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Shinohara N, Kurihara N, Naito W, Iwai A, Yasutaka T, Morioka T, Takatsuji T, Ogata M, Tatsu K. Wind velocity and dispersion/advection-diffusion of artificial droplets and droplet nuclei in a domed all-weather multi-purpose stadium. Sci Rep 2024; 14:26601. [PMID: 39496673 PMCID: PMC11535064 DOI: 10.1038/s41598-024-76806-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 10/16/2024] [Indexed: 11/06/2024] Open
Abstract
To evaluate the COVID-19 infection risk and the effectiveness of countermeasures at mass-gathering events, we measured the dispersion and advective diffusion of artificial droplets and artificial droplet nuclei at the Tokyo Dome, Japan (capacity 55,000 people). We also measured and evaluated the effectiveness of wearing masks and increasing the space between seating areas. If people were seated facing forward, artificial droplets did not reach the mouths of surrounding people, suggesting low risk of droplet transmission. For an artificially generated cough or sneeze, the volume of droplets deposited on the hair, back of the neck, and back of the human in front, and the backs of the seats in front, decreased by two to three orders of magnitude when a mask was worn, regardless of the type of mask. However, when the mask was worn with the nose out, the amount deposited on the back of the seat in front was reduced by only 17%. Even in seats with the highest particle concentration in the vicinity of the source, only 0.097%-0.24% of the generated droplet nuclei (1.0-3.0 μm) from the source were inhaled. Our results suggest that the infection risk at the Tokyo Dome via droplet and airborne transmission was low.
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Affiliation(s)
- Naohide Shinohara
- National Institute of Advanced Industrial Science and Technology (AIST), Research Institute of Science for Safety and Sustainability (RISS), 16-1 Onogawa, Tsukuba-City, Ibaraki, 305-8569, Japan.
| | - Noboru Kurihara
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), 1-1-1 Umezono, Tsukuba-City, Ibaraki, 305-8563, Japan
| | - Wataru Naito
- National Institute of Advanced Industrial Science and Technology (AIST), Research Institute of Science for Safety and Sustainability (RISS), 16-1 Onogawa, Tsukuba-City, Ibaraki, 305-8569, Japan
| | - Aya Iwai
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), 1-1-1 Umezono, Tsukuba-City, Ibaraki, 305-8563, Japan
| | - Tetsuo Yasutaka
- National Institute of Advanced Industrial Science and Technology (AIST), Geological survey of Japan, 1-1-1 Higashi, Tsukuba-City, Ibaraki, 305-8567, Japan
| | - Toshihiro Morioka
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), 1-1-1 Umezono, Tsukuba-City, Ibaraki, 305-8563, Japan
| | - Toshiyuki Takatsuji
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), 1-1-1 Umezono, Tsukuba-City, Ibaraki, 305-8563, Japan
| | - Masayuki Ogata
- Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-City, Tokyo, 192-0397, Japan
| | - Koichi Tatsu
- National Institute of Advanced Industrial Science and Technology (AIST), Research Institute of Science for Safety and Sustainability (RISS), 16-1 Onogawa, Tsukuba-City, Ibaraki, 305-8569, Japan
- Isuzu Motors Ltd, 8 Tsuchidana, Fujisawa-City, Kanagawa, 252-8501, Japan
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Dyrdak R, Hodcroft EB, Broddesson S, Grabbe M, Franklin H, Gisslén M, Holm ME, Lindh M, Nederby-Öhd J, Ringlander J, Sundqvist M, Neher RA, Albert J. Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020. Euro Surveill 2024; 29:2400021. [PMID: 39392000 PMCID: PMC11484920 DOI: 10.2807/1560-7917.es.2024.29.41.2400021] [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: 01/03/2024] [Accepted: 05/30/2024] [Indexed: 10/12/2024] Open
Abstract
BackgroundDespite the unprecedented measures implemented globally in early 2020 to prevent the spread of SARS-CoV-2, Sweden, as many other countries, experienced a severe first wave during the COVID-19 pandemic.AimWe investigated the introduction and spread of SARS-CoV-2 into Sweden.MethodsWe analysed stored respiratory specimens (n = 1,979), sampled 7 February-2 April 2020, by PCR for SARS-CoV-2 and sequenced PCR-positive specimens. Sequences generated from newly detected cases and stored positive specimens February-June 2020 (n = 954) were combined with sequences (Sweden: n = 730; other countries: n = 129,913) retrieved from other sources for Nextstrain clade assignment and phylogenetic analyses.ResultsTwelve previously unrecognised SARS-CoV-2 cases were identified: the earliest was sampled on 3 March, 1 week before recognised community transmission. We showed an early influx of clades 20A and 20B from Italy (201/328, 61% of cases exposed abroad) and clades 19A and 20C from Austria (61/328, 19%). Clade 20C dominated the first wave (20C: 908/1,684, 54%; 20B: 438/1,684, 26%; 20A: 263/1,684, 16%), and 800 of 1,684 (48%) Swedish sequences formed a country-specific 20C cluster defined by a spike mutation (G24368T). At the regional level, the proportion of clade 20C sequences correlated with an earlier weighted mean date of COVID-19 deaths.ConclusionCommunity transmission in Sweden started when mitigation efforts still focused on preventing influx. This created a transmission advantage for clade 20C, likely introduced from ongoing cryptic spread in Austria. Therefore, pandemic preparedness should have a comprehensive approach, including capacity for large-scale diagnostics to allow early detection of travel-related cases and community transmission.
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Affiliation(s)
- Robert Dyrdak
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Emma B Hodcroft
- Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Broddesson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Grabbe
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hildur Franklin
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden
- Public Health Agency of Sweden, Solna, Sweden
| | - Maricris E Holm
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Joanna Nederby-Öhd
- Department of Infectious Disease Prevention and Control, Stockholm Region, Stockholm, Sweden
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Johan Ringlander
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Martin Sundqvist
- Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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3
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Domènech-Montoliu S, Pac-Sa MR, Sala-Trull D, Del Rio-González A, Sanchéz-Urbano M, Satorres-Martinez P, Blasco-Gari R, Casanova-Suarez J, Gil-Fortuño M, López-Diago L, Notari-Rodríguez C, Pérez-Olaso Ó, Romeu-Garcia MA, Ruiz-Puig R, Aleixandre-Gorriz I, Domènech-León C, Arnedo-Pena A. Underreporting of Cases in the COVID-19 Outbreak of Borriana (Spain) during Mass Gathering Events in March 2020: A Cross-Sectional Study. EPIDEMIOLOGIA 2024; 5:499-510. [PMID: 39189253 PMCID: PMC11348374 DOI: 10.3390/epidemiologia5030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024] Open
Abstract
Determining the number of cases of an epidemic is the first function of epidemiological surveillance. An important underreporting of cases was observed in many locations during the first wave of the COVID-19 pandemic. To estimate this underreporting in the COVID-19 outbreak of Borriana (Valencia Community, Spain) in March 2020, a cross-sectional study was performed in June 2020 querying the public health register. Logistic regression models were used. Of a total of 468 symptomatic COVID-19 cases diagnosed in the outbreak through anti-SARS-CoV-2 serology, 36 cases were reported (7.7%), resulting in an underreporting proportion of 92.3% (95% confidence interval [CI], 89.5-94.6%), with 13 unreported cases for every reported case. Only positive SARS-CoV-2 polymerase chain reaction cases were predominantly reported due to a limited testing capacity and following a national protocol. Significant factors associated with underreporting included no medical assistance for COVID-19 disease, with an adjusted odds ratio [aOR] of 10.83 (95% CI 2.49-47.11); no chronic illness, aOR = 2.81 (95% CI 1.28-6.17); middle and lower social classes, aOR = 3.12 (95% CI 1.42-6.85); younger age, aOR = 0.97 (95% CI 0.94-0.99); and a shorter duration of illness, aOR = 0.98 (95% CI 0.97-0.99). To improve the surveillance of future epidemics, new approaches are recommended.
