similar odds of mortality (AOR 1.00, 95% CI 0.83-1.20) to patients treated with classes B, C, D or O or patients receiving no antihypertensive therapy (AOR 0.99, 95% CI 0.83-1.18). CONCLUSIONS There was no evidence that antihypertensive therapy is associated with increased risk of COVID-19 diagnosis or mortality; most classes of antihypertensive therapy showed negative associations with COVID-19 diagnosis.
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Affiliation(s)
- Emma Rezel‐Potts
- King's College LondonSchool of Population Health and Environmental SciencesLondonUK
- National Institute for Health Research Biomedical Research CentreGuy's and St Thomas' NHS Foundation Trust and King's College LondonLondonUK
| | - Abdel Douiri
- King's College LondonSchool of Population Health and Environmental SciencesLondonUK
- National Institute for Health Research Biomedical Research CentreGuy's and St Thomas' NHS Foundation Trust and King's College LondonLondonUK
- National Institute for Health Research Applied Research Collaboration South LondonGuy's and St Thomas' NHS Foundation Trust and King's College LondonLondonUK
| | | | - Martin C. Gulliford
- King's College LondonSchool of Population Health and Environmental SciencesLondonUK
- National Institute for Health Research Biomedical Research CentreGuy's and St Thomas' NHS Foundation Trust and King's College LondonLondonUK
- National Institute for Health Research Applied Research Collaboration South LondonGuy's and St Thomas' NHS Foundation Trust and King's College LondonLondonUK
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13
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Meybeck A, Huleux T, Tétart M, Thill P, Derdour V, Bocket L, Alidjinou EK, Patoz P, Robineau O, Ajana F. History of COVID-19 Symptoms and Seroprevalence of SARS-CoV-2 Antibodies in HIV-Infected Patients in Northern France after the First Wave of the Pandemic. Microorganisms 2021; 9:microorganisms9122491. [PMID: 34946093 PMCID: PMC8705918 DOI: 10.3390/microorganisms9122491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/11/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
To assess the prevalence of COVID-19 in people living with HIV (PLWHIV), we performed an epidemiological survey from 1 April through 1 August 2020 in an HIV reference center in Northern France. PLWHIV completed a questionnaire about risk exposures and symptoms consistent with COVID-19 and performed a SARS-CoV-2 serology. Among the 600 PLWHIV included, 16 have been infected with SARS-CoV-2. Symptoms consistent with COVID-19 were frequent both in SARS-CoV-2 positive and negative patients (67% vs. 32%, p = 0.02). Among SARS-CoV-2 infected patients, one (6%) has been hospitalized and five (31%) have been asymptomatic. Close contact with a confirmed COVID-19 case was the only factor associated with COVID-19 acquisition (40% vs. 13%, p = 0.01). The prevalence of COVID-19 in PLWHIV was 2.5%, half of the overall population estimate after the first wave of the pandemic in France. In conclusion, proportion of asymptomatic COVID-19 was high in PLWHIV. The prevalence of COVID-19 in PLWHIV was two times lower than in the general population.
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Affiliation(s)
- Agnès Meybeck
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
- Correspondence: ; Tel.: +33-320694605
| | - Thomas Huleux
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Macha Tétart
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Pauline Thill
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Vincent Derdour
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Laurence Bocket
- Laboratoire de Virologie, CHRU de Lille, 59000 Lille, France; (L.B.); (E.K.A.)
| | | | - Pierre Patoz
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Olivier Robineau
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
| | - Faiza Ajana
- Service des Maladies Infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, 59200 Tourcoing, France; (T.H.); (M.T.); (P.T.); (V.D.); (P.P.); (O.R.); (F.A.)
