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Lassaunière R, Polacek C, Utko M, Sørensen KM, Baig S, Ellegaard K, Escobar-Herrera LA, Fomsgaard A, Spiess K, Gunalan V, Bennedbæk M, Fonager J, Schwartz O, Planas D, Simon-Lorière E, Schneider UV, Sieber RN, Stegger M, Nielsen L, Hoppe M, Krause TG, Ullum H, Jokelainen P, Rasmussen M. Virus isolation and neutralisation of SARS-CoV-2 variants BA.2.86 and EG.5.1. Lancet Infect Dis 2023; 23:e509-e510. [PMID: 37949089 DOI: 10.1016/s1473-3099(23)00682-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Affiliation(s)
- Ria Lassaunière
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark.
| | - Charlotta Polacek
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | | | | | - Sharmin Baig
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Copenhagen 2300, Denmark
| | - Kirsten Ellegaard
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Copenhagen 2300, Denmark
| | | | - Anders Fomsgaard
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Katja Spiess
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Vithiagaran Gunalan
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Jannik Fonager
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Créteil, France
| | - Delphine Planas
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France; CNRS UMR 3569, Paris, France; Vaccine Research Institute, Créteil, France
| | | | - Uffe V Schneider
- Virus Preparedness, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
| | - Raphael N Sieber
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Copenhagen 2300, Denmark
| | - Marc Stegger
- Sequencing and Bioinformatics, Bacteria, Parasites & Fungi, Copenhagen 2300, Denmark; Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, WA, Australia
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Morten Hoppe
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - Tyra G Krause
- Epidemiological Infectious Disease Preparedness, Copenhagen 2300, Denmark
| | - Henrik Ullum
- Statens Serum Institut, Copenhagen 2300, Denmark
| | | | - Morten Rasmussen
- Virus Research and Development Laboratory, Virus & Microbiological Special Diagnostics, Copenhagen 2300, Denmark
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Noahsen P, Faber LL, Isidor S, Fonager J, Rasmussen M, Hansen HL. The COVID-19 pandemic in Greenland, epidemic features and impact of early strict measures, March 2020 to June 2022. Euro Surveill 2023; 28:2200767. [PMID: 37470739 PMCID: PMC10360370 DOI: 10.2807/1560-7917.es.2023.28.29.2200767] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/17/2023] [Indexed: 07/21/2023] Open
Abstract
BackgroundThe COVID-19 pandemic was of major concern in Greenland. There was a high possibility of rapid transmission in settlements, and an increased risk of morbidity and mortality because of comorbidities in the population and limited access to specialised healthcare in remote areas.AimTo describe the epidemiology of the COVID-19 pandemic in Greenland and evaluate the effects of a strict COVID-19 strategy until risk groups were immunised.MethodsWe studied the epidemiology during March 2020 to June 2022. We describe the non-pharmaceutical interventions (NPIs), PCR-confirmed COVID-19 cases and vaccination coverage with data from the registries of the Greenlandic health authority.ResultsWe found 21,419 confirmed cases per 100,000 inhabitants (54% female, 46% male), 342 per 100,000 were hospitalised and 16 per 100,000 were admitted to the intensive care unit. The COVID-19 mortality rate was 39 per 100,000, all those affected were aged above 65 years. No excess overall mortality was observed. The vaccination coverage by June 2022 was 71.67 and 41% for one, two and three doses, respectively.ConclusionSARS-CoV-2 circulation in Greenland was low, given strict restrictions until all eligible inhabitants had been offered immunisation. The main impact of the pandemic was from May 2021 onwards with increasing numbers of confirmed cases. This occurred after introduction of the vaccine programme, which may have had an influence on the severity of the associated morbidity and mortality experienced. Halting community transmission of SARS-CoV-2 with NPIs until the majority of the population had been immunised was a successful strategy in Greenland.
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Affiliation(s)
- Paneeraq Noahsen
- National Board of Health in Greenland, Nuuk, Greenland
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
- Aalborg University, Aalborg, Denmark
- Arctic Health Research Centre, Aalborg University Hospital, Aalborg, Denmark
| | | | - Silvia Isidor
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
| | - Jannik Fonager
- Virus Research and Development section, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development section, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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3
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Fomsgaard AS, Tahas SA, Spiess K, Polacek C, Fonager J, Belsham GJ. Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System. Viruses 2023; 15:1399. [PMID: 37376698 DOI: 10.3390/v15061399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.
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Affiliation(s)
- Anna S Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | | | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Charlotta Polacek
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
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4
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Spiess K, Gunalan V, Marving E, Nielsen SH, Jørgensen MGP, Fomsgaard AS, Nielsen L, Alfaro-Núñez A, Karst SM, Mortensen S, Rasmussen M, Lassaunière R, Rosenstierne MW, Polacek C, Fonager J, Cohen AS, Nielsen C, Fomsgaard A. Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations. Microbiol Spectr 2023; 11:e0359122. [PMID: 36625603 PMCID: PMC9927487 DOI: 10.1128/spectrum.03591-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023] Open
Abstract
Multiple mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) increase transmission, disease severity, and immune evasion and facilitate zoonotic or anthropozoonotic infections. Four such mutations, ΔH69/V70, L452R, E484K, and N501Y, occurred in the SARS-CoV-2 spike glycoprotein in combinations that allow the simultaneous detection of VOCs. Here, we present two flexible reverse transcription-quantitative PCR (RT-qPCR) platforms for small- and large-scale screening (also known as variant PCR) to detect these mutations and schemes for adapting the platforms to future mutations. The large-scale RT-qPCR platform was validated by pairwise matching of RT-qPCR results with whole-genome sequencing (WGS) consensus genomes, showing high specificity and sensitivity. Both platforms are valuable examples of complementing WGS to support the rapid detection of VOCs. Our mutational signature approach served as an important intervention measure for the Danish public health system to detect and delay the emergence of new VOCs. IMPORTANCE Denmark weathered the SARS-CoV-2 crisis with relatively low rates of infection and death. Intensive testing strategies with the aim of detecting SARS-CoV-2 in symptomatic and nonsymptomatic individuals were available by establishing a national test system called TestCenter Denmark. This testing regime included the detection of SARS-CoV-2 signature mutations, with referral to the national health system, thereby delaying outbreaks of variants of concern. Our study describes the design of the large-scale RT-qPCR platform established at TestCenter Denmark in conjunction with whole-genome sequencing to report mutations of concern to the national health system. Validation of the large-scale RT-qPCR platform using paired WGS consensus genomes showed high sensitivity and specificity. For smaller laboratories with limited infrastructure, we developed a flexible small-scale RT-qPCR platform to detect three signature mutations in a single run. The RT-qPCR platforms are important tools to support the control of the SARS-CoV-2 endemic in Denmark.
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Affiliation(s)
- Katja Spiess
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ellinor Marving
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Anna S. Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Line Nielsen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | - Alonzo Alfaro-Núñez
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Søren M. Karst
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - The Danish COVID-19 Genome Consortium (DCGC)
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
- Qlife ApS Symbion, Copenhagen, Denmark
| | - Shila Mortensen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassaunière
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Charlotta Polacek
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Arieh S. Cohen
- Test Center Denmark, Statens Serum Institut, Copenhagen, Denmark
| | - Claus Nielsen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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5
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Hansen CH, Friis NU, Bager P, Stegger M, Fonager J, Fomsgaard A, Gram MA, Christiansen LE, Ethelberg S, Legarth R, Krause TG, Ullum H, Valentiner-Branth P. Risk of reinfection, vaccine protection, and severity of infection with the BA.5 omicron subvariant: a nation-wide population-based study in Denmark. Lancet Infect Dis 2023; 23:167-176. [PMID: 36270311 PMCID: PMC9578720 DOI: 10.1016/s1473-3099(22)00595-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Estimates of immunity and severity for the SARS-CoV-2 omicron subvariant BA.5 are important to assess the public health impact associated with its rapid global spread despite vaccination. We estimated natural and vaccine immunity and severity of BA.5 relative to BA.2 in Denmark, a country with high mRNA-vaccination coverage and free-of-charge RT-PCR testing. METHODS This nation-wide population-based study in Denmark included residents aged 18 years or older who had taken an RT-PCR test between 10 April and 30 June, 2022 (ie, the outcome period), and who the national COVID-19 surveillance system identified as having information since February 2020 on RT-PCR tests, whole-genome sequencing, vaccinations, and hospitalisation with a positive RT-PCR test and COVID-19 as the main diagnosis. First, we used a case-control design, in which cases were people infected with BA.5 or BA.2 during the outcome period and controls were people who tested negative for SARS-CoV-2 infection during the outcome period. We calculated the protection provided by a previous PCR-confirmed omicron infection against BA.5 and BA.2 infection and hospitalisation among triple-vaccinated individuals. Second, we compared vaccination status in people infected with BA.5 versus BA.2 and estimated relative vaccine protection against each subvariant. Third, we compared rates of hospitalisation for COVID-19 among people infected with BA.5 versus BA.2. We estimated effects using logistic regression with adjustment for sex, age, region, PCR-test date, comorbidity and, as appropriate, vaccination and previous infection status. FINDINGS A total of 210 (2·4%) of 8678 of BA.5 cases, 192 (0·7%) of 29 292 of BA.2 cases, and 33 972 (19·0%) of 178 669 PCR-negative controls previously had an omicron infection, which was estimated in the adjusted analyses to offer 92·7% (95% CI 91·6-93·7) protection against BA.5 infection and 97·1% (96·6-97·5) protection against BA.2 infection. We found similarly high amounts of protection against hospitalisation owing to infection with BA.5 (96·4% [95% CI 74·2-99·5]) and BA.2 (91·2% [76·3-96·7]). Vaccine coverage (three mRNA doses vs none) was 9307 (94·2%) of 9878 among BA.5 cases and 30 581 (94·8%) of 32 272 among BA.2 cases, although in the adjusted analysis, there was a trend towards slightly higher vaccination coverage among BA.5 cases than BA.2 cases (OR 1·18 [95% CI 0·99-1·42]; p=0·064), possibly suggesting marginally poorer vaccine protection against BA.5. The rate of hospitalisation due to COVID-19 was higher among the BA.5 cases (210 [1·9%] of 11 314) than among the BA.2 cases (514 [1·4%] of 36 805), with an OR of 1·34 (95% CI 1·14-1·57) and an adjusted OR of 1·69 (95% CI 1·22-2·33), despite low and stable COVID-19 hospitalisation numbers during the study period. INTERPRETATION The study provides evidence that a previous omicron infection in triple-vaccinated individuals provides high amounts of protection against BA.5 and BA.2 infections. However, protection estimates greater than 90% might be too high if individuals with a previous infection were more likely than those without one to come forward for a test for reasons other than suspicion of COVID-19. Our analysis also showed that vaccine protection against BA.5 infection was similar to, or slightly weaker than, protection against BA.2 infection. Finally, there was evidence that BA.5 infections were associated with an increased risk of hospitalisation compared with BA.2 infections. FUNDING There was no funding source for this study.
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Affiliation(s)
- Christian Holm Hansen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark; Medical Reseasrch Council International Statistics and Epidemiology Group, London School of Hygiene & Tropical Medicine, London, UK
| | - Nikolaj Ulrik Friis
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Bager
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Mie Agermose Gram
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark; Department of Public Health, Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Legarth
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra Grove Krause
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Ullum
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Palle Valentiner-Branth
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
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Fomsgaard AS, Rasmussen M, Spiess K, Fomsgaard A, Belsham GJ, Fonager J. Improvements in metagenomic virus detection by simple pretreatment methods. J Clin Virol Plus 2022; 2:100120. [PMID: 36945677 PMCID: PMC10024160 DOI: 10.1016/j.jcvp.2022.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/20/2022] [Revised: 09/26/2022] [Accepted: 10/24/2022] [Indexed: 11/21/2022] Open
Abstract
Early detection of pathogens at the point of care helps reduce the threats to human and animal health from emerging pathogens. Initially, the disease-causing agent will be unknown and needs to be identified; this often requires specific laboratory facilities. Here we describe the development of an unbiased detection assay for RNA and DNA viruses using metagenomic Nanopore sequencing and simple methods that can be transferred into a field setting. Human clinical samples containing the RNA virus SARS-CoV-2 or the DNA viruses human papillomavirus (HPV) and molluscum contagiosum virus (MCV) were used as a test of concept. Firstly, the virus detection potential was optimized by investigating different pretreatments for reducing non-viral nucleic acid components. DNase I pretreatment followed by filtration increased the proportion of SARS-CoV-2 sequenced reads > 500-fold compared with no pretreatments. This was sufficient to achieve virus detection with high confidence and allowed variant identification. Next, we tested individual SARS-CoV-2 samples with various viral loads (measured as CT-values determined by RT-qPCR). Lastly, we tested the assay on clinical samples containing the DNA virus HPV and co-infection with MCV to show the assay's detection potential for DNA viruses. This protocol is fast (same day results). We hope to apply this method in other settings for point of care detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.