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Affiliation(s)
| | - Maria Rosario Pac-Sa
- Public Health Center, 12003 Castelló de la Plana, Spain; (M.R.P.-S.); (M.A.R.-G.)
| | - Diego Sala-Trull
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | | | - Manuel Sanchéz-Urbano
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | - Paloma Satorres-Martinez
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | - Roser Blasco-Gari
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | | | - Maria Gil-Fortuño
- Microbiology Service University Hospital de la Plana, 12540 Vila-Real, Spain; (M.G.-F.); (Ó.P.-O.)
| | - Laura López-Diago
- Clinical Analysis Service University Hospital de la Plana, 12540 Vila-Real, Spain; (L.L.-D.); (I.A.-G.)
| | - Cristina Notari-Rodríguez
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | - Óscar Pérez-Olaso
- Microbiology Service University Hospital de la Plana, 12540 Vila-Real, Spain; (M.G.-F.); (Ó.P.-O.)
| | | | - Raquel Ruiz-Puig
- Emergency Service University Hospital de la Plana, 12540 Vila-Real, Spain; (D.S.-T.); (M.S.-U.); (P.S.-M.); (R.B.-G.); (C.N.-R.); (R.R.-P.)
| | - Isabel Aleixandre-Gorriz
- Clinical Analysis Service University Hospital de la Plana, 12540 Vila-Real, Spain; (L.L.-D.); (I.A.-G.)
| | - Carmen Domènech-León
- Department of Medicine, University CEU Cardenal Herrera, 12006 Castelló de la Plana, Spain;
| | - Alberto Arnedo-Pena
- Public Health Center, 12003 Castelló de la Plana, Spain; (M.R.P.-S.); (M.A.R.-G.)
- Department of Health Science, Public University Navarra, 31006 Pamplona, Spain
- Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
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4
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Ragozzino S, Kuehl R, Leuzinger K, Schläpfer P, Urwyler P, Durovic A, Zingg S, von Rotz M, Battegay M, Widmer AF, Hirsch HH, Bassetti S, Tschudin-Sutter S. Secondary attack rate following on-site isolation of patients with suspected COVID-19 in multiple-bed rooms. Antimicrob Resist Infect Control 2024; 13:73. [PMID: 38971822 PMCID: PMC11227710 DOI: 10.1186/s13756-024-01430-4] [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: 12/18/2023] [Accepted: 06/28/2024] [Indexed: 07/08/2024] Open
Abstract
The implementation of isolation precautions for patients with suspected Coronavirus Disease 2019 (COVID-19) and pending test results is resource intensive. Due to the limited availability of single-bed rooms at our institution, we isolated patients with suspected COVID-19 together with patients without suspected COVID-19 on-site in multiple-bed rooms until SARS-CoV-2-test results were available. We evaluated the likelihood of SARS-CoV-2 transmission to individuals sharing the room with patients isolated on-site. This observational study was performed at the University Hospital Basel, Switzerland, from 03/20 - 11/20. Secondary attack rates were compared between patients hospitalized in multiple-bed rooms and exposed to individuals subjected to on-site isolation precautions (on-site isolation group), and patients exposed to individuals initially not identified as having COVID-19, and not placed under isolation precautions until the diagnosis was suspected (control group). Transmission events were confirmed by whole-genome sequencing. Among 1,218 patients with suspected COVID-19, 67 (5.5%) tested positive for SARS-CoV-2. Of these, 21 were isolated on-site potentially exposing 27 patients sharing the same room. Median contact time was 12 h (interquartile range 7-18 h). SARS-CoV-2 transmission was identified in none of the patients in the on-site isolation group vs. 10/63 (15.9%) in the control group (p = 0.03). Isolation on-site of suspected COVID-19-patients in multiple-bed rooms avoided single-room occupancy and subsequent in-hospital relocation for many patients without confirmed SARS-CoV-2-infection. The absence of secondary transmission among the exposed patients in the on-site isolation group allows for assessment of the risk/benefit ratio of this strategy given the limitation of a small sample size.
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Affiliation(s)
- Silvio Ragozzino
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Richard Kuehl
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Pascal Schläpfer
- Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Pascal Urwyler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Ana Durovic
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Sandra Zingg
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Matthias von Rotz
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Andreas F Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
- Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, University Basel, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland.
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Petersgraben 4, Basel, CH-4031, Switzerland.
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5
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Alahmari AA, Khan AA, Alamri FA, Almuzaini YS, Habash AK, Jokhdar H. Healthcare policies, precautionary measures and outcomes of mass gathering events in the era of COVID-19 pandemic: Expedited review. J Infect Public Health 2024; 17 Suppl 1:27-33. [PMID: 37059635 PMCID: PMC10049799 DOI: 10.1016/j.jiph.2023.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/14/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
With the onset of the COVID-19 pandemic in early 2020, several countries suspended or restricted mass gathering (MG) events to mitigate the risk of superspreading events. Prohibiting MGs aimed to lessen the likelihood of highly infectious persons coming into close contact with many others. Now that the world has opened its doors wide and removed most of precautionary measures, many questions arise. In this review, we aimed to summarize the current evidence regarding the policies and regulations that were implemented for the safe return of MG events. Besides, we highlighted the impact of the return of MG events during 2021 on the trajectory of COVID-19 spread. Canceling MG events can carry religious, societal, economic, and public negative consequences necessitating the safe return of these events. The experience with the COVID-19 pandemic was the foundation for the recommendations for the safe conduction of MG events during the pandemic by international public health bodies. When policymakers adequately applied precautionary measures and strategic approaches, we witnessed the safe holding of huge MG events without aggravating the COVID-19 situation or increasing the number of new cases beyond the capacity and readiness of the national healthcare system.
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Affiliation(s)
- Ahmed A Alahmari
- Global Centre for Mass Gatherings Medicine, Ministry of Health, Saudi Arabia
| | - Anas A Khan
- Department of Emergency Medicine, College of Medicine, King Saud University, Saudi Arabia
| | - Fahad A Alamri
- Global Centre of Mass Gatherings Medicine, Family Medicine, Primary Health Centre, Ministry of Health, Riyadh, Saudi Arabia.
| | - Yasir S Almuzaini
- Global Centre for Mass Gatherings Medicine, Ministry of Health, Saudi Arabia
| | - Alia K Habash
- Global Centre for Mass Gatherings Medicine, Ministry of Health, Saudi Arabia
| | - Hani Jokhdar
- Deputyship of Public Health, Ministry of Health, Riyadh, Saudi Arabia
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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [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: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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Seth-Smith H, Vesenbeckh S, Egli A, Ott S. SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing. BMJ Case Rep 2023; 16:e255255. [PMID: 38087481 PMCID: PMC10728978 DOI: 10.1136/bcr-2023-255255] [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] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
The evolution of SARS-CoV-2 within immunocompromised hosts who fail to clear the virus over many months has been proposed as a route to the development of Variants of Concern (VoCs). We present a case of an immunocompromised male patient with a prolonged SARS-CoV-2 infection. During hospitalisation, 7 weeks after first diagnosis, his condition worsened to require continuous ventilation support. Resolution of symptoms was observed after convalescent plasma therapy. Whole genome sequencing of the virus showed Pango lineage B.1.221. Between the first sample and the second from bronchoalveolar lavage fluid 7 weeks later, we identified eight mutations, including minor variants, which could be used to estimate the chronology of mutations. This suggests an elevated mutation rate, in-host accumulation of mutations and further evidence for sources of VoCs. Prolonged SARS-CoV-2 infections in immunocompromised hosts increase the likelihood of hospital stays and morbidity, and also pose an increased risk to global public health.