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14
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Launay T, Souty C, Vilcu AM, Turbelin C, Blanchon T, Guerrisi C, Hanslik T, Colizza V, Bardoulat I, Lemaître M, Boëlle PY. Common communicable diseases in the general population in France during the COVID-19 pandemic. PLoS One 2021; 16:e0258391. [PMID: 34634090 PMCID: PMC8504745 DOI: 10.1371/journal.pone.0258391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/26/2021] [Indexed: 12/02/2022] Open
Abstract
In France, social distancing measures have been adopted to contain the spread of COVID-19, culminating in national Lockdowns. The use of hand washing, hydro-alcoholic rubs and mask-wearing also increased over time. As these measures are likely to impact the transmission of many communicable diseases, we studied the changes in common infectious diseases incidence in France during the first year of COVID-19 circulation. We examined the weekly incidence of acute gastroenteritis, chickenpox, acute respiratory infections and bronchiolitis reported in general practitioner networks since January 2016. We obtained search engine query volume for French terms related to these diseases and sales data for relevant drugs over the same period. A periodic regression model was fit to disease incidence, drug sales and search query volume before the COVID-19 period and extrapolated afterwards. We compared the expected values with observations made in 2020. During the first lockdown period, incidence dropped by 67% for gastroenteritis, by 79% for bronchiolitis, by 49% for acute respiratory infection and 90% for chickenpox compared to the past years. Reductions with respect to the expected incidence reflected the strength of implemented measures. Incidence in children was impacted the most. Reduction in primary care consultations dropped during a short period at the beginning of the first lockdown period but remained more than 95% of the expected value afterwards. In primary care, the large decrease in reported gastroenteritis, chickenpox or bronchiolitis observed during the period where many barrier measures were implemented imply that the circulation of common viruses was reduced and informs on the overall effect of these measures.
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Affiliation(s)
- Titouan Launay
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Cécile Souty
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Ana-Maria Vilcu
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Clément Turbelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Caroline Guerrisi
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | - Vittoria Colizza
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
| | | | | | - Pierre-Yves Boëlle
- Sorbonne Université, INSERM, Institut Pierre Louis d’Épidémiologie et de Santé Publique, Paris, France
- Hôpital Saint-Antoine, Assistance Publique–Hôpitaux de Paris, Paris, France
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15
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Li L, Wang H, Liu A, Wang R, Zhi T, Zheng Y, Bao Y, Chen Y, Wang W. Comparison of 11 respiratory pathogens among hospitalized children before and during the COVID-19 epidemic in Shenzhen, China. Virol J 2021; 18:202. [PMID: 34627307 PMCID: PMC8501916 DOI: 10.1186/s12985-021-01669-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 12/16/2022] Open
Abstract
Background The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. Methods This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children’s Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. Results A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001). Conclusions Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.
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Affiliation(s)
- Li Li
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Heping Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Ailiang Liu
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Rongjun Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Tingting Zhi
- Department of Microbiology and Immunology, College of Basic Medicine, Guangdong Medical University, Dongguan, 523808, China
| | - Yuejie Zheng
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Yanming Bao
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China
| | - Yunsheng Chen
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China.
| | - Wenjian Wang
- Department of Respiratory Diseases, Shenzhen Children's Hospital, No. 7019 Yitian Road, Futian District, Shenzhen, 518038, Guangdong, China.
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17
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Grosso F, Castrofino A, Del Castillo G, Galli C, Binda S, Pellegrinelli L, Bubba L, Cereda D, Tirani M, Gramegna M, Bella A, Castaldi S, Pariani E. A comparative study between the incidence and epidemiological features of Influenza-Like Illness and laboratory-confirmed COVID-19 cases in the Italian epicenter (Lombardy). J Infect Public Health 2021; 14:674-680. [PMID: 33865059 PMCID: PMC7901382 DOI: 10.1016/j.jiph.2021.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/18/2021] [Accepted: 02/08/2021] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION In Lombardy, the influenza surveillance system relies on sentinel physicians that weekly report data on the number of Influenza-Like Illness (ILI) and a part of them also collect nasopharyngeal samples for virologic analyses. This study aims at comparing the ILI incidence of 2019-2020 influenza season with the incidence of COVID-19 cases in order to better understand the current epidemic and to evaluate whether the implementation of ILI surveillance system could succeed in early detection and monitoring of COVID-19 diffusion. METHODS The distribution of ILI cases in the seasons 2017-2018, 2018-2019 and 2019-2020 was taken in consideration and the curve trends were compared and analyzed according to geographical areas, age groups and time differences. RESULTS The curve trends presented a similar pattern up to the 9th week; in fact, a reduction in the ILI incidence rate was observed in the 2017-2018 and 2018-2019 season but in the 2019-2020 an increase in the reported ILI emerged. The relation between the numbers reported by 2019-2020 ILI surveillance and those reported for COVID-19 is supported by the curve trends, the correspondence between age groups, the correspondence by geographical location, and also by the results of the nasopharyngeal swab tests performed. DISCUSSION The influenza surveillance system is an effective tool for early detection of COVID-19. It may provide timely and high-quality data evaluating the SARS-CoV-2 burden among population with ILI. Implementation of the system has to be prioritized in order to identify any future novel respiratory pathogen with pandemic potential.
