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Integrated surveillance for respiratory viruses
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9 results
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Wastewater-based reproduction numbers and projections of COVID-19 cases in three areas in Japan, November 2021 to December 2022
More LessBackgroundWastewater surveillance has expanded globally as a means to monitor spread of infectious diseases. An inherent challenge is substantial noise and bias in wastewater data because of the sampling and quantification process, limiting the applicability of wastewater surveillance as a monitoring tool.
AimTo present an analytical framework for capturing the growth trend of circulating infections from wastewater data and conducting scenario analyses to guide policy decisions.
MethodsWe developed a mathematical model for translating the observed SARS-CoV-2 viral load in wastewater into effective reproduction numbers. We used an extended Kalman filter to infer underlying transmissions by smoothing out observational noise. We also illustrated the impact of different countermeasures such as expanded vaccinations and non-pharmaceutical interventions on the projected number of cases using three study areas in Japan during 2021–22 as an example.
ResultsObserved notified cases were matched with the range of cases estimated by our approach with wastewater data only, across different study areas and virus quantification methods, especially when the disease prevalence was high. Estimated reproduction numbers derived from wastewater data were consistent with notification-based reproduction numbers. Our projections showed that a 10–20% increase in vaccination coverage or a 10% reduction in contact rate may suffice to initiate a declining trend in study areas.
ConclusionOur study demonstrates how wastewater data can be used to track reproduction numbers and perform scenario modelling to inform policy decisions. The proposed framework complements conventional clinical surveillance, especially when reliable and timely epidemiological data are not available.
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Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023
More LessThe SARS-CoV-2 BA.2.86 Omicron subvariant was first detected in wastewater in Sweden in week 31 2023, using 21 highly specific markers from the 50 investigated. We report BA.2.86’s introduction and subsequent spread to all 14 regions performing wastewater sampling, and on 70 confirmed COVID-19 cases, along with the emergence of sublineages JN.1 and JN.2. Further, we investigated two novel mutations defining the unique BA.2.86 branching in Sweden. Our integrated approach enabled variant tracking, offering evidence for well-informed public health interventions.
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Establishing severe acute respiratory infection (SARI) surveillance in a sentinel hospital, Ireland, 2021 to 2022
More LessBackgroundIn 2020, due to the COVID-19 pandemic, the European Centre for Disease Prevention and Control (ECDC) accelerated development of European-level severe acute respiratory infection (SARI) surveillance.
AimWe aimed to establish SARI surveillance in one Irish hospital as part of a European network E-SARI-NET.
MethodsWe used routine emergency department records to identify cases in one adult acute hospital. The SARI case definition was adapted from the ECDC clinical criteria for a possible COVID-19 case. Clinical data were collected using an online questionnaire. Cases were tested for SARS-CoV-2, influenza and respiratory syncytial virus (RSV), including whole genome sequencing (WGS) on SARS-CoV-2 RNA-positive samples and viral characterisation/sequencing on influenza RNA-positive samples. Descriptive analysis was conducted for SARI cases hospitalised between July 2021 and April 2022.
ResultsOverall, we identified 437 SARI cases, the incidence ranged from two to 28 cases per week (0.7–9.2/100,000 hospital catchment population). Of 431 cases tested for SARS-CoV-2 RNA, 226 (52%) were positive. Of 349 (80%) cases tested for influenza and RSV RNA, 15 (4.3%) were positive for influenza and eight (2.3%) for RSV. Using WGS, we identified Delta- and Omicron-dominant periods. The resource-intensive nature of manual clinical data collection, specimen management and laboratory supply shortages for influenza and RSV testing were challenging.
ConclusionWe successfully established SARI surveillance as part of E-SARI-NET. Expansion to additional sentinel sites is planned following formal evaluation of the existing system. SARI surveillance requires multidisciplinary collaboration, automated data collection where possible, and dedicated personnel resources, including for specimen management.
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Using an influenza surveillance system to estimate the number of SARS-CoV-2 infections in Beijing, China, weeks 2 to 6 2023
More LessLi Zhang , Yi Zhang , Wei Duan , Shuangsheng Wu , Ying Sun , Chunna Ma , Quanyi Wang , Daitao Zhang and Peng YangWith COVID-19 public health control measures downgraded in China in January 2023, reported COVID-19 case numbers may underestimate the true numbers after the SARS-CoV-2 Omicron wave. Using a multiplier model based on our influenza surveillance system, we estimated that the overall incidence of SARS-CoV-2 infections was 392/100,000 population in Beijing during the 5 weeks following policy adjustment. No notable change occurred after the Spring Festival in early February. The multiplier model provides an opportunity for assessing the actual COVID-19 situation.