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Affiliation(s)
- Helena Seth-Smith
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Silvan Vesenbeckh
- Department of Pulmonology, University Hospital Zurich, Zurich, Switzerland
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Sebastian Ott
- Department of Pulmonology, Sankt Claraspital, Basel, Switzerland
- Department of Pulmonology, Inselspital University Hospital Bern, Bern, Switzerland
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8
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Zürcher K, Abela IA, Stange M, Dupont C, Mugglin C, Egli A, Trkola A, Egger M, Fenner L. Alpha Variant Coronavirus Outbreak in a Nursing Home Despite High Vaccination Coverage: Molecular, Epidemiological, and Immunological Studies. Clin Infect Dis 2023; 77:537-546. [PMID: 35522980 PMCID: PMC9129182 DOI: 10.1093/cid/ciab1005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Vaccination may control the coronavirus disease 2019 (COVID-19) pandemic, including in nursing homes where many high-risk people live. We conducted extensive outbreak investigations. METHODS We studied an outbreak at a nursing home in Switzerland, where the uptake of messenger RNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was 82% among residents as of 21 January 2021. After diagnosis of COVID-19 in a vaccinated symptomatic healthcare worker (HCW) on 22 February, we performed outbreak investigations in house A (47 residents; 37 HCWs), using SARS-CoV-2-specific polymerase chain reaction testing of nasopharyngeal swab samples. We performed whole-genome sequencing of SARS-CoV-2 and serological analyses. RESULTS We identified 17 individuals with positive polymerase chain reaction results, 10 residents (5 vaccinated) and 7 HCWs (3 vaccinated). The median age (interquartile range) was 86 (70-90) years among residents and 49 (29-59) years among HCWs. Of the 5 vaccinated residents, 3 had mild disease and 2 had no symptoms, whereas all 5 unvaccinated residents had mild to severe disease, and 2 died. Vaccine effectiveness for the prevention of infection among residents was 73.0% (95% confidence interval, 24.7%-90.1%). The 12 available genomes were all alpha variants. Neutralizing titers were significantly higher in vaccinated individuals on reexposure (>1 week after diagnosis) than in vaccinated, unexposed HCWs (P = .01). Transmission networks indicated 4 likely or possible transmissions from vaccinated to other individuals and 12 transmission events from unvaccinated individuals. CONCLUSIONS COVID-19 outbreaks can occur in nursing homes, including transmission from vaccinated persons to others. Outbreaks might occur silently, underlining the need for continued testing and basic infection control measures in these high-risk settings.
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Affiliation(s)
- Kathrin Zürcher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Irene A Abela
- Institute of Medical Virology, University of Zürich, Zurich, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Madlen Stange
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Carole Dupont
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Catrina Mugglin
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Kantonsärztlicher Dienst, Gesundheitsamt, Kanton Solothurn, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zürich, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Kantonsärztlicher Dienst, Gesundheitsamt, Kanton Solothurn, Switzerland
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9
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von Rotz M, Kuehl R, Durovic A, Zingg S, Apitz A, Wegner F, Seth-Smith HMB, Roloff T, Leuzinger K, Hirsch HH, Kuster S, Battegay M, Mariani L, Schaeren S, Bassetti S, Banderet-Uglioni F, Egli A, Tschudin-Sutter S. A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center. Antimicrob Resist Infect Control 2023; 12:38. [PMID: 37085891 PMCID: PMC10119817 DOI: 10.1186/s13756-023-01242-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020. METHODS At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains. RESULTS The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7%), more commonly affecting HCWs (16/24, 66.7%) than patients (8/24, 33.3%), followed by transmission between patients (6/33, 18.2%), and among HCWs and patients (3/33, 9.1%, respectively two HCWs and one patient). CONCLUSIONS Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.
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Affiliation(s)
- Matthias von Rotz
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Richard Kuehl
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Ana Durovic
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Sandra Zingg
- Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anett Apitz
- Employee Health Service, University Hospital Basel, Basel, Switzerland
| | - Fanny Wegner
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Tim Roloff
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland
- Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Sabine Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Luigi Mariani
- Department of Neurosurgery, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefan Schaeren
- Department of Traumatology and Orthopedics, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.
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10
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Nadeau SA, Vaughan TG, Beckmann C, Topolsky I, Chen C, Hodcroft E, Schär T, Nissen I, Santacroce N, Burcklen E, Ferreira P, Jablonski KP, Posada-Céspedes S, Capece V, Seidel S, Santamaria de Souza N, Martinez-Gomez JM, Cheng P, Bosshard PP, Levesque MP, Kufner V, Schmutz S, Zaheri M, Huber M, Trkola A, Cordey S, Laubscher F, Gonçalves AR, Aeby S, Pillonel T, Jacot D, Bertelli C, Greub G, Leuzinger K, Stange M, Mari A, Roloff T, Seth-Smith H, Hirsch HH, Egli A, Redondo M, Kobel O, Noppen C, du Plessis L, Beerenwinkel N, Neher RA, Beisel C, Stadler T. Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data. Sci Transl Med 2023; 15:eabn7979. [PMID: 36346321 PMCID: PMC9765449 DOI: 10.1126/scitranslmed.abn7979] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020-the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.
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Affiliation(s)
- Sarah A. Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Corresponding author. (T.S.); (S.A.N.)
| | - Timothy G. Vaughan
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | | | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Emma Hodcroft
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Institute for Social and Preventive Medicine, University of Bern; 3012, Bern, Switzerland
| | - Tobias Schär
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Ina Nissen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Natascha Santacroce
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Elodie Burcklen
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Pedro Ferreira
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Susana Posada-Céspedes
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Vincenzo Capece
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Sophie Seidel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | | | - Julia M. Martinez-Gomez
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Philipp P. Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Mitchell P. Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich; 8091, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich; 8057, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine; 1205, Geneva, Switzerland
| | - Ana Rita Gonçalves
- Swiss National Reference Centre for Influenza, University Hospitals of Geneva; 1205, Geneva, Switzerland
| | - Sébastien Aeby
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Damien Jacot
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Centre and University of Lausanne; 1011, Lausanne, Switzerland
| | - Karoline Leuzinger
- Division of Clinical Virology, University Hospital Basel; 4051, Basel, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland
| | - Madlen Stange
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Alfredo Mari
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Tim Roloff
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Helena Seth-Smith
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | - Hans H. Hirsch
- Division of Clinical Virology, University Hospital Basel; 4051, Basel, Switzerland.,Department of Biomedicine, University of Basel; 4031, Basel, Switzerland
| | - Adrian Egli
- Department of Biomedicine, University of Basel; 4031, Basel, Switzerland.,Division of Clinical Bacteriology and Mycology, University Hospital Basel; 4031, Basel, Switzerland
| | | | | | | | - Louis du Plessis
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland
| | - Richard A. Neher
- SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Biozentrum, University of Basel; 4056, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich; 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics; 1015, Lausanne, Switzerland.,Corresponding author. (T.S.); (S.A.N.)
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11
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Adzic F, Roberts BM, Hathway EA, Kaur Matharu R, Ciric L, Wild O, Cook M, Malki-Epshtein L. A post-occupancy study of ventilation effectiveness from high-resolution CO 2 monitoring at live theatre events to mitigate airborne transmission of SARS-CoV-2. BUILDING AND ENVIRONMENT 2022; 223:109392. [PMID: 35937085 PMCID: PMC9339161 DOI: 10.1016/j.buildenv.2022.109392] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/24/2022] [Accepted: 07/10/2022] [Indexed: 05/20/2023]
Abstract
Mass-gathering events were closed around the world in 2020 to minimise the spread of the SARS-CoV-2 virus. Emerging research on the transmission of SARS-CoV-2 emphasised the importance of sufficient ventilation. This paper presents the results of an indoor air quality (IAQ) monitoring study over 82 events in seven mechanically ventilated auditoria to support the UK government Events Research Programme. Indoor carbon dioxide concentration was measured at high resolution before, during, and after occupancy to allow for assessment of the ventilation systems. Generally, good indoor air quality was measured in all auditoria, with average IAQ found to be excellent or very good for 70% of spaces. In some auditoria, spatial variation in IAQ was identified, indicating poor mixing of the air. In addition, surface and air samples were taken and analysed for the presence of bacteria by culture and SARS-CoV-2 using RT-qPCR in one venue. SARS-CoV-2 RNA was detected on a small number of surfaces at very low copy numbers, which are unlikely to pose an infection risk. Under the ventilation strategies and occupancy levels investigated, it is likely that most theatres pose a low risk of long-range transmission of COVID-19.