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Affiliation(s)
- Francesca Grosso
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Ambra Castrofino
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | | | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Bubba
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | | | | | | | - Antonino Bella
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Silvana Castaldi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Health Management Department, Fondazione IRCCS Ca' Granda OMP, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy; Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), Genoa, Italy.
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18
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Galli C, Pellegrinelli L, Bubba L, Primache V, Anselmi G, Delbue S, Signorini L, Binda S, Cereda D, Gramegna M, Pariani E. When the COVID-19 Pandemic Surges during Influenza Season: Lessons Learnt from the Sentinel Laboratory-Based Surveillance of Influenza-Like Illness in Lombardy during the 2019-2020 Season. Viruses 2021; 13:v13040695. [PMID: 33923819 PMCID: PMC8073979 DOI: 10.3390/v13040695] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/17/2022] Open
Abstract
This paper outlines the role of Lombardy’s regional influenza reference laboratory (Northern Italy) in the surveillance of influenza-like illnesses (ILIs) in monitoring SARS-CoV-2 circulation by analyzing 631 consecutive nasopharyngeal swabs (NPSs) collected from ILI outpatients by sentinel physicians during the 2019–2020 season. The samples were tested by specific real-time RT-PCRs targeting SARS-CoV-2, influenza viruses, and RSVs. Results: Of these NPSs, 31% tested positive for influenza viruses, 10% for SARS-CoV-2, and 7% for RSV. No coinfections were detected. Influenza viruses and RSVs circulated throughout the surveillance period until the end of February (week 9-2020), when they suddenly ceased to circulate seven weeks earlier than during the previous five influenza seasons. After the first detection of SARS-CoV-2 in our ILI outpatients at the beginning of March (week 10-2020), SARS-CoV-2 remained the only virus identified throughout the surveillance period. Patients ≥ 65 years had a 3.2-fold greater risk of being infected with SARS-CoV-2, while school-age children (5–14 years) and children < 5 years proved to be the age groups most at risk of contracting influenza viruses and RSV, respectively. Our experience demonstrates that laboratory-based ILI surveillance networks are essential for identifying SARS-CoV-2 cases that would otherwise remain undetected, in order to stop their spread within our communities.
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Affiliation(s)
- Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Laura Bubba
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Valeria Primache
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Giovanni Anselmi
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (L.S.)
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (L.S.)
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
| | - Danilo Cereda
- DG Welfare, UO Prevenzione, Lombardy Region, 20124 Milan, Italy; (D.C.); (M.G.)
| | - Maria Gramegna
- DG Welfare, UO Prevenzione, Lombardy Region, 20124 Milan, Italy; (D.C.); (M.G.)
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy; (C.G.); (L.P.); (L.B.); (V.P.); (G.A.); (S.B.)
- Interuniversity Research Center on Influenza and Other Transmissible Infections (CIRI-IT), 16132 Genoa, Italy
- Correspondence: ; Tel.: +39-02-5031-5132
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Cumulative Effects of Particulate Matter Pollution and Meteorological Variables on the Risk of Influenza-Like Illness. Viruses 2021; 13:v13040556. [PMID: 33810283 PMCID: PMC8065612 DOI: 10.3390/v13040556] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
The cold season is usually accompanied by an increased incidence of respiratory infections and increased air pollution from combustion sources. As we are facing growing numbers of COVID-19 cases caused by the novel SARS-CoV-2 coronavirus, an understanding of the impact of air pollutants and meteorological variables on the incidence of respiratory infections is crucial. The incidence of influenza-like illness (ILI) can be used as a close proxy for the circulation of influenza viruses. Recently, SARS-CoV-2 has also been detected in patients with ILI. Using distributed lag nonlinear models, we analyzed the association between ILI, meteorological variables and particulate matter concentration in Bialystok, Poland, from 2013–2019. We found an exponential relationship between cumulative PM2.5 pollution and the incidence of ILI, which remained significant after adjusting for air temperatures and a long-term trend. Pollution had the greatest effect during the same week, but the risk of ILI was increased for the four following weeks. The risk of ILI was also increased by low air temperatures, low absolute humidity, and high wind speed. Altogether, our results show that all measures implemented to decrease PM2.5 concentrations would be beneficial to reduce the transmission of SARS-CoV-2 and other respiratory infections.
