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Kufner V, Frey AC, Burkhard SH, Schmutz S, Ziltener G, Zaheri M, Wiedmer CV, Plate A, Trkola A, Huber M, Mueller NJ. Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic. Swiss Med Wkly 2024; 154:3797. [PMID: 38587784 DOI: 10.57187/s.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
AIMS OF THE STUDY Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting. METHODS This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests. RESULTS Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures. CONCLUSIONS Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.
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Affiliation(s)
- Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea C Frey
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Sara H Burkhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Gabriela Ziltener
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Caroline V Wiedmer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Plate
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nicolas J Mueller
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
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2
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Chan T, Ginders J, Kuhlmeier E, Meli ML, Bönzli E, Meili T, Hüttl J, Hatt JM, Hindenlang Clerc K, Kipar A, Wyss F, Wenker C, Ryser-Degiorgis MP, Valenzuela Agüí C, Urban C, Beisel C, Stadler T, Hofmann-Lehmann R. Detection of SARS-CoV-2 RNA in a Zoo-Kept Red Fox ( Vulpes vulpes). Viruses 2024; 16:521. [PMID: 38675864 PMCID: PMC11054100 DOI: 10.3390/v16040521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Many different animal species are susceptible to SARS-CoV-2, including a few Canidae (domestic dog and raccoon dog). So far, only experimental evidence is available concerning SARS-CoV-2 infections in red foxes (Vulpes vulpes). This is the first report of SARS-CoV-2 RNA detection in a sample from a red fox. The RT-qPCR-positive fox was zoo-kept together with another fox and two bears in the Swiss Canton of Zurich. Combined material from a conjunctival and nasal swab collected for canine distemper virus diagnostics tested positive for SARS-CoV-2 RNA with Ct values of 36.9 (E gene assay) and 35.7 (RdRp gene assay). The sample was analysed for SARS-CoV-2 within a research project testing residual routine diagnostic samples from different animal species submitted between spring 2020 and December 2022 to improve knowledge on SARS-CoV-2 infections within different animal species and investigate their potential role in a One Health context. Within this project, 246 samples from 153 different animals from Swiss zoos and other wild animal species all tested SARS-CoV-2 RT-qPCR and/or serologically negative so far, except for the reported fox. The source of SARS-CoV-2 in the fox is unknown. The fox disappeared within the naturally structured enclosure, and the cadaver was not found. No further control measures were undertaken.
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Affiliation(s)
- Tatjana Chan
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Julia Ginders
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Evelyn Kuhlmeier
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Eva Bönzli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Theres Meili
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Julia Hüttl
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
| | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Department of Small Animals, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland;
| | | | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057 Zurich, Switzerland;
| | - Fabia Wyss
- Zoologischer Garten Basel AG, Binningerstrasse 40, 4054 Basel, Switzerland; (F.W.); (C.W.)
| | - Christian Wenker
- Zoologischer Garten Basel AG, Binningerstrasse 40, 4054 Basel, Switzerland; (F.W.); (C.W.)
| | | | - Cecilia Valenzuela Agüí
- Department of Biosystems Science and Engineering, ETH Zurich, Schanzenstrasse 44, Postfach, 4009 Basel, Switzerland; (C.V.A.); (C.B.); (T.S.)
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Christian Urban
- Functional Genomics Center, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland;
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Schanzenstrasse 44, Postfach, 4009 Basel, Switzerland; (C.V.A.); (C.B.); (T.S.)
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Schanzenstrasse 44, Postfach, 4009 Basel, Switzerland; (C.V.A.); (C.B.); (T.S.)
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (T.C.); (J.G.); (E.K.); (M.L.M.); (J.H.)