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Affiliation(s)
- Anna S. Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
- Corresponding author.
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, DK-2300 Copenhagen, Denmark
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7
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Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Mølbak K, Møller CH, Skov RL, Krause TG, Rasmussen M, Sieber RN, Johannesen TB, Lillebaek T, Fonager J, Fomsgaard A, Møller FT, Stegger M, Overvad M, Spiess K, Mortensen LH. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark. Nat Commun 2022. [PMID: 36180438 DOI: 10.1101/2022.01.28.22270044] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) continues to evolve and new variants emerge. Using nationwide Danish data, we estimate the transmission dynamics of SARS-CoV-2 Omicron subvariants BA.1 and BA.2 within households. Among 22,678 primary cases, we identified 17,319 secondary infections among 50,588 household contacts during a 1-7 day follow-up. The secondary attack rate (SAR) was 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. BA.2 was associated with increased susceptibility of infection for unvaccinated household contacts (Odds Ratio (OR) 1.99; 95%-CI 1.72-2.31), fully vaccinated contacts (OR 2.26; 95%-CI 1.95-2.62) and booster-vaccinated contacts (OR 2.65; 95%-CI 2.29-3.08), compared to BA.1. We also found increased infectiousness from unvaccinated primary cases infected with BA.2 compared to BA.1 (OR 2.47; 95%-CI 2.15-2.84), but not for fully vaccinated (OR 0.66; 95%-CI 0.57-0.78) or booster-vaccinated primary cases (OR 0.69; 95%-CI 0.59-0.82). Omicron BA.2 is inherently more transmissible than BA.1. Its immune-evasive properties also reduce the protective effect of vaccination against infection, but do not increase infectiousness of breakthrough infections from vaccinated individuals.
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Affiliation(s)
- Frederik Plesner Lyngse
- Department of Economics & Center for Economic Behavior and Inequality, University of Copenhagen, Copenhagen, Denmark.
- Danish Ministry of Health, Copenhagen, Denmark.
- Statens Serum Institut, Copenhagen, Denmark.
| | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew Denwood
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Engbo Christiansen
- Department of Applied Mathematics and Computer Science; Dynamical Systems, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kåre Mølbak
- Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Troels Lillebaek
- Statens Serum Institut, Copenhagen, Denmark
- Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Laust Hvas Mortensen
- Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Mølbak K, Møller CH, Skov RL, Krause TG, Rasmussen M, Sieber RN, Johannesen TB, Lillebaek T, Fonager J, Fomsgaard A, Møller FT, Stegger M, Overvad M, Spiess K, Mortensen LH. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark. Nat Commun 2022; 13:5760. [PMID: 36180438 PMCID: PMC9524324 DOI: 10.1038/s41467-022-33498-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/16/2022] [Indexed: 12/12/2022] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) continues to evolve and new variants emerge. Using nationwide Danish data, we estimate the transmission dynamics of SARS-CoV-2 Omicron subvariants BA.1 and BA.2 within households. Among 22,678 primary cases, we identified 17,319 secondary infections among 50,588 household contacts during a 1–7 day follow-up. The secondary attack rate (SAR) was 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. BA.2 was associated with increased susceptibility of infection for unvaccinated household contacts (Odds Ratio (OR) 1.99; 95%–CI 1.72-2.31), fully vaccinated contacts (OR 2.26; 95%–CI 1.95–2.62) and booster-vaccinated contacts (OR 2.65; 95%–CI 2.29–3.08), compared to BA.1. We also found increased infectiousness from unvaccinated primary cases infected with BA.2 compared to BA.1 (OR 2.47; 95%–CI 2.15–2.84), but not for fully vaccinated (OR 0.66; 95%–CI 0.57–0.78) or booster-vaccinated primary cases (OR 0.69; 95%–CI 0.59–0.82). Omicron BA.2 is inherently more transmissible than BA.1. Its immune-evasive properties also reduce the protective effect of vaccination against infection, but do not increase infectiousness of breakthrough infections from vaccinated individuals. In this study, the authors use household data from Denmark to investigate the transmissibility of the BA.1 and BA.2 Omicron SARS-CoV-2 subvariants. They find that the secondary attack rate was higher for BA.2, but that it had higher infectiousness only when cases were not vaccinated.
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Affiliation(s)
- Frederik Plesner Lyngse
- Department of Economics & Center for Economic Behavior and Inequality, University of Copenhagen, Copenhagen, Denmark. .,Danish Ministry of Health, Copenhagen, Denmark. .,Statens Serum Institut, Copenhagen, Denmark.
| | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew Denwood
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Engbo Christiansen
- Department of Applied Mathematics and Computer Science; Dynamical Systems, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kåre Mølbak
- Statens Serum Institut, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Troels Lillebaek
- Statens Serum Institut, Copenhagen, Denmark.,Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Laust Hvas Mortensen
- Statistics Denmark, Copenhagen, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Mølbak K, Møller CH, Skov RL, Krause TG, Rasmussen M, Sieber RN, Johannesen TB, Lillebaek T, Fonager J, Fomsgaard A, Møller FT, Stegger M, Overvad M, Spiess K, Mortensen LH. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark. Nat Commun 2022; 13:5760. [PMID: 36180438 DOI: 10.1101/2022.1101.1128.22270044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/16/2022] [Indexed: 05/23/2023] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) continues to evolve and new variants emerge. Using nationwide Danish data, we estimate the transmission dynamics of SARS-CoV-2 Omicron subvariants BA.1 and BA.2 within households. Among 22,678 primary cases, we identified 17,319 secondary infections among 50,588 household contacts during a 1-7 day follow-up. The secondary attack rate (SAR) was 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively. BA.2 was associated with increased susceptibility of infection for unvaccinated household contacts (Odds Ratio (OR) 1.99; 95%-CI 1.72-2.31), fully vaccinated contacts (OR 2.26; 95%-CI 1.95-2.62) and booster-vaccinated contacts (OR 2.65; 95%-CI 2.29-3.08), compared to BA.1. We also found increased infectiousness from unvaccinated primary cases infected with BA.2 compared to BA.1 (OR 2.47; 95%-CI 2.15-2.84), but not for fully vaccinated (OR 0.66; 95%-CI 0.57-0.78) or booster-vaccinated primary cases (OR 0.69; 95%-CI 0.59-0.82). Omicron BA.2 is inherently more transmissible than BA.1. Its immune-evasive properties also reduce the protective effect of vaccination against infection, but do not increase infectiousness of breakthrough infections from vaccinated individuals.
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Affiliation(s)
- Frederik Plesner Lyngse
- Department of Economics & Center for Economic Behavior and Inequality, University of Copenhagen, Copenhagen, Denmark.
- Danish Ministry of Health, Copenhagen, Denmark.
- Statens Serum Institut, Copenhagen, Denmark.
| | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew Denwood
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Engbo Christiansen
- Department of Applied Mathematics and Computer Science; Dynamical Systems, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kåre Mølbak
- Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Troels Lillebaek
- Statens Serum Institut, Copenhagen, Denmark
- Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Laust Hvas Mortensen
- Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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10
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Gram MA, Emborg HD, Schelde AB, Friis NU, Nielsen KF, Moustsen-Helms IR, Legarth R, Lam JUH, Chaine M, Malik AZ, Rasmussen M, Fonager J, Sieber RN, Stegger M, Ethelberg S, Valentiner-Branth P, Hansen CH. Vaccine effectiveness against SARS-CoV-2 infection or COVID-19 hospitalization with the Alpha, Delta, or Omicron SARS-CoV-2 variant: A nationwide Danish cohort study. PLoS Med 2022; 19:e1003992. [PMID: 36048766 PMCID: PMC9436060 DOI: 10.1371/journal.pmed.1003992] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/26/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The continued occurrence of more contagious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants and waning immunity over time require ongoing reevaluation of the vaccine effectiveness (VE). This study aimed to estimate the effectiveness in 2 age groups (12 to 59 and 60 years or above) of 2 or 3 vaccine doses (BNT162b2 mRNA or mRNA-1273) by time since vaccination against SARS-CoV-2 infection and Coronavirus Disease 2019 (COVID-19) hospitalization in an Alpha-, Delta-, or Omicron-dominated period. METHODS AND FINDINGS A Danish nationwide cohort study design was used to estimate VE against SARS-CoV-2 infection and COVID-19 hospitalization with the Alpha, Delta, or Omicron variant. Information was obtained from nationwide registries and linked using a unique personal identification number. The study included all previously uninfected residents in Denmark aged 12 years or above (18 years or above for the analysis of 3 doses) in the Alpha (February 20 to June 15, 2021), Delta (July 4 to November 20, 2021), and Omicron (December 21, 2021 to January 31, 2022) dominated periods. VE estimates including 95% confidence intervals (CIs) were calculated (1-hazard ratio∙100) using Cox proportional hazard regression models with underlying calendar time and adjustments for age, sex, comorbidity, and geographical region. Vaccination status was included as a time-varying exposure. In the oldest age group, VE against infection after 2 doses was 90.7% (95% CI: 88.2; 92.7) for the Alpha variant, 82.3% (95% CI: 75.5; 87.2) for the Delta variant, and 39.9% (95% CI: 26.3; 50.9) for the Omicron variant 14 to 30 days since vaccination. The VE waned over time and was 73.2% (Alpha, 95% CI: 57.1; 83.3), 50.0% (Delta, 95% CI: 46.7; 53.0), and 4.4% (Omicron, 95% CI: -0.1; 8.7) >120 days since vaccination. Higher estimates were observed after the third dose with VE estimates against infection of 86.1% (Delta, 95% CI: 83.3; 88.4) and 57.7% (Omicron, 95% CI: 55.9; 59.5) 14 to 30 days since vaccination. Among both age groups, VE against COVID-19 hospitalization 14 to 30 days since vaccination with 2 or 3 doses was 98.1% or above for the Alpha and Delta variants. Among both age groups, VE against COVID-19 hospitalization 14 to 30 days since vaccination with 2 or 3 doses was 95.5% or above for the Omicron variant. The main limitation of this study is the nonrandomized study design including potential differences between the unvaccinated (reference group) and vaccinated individuals. CONCLUSIONS Two vaccine doses provided high protection against SARS-CoV-2 infection and COVID-19 hospitalization with the Alpha and Delta variants with protection, notably against infection, waning over time. Two vaccine doses provided only limited and short-lived protection against SARS-CoV-2 infection with Omicron. However, the protection against COVID-19 hospitalization following Omicron SARS-CoV-2 infection was higher. The third vaccine dose substantially increased the level and duration of protection against infection with the Omicron variant and provided a high level of sustained protection against COVID-19 hospitalization among the +60-year-olds.
