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Jensen CB, Schneider UV, Madsen TV, Nielsen XC, Ma CMG, Severinsen JK, Hoegh AM, Botnen AB, Trebbien R, Lisby JG. Evaluation of the analytical and clinical performance of two RT-PCR based point-of-care tests; Cepheid Xpert® Xpress CoV-2/Flu/RSV plus and SD BioSensor STANDARD™ M10 Flu/RSV/SARS-CoV-2. J Clin Virol 2024; 172:105674. [PMID: 38643722 DOI: 10.1016/j.jcv.2024.105674] [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: 01/17/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Rapid and accurate detection of viral respiratory infections is important for infection control measures. This study compares the analytical and clinical performance of the Xpert® Xpress CoV-2/Flu/RSV plus test ("Xpert", Cepheid) and the STANDARD™ M10 Flu/RSV/SARS-CoV-2 test ("M10", SD Biosensor). Both tests are quadruplex RT-PCR assays for rapid diagnosis of SARS-CoV-2, influenza A/B and RSV. STUDY DESIGN Analytical sensitivities were determined by limit of detection for SARS-CoV-2, influenza A, influenza B and RSV, respectively. Additionally, the clinical performance of the Xpert and the M10 tests was evaluated against standard-of-care RT-PCR by testing of 492 clinical specimens. RESULTS The analytical sensitivities for Xpert versus M10 test was 10, 50, 50 and 300 versus 300, 200, 800 and 1500 copies/mL for SARS-CoV-2, influenza A, influenza B and RSV, respectively. Clinical sensitivity for the Xpert test was superior across all four pathogens compared to the M10 test. Xpert showed clinical sensitivity of 100 % in all Ct-ranges for all four pathogens whereas M10 showed clinical sensitivity of 100 % in the 25-30 Ct-range, 84-100 % in the 30-35 Ct-range and 47-67 % in the >35 Ct-range across the four pathogens. Translating into real-life clinical sensitivity, the Xpert would detect 100 % of all four pathogens, whereas M10 would detect 92.1, 92.4, 84.8 and 94.7 % for SARS-CoV-2, influenza A, influenza B and RSV. CONCLUSION This study demonstrates improved analytical and clinical performance of Xpert Xpress CoV-2/Flu/RSV plus compared to STANDARD M10 Flu/RSV/SARS-CoV-2, which is important for ensuring accuracy of diagnosis at all stages of a respiratory infection.
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Affiliation(s)
- Christel Barker Jensen
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Uffe Vest Schneider
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Tina Vasehus Madsen
- Zealand University Hospital Slagelse, Department of Clinical Microbiology, Ingemannsvej 46, 4200 Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- Zealand University Hospital Slagelse, Department of Clinical Microbiology, Ingemannsvej 46, 4200 Slagelse, Denmark
| | - Chih Man German Ma
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Jette Krogh Severinsen
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Anne Mette Hoegh
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Amanda Bolt Botnen
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Ramona Trebbien
- Statens Serum Institut, Department of Virus & Microbiological Special Diagnostics, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Jan Gorm Lisby
- Copenhagen University Hospital Hvidovre, Department of Clinical Microbiology, Kettegaard Allé 30, 2650 Hvidovre, Denmark.