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3
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Lam C, Johnson-Mackinnon J, Basile K, Fong W, Suster CJ, Gall M, Agius J, Chandra S, Draper J, Martinez E, Drew A, Wang Q, Chen SC, Kok J, Dwyer DE, Sintchenko V, Rockett RJ. A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs. Microbiol Spectr 2023; 11:e0220223. [PMID: 37966271 PMCID: PMC10715188 DOI: 10.1128/spectrum.02202-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE This study provides a laboratory framework to ensure ongoing relevance and performance of amplification-based whole genome sequencing to strengthen public health surveillance during extended outbreaks or pandemics. The framework integrates regular reviews of the performance of a genomic surveillance system and highlights the importance of ongoing monitoring and the identification and implementation of improvements to whole genome sequencing methods to enhance public health responses to pathogen outbreaks.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Kerri Basile
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Carl J.E. Suster
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Mailie Gall
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jessica Agius
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Shona Chandra
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Jenny Draper
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elena Martinez
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Alexander Drew
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C. Chen
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Dominic E. Dwyer
- Centre for Infectious Diseases and Microbiology - Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, Australia
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, The University of Sydney, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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4
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Weber A, Översti S, Kühnert D. Reconstructing relative transmission rates in Bayesian phylodynamics: Two-fold transmission advantage of Omicron in Berlin, Germany during December 2021. Virus Evol 2023; 9:vead070. [PMID: 38107332 PMCID: PMC10725310 DOI: 10.1093/ve/vead070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023] Open
Abstract
Phylodynamic methods have lately played a key role in understanding the spread of infectious diseases. During the coronavirus disease (COVID-19) pandemic, large scale genomic surveillance has further increased the potential of dynamic inference from viral genomes. With the continual emergence of novel severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, explicitly allowing transmission rate differences between simultaneously circulating variants in phylodynamic inference is crucial. In this study, we present and empirically validate an extension to the BEAST2 package birth-death skyline model (BDSKY), BDSKY[Formula: see text], which introduces a scaling factor for the transmission rate between independent, jointly inferred trees. In an extensive simulation study, we show that BDSKY[Formula: see text] robustly infers the relative transmission rates under different epidemic scenarios. Using publicly available genome data of SARS-CoV-2, we apply BDSKY[Formula: see text] to quantify the transmission advantage of the Omicron over the Delta variant in Berlin, Germany. We find the overall transmission rate of Omicron to be scaled by a factor of two with pronounced variation between the individual clusters of each variant. These results quantify the transmission advantage of Omicron over the previously circulating Delta variant, in a crucial period of pre-established non-pharmaceutical interventions. By inferring variant- as well as cluster-specific transmission rate scaling factors, we show the differences in transmission dynamics for each variant. This highlights the importance of incorporating lineage-specific transmission differences in phylodynamic inference.
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Affiliation(s)
- Ariane Weber
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
| | | | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group (tide), Max Planck Institute of Geoanthropology, Kahlaische Strasse 10, Jena, Thuringia 07745, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Saxony 04103, Germany
- Centre for Artificial Intelligence in Public Health Research, Robert Koch Institute, Ludwig-Witthöft-Straße 14, Wildau, Brandenburg 15745, Germany
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5
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Scholz U, Mundry R, Freund AM. Predicting the use of a COVID-19 contact tracing application: A study across two points of measurements. Appl Psychol Health Well Being 2023; 15:1673-1694. [PMID: 37339769 DOI: 10.1111/aphw.12461] [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: 11/01/2022] [Accepted: 05/24/2023] [Indexed: 06/22/2023]
Abstract
Contact tracing mobile applications (apps) were important in combating the COVID-19 pandemic. Most previous studies predicting contact tracing app use were cross-sectional and not theory-based. This study aimed at contributing to a better understanding of app use intentions and app use by applying an extended version of the protection motivation theory across two measurement points while accounting for the development of the pandemic. A total of N = 1525 participants from Switzerland (Mage = 53.70, SD = 18.73; 47% female; n = 270 completed both assessments) reported on risk perceptions, response efficacy, self-efficacy, social norms, trust in government, trust in the healthcare system, active search of COVID-19-related information, intentions for and actual (self-reported) app use. Analyses included country-specific incidences and death toll. Increases in response-efficacy, self-efficacy, trust in government, and the active search of COVID-19-related information predicted increased app-use intentions. Increases in self-efficacy, intentions, and the active search of COVID-19-related information predicted increased self-reported app use. Risk perceptions, incidence, and death toll were unrelated to both outcomes. Across an aggravation of the pandemic situation, intentions for and app use were primarily related to response-efficacy, self-efficacy, trust in government, and the active search of COVID-19-related information.