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20
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Di Domenico L, Pullano G, Sabbatini CE, Boëlle PY, Colizza V. Modelling safe protocols for reopening schools during the COVID-19 pandemic in France. Nat Commun 2021; 12:1073. [PMID: 33594076 PMCID: PMC7887250 DOI: 10.1038/s41467-021-21249-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
As countries in Europe implement strategies to control the COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Île-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on children's role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist to keep the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead to up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale test and trace is required to keep the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown.
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Affiliation(s)
- Laura Di Domenico
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Giulia Pullano
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- Orange Labs, Sociology and Economics of Network and Services (SENSE), Chatillon, France
| | - Chiara E Sabbatini
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Pierre-Yves Boëlle
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Pierre Louis Institute of Epidemiology and Public Health, Paris, France.
- Tokyo Tech World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.
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21
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Souty C, Guerrisi C, Masse S, Lina B, van der Werf S, Bernard-Stoecklin S, Turbelin C, Falchi A, Hanslik T, Blanchon T. Impact of the lockdown on the burden of COVID-19 in outpatient care in France, spring 2020. Infect Dis (Lond) 2021; 53:376-381. [PMID: 33512254 DOI: 10.1080/23744235.2021.1880024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To limit the spread of SARS-CoV-2 several countries implemented measures to reduce the number of contacts such as a national lockdown. We estimated the impact of the first lockdown on the burden of COVID-19 in the community in France. METHODS Physicians participating in the French Sentinelles network reported the number of patients with an acute respiratory infection (ARI) seen in consultation and performed nasopharyngeal swabs in a sample of these patients (first patient of the week). The swabs were tested by RT-PCR for the presence of SARS-CoV-2. Clinical and virological data were combined to estimate ARI incidence attributable to SARS-CoV-2 from 17 March to 10 May 2020. RESULTS The incidence of ARI attributable to COVID-19 decreased after the second week of the lockdown period from 142 (95%CI [101; 183]) to 41 (95%CI [21; 60]) per 100,000 population. A decrease was observed in all areas in metropolitan France. The youngest age groups (<15-years-old) were least affected with a cumulated incidence estimated to 14 per 100,000 population during the study period. CONCLUSIONS The data collected in primary care suggests that the first lockdown implemented in France during spring 2020 significantly reduced the incidence of acute respiratory infections including COVID-19 in France and limited the geographic spread of SARS-CoV-2.