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Emborg HD, Bolt Botnen A, Nielsen J, Vestergaard LS, Lomholt FK, Munkstrup C, Møller KL, Kjelsø C, Rasmussen SH, Trebbien R. Age-dependent influenza infection patterns and subtype circulation in Denmark, in seasons 2015/16 to 2021/22. Euro Surveill 2024; 29:2300263. [PMID: 38275020 PMCID: PMC10986648 DOI: 10.2807/1560-7917.es.2024.29.4.2300263] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/19/2023] [Indexed: 01/27/2024] Open
Abstract
BackgroundInfluenza was almost absent for 2 years following the implementation of strict public health measures to prevent the spread of SARS-CoV-2. The consequence of this on infections in different age groups is not yet known.AimTo describe the age groups infected with the influenza virus in 2021/22, the first post-pandemic influenza season in Denmark, compared with the previous six seasons, and subtypes circulating therein.MethodsInfection and hospitalisation incidences per season and age group were estimated from data in Danish registries. Influenza virus subtypes and lineages were available from samples sent to the National Influenza Centre at Statens Serum Institut.ResultsTest incidence followed a similar pattern in all seasons, being highest in 0-1-year-olds and individuals over 75 years, and lowest in 7-14-year-olds and young people 15 years to late twenties. When the influenza A virus subtypes A(H3N2) and A(H1N1)pdm09 co-circulated in seasons 2015/16 and 2017/18 to 2019/20, the proportion of A(H1N1)pdm09 was higher in 0-1-year-olds and lower in the over 85-year-olds compared with the overall proportion of A(H1N1)pdm09 in these seasons. The proportion of A(H3N2) was higher in the over 85 years age group compared with the overall proportion of A(H3N2). The 2016/17 and 2021/22 seasons were dominated by A(H3N2) but differed in age-specific trends, with the over 85 years age group initiating the 2016/17 season, while the 2021/22 season was initiated by the 15-25-year-olds, followed by 7-14-year-olds.ConclusionThe 2021/22 influenza season had a different age distribution compared with pre-COVID-19 pandemic seasons.
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Affiliation(s)
- Hanne-Dorthe Emborg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Denmark
| | - Amanda Bolt Botnen
- National Influenza Centre for WHO, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Denmark
| | - Jens Nielsen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Denmark
| | - Lasse S Vestergaard
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Denmark
| | | | - Charlotte Munkstrup
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Denmark
| | | | - Charlotte Kjelsø
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Denmark
| | | | - Ramona Trebbien
- National Influenza Centre for WHO, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Denmark
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3
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Kissling E, Maurel M, Emborg HD, Whitaker H, McMenamin J, Howard J, Trebbien R, Watson C, Findlay B, Pozo F, Bolt Botnen A, Harvey C, Rose A. Interim 2022/23 influenza vaccine effectiveness: six European studies, October 2022 to January 2023. Euro Surveill 2023; 28:2300116. [PMID: 37227299 PMCID: PMC10283457 DOI: 10.2807/1560-7917.es.2023.28.21.2300116] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/21/2023] [Indexed: 05/26/2023] Open
Abstract
BackgroundBetween October 2022 and January 2023, influenza A(H1N1)pdm09, A(H3N2) and B/Victoria viruses circulated in Europe with different influenza (sub)types dominating in different areas.AimTo provide interim 2022/23 influenza vaccine effectiveness (VE) estimates from six European studies, covering 16 countries in primary care, emergency care and hospital inpatient settings.MethodsAll studies used the test-negative design, but with differences in other study characteristics, such as data sources, patient selection, case definitions and included age groups. Overall and influenza (sub)type-specific VE was estimated for each study using logistic regression adjusted for potential confounders.ResultsThere were 20,477 influenza cases recruited across the six studies, of which 16,589 (81%) were influenza A. Among all ages and settings, VE against influenza A ranged from 27 to 44%. Against A(H1N1)pdm09 (all ages and settings), VE point estimates ranged from 28% to 46%, higher among children (< 18 years) at 49-77%. Against A(H3N2), overall VE ranged from 2% to 44%, also higher among children (62-70%). Against influenza B/Victoria, overall and age-specific VE were ≥ 50% (87-95% among children < 18 years).ConclusionsInterim results from six European studies during the 2022/23 influenza season indicate a ≥ 27% and ≥ 50% reduction in disease occurrence among all-age influenza vaccine recipients for influenza A and B, respectively, with higher reductions among children. Genetic virus characterisation results and end-of-season VE estimates will contribute to greater understanding of differences in influenza (sub)type-specific results across studies.
