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2. Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre

Author

Janssen, Reile, Cuypers, Lize, Laenen, Lies, Keyaerts, Els, Beuselinck, Kurt, Janssenswillen, Sunita, Slechten, Bram, Bode, Jannes, Wollants, Elke, Van Laethem, Kristel, Rector, Annabel, Bloemen, Mandy, Sijmons, Anke, de Schaetzen, Nathalie, Capron, Arnaud, Van Baelen, Kurt, Pascal, Thierry, Vermeiren, Céline, Bureau, Fabrice, Vandesompele, Jo, De Smet, Pieter, Uten, Wouter, Malonne, Hugues, Kerkhofs, Pierre, De Cock, Jo, Matheeussen, Veerle, Verhasselt, Bruno, Gillet, Laurent, Detry, Gautier, Bearzatto, Bertrand, Degosserie, Jonathan, Henin, Coralie, Pairoux, Gregor, Maes, Piet, Van Ranst, Marc, Lagrou, Katrien, Dequeker, Elisabeth, and André, Emmanuel

Published
2024
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5. Centralised Air Sampling From a Ventilation System for the Surveillance of Respiratory Pathogens.

Author

Happaerts, Michiel, Geenen, Caspar, Michiels, Jade, Gorissen, Sarah, Swinnen, Jens, Beuselinck, Kurt, Laenen, Lies, Raymenants, Joren, Lorent, Natalie, Ombelet, Sien, Keyaerts, Els, André, Emmanuel, and Yun, Geun Young

Subjects
AIR sampling, AIR conditioning, COMMUNICABLE diseases, RESPIRATORY organs, SCALABILITY, VENTILATION
Abstract

Background: The COVID‐19 pandemic has triggered a renewed interest in indoor air sampling for infectious disease surveillance. However, scalability is currently limited, as samples are usually collected in a single indoor space. An alternative is to place the device within a heating, ventilation, and air conditioning system (HVAC), but this approach has not been tested against room air sampling. Methods: In this observational study, we sampled the air in an indoor fitness centre for 2 or 6 h, simultaneously in three locations of the main exercise hall and in the return plenum of the HVAC system. Samples were collected twice weekly for 11 weeks. All samples were tested for 29 respiratory pathogens using PCR. We compared the ventilation system and exercise hall air with regard to the presence and quantity of pathogens. Findings: Samples collected in two locations in the exercise hall had a similar overall sensitivity to the HVAC sampler for detecting pathogens, while a third sampling location was associated with significantly lower sensitivity. Overall, the pathogen concentration was similar in the ventilation system and the exercise hall air (ratio: 1.0; 95% CI: 0.8–1.3). Interpretation: Our results show that air sampling within a ventilation system can have equal sensitivity for detecting respiratory pathogens, compared to room‐based sampling. Thus, placing samplers within central ventilation systems could increase the scalability of air sampling for infectious disease surveillance. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Author

de Vries, Jutte J.C., Brown, Julianne R., Fischer, Nicole, Sidorov, Igor A., Morfopoulou, Sofia, Huang, Jiabin, Munnink, Bas B. Oude, Sayiner, Arzu, Bulgurcu, Alihan, Rodriguez, Christophe, Gricourt, Guillaume, Keyaerts, Els, Beller, Leen, Bachofen, Claudia, Kubacki, Jakub, Cordey, Samuel, Laubscher, Florian, Schmitz, Dennis, Beer, Martin, Hoeper, Dirk, Huber, Michael, Kufner, Verena, Zaheri, Maryam, Lebrand, Aitana, Papa, Anna, van Boheemen, Sander, Kroes, Aloys C.M., Breuer, Judith, Lopez-Labrador, F. Xavier, and Claas, Eric C.J.

