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Rasmussen M, Møller FT, Gunalan V, Baig S, Bennedbæk M, Christiansen LE, Cohen AS, Ellegaard K, Fomsgaard A, Franck KT, Larsen NB, Larsen TG, Lassaunière R, Polacek C, Qvesel AG, Sieber RN, Rasmussen LD, Stegger M, Spiess K, Tang MHE, Vestergaard LS, Andersen TE, Hoegh SV, Pedersen RM, Skov MN, Steinke K, Sydenham TV, Hoppe M, Nielsen L, Krause TG, Ullum H, Jokelainen P. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Euro Surveill 2023; 28:2300460. [PMID: 37676147 PMCID: PMC10486197 DOI: 10.2807/1560-7917.es.2023.28.36.2300460] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/08/2023] Open
Abstract
We describe 10 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant BA.2.86 detected in Denmark, including molecular characteristics and results from wastewater surveillance that indicate that the variant is circulating in the country at a low level. This new variant with many spike gene mutations was classified as a variant under monitoring by the World Health Organization on 17 August 2023. Further global monitoring of COVID-19, BA.2.86 and other SARS-CoV-2 variants is highly warranted.
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Affiliation(s)
- Morten Rasmussen
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- These authors contributed equally to this work and share first authorship
| | - Frederik Trier Møller
- These authors contributed equally to this work and share first authorship
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Sharmin Baig
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Kirsten Ellegaard
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Kristina Træholt Franck
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Tine Graakjær Larsen
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassaunière
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Amanda Gammelby Qvesel
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael Niklaus Sieber
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Virus Surveillance and Research Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Katja Spiess
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Man-Hung Eric Tang
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Rune Micha Pedersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Marianne Nielsine Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Kat Steinke
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Thomas Vognbjerg Sydenham
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Morten Hoppe
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Tyra Grove Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | | | - Pikka Jokelainen
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
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Pedersen RM, Tornby DS, Bang LL, Madsen LW, Skov MN, Sydenham TV, Steinke K, Jensen TG, Johansen IS, Andersen TE. Rectally shed SARS-CoV-2 in COVID-19 inpatients is consistently lower than respiratory shedding and lacks infectivity. Clin Microbiol Infect 2021; 28:304.e1-304.e3. [PMID: 34763059 PMCID: PMC8575534 DOI: 10.1016/j.cmi.2021.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 10/30/2021] [Indexed: 12/18/2022]
Abstract
Objectives Assessment of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been propagated during intestinal passage and infectivity is conserved when shed rectally by hospitalized individuals. Methods An exploratory cohort study including 28 inpatients with coronavirus disease 2019 with estimation of RNA levels by RT-PCR and of viral infectivity by culturing of viral material sampled concomitantly and identically from pharynx and rectum. Results SARS-CoV-2 RNA was detected more frequently (91%, 30/33 versus 42%, 14/33, p <0.0001) and at higher concentrations (median levels 2 190 186 IU/mL versus 13 014 IU/mL, p <0.0001) in the pharyngeal swabs than in the rectal swabs. For all sample pairs (n = 33) the rectal swabs contained undetectable or lower SARS-CoV-2 RNA concentrations than their paired pharyngeal swabs. Replicative virus was found in 37% (11/30) of the PCR-positive pharyngeal swabs, whereas none of the PCR-positive rectal swabs could be cultured (0%, 0/14) despite containing SARS-CoV-2 RNA concentrations up to 1 544 691 IU/mL. Conclusions Our data draw into question whether SARS-CoV-2 is transmitted readily from faeces.
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Affiliation(s)
- Rune Micha Pedersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Ditte Sandfeld Tornby
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Line Lundegård Bang
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital and Research Unit of Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Marianne Nielsine Skov
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Thomas Vognbjerg Sydenham
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Kat Steinke
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Thøger Gorm Jensen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital and Research Unit of Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital and Research Unit of Clinical Microbiology, University of Southern Denmark, Odense, Denmark.