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Affiliation(s)
| | | | - Hanne-Dorthe Emborg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Ramona Trebbien
- Department of Virus and Microbiological Special diagnostics, National Influenza Center, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Francisco Pozo
- National Centre for Microbiology, National Influenza Reference Laboratory, WHO-National Influenza Centre, Institute of Health Carlos III, Madrid, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Institute of Health Carlos III, Madrid, Spain
| | - Amanda Bolt Botnen
- Department of Virus and Microbiological Special diagnostics, National Influenza Center, Statens Serum Institut, Copenhagen, Denmark
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Bolt Botnen A, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon 2023; 9:e12861. [PMID: 36699263 PMCID: PMC9868478 DOI: 10.1016/j.heliyon.2023.e12861] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
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Affiliation(s)
- Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Mads Bjørn Bjørnsen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
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5
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Jørgensen RL, Lerche CJ, Pedersen MS, Kirkby N, Botnen AB, Trebbien R, Nilsson-Møller S, Pinholt M, Nielsen ACY, Westh H, Lisby JG, Schneider UV. Emergence of circulating influenza A H3N2 viruses with genetic drift in the matrix gene: Be alert of false negative test results. APMIS 2022; 130:612-617. [PMID: 35836366 PMCID: PMC9544743 DOI: 10.1111/apm.13262] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022]
Abstract
In March 2022, we observed samples with a negative fluorescent signal (60.5%, n=43) for the influenza A matrix gene, and a stronger positive signal for subtype A(H3N2). Forty-three samples were positive in InfA (H3N2) (mean Cq 30.9, range 23.9-35.1) and 26 of the 43 samples were negative in InfA matrix (mean Cq 28.0, range 23.2-30.6). Our multiplex test is a laboratory developed four-target, four-color influenza A reverse-transcription PCR assay targeting the matrix gene, subtypes A(H3N2) and A(H1N1)pdm09. Several samples were negative when retested on commercial influenza Point-of-Care assays. As the matrix gene is a stand-alone target in most commercial diagnostic assays, we caution against false negative subtype A test results.
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Affiliation(s)
- Rikke Lind Jørgensen
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Christian Johann Lerche
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Martin Schou Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Nikolai Kirkby
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Ramona Trebbien
- National Influenza Center, Statens Serum Institut, Copenhagen, Denmark
| | - Stephen Nilsson-Møller
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Alex Christian Yde Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Denmark
| | - Jan Gorm Lisby
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Hvidovre, Denmark
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6
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Emborg HD, Vestergaard LS, Botnen AB, Nielsen J, Krause TG, Trebbien R. A late sharp increase in influenza detections and low interim vaccine effectiveness against the circulating A(H3N2) strain, Denmark, 2021/22 influenza season up to 25 March 2022. Euro Surveill 2022; 27. [PMID: 35426361 PMCID: PMC9012088 DOI: 10.2807/1560-7917.es.2022.27.15.2200278] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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] [Indexed: 01/29/2023] Open
Abstract
We estimated interim influenza A vaccine effectiveness (VE) following a late sharp rise in cases during an influenza A(H3N2)-dominated 2021/22 season, after lifting COVID-19 restrictions. In children aged 2–6 years offered a live attenuated influenza vaccine, adjusted VE was 62.7% (95% CI: 10.9–84.4) in hospitalised and 64.2% (95% CI: 50.5–74.1) in non-hospitalised children. In non-hospitalised patients aged 7–44 years, VE was 24.8% (95% CI: 12.8–35.2); VE was non-significant in remaining age groups and hospital/non-hospital settings.
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7
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Nyholm L, Koziol A, Marcos S, Botnen AB, Aizpurua O, Gopalakrishnan S, Limborg MT, Gilbert MTP, Alberdi A. Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research. iScience 2020; 23:101414. [PMID: 32777774 PMCID: PMC7416341 DOI: 10.1016/j.isci.2020.101414] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 04/08/2020] [Revised: 06/18/2020] [Accepted: 07/23/2020] [Indexed: 12/11/2022] Open
Abstract
From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.
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Affiliation(s)
- Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark.
| | - Adam Koziol
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Sofia Marcos
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen 1353, Denmark
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