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Affiliation(s)
- Mie Agermose Gram
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Hanne-Dorthe Emborg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Astrid Blicher Schelde
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Nikolaj Ulrik Friis
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Finderup Nielsen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Ida Rask Moustsen-Helms
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rebecca Legarth
- Division of Infectious Disease Preparedness, Data Integration and Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Janni Uyen Hoa Lam
- Division of Infectious Disease Preparedness, Data Integration and Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Manon Chaine
- Division of Infectious Disease Preparedness, Data Integration and Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Aisha Zahoor Malik
- Division of Infectious Disease Preparedness, Data Integration and Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael Niklaus Sieber
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- Department of Public Health, Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | - Palle Valentiner-Branth
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Holm Hansen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- MRC International Statistics and Epidemiology Group, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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11
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Vaughan AM, Cenciarelli O, Colombe S, Alves de Sousa L, Fischer N, Gossner CM, Pires J, Scardina G, Aspelund G, Avercenko M, Bengtsson S, Blomquist P, Caraglia A, Chazelle E, Cohen O, Diaz A, Dillon C, Dontsenko I, Kotkavaara K, Fafangel M, Ferraro F, Firth R, Fonager J, Frank C, Carrasco MG, Gkolfinopoulou K, Grenersen MP, Guzmán Herrador BR, Henczkó J, Hoornenborg E, Igoe D, Ilić M, Jansen K, Janță DG, Johansen TB, Kasradze A, Koch A, Kyncl J, Martins JV, McAuley A, Mellou K, Molnár Z, Mor Z, Mossong J, Novacek A, Orlikova H, Pem Novosel I, Rossi MK, Sadkowska-Todys M, Sawyer C, Schmid D, Sîrbu A, Sondén K, Tarantola A, Tavares M, Thordardottir M, Učakar V, Van Ewijk C, Varjas J, Vergison A, Vivancos R, Zakrzewska K, Pebody R, Haussig JM. A large multi-country outbreak of monkeypox across 41 countries in the WHO European Region, 7 March to 23 August 2022. Euro Surveill 2022; 27. [PMID: 36082686 PMCID: PMC9461311 DOI: 10.2807/1560-7917.es.2022.27.36.2200620] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Following the report of a non-travel-associated cluster of monkeypox cases by the United Kingdom in May 2022, 41 countries across the WHO European Region have reported 21,098 cases and two deaths by 23 August 2022. Nowcasting suggests a plateauing in case notifications. Most cases (97%) are MSM, with atypical rash-illness presentation. Spread is mainly through close contact during sexual activities. Few cases are reported among women and children. Targeted interventions of at-risk groups are needed to stop further transmission.
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Affiliation(s)
- Aisling M Vaughan
- World Health Organization (WHO) Regional Office for Europe, Copenhagen, Denmark
| | | | - Soledad Colombe
- Outbreak Research Team, Institute of Tropical Medicine, Antwerp, Belgium.,Global Outbreak Alert and Response Network (GOARN), Geneva, Switzerland.,World Health Organization (WHO) Regional Office for Europe, Copenhagen, Denmark
| | | | - Natalie Fischer
- Global Outbreak Alert and Response Network (GOARN), Geneva, Switzerland.,World Health Organization (WHO) Regional Office for Europe, Copenhagen, Denmark
| | - Celine M Gossner
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Jeff Pires
- World Health Organization (WHO) Regional Office for Europe, Copenhagen, Denmark
| | - Giuditta Scardina
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Gudrun Aspelund
- Centre for Health Security and Communicable Disease Control, The Directorate of Health, Reykjavik, Iceland
| | - Margarita Avercenko
- Infectious Disease Prevention and Control Unit, Department of Infectious Risks Analysis and Prevention, Centre for Disease Prevention and Control of Latvia, Riga, Latvia
| | - Sara Bengtsson
- Unit for Diagnostics Preparedness of Notifiable and High Consequence Pathogens, Public Health Agency of Sweden, Solna, Sweden
| | - Paula Blomquist
- Field Services, United Kingdom Health Security Agency, London, United Kingdom
| | - Anna Caraglia
- Directorate General of Health Prevention, Ministry of Health, Rome, Italy
| | - Emilie Chazelle
- Santé publique France, the French National Public Health Agency, Saint-Maurice, France
| | - Orna Cohen
- Division of Epidemiology, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Asuncion Diaz
- National Centre of Epidemiology, Carlos III Health Institute, CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Christina Dillon
- Health Services Executive, Health Protection Surveillance Centre, Dublin, Ireland
| | - Irina Dontsenko
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Katja Kotkavaara
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mario Fafangel
- Communicable Diseases Centre, National Institute of Public Health, Ljubljana, Slovenia
| | - Federica Ferraro
- Directorate General of Health Prevention, Ministry of Health, Rome, Italy
| | | | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Christina Frank
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Mireia G Carrasco
- Ministry of Health, Government of Andorra, Andorra la Vella, Andorra
| | - Kassiani Gkolfinopoulou
- Surveillance Coordination Department. Hellenic National Public Health Organization (EODY), Athens, Greece
| | | | - Bernardo R Guzmán Herrador
- Coordinating Centre for Health Alerts and Emergencies (CCAES), Directorate General of Public Health, Ministry of Health, Madrid, Spain
| | - Judit Henczkó
- Department of Microbiological Reference Laboratory, National Public Health Center, Budapest, Hungary
| | - Elske Hoornenborg
- Public Health Service of Amsterdam (GGD Amsterdam), Amsterdam, the Netherlands
| | - Derval Igoe
- Health Services Executive, Health Protection Surveillance Centre, Dublin, Ireland
| | - Maja Ilić
- Croatian Institute of Public Health, Zagreb, Croatia
| | - Klaus Jansen
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Denisa-Georgiana Janță
- National Centre of Surveillance and Control of Communicable Disease, National Institute of Public Health Romania, Bucharest, Romania
| | | | - Ana Kasradze
- Head of Public Health Emergency Preparedness and Response Division, National Center for Disease Control and Public Health, Tbilisi, Georgia
| | - Anders Koch
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Jan Kyncl
- Department of Infectious Diseases Epidemiology, National Institute of Public Health, Prague, Czech Republic
| | - João Vieira Martins
- Directorate of Information and Analysis, Directorate-General of Health, Lisbon, Portugal
| | - Andrew McAuley
- Public Health Scotland, Edinburgh, Scotland, United Kingdom
| | - Kassiani Mellou
- Directorate of Epidemiological Surveillance and Intervention for Infectious Diseases, Hellenic National Public Health Organization (EODY), Athens, Greece
| | - Zsuzsanna Molnár
- Department of Communicable Disease Epidemiology and Infection Control, National Public Health Center, Budapest, Hungary
| | - Zohar Mor
- School of Health Sciences, Ashkelon Academic College, Ashkelon, Israel.,Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Alina Novacek
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Hana Orlikova
- Department of Infectious Diseases Epidemiology, National Institute of Public Health, Prague, Czech Republic
| | | | - Maria K Rossi
- Public Health Scotland, Edinburgh, Scotland, United Kingdom
| | | | - Clare Sawyer
- Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, United Kingdom
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Anca Sîrbu
- National Centre of Surveillance and Control of Communicable Disease, National Institute of Public Health Romania, Bucharest, Romania
| | - Klara Sondén
- Unit for Diagnostics Preparedness of Notifiable and High Consequence Pathogens, Public Health Agency of Sweden, Solna, Sweden
| | - Arnaud Tarantola
- Santé publique France Regional Office, Saint-Denis, Île-de-France, France
| | - Margarida Tavares
- National Program for Sexually Transmitted Infections and HIV Infection, Directorate-General of Health, Lisbon, Portugal.,Laboratory for Integrative and Translational Research in Population Health (ITR), and EPIUnit - Institute of Public Health, University of Porto, Porto, Portugal.,Emerging Infectious Diseases Unit, Department of Infectious Diseases, Centro Hospitalar Universitário de São João, Porto, Portugal
| | - Marianna Thordardottir
- Centre for Health Security and Communicable Disease Control, The Directorate of Health, Reykjavik, Iceland
| | - Veronika Učakar
- Communicable Diseases Centre, National Institute of Public Health, Ljubljana, Slovenia
| | - Catharina Van Ewijk
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden.,National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Juta Varjas
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | | | - Roberto Vivancos
- Field Services, United Kingdom Health Security Agency, London, United Kingdom
| | - Karolina Zakrzewska
- National Institute of Public Health (NIH) - National Research Institute, Warsaw, Poland
| | - Richard Pebody
- World Health Organization (WHO) Regional Office for Europe, Copenhagen, Denmark
| | - Joana M Haussig
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
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12
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Mens H, Fjordside L, Fonager J, Gerstoft J. Emergence of the G118R Pan-Integrase Resistance Mutation as a Result of Low Compliance to a Dolutegravir-Based cART. Infect Dis Rep 2022; 14:501-504. [PMID: 35893472 PMCID: PMC9326666 DOI: 10.3390/idr14040053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/31/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
HIV-1 resistance towards integrase inhibitors is a potential threat of the success of HIV-1 combination treatment. G118R is a rare drug resistance mutation conferring pan-integrase resistance. Here, we describe the occurrence of G118R in a HIV-1 subtype-B-positive individual with major compliance problems, detected while the patient was on dolutegravir-based cART. We speculate the pre-selection of M184I/V aided the occurrence of G118R in this case, and discuss the robustness of dolutegravir-based therapies.
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Affiliation(s)
- Helene Mens
- Rigshospitalet, Department of Infectious Diseases, 2100 Copenhagen, Denmark; (L.F.); (J.G.)
- Correspondence: ; Tel.: +45-354-504-36
| | - Lasse Fjordside
- Rigshospitalet, Department of Infectious Diseases, 2100 Copenhagen, Denmark; (L.F.); (J.G.)
| | - Jannik Fonager
- Viruses and Microbial Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark;
| | - Jan Gerstoft
- Rigshospitalet, Department of Infectious Diseases, 2100 Copenhagen, Denmark; (L.F.); (J.G.)
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13
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Michaelsen TY, Bennedbæk M, Christiansen LE, Jørgensen MSF, Møller CH, Sørensen EA, Knutsson S, Brandt J, Jensen TBN, Chiche-Lapierre C, Collados EF, Sørensen T, Petersen C, Le-Quy V, Sereika M, Hansen FT, Rasmussen M, Fonager J, Karst SM, Marvig RL, Stegger M, Sieber RN, Skov R, Legarth R, Krause TG, Fomsgaard A, Albertsen M. Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark. Genome Med 2022; 14:47. [PMID: 35505393 PMCID: PMC9064402 DOI: 10.1186/s13073-022-01045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission of B.1.1.7 in Denmark. Methods We analyzed a comprehensive set of 60,178 SARS-CoV-2 genomes generated from high-throughput sequencing by the Danish COVID-19 Genome Consortium, representing 34% of all positive cases in the period 14 November 2020 to 7 February 2021. We calculated the transmissibility of B.1.1.7 relative to other lineages using Poisson regression. Including all 1976 high-quality B.1.1.7 genomes collected in the study period, we constructed a time-scaled phylogeny, which was coupled with detailed travel history and register data to outline the introduction and onward transmission of B.1.1.7 in Denmark. Results In a period with unchanged restrictions, we estimated an increased B.1.1.7 transmissibility of 58% (95% CI: [56%, 60%]) relative to other lineages. Epidemiological and phylogenetic analyses revealed that 37% of B.1.1.7 cases were related to the initial introduction in November 2020. The relative number of cases directly linked to introductions varied between 10 and 50% throughout the study period. Conclusions Our findings corroborate early estimates of increased transmissibility of B.1.1.7. Both substantial early expansion when B.1.1.7 was still unmonitored and continuous foreign introductions contributed considerably to case numbers. Finally, our study highlights the benefit of balanced travel restrictions and self-isolation procedures coupled with comprehensive surveillance efforts, to sustain epidemic control in the face of emerging variants. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01045-7.
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Affiliation(s)
- Thomas Y Michaelsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Marc Bennedbæk
- Centre of Excellence for Health, Immunity and Infection (CHIP), Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lasse E Christiansen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Mia S F Jørgensen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Camilla H Møller
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Emil A Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon Knutsson
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Jakob Brandt
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas B N Jensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Emilio F Collados
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Vang Le-Quy
- Unit for Research Data Services (CLAAUDIA), Aalborg University, Aalborg, Denmark
| | - Mantas Sereika
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Frederik T Hansen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Søren M Karst
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Robert Skov
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Rebecca Legarth
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra G Krause
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | | | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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14
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Fonager J, Bennedbæk M, Bager P, Wohlfahrt J, Ellegaard KM, Ingham AC, Edslev SM, Stegger M, Sieber RN, Lassauniere R, Fomsgaard A, Lillebaek T, Svarrer CW, Møller FT, Møller CH, Legarth R, Sydenham TV, Steinke K, Paulsen SJ, Castruita JAS, Schneider UV, Schouw CH, Nielsen XC, Overvad M, Nielsen RT, Marvig RL, Pedersen MS, Nielsen L, Nilsson LL, Bybjerg-Grauholm J, Tarpgaard IH, Ebsen TS, Lam JUH, Gunalan V, Rasmussen M. Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022. Euro Surveill 2022; 27. [PMID: 35272746 PMCID: PMC8915403 DOI: 10.2807/1560-7917.es.2022.27.10.2200181] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.