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Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021
More LessTorsten Houwaart , Samir Belhaj , Emran Tawalbeh , Dirk Nagels , Yara Fröhlich , Patrick Finzer , Pilar Ciruela , Aurora Sabrià , Mercè Herrero , Cristina Andrés , Andrés Antón , Assia Benmoumene , Dounia Asskali , Hussein Haidar , Janina von Dahlen , Jessica Nicolai , Mygg Stiller , Jacqueline Blum , Christian Lange , Carla Adelmann , Britta Schroer , Ute Osmers , Christiane Grice , Phillipp P. Kirfel , Hassan Jomaa , Daniel Strelow , Lisanna Hülse , Moritz Pigulla , Pascal Kreuzer , Alona Tyshaieva , Jonas Weber , Tobias Wienemann , Malte Kohns Vasconcelos , Katrin Hoffmann , Nadine Lübke , Sandra Hauka , Marcel Andree , Claus Jürgen Scholz , Nathalie Jazmati , Klaus Göbels , Rainer Zotz , Klaus Pfeffer , Jörg Timm , Lutz Ehlkes , Andreas Walker , Alexander T. Dilthey and German COVID-19 OMICS Initiative (DeCOI)BackgroundTracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective.
AimWe demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters.
MethodsGenomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021.
ResultsCluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf.
ConclusionIGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.
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Using routine emergency department data for syndromic surveillance of acute respiratory illness, Germany, week 10 2017 until week 10 2021
More LessBackgroundThe COVID-19 pandemic expanded the need for timely information on acute respiratory illness at population level.
AimWe explored the potential of routine emergency department data for syndromic surveillance of acute respiratory illness in Germany.
MethodsWe used routine attendance data from emergency departments, which continuously transferred data between week 10 2017 and 10 2021, with ICD-10 codes available for > 75% of attendances. Case definitions for acute respiratory infection (ARI), severe acute respiratory infection (SARI), influenza-like illness (ILI), respiratory syncytial virus infection (RSV) and COVID-19 were based on a combination of ICD-10 codes, and/or chief complaints, sometimes combined with information on hospitalisation and age.
ResultsWe included 1,372,958 attendances from eight emergency departments. The number of attendances dropped in March 2020 during the first COVID-19 pandemic wave, increased during summer, and declined again during the resurge of COVID-19 cases in autumn and winter of 2020/21. A pattern of seasonality of respiratory infections could be observed. By using different case definitions (i.e. for ARI, SARI, ILI, RSV) both the annual influenza seasons in the years 2017–2020 and the dynamics of the COVID-19 pandemic in 2020/21 were apparent. The absence of the 2020/21 influenza season was visible, parallel to the resurge of COVID-19 cases. SARI among ARI cases peaked in April–May 2020 (17%) and November 2020–January 2021 (14%).
ConclusionSyndromic surveillance using routine emergency department data can potentially be used to monitor the trends, timing, duration, magnitude and severity of illness caused by respiratory viruses, including both influenza viruses and SARS-CoV-2.
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Rapidly adapting primary care sentinel surveillance across seven countries in Europe for COVID-19 in the first half of 2020: strengths, challenges, and lessons learned
More LessJayshree Bagaria , Tessa Jansen , Diogo FP Marques , Mariette Hooiveld , Jim McMenamin , Simon de Lusignan , Ana-Maria Vilcu , Adam Meijer , Ana-Paula Rodrigues , Mia Brytting , Clara Mazagatos , Jade Cogdale , Sylvie van der Werf , Frederika Dijkstra , Raquel Guiomar , Theresa Enkirch , Marta Valenciano and I-MOVE-COVID-19 study teamAs the COVID-19 pandemic began in early 2020, primary care influenza sentinel surveillance networks within the Influenza - Monitoring Vaccine Effectiveness in Europe (I-MOVE) consortium rapidly adapted to COVID-19 surveillance. This study maps system adaptations and lessons learned about aligning influenza and COVID-19 surveillance following ECDC / WHO/Europe recommendations and preparing for other diseases possibly emerging in the future. Using a qualitative approach, we describe the adaptations of seven sentinel sites in five European Union countries and the United Kingdom during the first pandemic phase (March–September 2020). Adaptations to sentinel systems were substantial (2/7 sites), moderate (2/7) or minor (3/7 sites). Most adaptations encompassed patient referral and sample collection pathways, laboratory testing and data collection. Strengths included established networks of primary care providers, highly qualified testing laboratories and stakeholder commitments. One challenge was the decreasing number of samples due to altered patient pathways. Lessons learned included flexibility establishing new routines and new laboratory testing. To enable simultaneous sentinel surveillance of influenza and COVID-19, experiences of the sentinel sites and testing infrastructure should be considered. The contradicting aims of rapid case finding and contact tracing, which are needed for control during a pandemic and regular surveillance, should be carefully balanced.
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The impact of SARS-CoV-2 on respiratory syndromic and sentinel surveillance in Israel, 2020: a new perspective on established systems
More LessAharona Glatman-Freedman , Lea Gur-Arie , Hanna Sefty , Zalman Kaufman , Michal Bromberg , Rita Dichtiar , Alina Rosenberg , Rakefet Pando , Ital Nemet , Limor Kliker2, , Ella Mendelson , Lital Keinan-Boker , Neta S Zuckerman , Michal Mandelboim and on behalf of The Israeli Respiratory Viruses Surveillance Network (IRVSN)BackgroundThe 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.
AimWe 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.
MethodsWe 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.
ResultsSyndromic 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.
ConclusionOur 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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