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Affiliation(s)
- Cécile Souty
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé publique (IPLESP), Paris, France
| | - Caroline Guerrisi
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé publique (IPLESP), Paris, France
| | - Shirley Masse
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Bruno Lina
- Laboratoire de Virologie des HCL, Institut des Agents Infectieux, CNR des virus à transmission respiratoire (dont la grippe), Hôpital de la Croix Rousse, Lyon, France
| | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, CNRS UMR 3569, Institut Pasteur, Université de Paris, Paris, France
| | | | - Clément Turbelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé publique (IPLESP), Paris, France
| | - Alessandra Falchi
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Thomas Hanslik
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé publique (IPLESP), Paris, France.,Faculty of Health Sciences Simone Veil, University of Versailles Saint Quentin - University of Paris, Versailles, France.,Assistance Publique-Hôpitaux de Paris (APHP), Hôpital Ambroise Paré, Service de Médecine Interne, Boulogne-Billancourt, France
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé publique (IPLESP), Paris, France
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22
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Early indicators of intensive care unit bed requirement during the COVID-19 epidemic: A retrospective study in Ile-de-France region, France. PLoS One 2020; 15:e0241406. [PMID: 33206660 PMCID: PMC7673527 DOI: 10.1371/journal.pone.0241406] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
The aim of our retrospective study was to evaluate the earliest COVID19-related signal to anticipate requirements of intensive care unit (ICU) beds. Although the number of ICU beds is crucial during the COVID-19 epidemic, there is no recognized early indicator to anticipate it. In the Ile-de-France region, from February 20 to May 5, 2020, emergency medical service (EMS) calls and the response provided (ambulances) together the percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, general practitioner (GP) and emergency department (ED) visits, and hospital admissions of COVID-19 patients were recorded daily and compared to the number of ICU patients. Correlation curve analysis was performed to determine the best correlation coefficient, depending on the number of days the indicator has been shifted. Primary endpoint was the number of ICU patients. EMS calls, percentage of positive RT-PCR tests, ambulances used, ED and GP visits of COVID-19 patients were strongly associated (R2 ranging between 0.79 to 0.99, all P<0.001) with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipate ICU bed requirement. A qualitative analysis of the onset of the second wave period of the epidemic (August 1 to September 15, 2020) in the same region provided similar results. The daily number of COVID19-related telephone calls received by the EMS and corresponding dispatch ambulances, and the proportion of positive RT-PCR tests were the earliest indicators of the number of COVID19 patients requiring ICU care during the epidemic crisis, rapidly followed by ED and GP visits. This information may help health authorities to anticipate a future epidemic, including a second wave of COVID19, or decide additional social measures.
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23
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Abstract
Background: Liberal PCR testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key to contain the coronavirus disease 2019 (COVID-19) pandemic. Combined multi-sample testing in pools instead of single tests might enhance laboratory capacity and reduce costs, especially in low- and middle-income countries. Objective: The purpose of our study was to assess the value of a simple questionnaire to guide and further improve pooling strategies for SARS-CoV-2 laboratory testing. Methods: Pharyngeal swabs for SARS-CoV-2 testing were obtained from healthcare and police staff, hospital inpatients, and nursing home residents in the southwestern part of Germany. We designed a simple questionnaire, which included questions pertaining to a suggestive clinical symptomatology, recent travel history, and contact with confirmed cases to stratify an individual’s pre-test probability of having contracted COVID-19. The questionnaire was adapted repeatedly in face of the unfolding pandemic in response to the evolving epidemiology and observed clinical symptomatology. Based on the response patterns, samples were either tested individually or in multi-sample pools. We compared the pool positivity rate and the number of total PCR tests required to obtain individual results between this questionnaire-based pooling strategy and randomly assembled pools. Findings: Between March 11 and July 5, 2020, we processed 25,978 samples using random pooling (n = 6,012; 23.1%) or questionnaire-based pooling (n = 19,966; 76.9%). The overall prevalence of SARS-CoV-2 was 0.9% (n = 238). Pool positivity (14.6% vs. 1.2%) and individual SARS-CoV-2 prevalence (3.4% vs. 0.1%) were higher in the random pooling group than in the questionnaire group. The average number of PCR tests needed to obtain the individual result for one participant was 0.27 tests in the random pooling group, as compared to 0.09 in the questionnaire-based pooling group, leading to a laboratory capacity increase of 73% and 91%, respectively, as compared to single PCR testing. Conclusions: Strategies that combine pool testing with a questionnaire-based risk stratification can increase laboratory testing capacities for COVID-19 and might be important tools, particularly in resource-constrained settings.
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24
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Griffith GJ, Morris TT, Tudball MJ, Herbert A, Mancano G, Pike L, Sharp GC, Sterne J, Palmer TM, Davey Smith G, Tilling K, Zuccolo L, Davies NM, Hemani G. Collider bias undermines our understanding of COVID-19 disease risk and severity. Nat Commun 2020; 11:5749. [PMID: 33184277 PMCID: PMC7665028 DOI: 10.1038/s41467-020-19478-2] [Citation(s) in RCA: 468] [Impact Index Per Article: 117.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Numerous observational studies have attempted to identify risk factors for infection with SARS-CoV-2 and COVID-19 disease outcomes. Studies have used datasets sampled from patients admitted to hospital, people tested for active infection, or people who volunteered to participate. Here, we highlight the challenge of interpreting observational evidence from such non-representative samples. Collider bias can induce associations between two or more variables which affect the likelihood of an individual being sampled, distorting associations between these variables in the sample. Analysing UK Biobank data, compared to the wider cohort the participants tested for COVID-19 were highly selected for a range of genetic, behavioural, cardiovascular, demographic, and anthropometric traits. We discuss the mechanisms inducing these problems, and approaches that could help mitigate them. While collider bias should be explored in existing studies, the optimal way to mitigate the problem is to use appropriate sampling strategies at the study design stage.