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Affiliation(s)
- Filipa Adzic
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Ben M Roberts
- Building Energy Research Group, School of Architecture, Building and Civil Engineering, Loughborough University, UK
| | | | - Rupy Kaur Matharu
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Lena Ciric
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Oliver Wild
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
| | - Malcolm Cook
- Building Energy Research Group, School of Architecture, Building and Civil Engineering, Loughborough University, UK
| | - Liora Malki-Epshtein
- Department of Civil, Environmental and Geomatic Engineering, University College London, UK
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12
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Purushothaman S, Meola M, Egli A. Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:9834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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Affiliation(s)
- Srinithi Purushothaman
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Marco Meola
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, 4031 Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
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13
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Travel in the Time of COVID: A Review of International Travel Health in a Global Pandemic. Curr Infect Dis Rep 2022; 24:129-145. [PMID: 35965881 PMCID: PMC9361911 DOI: 10.1007/s11908-022-00784-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
Abstract
Abstract
Purpose of Review
This review critically considers the impact of the COVID-19 pandemic on global travel and the practice of travel medicine, highlights key innovations that have facilitated the resumption of travel, and anticipates how travel medicine providers should prepare for the future of international travel.
Recent Findings
Since asymptomatic transmission of the virus was first recognized in March 2020, extensive efforts have been made to characterize the pattern and dynamics of SARS-CoV-2 transmission aboard commercial aircraft, cruise ships, rail and bus transport, and in mass gatherings and quarantine facilities. Despite the negative impact of further waves of COVID-19 driven by the more transmissible Omicron variant, rapid increases of international tourist arrivals are occurring and modeling anticipates further growth. Mitigation of spread requires an integrated approach that combines masking, physical distancing, improving ventilation, testing, and quarantine. Vaccines and therapeutics have played a significant role in reopening society and accelerating the resumption of travel and further therapeutic innovation is likely.
Summary
COVID-19 is likely to persist as an endemic infection, and surveillance will assume an even more important role. The pandemic has provided an impetus to advance technology for telemedicine, to adopt mobile devices and GPS in contact tracing, and to apply digital applications in research. The future of travel medicine should continue to harness these novel platforms in the clinical, research, and educational arenas.
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14
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Yasutaka T, Murakami M, Iwasaki Y, Naito W, Onishi M, Fujita T, Imoto S. Assessment of COVID-19 risk and prevention effectiveness among spectators of mass gathering events. MICROBIAL RISK ANALYSIS 2022; 21:100215. [PMID: 35382415 PMCID: PMC8969296 DOI: 10.1016/j.mran.2022.100215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 03/29/2022] [Indexed: 05/12/2023]
Abstract
There is a need to evaluate and minimize the risk of novel coronavirus infections at mass gathering events, such as sports. In particular, to consider how to hold mass gathering events, it is important to clarify how the local infection prevalence, the number of spectators, the capacity proportion, and the implementation of preventions affect the infection risk. In this study, we used an environmental exposure model to analyze the relationship between infection risk and infection prevalence, the number of spectators, and the capacity proportion at mass gathering events in football and baseball games. In addition to assessing risk reduction through the implementation of various preventive measures, we assessed how face-mask-wearing proportion affects infection risk. Furthermore, the model was applied to estimate the number of infectors who entered the stadium and the number of newly infected individuals, and to compare them with actual reported cases. The model analysis revealed an 86-95% reduction in the infection risk due to the implementation of face-mask wearing and hand washing. Under conditions in which vaccine effectiveness was 20% and 80%, the risk reduction rates of infection among vaccinated spectators were 36% and 96%, respectively. Among the individual measures, face-mask wearing was particularly effective, and the infection risk increased as the face-mask-wearing proportion decreased. A linear relationship was observed between infection risk at mass gathering events and the infection prevalence. Furthermore, the number of newly infected individuals was also dependent on the number of spectators and the capacity proportion independent of the infection prevalence, confirming the importance of considering spectator capacity in infection risk management. These results highlight that it is beneficial for organisers to ensure prevention compliance and to mitigate or limit the number of spectators according to the prevalence of local infection. Both the estimated and reported numbers of newly infected individuals after the events were small, below 10 per 3-4 million spectators, despite a small gap between these numbers.
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Affiliation(s)
- Tetsuo Yasutaka
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Michio Murakami
- Department of Health Risk Communication, Fukushima Medical University School of Medicine, 1 Hikarigaoka, Fukushima, Fukushima 960-1295, Japan
- Division of Scientific Information and Public Policy, Center for Infectious Disease Education and Research (CiDER), Osaka University, Techno Alliance C209, 2-8 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichi Iwasaki
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Wataru Naito
- Research Institute of Science for Safety and Sustainability, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Masaki Onishi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tsukasa Fujita
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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15
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Callegari I, Schneider M, Berloffa G, Mühlethaler T, Holdermann S, Galli E, Roloff T, Boss R, Infanti L, Khanna N, Egli A, Buser A, Zimmer G, Derfuss T, Sanderson NSR. Potent neutralization by monoclonal human IgM against SARS-CoV-2 is impaired by class switch. EMBO Rep 2022; 23:e53956. [PMID: 35548920 PMCID: PMC9253785 DOI: 10.15252/embr.202153956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 01/11/2023] Open
Abstract
To investigate the class‐dependent properties of anti‐viral IgM antibodies, we use membrane antigen capture activated cell sorting to isolate spike‐protein‐specific B cells from donors recently infected with SARS‐CoV‐2, allowing production of recombinant antibodies. We isolate 20, spike‐protein‐specific antibodies of classes IgM, IgG, and IgA, none of which shows any antigen‐independent binding to human cells. Two antibodies of class IgM mediate virus neutralization at picomolar concentrations, but this potency is lost following artificial switch to IgG. Although, as expected, the IgG versions of the antibodies appear to have lower avidity than their IgM parents, this is not sufficient to explain the loss of potency.
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Affiliation(s)
- Ilaria Callegari
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mika Schneider
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Giuliano Berloffa
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Tobias Mühlethaler
- Biophysics Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Sebastian Holdermann
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Edoardo Galli
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Renate Boss
- Federal Food Safety and Veterinary Office, Bern, Switzerland
| | - Laura Infanti
- Regional Blood Transfusion Service, Swiss Red Cross, Basel, Switzerland
| | - Nina Khanna
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Andreas Buser
- Regional Blood Transfusion Service, Swiss Red Cross, Basel, Switzerland
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern & Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tobias Derfuss
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
| | - Nicholas S R Sanderson
- Department of Biomedicine, University of Basel and University Hospital Basel, Basel, Switzerland.,MS Center, Neurologic Clinic and Policlinic, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland
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16
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Qiu Z, Sun Y, He X, Wei J, Zhou R, Bai J, Du S. Application of genetic algorithm combined with improved SEIR model in predicting the epidemic trend of COVID-19, China. Sci Rep 2022; 12:8910. [PMID: 35618751 PMCID: PMC9133826 DOI: 10.1038/s41598-022-12958-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 05/17/2022] [Indexed: 01/23/2023] Open
Abstract
Since the outbreak of the 2019 Coronavirus disease (COVID-19) at the end of 2019, it has caused great adverse effects on the whole world, and it has been hindering the global economy. It is ergent to establish an infectious disease model for the current COVID-19 epidemic to predict the trend of the epidemic. Based on the SEIR model, the improved SEIR models were established with considering the incubation period, the isolated population, and genetic algorithm (GA) parameter optimization method. The improved SEIR models can predict the trend of the epidemic situation better and obtain the more accurate epidemic-related parameters. Comparing some key parameters, it is capable to evaluate the impact of different epidemic prevention measures and the implementation of different epidemic prevention levels on the COVID-19, which has significant guidance for further epidemic prevention measures.