Published
2021
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7. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

Author

López-Labrador, F. Xavier, Brown, Julianne R., Fischer, Nicole, Harvala, Heli, Van Boheemen, Sander, Cinek, Ondrej, Sayiner, Arzu, Madsen, Tina Vasehus, Auvinen, Eeva, Kufner, Verena, Huber, Michael, Rodriguez, Christophe, Jonges, Marcel, Hönemann, Mario, Susi, Petri, Sousa, Hugo, Klapper, Paul E., Pérez-Cataluňa, Alba, Hernandez, Marta, Molenkamp, Richard, der Hoek, Lia van, Schuurman, Rob, Couto, Natacha, Leuzinger, Karoline, Simmonds, Peter, Beer, Martin, Höper, Dirk, Kamminga, Sergio, Feltkamp, Mariet C.W., Rodríguez-Díaz, Jesús, Keyaerts, Els, Nielsen, Xiaohui Chen, Puchhammer-Stöckl, Elisabeth, Kroes, Aloys C.M., Buesa, Javier, Breuer, Judy, Claas, Eric C.J., and de Vries, Jutte J.C.

Published
2021
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8. Baseline predictors of hospital length of stay in children with respiratory syncytial virus infection: A retrospective analysis of three prospective observational studies

Author

Makariadou, Elli, primary, Keyaerts, Els, additional, Proesmans, Marijke, additional, Rector, Annabel, additional, Kirman, Joanna, additional, Ingham, Tristram, additional, Jones, Bernadette, additional, Miyairi, Isao, additional, Shinjoh, Masayoshi, additional, Tetsuka, Noriyuki, additional, Ispas, Gabriela, additional, and Fleischhackl, Roman, additional

Published
2024
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10. Diagnostic accuracy of digital RNA quantification versus real-time PCR for the detection of respiratory syncytial virus in nasopharyngeal aspirates from children with acute respiratory infection

Author

Bouzas, Maiara L., Oliveira, Juliana R., Queiroz, Artur, Fukutani, Kiyoshi F., Barral, Aldina, Rector, Annabel, Wollants, Elke, Keyaerts, Els, Van der Gucht, Winke, Van Ranst, Marc, Beuselinck, Kurt, de Oliveira, Camila I., Van Weyenbergh, Johan, and Nascimento-Carvalho, Cristiana M.

Published
2018
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12. Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks.

Author

Cuypers, Lize, Keyaerts, Els, Hong, Samuel Leandro, Gorissen, Sarah, Menezes, Soraya Maria, Starick, Marick, Van Elslande, Jan, Weemaes, Matthias, Wawina-Bokalanga, Tony, Marti-Carreras, Joan, Vanmechelen, Bert, Van Holm, Bram, Bloemen, Mandy, Dogne, Jean-Michel, Dufrasne, François, Durkin, Keith, Ruelle, Jean, De Mendonça, Ricardo, Wollants, Elke, Vermeersch, Pieter, COVID-19 Genomics Belgium Consortium, Boulouffe, Caroline, Djiena, Achille, Broucke, Caroline, Catry, Boudewijn, Lagrou, Katrien, Van Ranst, Marc, Neyts, Johan, Baele, Guy, Maes, Piet, André, Emmanuel, Dellicour, Simon, Van Weyenbergh, Johan, Cuypers, Lize, Keyaerts, Els, Hong, Samuel Leandro, Gorissen, Sarah, Menezes, Soraya Maria, Starick, Marick, Van Elslande, Jan, Weemaes, Matthias, Wawina-Bokalanga, Tony, Marti-Carreras, Joan, Vanmechelen, Bert, Van Holm, Bram, Bloemen, Mandy, Dogne, Jean-Michel, Dufrasne, François, Durkin, Keith, Ruelle, Jean, De Mendonça, Ricardo, Wollants, Elke, Vermeersch, Pieter, COVID-19 Genomics Belgium Consortium, Boulouffe, Caroline, Djiena, Achille, Broucke, Caroline, Catry, Boudewijn, Lagrou, Katrien, Van Ranst, Marc, Neyts, Johan, Baele, Guy, Maes, Piet, André, Emmanuel, Dellicour, Simon, and Van Weyenbergh, Johan