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Affiliation(s)
- Jannik Fonager
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Bager
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Jan Wohlfahrt
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael Niklaus Sieber
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassauniere
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.,Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | - Christina Wiid Svarrer
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Frederik Trier Møller
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Rebecca Legarth
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | | | - Kat Steinke
- Department of Clinical Microbiology, Odense University Hospital, Denmark
| | - Sarah Juel Paulsen
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | | | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | | | | | - Maria Overvad
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rikke Thoft Nielsen
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Martin Schou Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Herlev, Denmark
| | - Line Lynge Nilsson
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Herlev, Denmark
| | | | | | | | - Janni Uyen Hoa Lam
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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15
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Bang D, Fonager J, Johansen IS. Management of a human immunodeficiency virus case with discordant antiviral drug resistance profiles in cerebrospinal fluid compared with plasma: a case report. J Med Case Rep 2022; 16:62. [PMID: 35164871 PMCID: PMC8845297 DOI: 10.1186/s13256-022-03289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/13/2020] [Accepted: 01/21/2022] [Indexed: 11/12/2022] Open
Abstract
Background Human immunodeficiency virus-1-associated neurocognitive disorder is a known complication in individuals treated with antiretroviral therapy. Cerebrospinal fluid escape, which is defined as discordant higher cerebrospinal fluid viremia than plasma, may occur in antiretroviral therapy-experienced individuals. Different cerebrospinal fluid versus plasma mutation patterns have been observed in individuals with cerebrospinal fluid escape. Case presentation A 46-year-old adult African male with human immunodeficiency virus-1 infection and acquired immunodeficiency syndrome based on cerebral toxoplasmosis and a chronic hepatitis B virus infection developed cerebrospinal fluid escape. A different human immunodeficiency virus-1 genotypic drug resistance profile was observed in plasma compared with cerebrospinal fluid. Brain biopsy and cerebral magnetic resonance imaging indicated the development of human immunodeficiency virus encephalopathy. A discordant protease inhibitor mutation/wild-type T74PT in plasma but not in cerebrospinal fluid indicated poor central nervous system penetration due to the selective pressure of drug therapy. An intensified antiretroviral therapy regimen including dolutegravir with good central nervous system penetration improved conditions. Conclusions This case shows the importance of measuring human immunodeficiency virus drug resistance in cerebrospinal fluid, which might differ from resistance detected in plasma samples and target effective antiretroviral therapy treatment accordingly.
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Affiliation(s)
- Didi Bang
- Department of Clinical Microbiology, Copenhagen University Hospital, Amager and Hvidovre, Copenhagen, Denmark. .,Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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16
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Espenhain L, Funk T, Overvad M, Edslev SM, Fonager J, Ingham AC, Rasmussen M, Madsen SL, Espersen CH, Sieber RN, Stegger M, Gunalan V, Wilkowski B, Larsen NB, Legarth R, Cohen AS, Nielsen F, Lam JUH, Lavik KE, Karakis M, Spiess K, Marving E, Nielsen C, Wiid Svarrer C, Bybjerg-Grauholm J, Olsen SS, Jensen A, Krause TG, Müller L. Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021. Euro Surveill 2021; 26. [PMID: 34915977 PMCID: PMC8728489 DOI: 10.2807/1560-7917.es.2021.26.50.2101146] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
By 9 December 2021, 785 SARS-CoV-2 Omicron variant cases have been identified in Denmark. Most cases were fully (76%) or booster-vaccinated (7.1%); 34 (4.3%) had a previous SARS-CoV-2 infection. The majority of cases with available information reported symptoms (509/666; 76%) and most were infected in Denmark (588/644; 91%). One in five cases cannot be linked to previous cases, indicating widespread community transmission. Nine cases have been hospitalised, one required intensive care and no deaths have been registered.
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Affiliation(s)
- Laura Espenhain
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tjede Funk
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Maria Overvad
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Sarah Leth Madsen
- COVID-19 tracing Unit, Danish Patient Safety Authority, Copenhagen, Denmark
| | | | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Bartlomiej Wilkowski
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | | | - Rebecca Legarth
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Finn Nielsen
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Janni Uyen Hoa Lam
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Kjetil Erdogan Lavik
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Marianne Karakis
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Katja Spiess
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ellinor Marving
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Nielsen
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Christina Wiid Svarrer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Stefan Schytte Olsen
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Jensen
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra Grove Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Luise Müller
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
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17
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Lyngse FP, Mølbak K, Skov RL, Christiansen LE, Mortensen LH, Albertsen M, Møller CH, Krause TG, Rasmussen M, Michaelsen TY, Voldstedlund M, Fonager J, Steenhard N, Kirkeby CT. Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load. Nat Commun 2021; 12:7251. [PMID: 34903718 PMCID: PMC8669007 DOI: 10.1038/s41467-021-27202-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023] Open
Abstract
New lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and risk factors, such as age of primary case and viral load remains poorly understood. Here, we used comprehensive administrative data from Denmark, comprising the full population (January 11 to February 7, 2021), to estimate household transmissibility. This study included 5,241 households with primary cases; 808 were infected with lineage B.1.1.7 and 4,433 with other lineages. Here, we report an attack rate of 38% in households with a primary case infected with B.1.1.7 and 27% in households with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.
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Affiliation(s)
- Frederik Plesner Lyngse
- Department of Economics & Center for Economic Behaviour and Inequality, University of Copenhagen, Copenhagen, Denmark.
- Danish Ministry of Health, Copenhagen, Denmark.
- Statens Serum Institut, Copenhagen, Denmark.
| | - Kåre Mølbak
- Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Laust Hvas Mortensen
- Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | | | | | | | | | | | | | - Carsten Thure Kirkeby
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Lassaunière R, Polacek C, Fonager J, Bennedbæk M, Boding L, Rasmussen M, Fomsgaard A. Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021. Euro Surveill 2021; 26. [PMID: 34886943 PMCID: PMC8662802 DOI: 10.2807/1560-7917.es.2021.26.49.2101059] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Several factors may account for the recent increased spread of the SARS-CoV-2 Delta sub-lineage AY.4.2 in the United Kingdom, Romania, Poland, and Denmark. We evaluated the sensitivity of AY.4.2 to neutralisation by sera from 30 Comirnaty (BNT162b2 mRNA) vaccine recipients in Denmark in November 2021. AY.4.2 neutralisation was comparable to other circulating Delta lineages or sub-lineages. Conversely, the less prevalent B.1.617.2 with E484K showed a significant more than 4-fold reduction in neutralisation that warrants surveillance of strains with the acquired E484K mutation.
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Affiliation(s)
- Ria Lassaunière
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Boding
- Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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19
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van Wijhe M, Fischer TK, Fonager J. Identification of risk factors associated with national transmission and late presentation of HIV-1, Denmark, 2009 to 2017. Euro Surveill 2021; 26. [PMID: 34823639 PMCID: PMC8619873 DOI: 10.2807/1560-7917.es.2021.26.47.2002008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BackgroundDespite availability of pre-exposure prophylaxis (PrEP), the incidence of HIV-1 in Europe remained stable the past decade. Reduction of new HIV-1 infections requires more knowledge about the profiles of high-risk transmitters and late presenters (LP).AimWe aimed to investigate risk factors associated with HIV-1 transmission clusters and late presentation with HIV-1 in Denmark.MethodsBlood samples and epidemiological information were collected from newly diagnosed HIV-1 patients between 2009 and 2017. We genotyped pol genes and performed phylogenetic analyses to identify clusters. Risk factors for clustering and LP were investigated with partial proportional odds and logistic regression. Covariates included transmission mode, HIV-1 subtype, age, origin and cluster activity.ResultsWe included 1,040 individuals in the analysis, 59.6% identified with subtype B and 48.4% in a cluster. Risk factors for clustering included Danish origin (odds ratio (OR): 2.95; 95% confidence interval (CI): 2.21-3.96), non-LP (OR: 1.44; 95% CI: 1.12-1.86), and men who have sex with men (MSM). Increasing age and non-B subtype infection decreased risk (OR: 0.69; 95% CI: 0.50-0.94). Risk for late presentation was lower for active clusters (OR: 0.60; 95% CI: 0.44-0.82) and Danish origin (OR: 0.43; 95% CI: 0.27-0.67). Non-Danish MSM had a lower risk than non-Danish heterosexuals (OR: 0.34; 95% CI: 0.21-0.55).ConclusionHIV-1 transmission in Denmark is driven by early diagnosed, young, subtype B infected MSM. These may benefit most from PrEP. Non-Danish heterosexual HIV-1 patients could benefit from improved communication to achieve earlier diagnosis and treatment.
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Affiliation(s)
- Maarten van Wijhe
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Virus Research & Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Department of Research, University hospital of Nordsjælland, Hillerød, Denmark.,Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research & Development Laboratory, Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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20
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Rasmussen TB, Fonager J, Jørgensen CS, Lassaunière R, Hammer AS, Quaade ML, Boklund A, Lohse L, Strandbygaard B, Rasmussen M, Michaelsen TY, Mortensen S, Fomsgaard A, Belsham GJ, Bøtner A. Infection, recovery and re-infection of farmed mink with SARS-CoV-2. PLoS Pathog 2021; 17:e1010068. [PMID: 34780574 PMCID: PMC8629378 DOI: 10.1371/journal.ppat.1010068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/29/2021] [Accepted: 10/27/2021] [Indexed: 11/19/2022] Open
Abstract
Mink, on a farm with about 15,000 animals, became infected with SARS-CoV-2. Over 75% of tested animals were positive for SARS-CoV-2 RNA in throat swabs and 100% of tested animals were seropositive. The virus responsible had a deletion of nucleotides encoding residues H69 and V70 within the spike protein gene as well as the A22920T mutation, resulting in the Y453F substitution within this protein, seen previously in mink. The infected mink recovered and after free-testing of 300 mink (a level giving 93% confidence of detecting a 1% prevalence), the animals remained seropositive. During further follow-up studies, after a period of more than 2 months without any virus detection, over 75% of tested animals again scored positive for SARS-CoV-2 RNA. Whole genome sequencing showed that the viruses circulating during this re-infection were most closely related to those identified in the first outbreak on this farm but additional sequence changes had occurred. Animals had much higher levels of anti-SARS-CoV-2 antibodies in serum samples after the second round of infection than at free-testing or during recovery from initial infection, consistent with a boosted immune response. Thus, it was concluded that following recovery from an initial infection, seropositive mink were readily re-infected by SARS-CoV-2.