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Affiliation(s)
- Zhenzhen Qiu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Youyi Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Xuan He
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jing Wei
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Rui Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China.
| | - Jie Bai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Shouying Du
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 102488, China
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17
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Korencak M, Sivalingam S, Sahu A, Dressen D, Schmidt A, Brand F, Krawitz P, Hart L, Maria Eis-Hübinger A, Buness A, Streeck H. Reconstruction of the Origin of the First Major SARS-CoV-2 Outbreak in Germany. Comput Struct Biotechnol J 2022; 20:2292-2296. [PMID: 35574268 PMCID: PMC9088089 DOI: 10.1016/j.csbj.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/06/2022] [Accepted: 05/06/2022] [Indexed: 11/27/2022] Open
Abstract
The first major COVID-19 outbreak in Germany occurred in Heinsberg in February 2020 with 388 officially reported cases. Unexpectedly, the first outbreak happened in a small town with little to no travelers. We used phylogenetic analyses to investigate the origin and spread of the virus in this outbreak. We sequenced 90 (23%) SARS-CoV-2 genomes from the 388 reported cases including the samples from the first documented cases. Phylogenetic analyses of these sequences revealed mainly two circulating strains with 74 samples assigned to lineage B.3 and 6 samples assigned to lineage B.1. Lineage B.3 was introduced first and probably caused the initial spread. Using phylogenetic analysis tools, we were able to identify closely related strains in France and hypothesized the possible introduction from France.
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Affiliation(s)
- Marek Korencak
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Sugirthan Sivalingam
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Anshupa Sahu
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Dietmar Dressen
- Labor Mönchengladbach MVZ Dr. Stein & Kollegen GbR, Tomphecke 45, Mönchengladbach 41169, Germany
| | - Axel Schmidt
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Fabian Brand
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Libor Hart
- Department of Oral and Maxillofacial Surgery, University of Duisburg-Essen, Henricistr. 92, Essen 45136, Germany
| | | | - Andreas Buness
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
- Core Unit for Bioinformatics Data Analysis, Medical Faculty, University of Bonn, Venusberg-Campus 1, Bonn 53127, Germany
| | - Hendrik Streeck
- Institute of Virology, University Hospital Bonn, Venusberg-Campus 1, Bonn 53127, Germany
- Corresponding author.
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18
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Peter JK, Wegner F, Gsponer S, Helfenstein F, Roloff T, Tarnutzer R, Grosheintz K, Back M, Schaubhut C, Wagner S, Seth-Smith HMB, Scotton P, Redondo M, Beckmann C, Stadler T, Salzmann A, Kurth H, Leuzinger K, Bassetti S, Bingisser R, Siegemund M, Weisser M, Battegay M, Sutter ST, Lebrand A, Hirsch HH, Fuchs S, Egli A. SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination. Microorganisms 2022; 10:microorganisms10050857. [PMID: 35630302 PMCID: PMC9146960 DOI: 10.3390/microorganisms10050857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 12/14/2022] Open
Abstract
(1) Background: Some COVID-19 vaccine recipients show breakthrough infection. It remains unknown, which factors contribute to risks and severe outcomes. Our aim was to identify risk factors for SCoV2 breakthrough infections in fully vaccinated individuals. (2) Methods: We conducted a retrospective case-control study from 28 December 2020 to 25 October 2021. Data of all patients with breakthrough infection was compared to data of all vaccine recipients in the Canton of Basel-City, Switzerland. Further, breakthrough infections by Alpha- and Delta-variants were compared. (3) Results: Only 0.39% (488/126,586) of all vaccine recipients suffered from a breakthrough infection during the observational period, whereof most cases were asymptomatic or mild (97.2%). Breakthrough infections after full vaccination occurred in the median after 78 days (IQR 47-123.5). Factors with lower odds for breakthrough infection were age (OR 0.987) and previous COVID-19 infection prior to vaccination (OR 0.296). Factors with higher odds for breakthrough infection included vaccination with Pfizer/BioNTech instead of Moderna (OR 1.459), chronic disease (OR 2.109), and healthcare workers (OR 1.404). (4) Conclusions: Breakthrough infections are rare and mild but can occur early after vaccination. This implies that booster vaccination might be initiated earlier, especially for risk groups. Due to new variants emerging repeatedly, continuous monitoring of breakthrough infections is crucial.
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Affiliation(s)
- Jelissa Katharina Peter
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (F.W.); (T.R.); (H.M.B.S.-S.)
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
| | - Severin Gsponer
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Fabrice Helfenstein
- Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland;
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (F.W.); (T.R.); (H.M.B.S.-S.)
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
| | - Rahel Tarnutzer
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Kerstin Grosheintz
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Moritz Back
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Carla Schaubhut
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Sabina Wagner
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (F.W.); (T.R.); (H.M.B.S.-S.)
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
| | - Patrick Scotton
- Corona Vaccination Centre for the Canton of Basel-City, 4058 Basel, Switzerland;
| | - Maurice Redondo
- Viollier AG, 4123 Allschwil, Switzerland; (M.R.); (C.B.); (A.S.); (H.K.); (H.H.H.)
| | - Christiane Beckmann
- Viollier AG, 4123 Allschwil, Switzerland; (M.R.); (C.B.); (A.S.); (H.K.); (H.H.H.)
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
| | - Andrea Salzmann
- Viollier AG, 4123 Allschwil, Switzerland; (M.R.); (C.B.); (A.S.); (H.K.); (H.H.H.)
| | - Henriette Kurth
- Viollier AG, 4123 Allschwil, Switzerland; (M.R.); (C.B.); (A.S.); (H.K.); (H.H.H.)
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland;
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, 4031 Basel, Switzerland;
| | - Roland Bingisser
- Emergency Medicine, University Hospital Basel, 4031 Basel, Switzerland;
| | - Martin Siegemund
- Intensive Care Medicine, University Hospital Basel, 4031 Basel, Switzerland;
| | - Maja Weisser
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (M.W.); (M.B.); (S.T.S.)
| | - Manuel Battegay
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (M.W.); (M.B.); (S.T.S.)
| | - Sarah Tschudin Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (M.W.); (M.B.); (S.T.S.)
| | - Aitana Lebrand
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;
| | - Hans H. Hirsch
- Viollier AG, 4123 Allschwil, Switzerland; (M.R.); (C.B.); (A.S.); (H.K.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland; (M.W.); (M.B.); (S.T.S.)
| | - Simon Fuchs
- Department of Health Basel-City, 4052 Basel, Switzerland; (J.K.P.); (S.G.); (R.T.); (K.G.); (M.B.); (C.S.); (S.W.); (S.F.)
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (F.W.); (T.R.); (H.M.B.S.-S.)