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Niyonkuru M, Pedersen RM, Assing K, Andersen TE, Skov MN, Johansen IS, Madsen LW. Prolonged viral shedding of SARS-CoV-2 in two immunocompromised patients, a case report. BMC Infect Dis 2021; 21:743. [PMID: 34344321 PMCID: PMC8330202 DOI: 10.1186/s12879-021-06429-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/12/2021] [Indexed: 01/05/2023] Open
Abstract
Background The duration of viable Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) shedding in immunocompromised patients is still unknown. This case report describes the duration of viable SARS-CoV-2 in two immunocompromised patients with completely different clinical courses and further addresses the immunological aspects. Case presentations Oropharyngeal swaps were collected continuously during hospitalization for two immunocompromised patients infected with SARS-CoV-2 and sent for analysis to real time reverse transcription polymerase chain reaction (RT-PCR), viral culture assessed by plaque assay and full genome sequencing. Blood samples for flow cytometry and further immunological analysis were taken once during admission. One patient was without symptoms of Coronavirus disease 2019 (COVID-19) whereas the other had severe respiratory symptoms requiring a stay at an intensive care unit (ICU) and treatment with remdesivir and dexamethasone. Despite their difference in clinical courses, they both continuously shed SARS-CoV-2 with high viral loads in culture. Both patients had undetectable anti SARS-CoV-2 IgG levels about 2 weeks after the first positive real time RT-PCR test of SARS-CoV-2, marked expansions of virus reactive CD8+ T cells but cellular markers indicative of attenuated humoral immunity. Conclusions Our case illustrates the importance of distinguishing isolation guidelines for patients infected with SARS-CoV-2 according to their immunological status. Furthermore, it demonstrates the need for immune markers relating to viral shedding in immunocompromised patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06429-5.
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Affiliation(s)
- Melissa Niyonkuru
- Department of Infectious Diseases, Odense University Hospital, J.B Winsløws Vej 4, 5000, Odense C, Denmark. .,Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark.
| | - Rune Micha Pedersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Kristian Assing
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Thomas Emil Andersen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Marianne Nielsine Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital, J.B Winsløws Vej 4, 5000, Odense C, Denmark.,Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark
| | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital, J.B Winsløws Vej 4, 5000, Odense C, Denmark.,Research Unit for Infectious Diseases, University of Southern Denmark, Odense, Denmark
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Pedersen RM, Nielsen MTK, Möller S, Ethelberg S, Skov MN, Kolmos HJ, Scheutz F, Holt HM, Rosenvinge FS. Shiga toxin-producing Escherichia coli: incidence and clinical features in a setting with complete screening of patients with suspected infective diarrhoea. Clin Microbiol Infect 2017; 24:635-639. [PMID: 29030168 DOI: 10.1016/j.cmi.2017.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Shiga toxin-producing Escherichia coli (STEC) causes diarrhoeal disease, bloody diarrhoea, and haemolytic uraemic syndrome. The aim of this study was to describe the incidence of STEC and the clinical features of STEC patients from a well-defined Danish population in which all fecal samples of patients with suspected infective gastroenteritis were analysed for STEC. METHODS In this population-based cohort study, all stool samples referred to two clinical microbiology laboratories were screened for STEC by culture and/or PCR. Epidemiological (n=170) and clinical (n=209) characteristics were analysed using data from local and national registries. RESULTS Overall, 75,132 samples from 30,073 patients were screened resulting in 217 unique STEC-isolates. The epidemiological analysis showed an incidence of 10.1 cases per 100,000 person-years, which was more than twofold higher than the incidence in the rest of Denmark (3.4 cases per 100,000 person-years, p <0.001). Three groups were associated with a higher incidence: age <5 years (n=28, p <0.001), age ≥65 years (n=38, p 0.045), and foreign ethnicity (n=27, p 0.003). In the clinical analysis, patients with STEC harbouring only the Shiga toxin 1 gene (stx1-only isolates) showed a lower frequency of acute (n=11, p <0.05) and bloody diarrhoea (n=5, p <0.05) and a higher frequency of gastrointestinal symptoms for ≥3 months (n=8, p <0.05) than the other STEC patients. CONCLUSIONS We report a more than twofold higher incidence in the project area compared with the rest of Denmark, indicating that patients remain undiagnosed when selective STEC screening is used. We found an association between patients with stx1-only isolates and long-term gastrointestinal symptoms.
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Affiliation(s)
- R M Pedersen
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark.
| | - M T K Nielsen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - S Möller
- OPEN - Odense Patient Data Explorative Network, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - S Ethelberg
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - M N Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - H J Kolmos
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - F Scheutz
- The International Collaborating Centre for Reference and Research on Escherichia and Klebsiella, Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - H M Holt
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - F S Rosenvinge
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark; Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
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