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Affiliation(s)
- Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Jannik Fonager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Charlotte Sværke Jørgensen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Ria Lassaunière
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Michelle Lauge Quaade
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Anette Boklund
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Louise Lohse
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Bertel Strandbygaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Morten Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | | | - Sten Mortensen
- Danish Veterinary and Food Administration, Glostrup, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen S, Denmark
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail: (GJB); (AB)
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail: (GJB); (AB)
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21
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Bager P, Wohlfahrt J, Fonager J, Rasmussen M, Albertsen M, Michaelsen TY, Møller CH, Ethelberg S, Legarth R, Button MSF, Gubbels S, Voldstedlund M, Mølbak K, Skov RL, Fomsgaard A, Krause TG. Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study. Lancet Infect Dis 2021; 21:1507-1517. [PMID: 34171231 PMCID: PMC8219488 DOI: 10.1016/s1473-3099(21)00290-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND The more infectious SARS-CoV-2 lineage B.1.1.7 rapidly spread in Europe after December, 2020, and a concern that B.1.1.7 could cause more severe disease has been raised. Taking advantage of Denmark's high RT-PCR testing and whole genome sequencing capacities, we used national health register data to assess the risk of COVID-19 hospitalisation in individuals infected with B.1.1.7 compared with those with other SARS-CoV-2 lineages. METHODS We did an observational cohort study of all SARS-CoV-2-positive cases confirmed by RT-PCR in Denmark, sampled between Jan 1 and March 24, 2021, with 14 days of follow-up for COVID-19 hospitalisation. Cases were identified in the national COVID-19 surveillance system database, which includes data from the Danish Microbiology Database (RT-PCR test results), the Danish COVID-19 Genome Consortium, the National Patient Registry, the Civil Registration System, as well as other nationwide registers. Among all cases, COVID-19 hospitalisation was defined as first admission lasting longer than 12 h within 14 days of a sample with a positive RT-PCR result. The study population and main analysis were restricted to the proportion of cases with viral genome data. We calculated the risk ratio (RR) of admission according to infection with B.1.1.7 versus other co-existing lineages with a Poisson regression model with robust SEs, adjusted a priori for sex, age, calendar time, region, and comorbidities. The contribution of each covariate to confounding of the crude RR was evaluated afterwards by a stepwise forward inclusion. FINDINGS Between Jan 1 and March 24, 2021, 50 958 individuals with a positive SARS-CoV-2 test and at least 14 days of follow-up for hospitalisation were identified; 30 572 (60·0%) had genome data, of whom 10 544 (34·5%) were infected with B.1.1.7. 1944 (6·4%) individuals had a COVID-19 hospitalisation and of these, 571 (29·4%) had a B.1.1.7 infection and 1373 (70·6%) had an infection with other SARS-CoV-2 lineages. Although the overall number of hospitalisations decreased during the study period, the proportion of individuals infected with B.1.1.7 increased from 3·5% to 92·1% per week. B.1.1.7 was associated with a crude RR of hospital admission of 0·79 (95% CI 0·72-0·87; p<0·0001) and an adjusted RR of 1·42 (95% CI 1·25-1·60; p<0·0001). The adjusted RR was increased in all strata of age and calendar period-the two covariates with the largest contribution to confounding of the crude RR. INTERPRETATION Infection with SARS-CoV-2 lineage B.1.1.7 was associated with an increased risk of hospitalisation compared with that of other lineages in an analysis adjusted for covariates. The overall effect on hospitalisations in Denmark was lessened due to a strict lockdown, but our findings could support hospital preparedness and modelling of the projected impact of the epidemic in countries with uncontrolled spread of B.1.1.7. FUNDING None.
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Affiliation(s)
- Peter Bager
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark; Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
| | - Jan Wohlfahrt
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Camilla Holten Møller
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Ethelberg
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rebecca Legarth
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Sophie Gubbels
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Marianne Voldstedlund
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Kåre Mølbak
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark; Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert Leo Skov
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra Grove Krause
- Division of Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
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22
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Lassaunière R, Fonager J, Rasmussen M, Frische A, Polacek C, Rasmussen TB, Lohse L, Belsham GJ, Underwood A, Winckelmann AA, Bollerup S, Bukh J, Weis N, Sækmose SG, Aagaard B, Alfaro-Núñez A, Mølbak K, Bøtner A, Fomsgaard A. In vitro Characterization of Fitness and Convalescent Antibody Neutralization of SARS-CoV-2 Cluster 5 Variant Emerging in Mink at Danish Farms. Front Microbiol 2021; 12:698944. [PMID: 34248922 PMCID: PMC8267889 DOI: 10.3389/fmicb.2021.698944] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 04/22/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
In addition to humans, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can transmit to animals that include hamsters, cats, dogs, mink, ferrets, tigers, lions, cynomolgus macaques, rhesus macaques, and treeshrew. Among these, mink are particularly susceptible. Indeed, 10 countries in Europe and North America reported SARS-CoV-2 infection among mink on fur farms. In Denmark, SARS-CoV-2 spread rapidly among mink farms and spilled-over back into humans, acquiring mutations/deletions with unknown consequences for virulence and antigenicity. Here we describe a mink-associated SARS-CoV-2 variant (Cluster 5) characterized by 11 amino acid substitutions and four amino acid deletions relative to Wuhan-Hu-1. Temporal virus titration, together with genomic and subgenomic viral RNA quantitation, demonstrated a modest in vitro fitness attenuation of the Cluster 5 virus in the Vero-E6 cell line. Potential alterations in antigenicity conferred by amino acid changes in the spike protein that include three substitutions (Y453F, I692V, and M1229I) and a loss of two amino acid residues 69 and 70 (ΔH69/V70), were evaluated in a virus microneutralization assay. Compared to a reference strain, the Cluster 5 variant showed reduced neutralization in a proportion of convalescent human COVID-19 samples. The findings underscore the need for active surveillance SARS-CoV-2 infection and virus evolution in susceptible animal hosts.
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Affiliation(s)
- Ria Lassaunière
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Frische
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Thomas Bruun Rasmussen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Lohse
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Underwood
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Anni Assing Winckelmann
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Signe Bollerup
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Bitten Aagaard
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Alonzo Alfaro-Núñez
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Kåre Mølbak
- Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Division of Infectious Diseases Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Anette Bøtner
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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23
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Høy Marbjerg L, Jacobsen C, Fonager J, Bøgelund C, Rasmussen M, Fomsgaard A, Banner J, Vorobieva Solholm Jensen V. Possible Involvement of Central Nervous System in COVID-19 and Sequence Variability of SARS-CoV-2 Revealed in Autopsy Tissue Samples: A Case Report. Clin Pathol 2021; 14:2632010X211006096. [PMID: 33855294 PMCID: PMC8013633 DOI: 10.1177/2632010x211006096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/25/2021] [Indexed: 11/16/2022]
Abstract
The case presented here illustrates that interdisciplinary teamwork can be essential for the understanding of the COVID-19 disease presentation and enlightening of the pathophysiology. A 60-year-old woman without any comorbidities, apart from overweight, was found dead in her apartment after 14 days of home isolation due to suspicion of COVID-19. A forensic autopsy was performed. This revealed severely condensed, almost airless, firm lungs, and the cause of death was severe acute respiratory distress syndrome-associated with COVID-19 (SARS-CoV-2). In addition, SARS-CoV-2 was detected with reverse transcription polymerase chain reaction (RT-PCR) in cerebrospinal fluid, lung tissue, and tracheal sample and specific antibodies for SARS-CoV-2 were detected in cerebrospinal fluid and serum. Subsequent sequencing of the SARS-CoV-2 virus showed variation in nucleotides at 3 sites between SARS-CoV-2 isolates recovered from the tracheal sample, cerebrospinal fluid, and tissues from both lungs, and phylogenetic analysis revealed that the spinal fluid sample differed the most from the other 3 samples. This case supports the hypothesis that SARS-CoV-2 may be neuroinvasive and cause central nervous system infection.
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Affiliation(s)
- Lis Høy Marbjerg
- Division of Infectious Disease Preparedness, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Christina Jacobsen
- Section of Forensic Pathology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jannik Fonager
- Division of Infectious Disease Preparedness, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Claus Bøgelund
- Section of Forensic Pathology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Division of Infectious Disease Preparedness, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Division of Infectious Disease Preparedness, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jytte Banner
- Section of Forensic Pathology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Veronika Vorobieva Solholm Jensen
- Division of Infectious Disease Preparedness, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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24
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Larsen HD, Fonager J, Lomholt FK, Dalby T, Benedetti G, Kristensen B, Urth TR, Rasmussen M, Lassaunière R, Rasmussen TB, Strandbygaard B, Lohse L, Chaine M, Møller KL, Berthelsen ASN, Nørgaard SK, Sönksen UW, Boklund AE, Hammer AS, Belsham GJ, Krause TG, Mortensen S, Bøtner A, Fomsgaard A, Mølbak K. Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020. ACTA ACUST UNITED AC 2021; 26. [PMID: 33541485 PMCID: PMC7863232 DOI: 10.2807/1560-7917.es.2021.26.5.210009] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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] [Indexed: 01/05/2023]
Abstract
In June–November 2020, SARS-CoV-2-infected mink were detected in 290 of 1,147 Danish mink farms. In North Denmark Region, 30% (324/1,092) of people found connected to mink farms tested SARS-CoV-2-PCR-positive and approximately 27% (95% confidence interval (CI): 25–30) of SARS-CoV-2-strains from humans in the community were mink-associated. Measures proved insufficient to mitigate spread. On 4 November, the government ordered culling of all Danish mink. Farmed mink constitute a potential virus reservoir challenging pandemic control.
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Affiliation(s)
| | | | | | - Tine Dalby
- Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anette Ella Boklund
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Sten Mortensen
- Department of Animal Health, Danish Veterinary and Food administration, Copenhagen, Denmark
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Statens Serum Institut, Copenhagen, Denmark
| | | | - Kåre Mølbak
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Statens Serum Institut, Copenhagen, Denmark
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25
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Hammer AS, Quaade ML, Rasmussen TB, Fonager J, Rasmussen M, Mundbjerg K, Lohse L, Strandbygaard B, Jørgensen CS, Alfaro-Núñez A, Rosenstierne MW, Boklund A, Halasa T, Fomsgaard A, Belsham GJ, Bøtner A. SARS-CoV-2 Transmission between Mink (Neovison vison) and Humans, Denmark. Emerg Infect Dis 2020; 27:547-551. [PMID: 33207152 PMCID: PMC7853580 DOI: 10.3201/eid2702.203794] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 has caused a pandemic in humans. Farmed mink (Neovison vison) are also susceptible. In Denmark, this virus has spread rapidly among farmed mink, resulting in some respiratory disease. Full-length virus genome sequencing revealed novel virus variants in mink. These variants subsequently appeared within the local human community.
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26
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van de Laar MJ, Bosman A, Pharris A, Andersson E, Assoumou L, Ay E, Bannert N, Bartmeyer B, Brady M, Chaix ML, Descamps D, Dauwe K, Fonager J, Hauser A, Lunar M, Mezei M, Neary M, Poljak M, van Sighem A, Verhofstede C, Amato-Gauci AJ, Broberg EK. Piloting a surveillance system for HIV drug resistance in the European Union. ACTA ACUST UNITED AC 2020; 24. [PMID: 31088600 PMCID: PMC6518967 DOI: 10.2807/1560-7917.es.2019.24.19.1800390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background A steady increase in HIV drug resistance (HIVDR) has been demonstrated globally in individuals initiating first-line antiretroviral therapy (ART). To support effective use of ART and prevent spread of HIVDR, monitoring is essential. Aim We piloted a surveillance system for transmitted HIVDR to assess the feasibility of implementation at the European level. Method All 31 countries in the European Union and European Economic Area were invited to retrospectively submit data on individuals newly diagnosed with HIV in 2015 who were tested for antiviral susceptibility before ART, either as case-based or as aggregate data. We used the Stanford HIV database algorithm to translate genetic sequences into levels of drug resistance. Results Nine countries participated, with six reporting case-based data on 1,680 individuals and four reporting aggregated data on 1,402 cases. Sequence data were available for 1,417 cases: 14.5% of individuals (n = 244) showed resistance to at least one antiretroviral drug. In case-based surveillance, the highest levels of transmitted HIVDR were observed for non-nucleoside reverse-transcriptase inhibitors (NNRTIs) with resistance detected in 8.6% (n = 145), followed by resistance to nucleoside reverse-transcriptase inhibitors (NRTI) (5.1%; n = 85) and protease inhibitors (2.0%; n = 34). Conclusion We conclude that standard reporting of HIVDR data was feasible in the participating countries. Legal barriers for data sharing, consensus on definitions and standardisation of interpretation algorithms should be clarified in the process of enhancing European-wide HIV surveillance with drug resistance information.