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, 4031 Basel, Switzerland
- Correspondence:
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19
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Delaugerre C, Foissac F, Abdoul H, Masson G, Choupeaux L, Dufour E, Gastli N, Delarue SM, Néré ML, Minier M, Gabassi A, Salmona M, Seguineau M, Schmitt S, Tonglet S, Olivier A, Poyart C, Le Goff J, Lescure X, Kernéis S, Tréluyer JM. Prevention of SARS-CoV-2 transmission during a large, live, indoor gathering (SPRING): a non-inferiority, randomised, controlled trial. THE LANCET. INFECTIOUS DISEASES 2022; 22:341-348. [PMID: 34843662 PMCID: PMC8626094 DOI: 10.1016/s1473-3099(21)00673-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Mass indoor gatherings were banned in early 2020 to prevent the spread of SARS-CoV-2. We aimed to assess, under controlled conditions, whether infection rates among attendees at a large, indoor gathering event would be similar to those in non-attendees, given implementation of a comprehensive prevention strategy including antigen-screening within 3 days, medical mask wearing, and optimised ventilation. METHODS The non-inferiority, prospective, open-label, randomised, controlled SPRING trial was done on attendees at a live indoor concert held in the Accor Arena on May 29, 2021 in Paris, France. Participants, aged 18-45 years, recruited via a dedicated website, had no comorbidities, COVID-19 symptoms, or recent case contact, and had had a negative rapid antigen diagnostic test within 3 days before the concert. Participants were randomly allocated in a 2:1 ratio to the experimental group (attendees) or to the control group (non-attendees). The allocation sequence was computer-generated by means of permuted blocks of sizes three, six, or nine, with no stratification. The primary outcome measure was the number of patients who were SARS-CoV-2-positive by RT-PCR test on self-collected saliva 7 days post-gathering in the per-protocol population (non-inferiority margin <0·35%). This trial is registered with ClinicalTrials.gov, NCT04872075. FINDINGS Between May 11 and 25, 2021, 18 845 individuals registered on the dedicated website, and 10 953 were randomly selected for a pre-enrolment on-site visit. Among 6968 who kept the appointment and were screened, 6678 participants were randomly assigned (4451 were assigned to be attendees and 2227 to be non-attendees; median age 28 years; 59% women); 88% (3917) of attendees and 87% (1947) of non-attendees complied with follow-up requirements. The day 7 RT-PCR was positive for eight of the 3917 attendees (observed incidence, 0·20%; 95% CI 0·09-0·40) and three of the 1947 non-attendees (0·15%; 0·03-0·45; absolute difference, 95% CI -0·26% to 0·28%), findings that met the non-inferiority criterion for the primary endpoint. INTERPRETATION Participation in a large, indoor, live gathering without physical distancing was not associated with increased SARS-CoV-2-transmission risk, provided a comprehensive preventive intervention was implemented. FUNDING French Ministry of Health. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Constance Delaugerre
- Service de Virologie, AP-HP, Hôpital Saint Louis, Paris, France; Université de Paris, INSERM, U944, Paris, France.
| | - Frantz Foissac
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France; Université de Paris, EA 7323 Pharmacologie et thérapeutique de l'enfant et de la femme enceinte, Paris, France
| | - Hendy Abdoul
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France; Université de Paris, EA 7323 Pharmacologie et thérapeutique de l'enfant et de la femme enceinte, Paris, France
| | - Guillaume Masson
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France
| | - Laure Choupeaux
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France
| | - Eric Dufour
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France
| | - Nabil Gastli
- Plateforme COVID IDF, AP-HP. Centre Université de Paris, F-75014 Paris, France
| | | | | | - Marine Minier
- Service de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Audrey Gabassi
- Service de Virologie, AP-HP, Hôpital Saint Louis, Paris, France
| | - Maud Salmona
- Service de Virologie, AP-HP, Hôpital Saint Louis, Paris, France; Université de Paris, INSERM, Equipe INSIGHT, U976, Paris, France
| | - Malika Seguineau
- PRODISS, Syndicat national du spectacle vivant et de variété, Paris, France
| | - Sarah Schmitt
- PRODISS, Syndicat national du spectacle vivant et de variété, Paris, France
| | | | | | - Claire Poyart
- Université de Paris, INSERM, Institut Cochin 1016, Paris, France; Bactériologie, AP-HP Centre, Hôpital Cochin, Paris, France
| | - Jerôme Le Goff
- Service de Virologie, AP-HP, Hôpital Saint Louis, Paris, France; Université de Paris, INSERM, Equipe INSIGHT, U976, Paris, France
| | - Xavier Lescure
- Service de maladies infectieuses et tropicales, AP-HP, Hôpital Bichat, Paris, France; Université de Paris, INSERM, IAME, Paris, France
| | - Solen Kernéis
- Equipe de Prévention du Risque Infectieux, AP-HP, Hôpital Bichat, Paris, France; AP-HP, Hôpital Bichat, Paris, France; Epidemiology and Modelling of Antibiotic Evasion, Institut Pasteur, Paris, France
| | - Jean-Marc Tréluyer
- Unité de Recherche Clinique-Centre Investigation Clinique, APHP, Hôpital Necker-Enfants malades, Paris, France
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20
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Aggarwal D, Page AJ, Schaefer U, Savva GM, Myers R, Volz E, Ellaby N, Platt S, Groves N, Gallagher E, Tumelty NM, Le Viet T, Hughes GJ, Chen C, Turner C, Logan S, Harrison A, Peacock SJ, Chand M, Harrison EM. Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nat Commun 2022; 13:1012. [PMID: 35197443 PMCID: PMC8866425 DOI: 10.1038/s41467-022-28371-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/18/2022] [Indexed: 01/16/2023] Open
Abstract
Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.
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Affiliation(s)
- Dinesh Aggarwal
- University of Cambridge, Department of Medicine, Cambridge, UK.
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Ulf Schaefer
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Richard Myers
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Erik Volz
- Imperial College London, Department of Infectious Disease Epidemiology, London, UK
| | - Nicholas Ellaby
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Steven Platt
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Natalie Groves
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | | | - Niamh M Tumelty
- University of Cambridge, Cambridge University Libraries, Cambridge, UK
| | - Thanh Le Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Gareth J Hughes
- Public Health England National Infections Service, Field Service, Leeds, UK
| | - Cong Chen
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Charlie Turner
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Sophie Logan
- Public Health England, National Infections Service, Field Service, Nottingham, UK
| | - Abbie Harrison
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Sharon J Peacock
- University of Cambridge, Department of Medicine, Cambridge, UK
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Meera Chand
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK
| | - Ewan M Harrison
- University of Cambridge, Department of Medicine, Cambridge, UK.
- Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK.
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.
- University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK.
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21
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Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. J Clin Microbiol 2022; 60:e0169821. [PMID: 34757834 PMCID: PMC8769736 DOI: 10.1128/jcm.01698-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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Affiliation(s)
- Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Yannick Gerth
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jonas Fuchs
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Paul Savelkoul
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jozef Dingemans
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Brian van der Veer
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Hadar Golan Berman
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Dana G. Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Oliver Nolte
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EPIGEN), Akershus University Hospital and University of Oslo, Lørenskog, Norway
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
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22
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Brüningk SC, Klatt J, Stange M, Mari A, Brunner M, Roloff TC, Seth-Smith HMB, Schweitzer M, Leuzinger K, Søgaard KK, Albertos Torres D, Gensch A, Schlotterbeck AK, Nickel CH, Ritz N, Heininger U, Bielicki J, Rentsch K, Fuchs S, Bingisser R, Siegemund M, Pargger H, Ciardo D, Dubuis O, Buser A, Tschudin-Sutter S, Battegay M, Schneider-Sliwa R, Borgwardt KM, Hirsch HH, Egli A. OUP accepted manuscript. Virus Evol 2022; 8:veac002. [PMID: 35310621 PMCID: PMC8927799 DOI: 10.1093/ve/veac002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/07/2021] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
Transmission chains within small urban areas (accommodating ∼30 per cent of the European population) greatly contribute to case burden and economic impact during the ongoing coronavirus pandemic and should be a focus for preventive measures to achieve containment. Here, at very high spatio-temporal resolution, we analysed determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in a European urban area, Basel-City (Switzerland). We combined detailed epidemiological, intra-city mobility and socio-economic data sets with whole-genome sequencing during the first SARS-CoV-2 wave. For this, we succeeded in sequencing 44 per cent of all reported cases from Basel-City and performed phylogenetic clustering and compartmental modelling based on the dominating viral variant (B.1-C15324T; 60 per cent of cases) to identify drivers and patterns of transmission. Based on these results we simulated vaccination scenarios and corresponding healthcare system burden (intensive care unit (ICU) occupancy). Transmissions were driven by socio-economically weaker and highly mobile population groups with mostly cryptic transmissions which lacked genetic and identifiable epidemiological links. Amongst more senior population transmission was clustered. Simulated vaccination scenarios assuming 60–90 per cent transmission reduction and 70–90 per cent reduction of severe cases showed that prioritising mobile, socio-economically weaker populations for vaccination would effectively reduce case numbers. However, long-term ICU occupation would also be effectively reduced if senior population groups were prioritised, provided there were no changes in testing and prevention strategies. Reducing SARS-CoV-2 transmission through vaccination strongly depends on the efficacy of the deployed vaccine. A combined strategy of protecting risk groups by extensive testing coupled with vaccination of the drivers of transmission (i.e. highly mobile groups) would be most effective at reducing the spread of SARS-CoV-2 within an urban area.