Abstract

Coronavirus Disease 2019 (COVID-19) vaccination has resulted in excellent protection against fatal disease, including in older adults. However, risk factors for post-vaccination fatal COVID-19 are largely unknown. We comprehensively studied three large nursing home outbreaks (20-35% fatal cases among residents) by combining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aerosol monitoring, whole-genome phylogenetic analysis and immunovirological profiling of nasal mucosa by digital nCounter transcriptomics. Phylogenetic investigations indicated that each outbreak stemmed from a single introduction event, although with different variants (Delta, Gamma and Mu). SARS-CoV-2 was detected in aerosol samples up to 52 d after the initial infection. Combining demographic, immune and viral parameters, the best predictive models for mortality comprised IFNB1 or age, viral ORF7a and ACE2 receptor transcripts. Comparison with published pre-vaccine fatal COVID-19 transcriptomic and genomic signatures uncovered a unique IRF3 low/IRF7 high immune signature in post-vaccine fatal COVID-19 outbreaks. A multi-layered strategy, including environmental sampling, immunomonitoring and early antiviral therapy, should be considered to prevent post-vaccination COVID-19 mortality in nursing homes., 0, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2023

14. Severity of COVID-19 among Hospitalized Patients: Omicron Remains a Severe Threat for Immunocompromised Hosts

Author

Nevejan, Louis, primary, Ombelet, Sien, additional, Laenen, Lies, additional, Keyaerts, Els, additional, Demuyser, Thomas, additional, Seyler, Lucie, additional, Soetens, Oriane, additional, Van Nedervelde, Els, additional, Naesens, Reinout, additional, Geysels, Dieter, additional, Verstrepen, Walter, additional, Cattoir, Lien, additional, Martens, Steven, additional, Michel, Charlotte, additional, Mathieu, Elise, additional, Reynders, Marijke, additional, Evenepoel, Anton, additional, Hellemans, Jorn, additional, Vanhee, Merijn, additional, Magerman, Koen, additional, Maes, Justine, additional, Matheeussen, Veerle, additional, Boogaerts, Hélène, additional, Lagrou, Katrien, additional, Cuypers, Lize, additional, and André, Emmanuel, additional

Published
2022
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15. Immunovirological and environmental screening reveals actionable risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks

Author

COVID-19 Genomics Belgium Consortium, Cuypers, Lize, Keyaerts, Els, Hong, Samuel Leandro, Gorissen, Sarah, Menezes, Soraya Maria, Starick, Marick, Van Elslande, Jan, Weemaes, Matthias, Wawina-Bokalanga, Tony, Marti-Carreras, Joan, Vanmechelen, Bert, Van Holm, Bram, Bloemen, Mandy, Dogné, Jean-Michel, Dufrasne, François, Durkin, Keith, Ruelle, Jean, De Mendonca, Ricardo, Wollants, Elke, Vermeersch, Pieter, Boulouffe, Caroline, Djiena, Achille, Broucke, Caroline, Catry, Boudewijn, Lagrou, Katrien, Van Ranst, Marc, Neyts, Johan, Baele, Guy, Maes, Piet, André, Emmanuel, Dellicour, Simon, Van Weyenbergh, Johan, UCL - SSS/IREC/MBLG - Pôle de Microbiologie médicale, UCL - (SLuc) Service de microbiologie, Supporting clinical sciences, Microbiology and Infection Control, and Clinical Biology

Subjects
Epidemiology, SARS-CoV-2, Vaccination, Immunovirological screening, COVID-19, infectious diseases, Nursing Homes, Disease Outbreaks, Immunology and Microbiology(all), Virology, environmental screening, Humans, Genetics(clinical), post-vaccination, Phylogeny, nursing home outbreaks, Aged
Abstract