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Affiliation(s)
| | | | - Anastasia Pharris
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Emmi Andersson
- Department of Clinical Microbiology, Karolinska University Laboratory, Stockholm, Sweden.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lambert Assoumou
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Eva Ay
- National Public Health Institute, Department of Retroviruses, Budapest, Hungary
| | | | | | - Melissa Brady
- Health Service Executive (HSE), Health Protection Surveillance Centre, Dublin, Ireland
| | - Marie-Laure Chaix
- Paris Diderot University, Paris, France.,Laboratoire de Virologie, APHP, Saint Louis Hospital, INSERM UMR944, Paris, France
| | - Diane Descamps
- Laboratoire de Virologie, Bichat-Claude Bernard University Hospital, INSERM UMR_1137, Paris, France.,Paris Diderot University, Paris, France
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | | | - Maja Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maria Mezei
- National Public Health Institute, Department of Retroviruses, Budapest, Hungary
| | - Martha Neary
- University College Dublin (UCD), National Virus Reference Laboratory, Dublin, Ireland
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Chris Verhofstede
- Aids Reference Laboratory, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Eeva K Broberg
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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27
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Fonager J, Fischer TK. A2 Phylogenetic investigation of transmitted HIV-1 drug resistance mutations in Denmark, 2009–17. Virus Evol 2019. [PMCID: PMC6735854 DOI: 10.1093/ve/vez002.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Transmission of HIV-1 resistance mutations among therapy-naïve patients impairs the efficiency of antiretroviral therapy (ART). Therefore, genotypic resistance testing of patients is recommended at baseline, as this both allows for the selection of the correct ART regimen and for surveillance of transmitted drug resistance mutations (TDRM) among therapy naive HIV-1 patients. In Denmark, the occurrence of TDRM in newly diagnosed and therapy naïve HIV-1 patients is monitored through the SERO project. Here, we investigated if the prevalence of TDRM differed between patients within and outside of phylogenetically identified transmission clusters. Samples from 1,227 newly diagnosed HIV-1 patients were sent along with epidemiological information to the Virological Surveillance and Research group at Statens Serum Institut. HIV-1 RNA extraction, RT-PCR and Sanger sequencing of the pol gene was performed using an in-house assay. The sequences were analyzed using BioNumerics v. 6.6 and manually checked for the presence of mixed mutations and analyzed for mutations using the HIVDB 8.4 algorithm implemented at the Stanford database. Sequence alignments were performed in Mafft, and phylogenetic analysis was performed using Mega 6.0 using the Maximum likelihood general time reversible model with 100 bootstrap replicates. Clusters were identified with ClusterPicker at default settings (cluster support = 90%, genetic distance 4.5%). Active clusters contained newly diagnosed patients from the 2015 to 2017 period. HIV-1 sequences from 588 patients belonged to one of 154 clusters, and sequences from 639 patients did not belong to a cluster. Patients in clusters were significantly more likely to be men who have sex with men and subtype B and significantly less likely to be late presenters (Fisher’s test P < 0.05). The TDRM prevalence was significantly higher for patients outside of clusters than within clusters, 16.6 per cent versus 12.1 per cent, respectively (Fisher’s test P < 0.05); however, no significant differences were found in the TDRM prevalence between the 75 active and 79 inactive clusters, nor between small (<3 patients) and large (≥3 patients) clusters. E138A, V179D, and K103N were the three most prevalent TDRMs for both patient groups, whereas M41L differed between them. In Denmark, the TDRM prevalence is lower within clusters than outside, indicating that TDRM cases are either imported and/or belong to yet unidentified clusters.
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Affiliation(s)
- J Fonager
- Department of Microbiological Special Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - T K Fischer
- Department of Microbiological Special Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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28
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Fischer TK, Rasmussen LD, Fonager J. Taking gastro-surveillance into the 21st century. J Clin Virol 2019; 117:43-48. [PMID: 31176211 DOI: 10.1016/j.jcv.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/28/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Enteric viruses, particularly rotaviruses and noroviruses, are leading causes of gastroenteritis worldwide. Human rotaviruses are ubiquitous and globally almost every child has been infected by 3-5 years of age. Noroviruses affect people of all ages and is the leading cause of foodborne outbreaks. Rota- and noroviruses account for ˜40% and ˜17% of diarrhea-associated hospitalizations, and ˜200,000 deaths annually respectively, with most deaths occurring in developing countries. Two rotavirus vaccines have currently been implemented in ˜95 countries and several norovirus vaccine candidates are currently in development and/or clinical testing. Surveillance of enteric viruses is an important part of outbreak investigations as well as pre- and post-vaccine impact studies but is even in developed countries often limited to investigation of sporadic cases or comprehensive outbreaks. Conventional methods for enteric virus detection and subtyping relies on standard RT-PCR methods, supplemented with Sanger-sequencing. However, for viruses with even moderate mutationrates, PCR-based-typing of only limited parts of the virus genome is challenging and requires regular update of primers. Full-genomecharacterization technologies based on sequence independent methods based on next generation sequencing (NGS), have demonstrated great potential for enteric virus detection and/or typing in both clinical and environmental samples. However, cost-benefits must balance for such methods to be widely accepted for public health purposes. In Europe as also globally, routine use of NGS-methods for surveillance of enteric viruses is currently limited to few national public health laboratories. What important lessons can be learned from these and what is the future of NGS-based surveillance?
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Affiliation(s)
- Thea K Fischer
- Department of Clinical Research, Nordsjaellands Hospital, Hilleroed, Denmark; Departments of Infectious Diseases and Global Health, Clinical Institute, University of Southern Denmark, Denmark; National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
| | - Lasse D Rasmussen
- National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research & Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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29
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Abstract
This study describes the prevalence of human immunodeficiency virus (HIV) drug resistance mutations among 1,815 patients in Denmark from 2004 to 2016 and characterises transmission clusters. POL sequences were analysed for subtype, drug resistance mutations and phylogenetic relationship. The prevalence of surveillance drug resistance mutations (SDRM) was 6.7%, while the prevalence of drug resistance mutations (DRM) with a clinical impact was 12.3%. We identified 197 transmission clusters with 706 patients. Patients 40 years or older were less likely to be members of a transmission cluster and patients in transmission clusters were less likely to be infected abroad. The proportion of late presenters (LP) was lower in active compared with inactive clusters. Large active clusters consisted of more men who have sex with men (MSM), had members more frequently infected in Denmark and contained a significantly lower proportion of LP and significantly fewer patients with DRM than small active clusters. Subtyping demonstrated that the Danish HIV epidemic is gradually becoming more composed of non-B subtypes/circulating recombinant forms. This study shows that active HIV-1 transmission has become increasingly MSM-dominated and that the recent increase in SDRM and DRM prevalence is not associated with more sustained transmission within identified transmission networks or clusters.
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Affiliation(s)
- Andreas Petersen
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark,European Public Health Microbiology (EUPHEM) training programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Susan A Cowan
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Nielsen
- Infectious Disease Epidemiology & Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus & Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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30
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Redd AD, Helleberg M, Sievers M, Schmidt SD, Doria-Rose NA, Bruno D, Traeger S, Martens C, Fonager J, Kronborg G, Packman Z, Mascola JR, Porcella SF, Gerstoft J, Quinn TC. Limited anti-HIV neutralizing antibody breadth and potency before and after HIV superinfection in Danish men who have sex with men. Infect Dis (Lond) 2018; 51:56-61. [PMID: 30317905 DOI: 10.1080/23744235.2018.1500708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND The role of the anti-HIV neutralizing antibody response in protecting against HIV superinfection, and changes in neutralizing antibody potency and breadth after HIV superinfection have not been fully elucidated. This study examined the rate of HIV superinfection in men who have sex with men (MSM) also diagnosed with syphilis in Denmark, and the anti-HIV neutralizing antibody response in men who became superinfected. MATERIALS AND METHODS MSM enrolled in the Danish HIV cohort who acquired syphilis were examined longitudinally for HIV superinfection using a validated next-generation sequencing assay. HIV superinfection cases were matched 3:1 to controls, and neutralizing antibody responses before (cases/controls) and after (cases) HIV superinfection were determined using a 20-pseudovirus panel. RESULTS Four cases of HIV superinfection were identified from 95 MSM screened for a rate of HIV superinfection of 1.56/100 pys (95% CI = 0.43-4.01). Prior to HIV superinfection neutralizing antibody responses were low in breadth and potency, and did not differ between cases and controls (p = 1.0). In cases, neutralizing antibody responses increased modestly after HIV superinfection. CONCLUSIONS These data support the theory that the natural neutralizing antibody response to HIV infection may not be the controlling factor in protecting against a subsequent HIV challenge.
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Affiliation(s)
- Andrew D Redd
- a Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH , Bethesda , USA.,b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Marie Helleberg
- c Department of Infectious Diseases , Copenhagen University Hospital , Rigshospitalet , Denmark
| | - Matthew Sievers
- b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | | | | | - Daniel Bruno
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Shelby Traeger
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Craig Martens
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Jannik Fonager
- f Section for Virus Surveillance and Research, Department of Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness , Statens Serum Institut , Copenhagen , Denmark
| | - Gitte Kronborg
- g Department of Infectious Diseases , Copenhagen University Hospital , Hvidovre , Denmark
| | - Zoe Packman
- h Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - John R Mascola
- d Vaccine Research Center, NIAID, NIH , Bethesda , MD , USA
| | - Stephen F Porcella
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Jan Gerstoft
- c Department of Infectious Diseases , Copenhagen University Hospital , Rigshospitalet , Denmark
| | - Thomas C Quinn
- a Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH , Bethesda , USA.,b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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31
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Barnadas C, Schmidt DJ, Fischer TK, Fonager J. Molecular epidemiology of human adenovirus infections in Denmark, 2011-2016. J Clin Virol 2018; 104:16-22. [PMID: 29704734 PMCID: PMC7106356 DOI: 10.1016/j.jcv.2018.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 01/03/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Abstract
We developed new primers to improve genotyping of HAdV D. Six out of seven HAdV species from at least 13 HAdV types were identified. Young children (<5 years old) were more likely to be positive for HAdV. Co-infections with other gastrointestinal or respiratory viruses were common. A HAdV surveillance system is required to monitor circulating species and types.
Background Human adenoviruses (HAdVs) can cause respiratory tract infections, conjunctivitis, diarrhoea and outbreaks have been reported. However, little is known about the disease burden and the molecular epidemiology of HAdV. Objectives To retrospectively perform a molecular characterization of HAdV positive samples received at Statens Serum Institut during the period 2011–2016 and to compare this with demographic information, geographic location, sample collection date and type and co-infection with other viral pathogens. Study design 152 HAdV positive samples were genotyped by Sanger sequencing of a fragment of the hexon gene using published primers along with a newly developed primer set for enhanced genotyping of HAdV D. Phylogenetic analysis was used for genotyping and genotypes were compared with epidemiological information. In addition, HAdV burden and co-infection was evaluated for samples tested in laboratory analysis packages. Results Six out of seven HAdV species were identified and represented by 13 types. Young children (<5 years old) were more likely to be positive for HAdV and co-infections with other gastrointestinal or respiratory viruses were common. Possible outbreaks of ocular infections due to HAdV D could not be confirmed. Conclusion A diverse set of HAdV species were circulating in Denmark in the study period and although possible transmission clusters were identified, this could not be verified with current genotyping methods Young children were commonly affected by HAdV infection and co-infections with other viral pathogens were frequent suggesting a possible underestimation of the real HAdV burden.
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Affiliation(s)
- Céline Barnadas
- European Public Health Microbiology (EUPHEM) Training Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden; Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institute, Copenhagen, Denmark
| | - Dennis Jelsbak Schmidt
- Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institute, Copenhagen, Denmark
| | - Thea K Fischer
- Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institute, Copenhagen, Denmark; Department of Infectious Diseases and Centre for Global Health, University of Southern Denmark, Denmark
| | - Jannik Fonager
- Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institute, Copenhagen, Denmark.
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32
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Fonager J, Stegger M, Rasmussen LD, Poulsen MW, Rønn J, Andersen PS, Fischer TK. A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants. Sci Rep 2017; 7:813. [PMID: 28400558 PMCID: PMC5429772 DOI: 10.1038/s41598-017-00926-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 03/21/2017] [Indexed: 12/16/2022] Open
Abstract
Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.
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Affiliation(s)
- Jannik Fonager
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Mille Weismann Poulsen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Rønn
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thea Kølsen Fischer
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Infectious Diseases and Centre for Global health, Clinical Unit, University of Southern Denmark, Odense, Denmark
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Fougère A, Jackson AP, Bechtsi DP, Braks JAM, Annoura T, Fonager J, Spaccapelo R, Ramesar J, Chevalley-Maurel S, Klop O, van der Laan AMA, Tanke HJ, Kocken CHM, Pasini EM, Khan SM, Böhme U, van Ooij C, Otto TD, Janse CJ, Franke-Fayard B. Correction: Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole. PLoS Pathog 2017; 13:e1006128. [PMID: 28095481 PMCID: PMC5240906 DOI: 10.1371/journal.ppat.1006128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Fougère A, Jackson AP, Paraskevi Bechtsi D, Braks JAM, Annoura T, Fonager J, Spaccapelo R, Ramesar J, Chevalley-Maurel S, Klop O, van der Laan AMA, Tanke HJ, Kocken CHM, Pasini EM, Khan SM, Böhme U, van Ooij C, Otto TD, Janse CJ, Franke-Fayard B. Correction: Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole. PLoS Pathog 2016; 12:e1006107. [PMID: 27973555 PMCID: PMC5156361 DOI: 10.1371/journal.ppat.1006107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.ppat.1005917.].