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Affiliation(s)
- Gareth J Griffith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tim T Morris
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Matthew J Tudball
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Annie Herbert
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Giulia Mancano
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Lindsey Pike
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Jonathan Sterne
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Tom M Palmer
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Kate Tilling
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Luisa Zuccolo
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Neil M Davies
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
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25
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Piarroux R, Batteux F, Rebaudet S, Boelle PY. Les indicateurs d’alerte et de surveillance de la Covid-19. ANNALES FRANCAISES DE MEDECINE D URGENCE 2020. [DOI: 10.3166/afmu-2020-0277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Face à la crise sanitaire provoquée par la pandémie de Covid-19 en France, Santé publique France a mis en place un système de surveillance évolutif fondé sur des définitions de cas possible, probable et confirmé. Le décompte quotidien se limite cependant aux cas confirmés par reverse transcriptase polymerase chain reaction ou sérologie SARS-CoV-2 (actuellement via la plateforme SI-DEP), aux cas hospitalisés (via le Système d’information pour le suivi des victimes d’attentats) et aux décès hospitaliers par Covid-19. Ce suivi de la circulation virale est forcément non exhaustif, et l’estimation de l’incidence est complétée par d’autres indicateurs comme les appels au 15, les recours à SOS Médecins, les passages dans les services d’accueil des urgences, les consultations de médecine de ville via le réseau Sentinelle. Le suivi de la mortalité non hospitalière s’est heurté aux délais de transmission des certificats de décès et au manque de diagnostic fiable. Seule la létalité hospitalière a pu être mesurée de manière fiable. Moyennant un certain nombre de précautions statistiques et d’hypothèses de travail, les modèles ont permis d’anticiper l’évolution de l’épidémie à partir de deux indicateurs essentiels : le ratio de reproduction R et le temps de doublement épidémique. En Île-de-France, l’Assistance publique– Hôpitaux de Paris a complété ce tableau de bord grâce à son entrepôt de données de santé et a ainsi pu modéliser de manière fine le parcours de soins des patients. L’ensemble de ces indicateurs a été essentiel pour assurer une planification de la réponse à la crise.
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26
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Dai Y, Wang J. Identifying the outbreak signal of COVID-19 before the response of the traditional disease monitoring system. PLoS Negl Trop Dis 2020; 14:e0008758. [PMID: 33001985 PMCID: PMC7553315 DOI: 10.1371/journal.pntd.0008758] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/13/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022] Open
Abstract
SYNOPSIS Early identification of the emergence of an outbreak of a novel infectious disease is critical to generating a timely response. The traditional monitoring system is adequate for detecting the outbreak of common diseases; however, it is insufficient for the discovery of novel infectious diseases. In this study, we used COVID-19 as an example to compare the delay time of different tools for identifying disease outbreaks. The results showed that both the abnormal spike in influenza-like illnesses and the peak of online searches of key terms could provide early signals. We emphasize the importance of testing these findings and discussing the broader potential to use syndromic surveillance, internet searches, and social media data together with traditional disease surveillance systems for early detection and understanding of novel emerging infectious diseases.