Coronavirus Disease 2019 (COVID-19) vaccination has resulted in excellent protection against fatal disease, including in older adults. However, risk factors for post-vaccination fatal COVID-19 are largely unknown. We comprehensively studied three large nursing home outbreaks (20-35% fatal cases among residents) by combining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) aerosol monitoring, whole-genome phylogenetic analysis and immunovirological profiling of nasal mucosa by digital nCounter transcriptomics. Phylogenetic investigations indicated that each outbreak stemmed from a single introduction event, although with different variants (Delta, Gamma and Mu). SARS-CoV-2 was detected in aerosol samples up to 52 d after the initial infection. Combining demographic, immune and viral parameters, the best predictive models for mortality comprised IFNB1 or age, viral ORF7a and ACE2 receptor transcripts. Comparison with published pre-vaccine fatal COVID-19 transcriptomic and genomic signatures uncovered a unique IRF3 low/IRF7 high immune signature in post-vaccine fatal COVID-19 outbreaks. A multi-layered strategy, including environmental sampling, immunomonitoring and early antiviral therapy, should be considered to prevent post-vaccination COVID-19 mortality in nursing homes.

Published
2023

16. Natural ventilation, low CO2 and air filtration are associated with reduced indoor air respiratory pathogens

Author

Raymenants, Joren, primary, Geenen, Caspar, additional, Budts, Lore, additional, Thibaut, Jonathan, additional, Thijssen, Marijn, additional, De Mulder, Hannelore, additional, Gorissen, Sarah, additional, Craessaerts, Bastiaan, additional, Laenen, Lies, additional, Beuselinck, Kurt, additional, Ombelet, Sien, additional, Keyaerts, Els, additional, and André, Emmanuel, additional

Published
2022
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17. Environmental circulation of adenovirus 40/41 and SARS-CoV-2 in the context of the emergence of acute hepatitis of unknown origin

Author

Wollants, Elke, primary, Keyaerts, Els, additional, Cuypers, Lize, additional, Bloemen, Mandy, additional, Thijssen, Marijn, additional, Ombelet, Sien, additional, Raymenants, Joren, additional, Beuselinck, Kurt, additional, Laenen, Lies, additional, Budts, Lore, additional, Pussig, Bram, additional, Lagrou, Katrien, additional, Van Ranst, Marc, additional, and André, Emmanuel, additional

Published
2022
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18. Risk factors for disease severity and increased medical resource utilization in respiratory syncytial virus (+) hospitalized children: A descriptive study conducted in four Belgian hospitals

Author

Proesmans, Marijke, primary, Rector, Annabel, additional, Keyaerts, Els, additional, Vandendijck, Yannick, additional, Vermeulen, Francois, additional, Sauer, Kate, additional, Reynders, Marijke, additional, Verschelde, Ann, additional, Laffut, Wim, additional, Garmyn, Kristien, additional, Fleischhackl, Roman, additional, Bollekens, Jacques, additional, and Ispas, Gabriela, additional

Published
2022
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22. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Author

Salimi, Vahid, primary, Viegas, Mariana, additional, Trento, Alfonsina, additional, Agoti, Charles N., additional, Anderson, Larry J., additional, Avadhanula, Vasanthi, additional, Bahl, Justin, additional, Bont, Louis, additional, Brister, J. Rodney, additional, Cane, Patricia A., additional, Galiano, Mónica, additional, Graham, Barney S., additional, Hatcher, Eneida L., additional, Hellferscee, Orienka, additional, Henke, David M., additional, Hirve, Siddhivinayak, additional, Jackson, Sandra, additional, Keyaerts, Els, additional, Kragten-Tabatabaie, Leyla, additional, Lindstrom, Stephen, additional, Nauwelaers, Inne, additional, Nokes, D. James, additional, Openshaw, Peter J., additional, Peret, Teresa C., additional, Piedra, Pedro A., additional, Ramaekers, Kaat, additional, Rector, Annabel, additional, Trovão, Nídia Sequeira, additional, von Gottberg, Anne, additional, Zambon, Maria, additional, Zhang, Wenqing, additional, Williams, Thomas C., additional, Barr, Ian G., additional, and Buchholz, Ursula J., additional

Published
2021
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23. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Author