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Affiliation(s)
- Urte Scholz
- Department of Psychology, University of Zurich, Zurich, Switzerland
- University Research Priority Program Dynamic of Healthy Aging, University of Zurich, Zurich, Switzerland
| | - Roger Mundry
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department for Primate Cognition, Georg-August-University Göttingen, Göttingen, Germany
- Leibniz Science Campus Primate Cognition, Göttingen, Germany
| | - Alexandra M Freund
- Department of Psychology, University of Zurich, Zurich, Switzerland
- University Research Priority Program Dynamic of Healthy Aging, University of Zurich, Zurich, Switzerland
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6
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Heron L, Mugglin C, Zürcher K, Brumann E, Keune-Dübi B, Low N, Fenner L. Contact tracing for COVID-19 in a Swiss canton: analysis of key performance indicators. Swiss Med Wkly 2023; 153:40112. [PMID: 37955850 DOI: 10.57187/smw.2023.40112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Contact tracing (CT) has played an important role in strategies to control COVID-19. However, there is limited evidence on the performance of digital tools for CT and no consensus on which indicators to use to monitor their performance. We aimed to describe the system and analyse outcomes of CT with a partially automated workflow in the Swiss canton of Solothurn, using key performance indicators (KPIs). METHODS We describe the process of CT used in the canton of Solothurn between November 2020 and February 2022, including forward and backward CT. We developed 16 KPIs representing CT structure (S1-2), process (P1-11) and outcome (O1-3) based on previous literature to analyse the relative performance of CT. We report the changes in the indicators over waves of SARS-CoV-2 infections caused by several viral variants. RESULTS The CT team in Solothurn processed 57,363 index cases and 71,809 contacts over a 15-month period. The CT team successfully contacted 99% of positive cases within 24 hours (KPI P7) throughout the pandemic and returned almost all test results on the same or next day (KPI P6), before the delta variant emerged. Three-quarters of contacts were notified within 24 hours of the CT interview with the index (KPI P8) before the emergence of the alpha, delta and omicron variants, when the proportions decreased to 64%, 36% and 54%, respectively. The percentage of new symptomatic cases tested and interviewed within 3 days of symptom onset was high at >70% (KPI P10) and contacts started quarantine within a median of 3 days of index case symptom onset (KPI P3). About a fifth of new index cases had already been in quarantine by the time of their positive test (KPI O1), before the delta variant emerged. The percentage of index cases in isolation by day of testing remained at almost 100% throughout the period of analysis (KPI O2). CONCLUSIONS The CT in Solothurn used a partially automated workflow and continued to perform well throughout the pandemic, although the relative performance of the CT system declined at higher caseloads. CT remains an important tool for controlling the spread of infectious diseases, but clearer standards should improve the performance, comparability and monitoring of infection in real time as part of pandemic preparedness efforts.
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Affiliation(s)
- Leonie Heron
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Catrina Mugglin
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Kathrin Zürcher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erich Brumann
- Cantonal Physician's Office, Canton of Solothurn, Solothurn, Switzerland
| | - Bettina Keune-Dübi
- Cantonal Physician's Office, Canton of Solothurn, Solothurn, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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7
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Ge Y, Wu X, Zhang W, Wang X, Zhang D, Wang J, Liu H, Ren Z, Ruktanonchai NW, Ruktanonchai CW, Cleary E, Yao Y, Wesolowski A, Cummings DAT, Li Z, Tatem AJ, Lai S. Effects of public-health measures for zeroing out different SARS-CoV-2 variants. Nat Commun 2023; 14:5270. [PMID: 37644012 PMCID: PMC10465600 DOI: 10.1038/s41467-023-40940-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Targeted public health interventions for an emerging epidemic are essential for preventing pandemics. During 2020-2022, China invested significant efforts in strict zero-COVID measures to contain outbreaks of varying scales caused by different SARS-CoV-2 variants. Based on a multi-year empirical dataset containing 131 outbreaks observed in China from April 2020 to May 2022 and simulated scenarios, we ranked the relative intervention effectiveness by their reduction in instantaneous reproduction number. We found that, overall, social distancing measures (38% reduction, 95% prediction interval 31-45%), face masks (30%, 17-42%) and close contact tracing (28%, 24-31%) were most effective. Contact tracing was crucial in containing outbreaks during the initial phases, while social distancing measures became increasingly prominent as the spread persisted. In addition, infections with higher transmissibility and a shorter latent period posed more challenges for these measures. Our findings provide quantitative evidence on the effects of public-health measures for zeroing out emerging contagions in different contexts.