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Affiliation(s)
- Yaoyao Dai
- Department of Infectious Diseases, Center for Disease Control and Prevention of Nantong City, Nantong, China
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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27
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Boëlle PY, Delory T, Maynadier X, Janssen C, Piarroux R, Pichenot M, Lemaire X, Baclet N, Weyrich P, Melliez H, Meybeck A, Lanoix JP, Robineau O. Trajectories of Hospitalization in COVID-19 Patients: An Observational Study in France. J Clin Med 2020; 9:E3148. [PMID: 33003375 PMCID: PMC7600846 DOI: 10.3390/jcm9103148] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/20/2020] [Accepted: 09/27/2020] [Indexed: 12/16/2022] Open
Abstract
Describing the characteristics of COVID-19 patients in the hospital is of importance to assist in the management of hospital capacity in the future. Here, we analyze the trajectories of 1321 patients admitted to hospitals in northern and eastern France. We found that the time from onset to hospitalization decreased with age, from 7.3 days in the 20-65 year-olds to 4.5 in the >80 year-olds (p < 0.0001). Overall, the length of stay in the hospital was 15.9 days, and the death rate was 20%. One patient out of four was admitted to the intensive care unit (ICU) for approximately one month. The characteristics of trajectories changed with age: fewer older patients were admitted to the ICU and the death rate was larger in the elderly. Admission shortly after onset was associated with increased mortality (odds-ratio (OR) = 1.8, Confidence Interval (CI) 95% [1.3, 2.6]) as well as male sex (OR = 2.1, CI 95% [1.5, 2.9]). Time from admission within the hospital to the transfer to ICU was short. The age- and sex-adjusted mortality rate decreased over the course of the epidemic, suggesting improvement in care over time. In the SARS-CoV-2 epidemic, the urgent need for ICU at admission and the prolonged length of stay in ICU are a challenge for bed management and organization of care.
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Affiliation(s)
- Pierre-Yves Boëlle
- Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, Assistance Publique – Hôpitaux de Paris, 75012 Paris, France; (T.D.); (X.M.); (R.P.)
| | - Tristan Delory
- Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, Assistance Publique – Hôpitaux de Paris, 75012 Paris, France; (T.D.); (X.M.); (R.P.)
- Centre Hospitalier Annecy Genevois, 74370 Epagny–Metz-Tessy, France;
| | - Xavier Maynadier
- Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, Assistance Publique – Hôpitaux de Paris, 75012 Paris, France; (T.D.); (X.M.); (R.P.)
| | - Cécile Janssen
- Centre Hospitalier Annecy Genevois, 74370 Epagny–Metz-Tessy, France;
| | - Renaud Piarroux
- Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, Assistance Publique – Hôpitaux de Paris, 75012 Paris, France; (T.D.); (X.M.); (R.P.)
| | - Marie Pichenot
- Centre Hospitalier Victor Provot, 59100 Roubaix, France;
| | - Xavier Lemaire
- Service Maladies infectieuses, Centre Hospitalier de Douai, 59500 Douai, France;
| | - Nicolas Baclet
- Department of Infectious Diseases, Lille Catholic Hospitals, F-59160 Lille, France; (N.B.); (P.W.)
| | - Pierre Weyrich
- Department of Infectious Diseases, Lille Catholic Hospitals, F-59160 Lille, France; (N.B.); (P.W.)
| | - Hugues Melliez
- Service de médecine interne, Hôpital de la région de Saint-Omer, 62570 Helfaut, France;
| | - Agnès Meybeck
- Service Universitaire des maladies Infectieuses et du Voyageur, 59200 Tourcoing, France;
| | - Jean-Philippe Lanoix
- Service de Maladies Infectieuses et tropicales, CHU Amiens-Picardie, 80000 Amiens, France;
- AGIR UR UPJV 4294, CURS, Université Picardie Jules Verne, 80000 Amiens, France
| | - Olivier Robineau
- Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique, INSERM, Assistance Publique – Hôpitaux de Paris, 75012 Paris, France; (T.D.); (X.M.); (R.P.)