CTI Bont, Infectieziekten onderzoek1 (Bont), Child Health, Infection & Immunity, Salimi, Vahid, Viegas, Mariana, Trento, Alfonsina, Agoti, Charles N, Anderson, Larry J, Avadhanula, Vasanthi, Bahl, Justin, Bont, Louis, Brister, J Rodney, Cane, Patricia A, Galiano, Mónica, Graham, Barney S, Hatcher, Eneida L, Hellferscee, Orienka, Henke, David M, Hirve, Siddhivinayak, Jackson, Sandra, Keyaerts, Els, Kragten-Tabatabaie, Leyla, Lindstrom, Stephen, Nauwelaers, Inne, Nokes, D James, Openshaw, Peter J, Peret, Teresa C, Piedra, Pedro A, Ramaekers, Kaat, Rector, Annabel, Trovão, Nídia Sequeira, von Gottberg, Anne, Zambon, Maria, Zhang, Wenqing, Williams, Thomas C, Barr, Ian G, Buchholz, Ursula J, CTI Bont, Infectieziekten onderzoek1 (Bont), Child Health, Infection & Immunity, Salimi, Vahid, Viegas, Mariana, Trento, Alfonsina, Agoti, Charles N, Anderson, Larry J, Avadhanula, Vasanthi, Bahl, Justin, Bont, Louis, Brister, J Rodney, Cane, Patricia A, Galiano, Mónica, Graham, Barney S, Hatcher, Eneida L, Hellferscee, Orienka, Henke, David M, Hirve, Siddhivinayak, Jackson, Sandra, Keyaerts, Els, Kragten-Tabatabaie, Leyla, Lindstrom, Stephen, Nauwelaers, Inne, Nokes, D James, Openshaw, Peter J, Peret, Teresa C, Piedra, Pedro A, Ramaekers, Kaat, Rector, Annabel, Trovão, Nídia Sequeira, von Gottberg, Anne, Zambon, Maria, Zhang, Wenqing, Williams, Thomas C, Barr, Ian G, and Buchholz, Ursula J

Published
2021

24. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Author

de Vries, Jutte J C; https://orcid.org/0000-0003-2530-6260, Brown, Julianne R; https://orcid.org/0000-0002-4681-9586, Fischer, Nicole, Sidorov, Igor A, Morfopoulou, Sofia; https://orcid.org/0000-0001-8181-4548, Huang, Jiabin; https://orcid.org/0000-0002-3480-7115, Munnink, Bas B Oude; https://orcid.org/0000-0002-9394-1189, Sayiner, Arzu, Bulgurcu, Alihan; https://orcid.org/0000-0001-7422-4494, Rodriguez, Christophe, Gricourt, Guillaume; https://orcid.org/0000-0003-0143-5535, Keyaerts, Els, Beller, Leen, Bachofen, Claudia; https://orcid.org/0000-0002-0799-8083, Kubacki, Jakub; https://orcid.org/0000-0001-7085-3533, Cordey, Samuel, Laubscher, Florian, Schmitz, Dennis, Beer, Martin, Hoeper, Dirk, Huber, Michael, Kufner, Verena, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Lebrand, Aitana; https://orcid.org/0000-0002-3984-6842, Papa, Anna, van Boheemen, Sander, Kroes, Aloys C M; https://orcid.org/0000-0002-9866-2461, Breuer, Judith, Lopez-Labrador, F Xavier; https://orcid.org/0000-0002-9403-8258, Claas, Eric C J, de Vries, Jutte J C; https://orcid.org/0000-0003-2530-6260, Brown, Julianne R; https://orcid.org/0000-0002-4681-9586, Fischer, Nicole, Sidorov, Igor A, Morfopoulou, Sofia; https://orcid.org/0000-0001-8181-4548, Huang, Jiabin; https://orcid.org/0000-0002-3480-7115, Munnink, Bas B Oude; https://orcid.org/0000-0002-9394-1189, Sayiner, Arzu, Bulgurcu, Alihan; https://orcid.org/0000-0001-7422-4494, Rodriguez, Christophe, Gricourt, Guillaume; https://orcid.org/0000-0003-0143-5535, Keyaerts, Els, Beller, Leen, Bachofen, Claudia; https://orcid.org/0000-0002-0799-8083, Kubacki, Jakub; https://orcid.org/0000-0001-7085-3533, Cordey, Samuel, Laubscher, Florian, Schmitz, Dennis, Beer, Martin, Hoeper, Dirk, Huber, Michael, Kufner, Verena, Zaheri, Maryam; https://orcid.org/0000-0003-2777-835X, Lebrand, Aitana; https://orcid.org/0000-0002-3984-6842, Papa, Anna, van Boheemen, Sander, Kroes, Aloys C M; https://orcid.org/0000-0002-9866-2461, Breuer, Judith, Lopez-Labrador, F Xavier; https://orcid.org/0000-0002-9403-8258, and Claas, Eric C J