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23
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Choi Y, Ladoy A, De Ridder D, Jacot D, Vuilleumier S, Bertelli C, Guessous I, Pillonel T, Joost S, Greub G. Detection of SARS-CoV-2 infection clusters: The useful combination of spatiotemporal clustering and genomic analyses. Front Public Health 2022; 10:1016169. [PMID: 36568782 PMCID: PMC9771593 DOI: 10.3389/fpubh.2022.1016169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/15/2022] [Indexed: 12/04/2022] Open
Abstract
Background The need for effective public health surveillance systems to track virus spread for targeted interventions was highlighted during the COVID-19 pandemic. It spurred an interest in the use of spatiotemporal clustering and genomic analyses to identify high-risk areas and track the spread of the SARS-CoV-2 virus. However, these two approaches are rarely combined in surveillance systems to complement each one's limitations; spatiotemporal clustering approaches usually consider only one source of virus transmission (i.e., the residential setting) to detect case clusters, while genomic studies require significant resources and processing time that can delay decision-making. Here, we clarify the differences and possible synergies of these two approaches in the context of infectious disease surveillance systems by investigating to what extent geographically-defined clusters are confirmed as transmission clusters based on genome sequences, and how genomic-based analyses can improve the epidemiological investigations associated with spatiotemporal cluster detection. Methods For this purpose, we sequenced the SARS-CoV-2 genomes of 172 cases that were part of a collection of spatiotemporal clusters found in a Swiss state (Vaud) during the first epidemic wave. We subsequently examined intra-cluster genetic similarities and spatiotemporal distributions across virus genotypes. Results Our results suggest that the congruence between the two approaches might depend on geographic features of the area (rural/urban) and epidemic context (e.g., lockdown). We also identified two potential superspreading events that started from cases in the main urban area of the state, leading to smaller spreading events in neighboring regions, as well as a large spreading in a geographically-isolated area. These superspreading events were characterized by specific mutations assumed to originate from Mulhouse and Milan, respectively. Our analyses propose synergistic benefits of using two complementary approaches in public health surveillance, saving resources and improving surveillance efficiency.
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Affiliation(s)
- Yangji Choi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Anaïs Ladoy
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland
| | - David De Ridder
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,Faculty of Medicine, University of Geneva (UNIGE), Geneva, Switzerland.,Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Damien Jacot
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Séverine Vuilleumier
- La Source School of Nursing, University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Idris Guessous
- Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,Faculty of Medicine, University of Geneva (UNIGE), Geneva, Switzerland.,Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Geneva, Switzerland.,La Source School of Nursing, University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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24
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Basheer A, Zahoor I. Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan. Microorganisms 2021; 9:2609. [PMID: 34946210 PMCID: PMC8708969 DOI: 10.3390/microorganisms9122609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/17/2022] Open
Abstract
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.
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Affiliation(s)
| | - Imran Zahoor
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan;
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25
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Basheer A, Zahoor I. Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan. Microorganisms 2021; 9:microorganisms9122609. [PMID: 34946210 DOI: 10.1101/2021.07.28.21261233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023] Open
Abstract
The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.
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Affiliation(s)
- Atia Basheer
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
| | - Imran Zahoor
- Genetics and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki 55300, Pakistan
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26
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Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics 2021; 37:100480. [PMID: 34488035 PMCID: PMC8452947 DOI: 10.1016/j.epidem.2021.100480] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/30/2021] [Accepted: 06/15/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.7. Based on initial data from the UK and later data from other countries, this variant was estimated to have a transmission fitness advantage of around 40-80 % (Volz et al., 2021; Leung et al., 2021; Davies et al., 2021). AIM This study aims to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time based on data from Switzerland. METHODS We generated whole genome sequences from 11.8 % of all confirmed SARS-CoV-2 cases in Switzerland between 14 December 2020 and 11 March 2021. Based on these data, we determine the daily frequency of the B.1.1.7 variant and quantify the variant's transmission fitness advantage on a national and a regional scale. RESULTS We estimate B.1.1.7 had a transmission fitness advantage of 43-52 % compared to the other variants circulating in Switzerland during the study period. Further, we estimate B.1.1.7 had a reproductive number above 1 from 01 January 2021 until the end of the study period, compared to below 1 for the other variants. Specifically, we estimate the reproductive number for B.1.1.7 was 1.24 [1.07-1.41] from 01 January until 17 January 2021 and 1.18 [1.06-1.30] from 18 January until 01 March 2021 based on the whole genome sequencing data. From 10 March to 16 March 2021, once B.1.1.7 was dominant, we estimate the reproductive number was 1.14 [1.00-1.26] based on all confirmed cases. For reference, Switzerland applied more non-pharmaceutical interventions to combat SARS-CoV-2 on 18 January 2021 and lifted some measures again on 01 March 2021. CONCLUSION The observed increase in B.1.1.7 frequency in Switzerland during the study period is as expected based on observations in the UK. In absolute numbers, B.1.1.7 increased exponentially with an estimated doubling time of around 2-3.5 weeks. To monitor the ongoing spread of B.1.1.7, our plots are available online.
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Affiliation(s)
- Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Sarah Ann Nadeau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Marc Manceau
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Jana S Huisman
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland; Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Kim Philipp Jablonski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | | | | | | | - Lorenz Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | - Martin Risch
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Sinem Kas
- Dr Risch, Labormedizinisches Zentrum, Switzerland
| | | | - Tim Roloff
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Madlen Stange
- Swiss Institute of Bioinformatics, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Center for Emerging Viral Diseases and Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland; Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland; Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Rebecca Denes
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mirjam Feldkamp
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ina Nissen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Natascha Santacroce
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Elodie Burcklen
- Genomic Facility Basel, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | | | - Maria Domenica Moccia
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Simon Grüter
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Timothy Sykes
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Griffin White
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Laura Neff
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Doris Popovic
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Jay Tracy
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zürich and University of Zurich, Zurich, Switzerland
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland; Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Ioannis Xenarios
- Health 2030 Genome Center, Geneva, Switzerland; University of Geneva Medical School, Geneva, Switzerland
| | | | | | | | | | | | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Swiss Federal Institute of Technology, Zurich, Switzerland; Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
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27
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Domènech-Montoliu S, Pac-Sa MR, Vidal-Utrillas P, Latorre-Poveda M, Del Rio-González A, Ferrando-Rubert S, Ferrer-Abad G, Sánchez-Urbano M, Aparisi-Esteve L, Badenes-Marques G, Cervera-Ferrer B, Clerig-Arnau U, Dols-Bernad C, Fontal-Carcel M, Gomez-Lanas L, Jovani-Sales D, León-Domingo MC, Llopico-Vilanova MD, Moros-Blasco M, Notari-Rodríguez C, Ruíz-Puig R, Valls-López S, Arnedo-Pena A. "Mass gathering events and COVID-19 transmission in Borriana (Spain): A retrospective cohort study". PLoS One 2021; 16:e0256747. [PMID: 34437628 PMCID: PMC8389516 DOI: 10.1371/journal.pone.0256747] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/13/2021] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE Mass gathering events (MGEs) are associated with the transmission of COVID-19. Between 6 and 10 March 2020, several MGEs related to the Falles festival took place in Borriana, a municipality in the province of Castellon (Spain). The aim of this study was to estimate the incidence of COVID-19 and its association with these MGEs, and to quantify the potential risk factors of its occurrence. METHODS During May and June 2020, a population-based retrospective cohort study was carried out by the Public Health Center of Castelló and the Hospital de la Plana in Vila-real. Participants were obtained from a representative sample of 1663 people with potential exposure at six MGEs. A questionnaire survey was carried out to obtain information about attendance at MGEs and COVID-19 disease. In addition, a serologic survey of antibodies against SARS-Cov-2 was implemented. Inverse probability weighted regression was used in the statistical analysis. RESULTS A total of 1338 subjects participated in the questionnaire survey (80.5%), 997 of whom undertook the serologic survey. Five hundred and seventy cases were observed with an attack rate (AR) of 42.6%; average age was 36 years, 62.3% were female, 536 cases were confirmed by laboratory tests, and 514 cases were found with SARS-CoV-2 total antibodies. Considering MGE exposure, AR was 39.2% (496/1264). A dose-response relationship was found between MGE attendance and the disease, (adjusted relative risk [aRR] = 4.11 95% confidence interval [CI]3.25-5.19). Two MGEs with a dinner and dance in the same building had higher risks. Associated risk factors with the incidence were older age, obesity, and upper and middle class versus lower class; current smoking was protective. CONCLUSIONS The study suggests the significance of MGEs in the COVID-19 transmission that could explain the subsequent outbreak in Borriana.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lorna Gomez-Lanas
- Emergency Service, Hospital de la Plana, Vila-real, Castellon, Spain
| | | | | | | | | | | | - Raquel Ruíz-Puig
- Emergency Service, Hospital de la Plana, Vila-real, Castellon, Spain
| | - Sonia Valls-López
- Emergency Service, Hospital de la Plana, Vila-real, Castellon, Spain
| | - Alberto Arnedo-Pena
- Public Health Center, Castelló de la Plana, Castellon, Spain
- Department of Health Science, Public University Navarra, Pamplona, Spain
- Epidemiology and Public Health (CIBERESP), Madrid, Spain
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28
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Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, González-Candelas F, Stadler T, Neher RA. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature 2021; 595:707-712. [PMID: 34098568 DOI: 10.1038/s41586-021-03677-y] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Following its emergence in late 2019, the spread of SARS-CoV-21,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail3-5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes.