- Service Universitaire des maladies Infectieuses et du Voyageur, 59200 Tourcoing, France;
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28
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Petti S, Cowling BJ. Ecologic association between influenza and COVID-19 mortality rates in European countries. Epidemiol Infect 2020; 148:e209. [PMID: 32912363 PMCID: PMC7506171 DOI: 10.1017/s0950268820002125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/12/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
Ecologic studies investigating COVID-19 mortality determinants, used to make predictions and design public health control measures, generally focused on population-based variable counterparts of individual-based risk factors. Influenza is not causally associated with COVID-19, but shares population-based determinants, such as similar incidence/mortality trends, transmission patterns, efficacy of non-pharmaceutical interventions, comorbidities and underdiagnosis. We investigated the ecologic association between influenza mortality rates and COVID-19 mortality rates in the European context. We considered the 3-year average influenza (2014-2016) and COVID-19 (31 May 2020) crude mortality rates in 34 countries using EUROSTAT and ECDC databases and performed correlation and regression analyses. The two variables - log transformed, showed significant Spearman's correlation ρ = 0.439 (P = 0.01), and regression coefficients, b = 0.743 (95% confidence interval, 0.272-1.214; R2 = 0.244; P = 0.003), b = 0.472 (95% confidence interval, 0.067-0.878; R2 = 0.549; P = 0.02), unadjusted and adjusted for confounders (population size and cardiovascular disease mortality), respectively. Common significant determinants of both COVID-19 and influenza mortality rates were life expectancy, influenza vaccination in the elderly (direct associations), number of hospital beds per population unit and crude cardiovascular disease mortality rate (inverse associations). This analysis suggests that influenza mortality rates were independently associated with COVID-19 mortality rates in Europe, with implications for public health preparedness, and implies preliminary undetected SARS-CoV-2 spread in Europe.
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Affiliation(s)
- S. Petti
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - B. J. Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Delatorre E, Mir D, Gräf T, Bello G. Tracking the onset date of the community spread of SARS-CoV-2 in western countries. Mem Inst Oswaldo Cruz 2020; 115:e200183. [PMID: 32901696 PMCID: PMC7472723 DOI: 10.1590/0074-02760200183] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/12/2020] [Indexed: 01/21/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread around the world during 2020, but the precise time in which the virus began to spread locally is difficult to trace for most countries. Here, we estimate the probable onset date of the community spread of SARS-CoV-2 for heavily affected countries from Western Europe and the Americas on the basis of the cumulative number of deaths reported during the early stage of the epidemic. Our results support that SARS-CoV-2 probably started to spread locally in all western countries analysed between mid-January and mid-February 2020, thus long before community transmission was officially recognised and control measures were implemented.
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Affiliation(s)
- Edson Delatorre
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia, Alegre, ES, Brasil
| | - Daiana Mir
- Universidad de la República, Centro Universitario Regional del Litoral Norte, Unidad de Genómica y Bioinformática, Salto, Uruguay
| | - Tiago Gräf
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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Hansen JC. Commentaire cindynique sur l’épidémiologie de la pandémie COVID-19. MÉDECINE DE CATASTROPHE - URGENCES COLLECTIVES 2020. [PMCID: PMC7455198 DOI: 10.1016/j.pxur.2020.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Silverman JD, Hupert N, Washburne AD. Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States. Sci Transl Med 2020; 12:scitranslmed.abc1126. [PMID: 32571980 PMCID: PMC7319260 DOI: 10.1126/scitranslmed.abc1126] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022]
Abstract
Detection of SARS-CoV-2 infections to date has relied heavily on RT-PCR testing. However, limited test availability, high false-negative rates, and the existence of asymptomatic or sub-clinical infections have resulted in an under-counting of the true prevalence of SARS-CoV-2. Here, we show how influenza-like illness (ILI) outpatient surveillance data can be used to estimate the prevalence of SARS-CoV-2. We found a surge of non-influenza ILI above the seasonal average in March 2020 and showed that this surge correlated with COVID-19 case counts across states. If 1/3 of patients infected with SARS-CoV-2 in the US sought care, this ILI surge would have corresponded to more than 8.7 million new SARS-CoV-2 infections across the US during the three-week period from March 8 to March 28, 2020. Combining excess ILI counts with the date of onset of community transmission in the US, we also show that the early epidemic in the US was unlikely to have been doubling slower than every 4 days. Together these results suggest a conceptual model for the COVID-19 epidemic in the US characterized by rapid spread across the US with over 80% infected patients remaining undetected. We emphasize the importance of testing these findings with seroprevalence data and discuss the broader potential to use syndromic surveillance for early detection and understanding of emerging infectious diseases.
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Affiliation(s)
- Justin D Silverman
- College of Information Science and Technology, Penn State University, University Park, PA 16802, USA. .,Department of Medicine, Penn State University, Hershey, PA 17033, USA
| | - Nathaniel Hupert
- Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.,New York-Presbyterian Hospital, New York, NY 10065, USA
| | - Alex D Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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