Abstract

Introduction: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories. Methods: Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analyzed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analyzed. Results: Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection. Conclusion: A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the

Published
2021

25. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples

Author

de Vries, Jutte J.C., primary, Brown, Julianne R., additional, Fischer, Nicole, additional, Sidorov, Igor A., additional, Morfopoulou, Sofia, additional, Huang, Jiabin, additional, Oude Munnink, Bas B., additional, Sayiner, Arzu, additional, Bulgurcu, Alihan, additional, Rodriguez, Christophe, additional, Gricourt, Guillaume, additional, Keyaerts, Els, additional, Beller, Leen, additional, Bachofen, Claudia, additional, Kubacki, Jakub, additional, Cordey, Samuel, additional, Laubscher, Florian, additional, Schmitz, Dennis, additional, Beer, Martin, additional, Hoeper, Dirk, additional, Huber, Michael, additional, Kufner, Verena, additional, Zaheri, Maryam, additional, Lebrand, Aitana, additional, Papa, Anna, additional, van Boheemen, Sander, additional, Kroes, Aloys C.M., additional, Breuer, Judith, additional, Lopez-Labrador, F. Xavier, additional, and Claas, Eric C.J., additional

Published
2021
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26. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

Author

López-Labrador, F Xavier, Brown, Julianne R, Fischer, Nicole, Harvala, Heli, Van Boheemen, Sander, Cinek, Ondrej, Sayiner, Arzu, Madsen, Tina Vasehus, Auvinen, Eeva, Kufner, Verena, Huber, Michael, Rodriguez, Christophe, Jonges, Marcel, Hönemann, Mario, Susi, Petri, Sousa, Hugo, Klapper, Paul E, Pérez-Cataluña, Alba, Hernandez, Marta, Molenkamp, Richard, der Hoek, Lia van, Schuurman, Rob, Couto, Natacha, Leuzinger, Karoline, Simmonds, Peter, Beer, Martin, Höper, Dirk, Kamminga, Sergio, Feltkamp, Mariet C W, Rodríguez-Díaz, Jesús, Keyaerts, Els, Nielsen, Xiaohui Chen, Puchhammer-Stöckl, Elisabeth, Kroes, Aloys C M, Buesa, Javier, Breuer, Judy, Claas, Eric C J, de Vries, Jutte J C, López-Labrador, F Xavier, Brown, Julianne R, Fischer, Nicole, Harvala, Heli, Van Boheemen, Sander, Cinek, Ondrej, Sayiner, Arzu, Madsen, Tina Vasehus, Auvinen, Eeva, Kufner, Verena, Huber, Michael, Rodriguez, Christophe, Jonges, Marcel, Hönemann, Mario, Susi, Petri, Sousa, Hugo, Klapper, Paul E, Pérez-Cataluña, Alba, Hernandez, Marta, Molenkamp, Richard, der Hoek, Lia van, Schuurman, Rob, Couto, Natacha, Leuzinger, Karoline, Simmonds, Peter, Beer, Martin, Höper, Dirk, Kamminga, Sergio, Feltkamp, Mariet C W, Rodríguez-Díaz, Jesús, Keyaerts, Els, Nielsen, Xiaohui Chen, Puchhammer-Stöckl, Elisabeth, Kroes, Aloys C M, Buesa, Javier, Breuer, Judy, Claas, Eric C J, and de Vries, Jutte J C

Abstract

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.