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Affiliation(s)
- Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Basel, Switzerland. .,Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.
| | - Moira Zuber
- Biozentrum, University of Basel, Basel, Switzerland
| | - Sarah Nadeau
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Timothy G Vaughan
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Katharine H D Crawford
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Iñaki Comas
- Tuberculosis Genomics Unit, Biomedicine Institute of Valencia (IBV-CSIC), Valencia, Spain.,CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | | | - Tanja Stadler
- Swiss Institute of Bioinformatics, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland. .,Swiss Institute of Bioinformatics, Basel, Switzerland.
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29
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Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. Microorganisms 2021; 9:microorganisms9051094. [PMID: 34069681 PMCID: PMC8160703 DOI: 10.3390/microorganisms9051094] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/09/2021] [Accepted: 05/15/2021] [Indexed: 01/18/2023] Open
Abstract
A variety of antiviral treatments for COVID-19 have been investigated, involving many repurposed drugs. Currently, the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp, encoded by nsp12-nsp7-nsp8) has been targeted by numerous inhibitors, e.g., remdesivir, the only provisionally approved treatment to-date, although the clinical impact of these interventions remains inconclusive. However, the potential emergence of antiviral resistance poses a threat to the efficacy of any successful therapies on a wide scale. Here, we propose a framework to monitor the emergence of antiviral resistance, and as a proof of concept, we address the interaction between RdRp and remdesivir. We show that SARS-CoV-2 RdRp is under purifying selection, that potential escape mutations are rare in circulating lineages, and that those mutations, where present, do not destabilise RdRp. In more than 56,000 viral genomes from 105 countries from the first pandemic wave, we found negative selective pressure affecting nsp12 (Tajima’s D = −2.62), with potential antiviral escape mutations in only 0.3% of sequenced genomes. Potential escape mutations included known key residues, such as Nsp12:Val473 and Nsp12:Arg555. Of the potential escape mutations involved globally, in silico structural models found that they were unlikely to be associated with loss of stability in RdRp. No potential escape mutation was found in a local cohort of remdesivir treated patients. Collectively, these findings indicate that RdRp is a suitable drug target, and that remdesivir does not seem to exert high selective pressure. We anticipate our framework to be the starting point of a larger effort for a global monitoring of drug resistance throughout the COVID-19 pandemic.
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30
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Goncalves Cabecinhas AR, Roloff T, Stange M, Bertelli C, Huber M, Ramette A, Chen C, Nadeau S, Gerth Y, Yerly S, Opota O, Pillonel T, Schuster T, Metzger CMJA, Sieber J, Bel M, Wohlwend N, Baumann C, Koch MC, Bittel P, Leuzinger K, Brunner M, Suter-Riniker F, Berlinger L, Søgaard KK, Beckmann C, Noppen C, Redondo M, Steffen I, Seth-Smith HMB, Mari A, Lienhard R, Risch M, Nolte O, Eckerle I, Martinetti Lucchini G, Hodcroft EB, Neher RA, Stadler T, Hirsch HH, Leib SL, Risch L, Kaiser L, Trkola A, Greub G, Egli A. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021-Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms 2021; 9:677. [PMID: 33806013 PMCID: PMC8064472 DOI: 10.3390/microorganisms9040677] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
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Affiliation(s)
- Ana Rita Goncalves Cabecinhas
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Chaoran Chen
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Yannick Gerth
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Tobias Schuster
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Cesar M. J. A. Metzger
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Jonas Sieber
- Spiez Laboratory, Federal Office for Civil Protection FOCP, 3700 Spiez, Switzerland; (C.M.J.A.M.); (J.S.)
| | - Michael Bel
- Federal Office of Public Health FOPH, 3097 Berne, Switzerland; (T.S.); (M.B.)
| | - Nadia Wohlwend
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
| | - Christian Baumann
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Michel C. Koch
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Myrta Brunner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
| | - Franziska Suter-Riniker
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | | | - Kirstine K. Søgaard
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
| | | | - Christoph Noppen
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | - Maurice Redondo
- Viollier AG, 4123 Allschwil, Switzerland; (C.B.); (C.N.); (M.R.)
| | | | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Clinical Bacteriology and Mycology, University Hospital Basel & University of Basel, 4031 Basel, Switzerland
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
| | - Reto Lienhard
- ADMED Microbiology, 2300 La Chaux-de-Fonds, Switzerland;
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
| | - Oliver Nolte
- Center for Laboratory Medicine, 9001 Saint Gall, Switzerland; (Y.G.); (O.N.)
| | - Isabella Eckerle
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Gladys Martinetti Lucchini
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
- EOC Microbiological Laboratory, 6500 Bellinzona, Switzerland
| | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland;
| | - Richard A. Neher
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Tanja Stadler
- Swiss Institute for Bioinformatics (SIB), 1015 Lausanne, Switzerland; (R.A.N.); (T.S.)
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; (C.C.); (S.N.)
| | - Hans H. Hirsch
- Clinical Virology, University Hospital Basel, 4031 Basel, Switzerland; (K.L.); (H.H.H.)
- Transplantation & Clinical Virology, Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, 3012 Bern, Switzerland; (A.R.); (C.B.); (M.C.K.); (P.B.); (F.S.-R.); (S.L.L.)
| | - Lorenz Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr. Risch, 9470 Buchs SG, Switzerland; (N.W.); (M.R.); (L.R.)
- Faculty of Medical Sciences, Private University of the Principality of Liechtenstein, 9495 Triesen, Liechtenstein
- Centre of Laboratory Medicine, University Institute of Clinical Chemistry, University of Bern, 3010 Bern, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, 1205 Geneva, Switzerland; (A.R.G.C.); (S.Y.); (I.E.); (L.K.)
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; (M.H.); (A.T.)
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland; (C.B.); (O.O.); (T.P.); (G.G.)
| | - Adrian Egli
- Center for Emerging Viral Diseases, University Hospital Geneva, 1205 Geneva, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, 4056 Basel, Switzerland; (T.R.); (M.S.); (M.B.); (K.K.S.); (H.M.B.S.-S.); (A.M.)
- Coordination Commission of Clinical Microbiology, Swiss Society of Microbiology, 1033 Cheseaux, Switzerland;
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