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Affiliation(s)
- Yong Ge
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Poyang Lake Wetland and Watershed Research Ministry of Education, Jiangxi Normal University, Nanchang, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
| | - Xilin Wu
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wenbin Zhang
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Xiaoli Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Die Zhang
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Poyang Lake Wetland and Watershed Research Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Jianghao Wang
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haiyan Liu
- Marine Data Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhoupeng Ren
- State Key Laboratory of Resources and Environmental Information System, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | | | | | - Eimear Cleary
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Yongcheng Yao
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
- School of Mathematics and Statistics, Zhengzhou Normal University, Zhengzhou, China
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Derek A T Cummings
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Zhongjie Li
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Andrew J Tatem
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK
| | - Shengjie Lai
- WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK.
- Institute for Life Sciences, University of Southampton, Southampton, UK.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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8
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Kuhlmeier E, Chan T, Agüí CV, Willi B, Wolfensberger A, Beisel C, Topolsky I, Beerenwinkel N, Stadler T, Jones S, Tyson G, Hosie MJ, Reitt K, Hüttl J, Meli ML, Hofmann-Lehmann R. Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland. Viruses 2023; 15:245. [PMID: 36680285 PMCID: PMC9864232 DOI: 10.3390/v15010245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
In human beings, there are five reported variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). However, in contrast to human beings, descriptions of infections of animals with specific variants are still rare. The aim of this study is to systematically investigate SARS-CoV-2 infections in companion animals in close contact with SARS-CoV-2-positive owners ("COVID-19 households") with a focus on the Delta variant. Samples, obtained from companion animals and their owners were analyzed using a real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) and next-generation sequencing (NGS). Animals were also tested for antibodies and neutralizing activity against SARS-CoV-2. Eleven cats and three dogs in nine COVID-19-positive households were RT-qPCR and/or serologically positive for the SARS-CoV-2 Delta variant. For seven animals, the genetic sequence could be determined. The animals were infected by one of the pangolin lineages B.1.617.2, AY.4, AY.43 and AY.129 and between zero and three single-nucleotide polymorphisms (SNPs) were detected between the viral genomes of animals and their owners, indicating within-household transmission between animal and owner and in multi-pet households also between the animals. NGS data identified SNPs that occur at a higher frequency in the viral sequences of companion animals than in viral sequences of humans, as well as SNPs, which were exclusively found in the animals investigated in the current study and not in their owners. In conclusion, our study is the first to describe the SARS-CoV-2 Delta variant transmission to animals in Switzerland and provides the first-ever description of Delta-variant pangolin lineages AY.129 and AY.4 in animals. Our results reinforce the need of a One Health approach in the monitoring of SARS-CoV-2 in animals.
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Affiliation(s)
- Evelyn Kuhlmeier
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Tatjana Chan
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Cecilia Valenzuela Agüí
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Barbara Willi
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Aline Wolfensberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | | | - Sarah Jones
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Grace Tyson
- School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Margaret J. Hosie
- MRC-University of Glasgow Centre for Virus, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK
| | - Katja Reitt
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Julia Hüttl
- Center for Laboratory Medicine, Veterinary Diagnostic Services, Frohbergstrasse 3, 9001 St. Gallen, Switzerland
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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