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Fougère A, Jackson AP, Paraskevi Bechtsi D, Braks JAM, Annoura T, Fonager J, Spaccapelo R, Ramesar J, Chevalley-Maurel S, Klop O, van der Laan AMA, Tanke HJ, Kocken CHM, Pasini EM, Khan SM, Böhme U, van Ooij C, Otto TD, Janse CJ, Franke-Fayard B. Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole. PLoS Pathog 2016; 12:e1005917. [PMID: 27851824 PMCID: PMC5113031 DOI: 10.1371/journal.ppat.1005917] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/06/2016] [Indexed: 01/05/2023] Open
Abstract
Many variant proteins encoded by Plasmodium-specific multigene families are exported into red blood cells (RBC). P. falciparum-specific variant proteins encoded by the var, stevor and rifin multigene families are exported onto the surface of infected red blood cells (iRBC) and mediate interactions between iRBC and host cells resulting in tissue sequestration and rosetting. However, the precise function of most other Plasmodium multigene families encoding exported proteins is unknown. To understand the role of RBC-exported proteins of rodent malaria parasites (RMP) we analysed the expression and cellular location by fluorescent-tagging of members of the pir, fam-a and fam-b multigene families. Furthermore, we performed phylogenetic analyses of the fam-a and fam-b multigene families, which indicate that both families have a history of functional differentiation unique to RMP. We demonstrate for all three families that expression of family members in iRBC is not mutually exclusive. Most tagged proteins were transported into the iRBC cytoplasm but not onto the iRBC plasma membrane, indicating that they are unlikely to play a direct role in iRBC-host cell interactions. Unexpectedly, most family members are also expressed during the liver stage, where they are transported into the parasitophorous vacuole. This suggests that these protein families promote parasite development in both the liver and blood, either by supporting parasite development within hepatocytes and erythrocytes and/or by manipulating the host immune response. Indeed, in the case of Fam-A, which have a steroidogenic acute regulatory-related lipid transfer (START) domain, we found that several family members can transfer phosphatidylcholine in vitro. These observations indicate that these proteins may transport (host) phosphatidylcholine for membrane synthesis. This is the first demonstration of a biological function of any exported variant protein family of rodent malaria parasites. Malaria-parasites invade and multiply in hepatocytes and erythrocytes. The human parasite P. falciparum transports proteins encoded by multigene families onto the surface of erythrocytes, mediating interactions between infected red blood cells (iRBCs) and other host-cells and are thought to play a key role in parasite survival during blood-stage development. The function of other exported Plasmodium protein families remains largely unknown. We provide novel insights into expression and cellular location of proteins encoded by three large multigene families of rodent malaria parasites (Fam-a, Fam-b and PIR). Multiple members of the same family are expressed in a single iRBC, unlike P. falciparum PfEMP1 proteins where individual iRBCs express only a single member. Most proteins we examined are located in the RBC cytoplasm and are not transported onto the iRBC surface membrane, indicating that these proteins are unlikely to mediate interactions between iRBCs and host-cells. Unexpectedly, liver stages also express many of these proteins, where they locate to the vacuole surrounding the parasite inside the hepatocyte. In support of a role of these proteins for parasite growth within their host cells we provide evidence that Fam-A proteins have a role in uptake and transport of (host) phosphatidylcholine for parasite-membrane synthesis.
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Affiliation(s)
- Aurélie Fougère
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Experimental Medicine, University of Perugia, Italy
| | - Andrew P. Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UnitedKingdom
| | | | - Joanna A. M. Braks
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Takeshi Annoura
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Department of Parasitology, National Institute of Infectious Diseases (NIID), Tokyo, Japan
| | - Jannik Fonager
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Department of Microbiological Diagnostics and Virology, Statens Serum Institute, Copenhagen, Denmark
| | | | - Jai Ramesar
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Séverine Chevalley-Maurel
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Onny Klop
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | | | - Hans J. Tanke
- Department of Molecular Cell Biology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Erica M. Pasini
- Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Shahid M. Khan
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ulrike Böhme
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UnitedKingdom
| | - Christiaan van Ooij
- The Francis Crick Institute, Mill Hill Laboratory, Mill Hill, London, UnitedKingdom
| | - Thomas D. Otto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UnitedKingdom
| | - Chris J. Janse
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Blandine Franke-Fayard
- Leiden Malaria Research Group, Parasitology, Center of infectious Diseases, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- * E-mail:
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Fonager J, Rasmussen LD, Fischer TK. Letter to the editor: A norovirus intervariant GII.4 recombinant in Victoria, Australia, June 2016: the next epidemic variant? Reflections and a note of caution. ACTA ACUST UNITED AC 2016; 21:30372. [PMID: 27762209 PMCID: PMC5073193 DOI: 10.2807/1560-7917.es.2016.21.41.30372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jannik Fonager
- Virology Surveillance and Research Section, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, Medstrand P, Albert J. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol 2016; 2:vew010. [PMID: 27774303 PMCID: PMC4989887 DOI: 10.1093/ve/vew010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [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] [Indexed: 11/13/2022] Open
Abstract
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions.
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Affiliation(s)
- Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden; Nuffield Department of Medicine, University of Oxford, Oxford, UK; REGA Institute, Katholieke Universiteit, Leuven, Belgium
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Anne Audelin
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Skar
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
| | - Louise Bruun Jørgensen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Per Björkman
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jan Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Rasmussen LD, Fonager J, Knudsen LK, Andersen PHS, Rønn J, Poulsen MW, Franck KT, Fischer TK. Phylogenetic and epidemiological analysis of measles outbreaks in Denmark, 2013 to 2014. Euro Surveill 2015; 20:30027. [DOI: 10.2807/1560-7917.es.2015.20.39.30027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/22/2015] [Indexed: 11/20/2022] Open
Abstract
Despite the introduction of safe, effective vaccines decades ago and joint global public health efforts to eliminate measles, this vaccine-preventable disease continues to pose threats to children’s health worldwide. During 2013 and 2014, measles virus was introduced into Denmark through several independent importations. This resulted in a number of secondary cases (n = 7), with two clusters in 2013 and one in 2014. In total, there were 44 cases of measles. Most cases (n = 41) were laboratory confirmed by detection of measles virus genome by real-time reverse transcription (RT)-PCR and IgM antibodies. The viruses from confirmed cases were genotyped by sequencing. Only one genotype circulated each year, i.e. D8 and B3, respectively. Sequencing of measles virus from different clinical specimens from the same patients revealed that sequence variants of measles viruses might co-exist and co-transmit during an outbreak. The majority of the cases were unvaccinated (n = 27) or recipients of one dose of measles-mumps-rubella (MMR) vaccine (n = 7). In addition, two fully vaccinated adult cases were reported in 2014. We demonstrate the transmission of measles virus in a population in which the two-dose MMR vaccination coverage rate was 80% and how even vaccinated individuals may be at risk of contracting measles once transmission has been established.
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Affiliation(s)
- Lasse Dam Rasmussen
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Lisbet Krause Knudsen
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Jesper Rønn
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Thea Kølsen Fischer
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Centre for Global Health, University of Southern Denmark, Odense, Denmark
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Franck KT, Fonager J, Ersbøll AK, Böttiger B. Norovirus epidemiology in community and health care settings and association with patient age, Denmark. Emerg Infect Dis 2015; 20:1123-31. [PMID: 24960024 PMCID: PMC4073851 DOI: 10.3201/eid2007.130781] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Norovirus GII.4 predominated in patients ≥60 years of age and in health care settings. Norovirus (NoV) is a major cause of gastroenteritis. NoV genotype II.4 (GII.4) is the predominant genotype in health care settings but the reason for this finding is unknown. Stool samples containing isolates with a known NoV genotype from 2,109 patients in Denmark (patients consulting a general practitioner or outpatient clinic, inpatients, and patients from foodborne outbreaks) were used to determine genotype distribution in relation to age and setting. NoV GII.4 was more prevalent among inpatients than among patients in community settings or those who became infected during foodborne outbreaks. In community and health care settings, we found an association between infection with GII.4 and increasing age. Norovirus GII.4 predominated in patients ≥60 years of age and in health care settings. A larger proportion of children than adults were infected with NoV GII.3 or GII.P21. Susceptibility to NoV infection might depend on patient age and infecting NoV genotype. Cohort studies are warranted to test this hypothesis.
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Holzknecht BJ, Franck KT, Nielsen RT, Böttiger B, Fischer TK, Fonager J. Sequence analysis of the capsid gene during a genotype II.4 dominated norovirus season in one university hospital: identification of possible transmission routes. PLoS One 2015; 10:e0115331. [PMID: 25590635 PMCID: PMC4295850 DOI: 10.1371/journal.pone.0115331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/21/2014] [Indexed: 12/13/2022] Open
Abstract
Norovirus (NoV) is a leading cause of gastroenteritis and genotype II.4 (GII.4) is responsible for the majority of nosocomial NoV infections. Our objective was to examine whether sequencing of the capsid gene might be a useful tool for the hospital outbreak investigation to define possible transmission routes. All NoV positive samples submitted from one university hospital during the 2007/8 season were selected. Genotyping of selected samples by partial polymerase gene sequencing had shown that the majority belonged to the GII.4 variant Den Haag 2006b and had identical polymerase sequences. Sequences of the capsid gene (1412 nucleotides) were obtained from the first available sample from 55 patients. From six immunocompromised patients with persistent infections a second sample was also included. As a control for a point-source outbreak, five samples from a foodborne outbreak caused by the same GII.4 variant were analyzed. Forty-seven of the inpatients (85%) were infected with the GII.4 variant Den Haag 2006b. Phylogenetic analysis of the Den Haag 2006b sequences identified four distinct outbreaks in different departments and a fifth outbreak with possible inter-department spread. In addition, a more heterogeneous cluster with evidence of repeated introductions from the community, but also possible inter-department spread was observed. In all six patients with paired sequences, evidence for in vivo evolution of the virus was found. Capsid gene sequencing showed substantial sequence variation among NoV GII.4 variant Den Haag 2006b strains from one single institution during a nine months' period. This method proved useful to understand the local epidemiology and, when used promptly, has the potential to make infection control measures more targeted.
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Affiliation(s)
- Barbara Juliane Holzknecht
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - Kristina Træholt Franck
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Rikke Thoft Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital Herlev, Herlev, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Blenda Böttiger
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Malmö, Sweden
| | - Thea Kølsen Fischer
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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van Alphen LB, Dorléans F, Schultz AC, Fonager J, Ethelberg S, Dalgaard C, Adelhardt M, Engberg JH, Fischer TK, Lassen SG. The application of new molecular methods in the investigation of a waterborne outbreak of norovirus in Denmark, 2012. PLoS One 2014; 9:e105053. [PMID: 25222495 PMCID: PMC4164364 DOI: 10.1371/journal.pone.0105053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/19/2014] [Indexed: 01/15/2023] Open
Abstract
In December 2012, an outbreak of acute gastrointestinal illness occurred in a geographical distinct area in Denmark covering 368 households. A combined microbiological, epidemiological and environmental investigation was initiated to understand the outbreak magnitude, pathogen(s) and vehicle in order to control the outbreak. Norovirus GII.4 New Orleans 2009 variant was detected in 15 of 17 individual stool samples from 14 households. Norovirus genomic material from water samples was detected and quantified and sequencing of longer parts of the viral capsid region (>1000 nt) were applied to patient and water samples. All five purposely selected water samples tested positive for norovirus GII in levels up to 1.8×104 genomic units per 200 ml. Identical norovirus sequences were found in all 5 sequenced stool samples and 1 sequenced water sample, a second sequenced water sample showed 1 nt (<0.1%) difference. In a cohort study, including 256 participants, cases were defined as residents of the area experiencing diarrhoea or vomiting onset on 12–14 December 2012. We found an attack rate of 51%. Being a case was associated with drinking tap-water on 12–13 December (relative risk = 6.0, 95%CI: 1.6–22) and a dose-response relation for the mean glasses of tap-water consumed was observed. Environmental investigations suggested contamination from a sewage pipe to the drinking water due to fall in pressure during water supply system renovations. The combined microbiological, epidemiological and environmental investigations strongly indicates the outbreak was caused by norovirus contamination of the water supply system.