Published
2020

29. Plasma exchange-associated immunoglobulin M-negative hantavirus disease after a camping holiday in southern France

Author

Keyaerts, Els, Ghijsels, Erik, Lemey, Philippe, Maes, Piet, Zachee, Pierre, Daelemans, Ronald, Vervoort, Tony, Mertens, Gerhard, Van Ranst, Marc, and Clement, Jan

Subjects
Bunyaviruses -- Risk factors, Bunyaviruses -- Research, Hantaviruses -- Risk factors, Hantaviruses -- Research, Hantavirus infections -- Care and treatment, Hantavirus infections -- Case studies, Health, Health care industry
Published
2004

38. Exhaled breath condensate sampling is not a new method for detection of respiratory viruses

Author

Maes Piet, Sisk Maura, Talboom Ive, Narongsack Phouthalack, De Roy Rikka, Keyaerts Els, De Coster Sarah, Houspie Lieselot, Verbeeck Jannick, and Van Ranst Marc

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. Methods In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. Results Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. Conclusion Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.

Published
2011
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39. A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium

Author

Berkhout Ben, Pyrc Krzysztof, Maes Piet, Li Sandra, Zlateva Kalina, Keyaerts Els, Vijgen Leen, Moës Elien, van der Hoek Lia, and Van Ranst Marc

Subjects
Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Four human coronaviruses are currently known to infect the respiratory tract: human coronaviruses OC43 (HCoV-OC43) and 229E (HCoV-229E), SARS associated coronavirus (SARS-CoV) and the recently identified human coronavirus NL63 (HCoV-NL63). In this study we explored the incidence of HCoV-NL63 infection in children diagnosed with respiratory tract infections in Belgium. Methods Samples from children hospitalized with respiratory diseases during the winter seasons of 2003 and 2004 were evaluated for the presence of HCoV-NL63 using a optimized pancoronavirus RT-PCR assay. Results Seven HCoV-NL63 positive samples were identified, six were collected during January/February 2003 and one at the end of February 2004. Conclusions Our results support the notation that HCoV-NL63 can cause serious respiratory symptoms in children. Sequence analysis of the S gene showed that our isolates could be classified into two subtypes corresponding to the two prototype HCoV-NL63 sequences isolated in The Netherlands in 1988 and 2003, indicating that these two subtypes may currently be cocirculating.

Published
2005
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40. A Pancoronavirus RT-PCR Assay for Detection of All Known Coronaviruses

Author

Vijgen, Leen, Moës, Elien, Keyaerts, Els, Li, Sandra, and Van Ranst, Marc

Subjects
Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, viruses, coronavirus, virus diseases, sequencing, Sequence Analysis, DNA, RNA-Dependent RNA Polymerase, Article, polymerase gene, Sequence Homology, Nucleic Acid, pancoronavirus RT-PCR, degenerate primers, Humans, Coronavirus Infections, Phylogeny
Abstract

The recent discoveries of novel human coronaviruses, including the coronavirus causing SARS, and the previously unrecognized human coronaviruses HCoV-NL63 and HCoV-HKU1, indicate that the family Coronaviridae harbors more members than was previously assumed. All human coronaviruses characterized at present are associated with respiratory illnesses, ranging from mild common colds to more severe lower respiratory tract infections. Since the etiology of a relatively large percentage of respiratory tract diseases remains unidentified, it is possible that for a certain number of these illnesses, a yet unknown viral causative agent may be found. Screening for the presence of novel coronaviruses requires the use of a method that can detect all coronaviruses known at present. In this chapter, we describe a pancoronavirus degenerate primer-based method that allows the detection of all known and possibly unknown coronaviruses by RT-PCR amplification and sequencing of a 251-bp fragment of the coronavirus polymerase gene.

Published
2007

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