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Affiliation(s)
- Lieke B. van Alphen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- European Programme of Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- * E-mail:
| | - Frédérique Dorléans
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anna Charlotte Schultz
- National Food Institute, Division of Food Microbiology, Danish Technical University (DTU), Lyngby, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - Camilla Dalgaard
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Marianne Adelhardt
- Danish Health and Medicines Authority, Public Health Medical Officers East, Denmark
| | | | - Thea Kølsen Fischer
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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St-Martin G, Knudsen LK, Engsig FN, Panum I, Andersen PHS, Rønn J, Fonager J, Fischer TK. Mumps resurgence in Denmark. J Clin Virol 2014; 61:435-8. [PMID: 25218244 DOI: 10.1016/j.jcv.2014.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 05/27/2014] [Revised: 08/11/2014] [Accepted: 08/16/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND The past decade has witnessed a resurgence of parotitisvirus (mumps) in several countries where seemingly good mumps control otherwise had been achieved through vaccination. Recently detection of mumps has increased in Denmark. OBJECTIVES To describe the age-specific changes and time trends of parotitisvirus detection in Denmark over a 10 year period. STUDY DESIGN Retrospective cohort study based on national laboratory data for parotitisvirus typing surveillance and national epidemiology data for mumps reporting. RESULTS The parotitisvirus detection rate has increased almost 10 times during the past 10 years from an incidence <0.1 per 100,000 in 2003 to 0.96 per 100,000 in 2013. The age distribution has shifted from children to young adults, and most cases are unvaccinated (54%) or vaccinated once (41%). The increase is due mainly to the existence of cohorts with low MMR vaccine coverage. CONCLUSION Analysis of mumps surveillance data from Denmark documents that the incidence of mumps is increasing, and that the resurgence of parotitisvirus is primarily occurring among young Danish adults. Almost half of the infected clinical mumps cases had received the first dose of MMR.
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Affiliation(s)
- Gry St-Martin
- Section for Virus Surveillance and Research, Department for Microbiological Diagnostics and Virology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Lisbet Krause Knudsen
- Department of Infectious Disease Epidemiology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Frederik Neess Engsig
- Department for Microbiological Diagnostics and Virology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Inge Panum
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Peter H S Andersen
- Department of Infectious Disease Epidemiology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Jesper Rønn
- Section for Virus Surveillance and Research, Department for Microbiological Diagnostics and Virology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Jannik Fonager
- Section for Virus Surveillance and Research, Department for Microbiological Diagnostics and Virology, Statens Serum Institut SSI, Copenhagen, Denmark
| | - Thea Kølsen Fischer
- Section for Virus Surveillance and Research, Department for Microbiological Diagnostics and Virology, Statens Serum Institut SSI, Copenhagen, Denmark.
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Franck KT, Lisby M, Fonager J, Schultz AC, Böttiger B, Villif A, Absalonsen H, Ethelberg S. Sources of Calicivirus contamination in foodborne outbreaks in Denmark, 2005-2011--the role of the asymptomatic food handler. J Infect Dis 2014; 211:563-70. [PMID: 25156563 DOI: 10.1093/infdis/jiu479] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Norovirus (NoV) is the predominant cause of foodborne disease outbreaks. Virus contamination may occur during all steps of food processing, from production to preparation and serving. The relative importance of these different routes of contamination is unknown. METHODS The purpose of this study was to estimate the proportions of outbreaks caused by asymptomatic and symptomatic food handlers (FHs). Reports of foodborne NoV and sapovirus outbreaks (n=191) that occurred over a 7-year period were extracted, reviewed, and categorized according to the available evidence for source of contamination. RESULTS In 64 (34%) of the outbreaks, contamination from FHs took place during preparation or serving of food. In the majority of these outbreaks (n=41; 64%), the FHs were asymptomatic during food handling. Some had been in contact with ill household members before handling the food and remained asymptomatic; others developed symptoms shortly after or were post-symptomatic. In 51 (27%) of the outbreaks, contamination occurred during production of the food, and in 55 (29%) of the outbreaks, contamination had supposedly occurred after serving a guest at a self-serve buffet. CONCLUSIONS Guidelines regarding exclusion of FHs where household members suffer from gastroenteritis could limit the number of outbreaks.
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Affiliation(s)
- Kristina T Franck
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen Research Unit for Clinical Microbiology, University of Southern Denmark, Odense
| | - Morten Lisby
- Danish Veterinary and Food Administration, Glostrup
| | - Jannik Fonager
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen
| | - Anna C Schultz
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Blenda Böttiger
- Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen Medical Microbiology, Lund University, Malmö, Sweden
| | | | | | - Steen Ethelberg
- Infectious Diseases Epidemiology, Statens Serum Institut, Copenhagen, Denmark
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Abstract
We report here new recombinants between the norovirus II.4 Sydney 2012 and the II.4 New Orleans 2009 variants. This demonstrates that the II.4 Sydney 2012 variant is undergoing further diversification and suggests a potential for rapid evolution. We also provide primers, which allow the amplification and sequencing of both the current New Orleans 2009 and Sydney 2012 variants and the new II.4 New Orleans 2009/II.4 Sydney 2012 recombinants for more accurate surveillance and transmission tracking.
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Affiliation(s)
- J Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
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Fonager J, Hindbæk LS, Fischer TK. Rapid emergence and antigenic diversification of the norovirus 2012 Sydney variant in Denmark, October to December, 2012. Euro Surveill 2013; 18:20413. [PMID: 23470017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Affiliation(s)
- J Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
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Fonager J, Hindbæk LS, Fischer TK. Rapid emergence and antigenic diversification of the norovirus 2012 Sydney variant in Denmark, October to December, 2012. Euro Surveill 2013. [DOI: 10.2807/ese.18.09.20413-en] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The norovirus (NoV) season in Denmark in late 2012 was characterised by an increase in the number of NoV infections caused mainly by the 2012 Sydney variant, but also by the 2009 New Orleans variant. Analysis of approximately 85% of the capsid gene from 10 Sydney 2012 and 9 New Orleans 2009 isolates showed rapid antigenic diversification of the Sydney 2012 variant shortly after its emergence. We also present new primers useful for transmission tracking.
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Affiliation(s)
- J Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - L S Hindbæk
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - T K Fischer
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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van Beek J, Ambert-Balay K, Botteldoorn N, Eden JS, Fonager J, Hewitt J, Iritani N, Kroneman A, Vennema H, Vinjé J, White PA, Koopmans M. Indications for worldwide increased norovirus activity associated with emergence of a new variant of genotype II.4, late 2012. Euro Surveill 2013; 18:8-9. [PMID: 23305715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Globally, surveillance systems showed an increasein norovirus activity in late 2012. Molecular datashared through the NoroNet network suggest thatthis increase is related to the emergence of a newnorovirus genotype II.4 variant, termed Sydney 2012.Healthcare institutions are advised to be prepared fora severe norovirus season.
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Affiliation(s)
- J van Beek
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
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van Beek J, Ambert-Balay K, Botteldoorn N, Eden JS, Fonager J, Hewitt J, Iritani N, Kroneman A, Vennema H, Vinjé J, White PA, Koopmans M, on behalf of NoroNet C. Indications for worldwide increased norovirus activity associated with emergence of a new variant of genotype II.4, late 2012. Euro Surveill 2013. [DOI: 10.2807/ese.18.01.20345-en] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Globally, surveillance systems showed an increase in norovirus activity in late 2012. Molecular data shared through the NoroNet network suggest that this increase is related to the emergence of a new norovirus genotype II.4 variant, termed Sydney 2012. Healthcare institutions are advised to be prepared for a severe norovirus season.
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Affiliation(s)
- J van Beek
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - K Ambert-Balay
- National Reference Centre for Enteric Viruses, Dijon, France
| | - N Botteldoorn
- Scientific Institute of Public Health, Brussels, Belgium
| | - J S Eden
- University of New South Wales, Sydney, Australia
| | - J Fonager
- Statens Serum Institut, Copenhagen, Denmark
| | - J Hewitt
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - N Iritani
- Osaka City Institute of Public Health and Environmental Sciences, Osaka, Japan
| | - A Kroneman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - H Vennema
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - J Vinjé
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - P A White
- University of New South Wales, Sydney, Australia
| | - M Koopmans
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Pasini EM, Braks JA, Fonager J, Klop O, Aime E, Spaccapelo R, Otto TD, Berriman M, Hiss JA, Thomas AW, Mann M, Janse CJ, Kocken CHM, Franke-Fayard B. Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins. Mol Cell Proteomics 2012. [PMID: 23197789 PMCID: PMC3567864 DOI: 10.1074/mcp.m112.021238] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Malaria parasites actively remodel the infected red blood cell (irbc) by exporting proteins into the host cell cytoplasm. The human parasite Plasmodium falciparum exports particularly large numbers of proteins, including proteins that establish a vesicular network allowing the trafficking of proteins onto the surface of irbcs that are responsible for tissue sequestration. Like P. falciparum, the rodent parasite P. berghei ANKA sequesters via irbc interactions with the host receptor CD36. We have applied proteomic, genomic, and reverse-genetic approaches to identify P. berghei proteins potentially involved in the transport of proteins to the irbc surface. A comparative proteomics analysis of P. berghei non-sequestering and sequestering parasites was used to determine changes in the irbc membrane associated with sequestration. Subsequent tagging experiments identified 13 proteins (Plasmodium export element (PEXEL)-positive as well as PEXEL-negative) that are exported into the irbc cytoplasm and have distinct localization patterns: a dispersed and/or patchy distribution, a punctate vesicle-like pattern in the cytoplasm, or a distinct location at the irbc membrane. Members of the PEXEL-negative BIR and PEXEL-positive Pb-fam-3 show a dispersed localization in the irbc cytoplasm, but not at the irbc surface. Two of the identified exported proteins are transported to the irbc membrane and were named erythrocyte membrane associated proteins. EMAP1 is a member of the PEXEL-negative Pb-fam-1 family, and EMAP2 is a PEXEL-positive protein encoded by a single copy gene; neither protein plays a direct role in sequestration. Our observations clearly indicate that P. berghei traffics a diverse range of proteins to different cellular locations via mechanisms that are analogous to those employed by P. falciparum. This information can be exploited to generate transgenic humanized rodent P. berghei parasites expressing chimeric P. berghei/P. falciparum proteins on the surface of rodent irbc, thereby opening new avenues for in vivo screening adjunct therapies that block sequestration.
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Affiliation(s)
- Erica M Pasini
- Biomedical Primate Research Centre, 2288 GJ Rijswijk, The Netherlands
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Fonager J, Pasini EM, Braks JAM, Klop O, Ramesar J, Remarque EJ, Vroegrijk IOCM, van Duinen SG, Thomas AW, Khan SM, Mann M, Kocken CHM, Janse CJ, Franke-Fayard BMD. Reduced CD36-dependent tissue sequestration of Plasmodium-infected erythrocytes is detrimental to malaria parasite growth in vivo. ACTA ACUST UNITED AC 2011; 209:93-107. [PMID: 22184632 PMCID: PMC3260870 DOI: 10.1084/jem.20110762] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Adherence of parasite-infected red blood cells (irbc) to the vascular endothelium of organs plays a key role in the pathogenesis of Plasmodium falciparum malaria. The prevailing hypothesis of why irbc adhere and sequester in tissues is that this acts as a mechanism of avoiding spleen-mediated clearance. Irbc of the rodent parasite Plasmodium berghei ANKA sequester in a fashion analogous to P. falciparum by adhering to the host receptor CD36. To experimentally determine the significance of sequestration for parasite growth, we generated a mutant P. berghei ANKA parasite with a reduced CD36-mediated adherence. Although the cognate parasite ligand binding to CD36 is unknown, we show that nonsequestering parasites have reduced growth and we provide evidence that in addition to avoiding spleen removal, other factors related to CD36-mediated sequestration are beneficial for parasite growth. These results reveal for the first time the importance of sequestration to a malaria infection, with implications for the development of strategies aimed at reducing pathology by inhibiting tissue sequestration.
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Affiliation(s)
- Jannik Fonager
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
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