Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre.
Belgium
COVID-19
High-throughput testing
National reference centre
Quality assurance
SARS-CoV-2
Journal
Virology journal
ISSN: 1743-422X
Titre abrégé: Virol J
Pays: England
ID NLM: 101231645
Informations de publication
Date de publication:
10 Feb 2024
10 Feb 2024
Historique:
received:
28
07
2023
accepted:
29
01
2024
medline:
11
2
2024
pubmed:
11
2
2024
entrez:
10
2
2024
Statut:
epublish
Résumé
Since the onset of the coronavirus disease (COVID-19) pandemic in Belgium, UZ/KU Leuven has played a crucial role as the National Reference Centre (NRC) for respiratory pathogens, to be the first Belgian laboratory to develop and implement laboratory developed diagnostic assays for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and later to assess the quality of commercial kits. To meet the growing demand for decentralised testing, both clinical laboratories and government-supported high-throughput platforms were gradually deployed across Belgium. Consequently, the role of the NRC transitioned from a specialised testing laboratory to strengthening capacity and coordinating quality assurance. Here, we outline the measures taken by the NRC, the national public health institute Sciensano and the executing clinical laboratories to ensure effective quality management of molecular testing throughout the initial two years of the pandemic (March 2020 to March 2022).
Identifiants
pubmed: 38341597
doi: 10.1186/s12985-024-02308-y
pii: 10.1186/s12985-024-02308-y
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
40Subventions
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Sciensano (Belgium)
ID : NRC
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Federal Public Service Public Health Belgium
ID : COVID-19 testing
Organisme : Fonds Wetenschappelijk Onderzoek
ID : G0H4420N
Organisme : Fonds Wetenschappelijk Onderzoek
ID : G0H4420N
Investigateurs
Emmanuel André
(E)
Piet Maes
(P)
Guy Baele
(G)
Simon Dellicour
(S)
Lize Cuypers
(L)
Marc Van Ranst
(M)
Barney Potter
(B)
Samuel Hong
(S)
François E Dufrasne
(FE)
Guillaume Bayon-Vicente
(G)
Ruddy Wattiez
(R)
Carl Vael
(C)
Lynsey Berckmans
(L)
Philippe Selhorst
(P)
Kevin K Ariën
(KK)
Arnaud Marchant
(A)
Coralie Henin
(C)
Benoit Haerlingen
(B)
Ricardo De Mendonca
(R)
Marie-Luce Delforge
(ML)
Sonia Van Dooren
(S)
Bruno Hinckel
(B)
Hideo Imamura
(H)
Toon Janssen
(T)
Ben Caljon
(B)
Oriane Soetens
(O)
Denis Piérard
(D)
Thomas Demuyser
(T)
Charlotte Michel
(C)
Olivier Vandenberg
(O)
Sigi van den Wijngaert
(S)
Giulia Zorzi
(G)
Jean Ruelle
(J)
Benoit Kabamba Mukadi
(BK)
Jean-Luc Gala
(JL)
Bertrand Bearzatto
(B)
Jérôme Ambroise
(J)
Philippe Van Lint
(P)
Walter Verstrepen
(W)
Reinout Naesens
(R)
Michael Peeters
(M)
Kate Bakelants
(K)
Sarah Denayer
(S)
Sofieke Klamer
(S)
Pascale Hilbert
(P)
Sylvain Brohée
(S)
Pierre-Emmanuel Léonard
(PE)
Deniz Karadurmus
(D)
Jeremie Gras
(J)
Damien Féret
(D)
Barbara Lambert
(B)
Anne Vankeerberghen
(A)
Astrid Holderbeke
(A)
Hans De Beenhouwer
(H)
Lien Cattoir
(L)
Christine Lammens
(C)
Basil Britto Xavier
(BB)
Marie Le Mercier
(M)
Jasmine Coppens
(J)
Veerle Matheeussen
(V)
Herman Goossens
(H)
Geert A Martens
(GA)
Koen Swaert
(K)
Frederik Van Hoecke
(F)
Dieter Desmet
(D)
Merijn Vanhee
(M)
Pierre Bogaerts
(P)
Jonathan Degosserie
(J)
Olivier Denis
(O)
Te-Din Huang
(TD)
Dagmar Obbels
(D)
Hanne Valgaeren
(H)
Johan Frans
(J)
Annick Smismans
(A)
Paul-Emile Claus
(PE)
Truus Goegebuer
(T)
Ann Lemmens
(A)
Bea Van den Poel
(B)
Sonja De Bock
(S)
Wim Laffut
(W)
Ellen Van Even
(E)
Jos Van Acker
(J)
Charlotte Verfaillie
(C)
Elke Vanlaere
(E)
Klara De Rauw
(K)
Brigitte Maes
(B)
Guy Froyen
(G)
Bert Cruys
(B)
Ellen Geerdens
(E)
Luc Waumans
(L)
Britt Van Meensel
(B)
Reinoud Cartuyvels
(R)
Severine Berden
(S)
Marijke Raymaekers
(M)
Bruno Verhasselt
(B)
Cécile Meex
(C)
Keith Durkin
(K)
Laurent Gillet
(L)
Maria Artesi
(M)
Marie-Pierre Hayette
(MP)
Sébastien Bontems
(S)
Vincent Bours
(V)
Claire Gourzonès
(C)
Olivier Ek
(O)
Fabrice Bureau
(F)
Jorn Hellemans
(J)
Patrick Descheemaeker
(P)
Marijke Reynders
(M)
Informations de copyright
© 2024. The Author(s).
Références
Federal Public Service of Social Security (2011) Royal Decree for the financing of referral centres for human microbiology. http://www.ejustice.just.fgov.be/eli/besluit/2011/02/09/2011022071/staatsblad . Accessed 24 Jan 2023.
Coupeau D, Burton N, Lejeune N, Loret S, Petit A, Pejakovic S, Poulain S, et al. SARS-CoV-2 detection for diagnosis purposes in the setting of a molecular biology research lab. Methods Protoc. 2020;3(3):59. https://doi.org/10.3390/mps3030059 .
doi: 10.3390/mps3030059
pubmed: 32824827
pmcid: 7564796
Hans L, Steegen K, Ketseolou I, Mahlumba Z, Cassim N, Wiggill T, et al. Preparing for the next pandemic: lessons from rapid scale-up of SARS-CoV-2 testing in a South African high-throughput automated HIV molecular laboratory. Int J Infect Dis. 2021;110:1–3. https://doi.org/10.1016/j.ijid.2021.06.019 .
doi: 10.1016/j.ijid.2021.06.019
pubmed: 34139371
pmcid: 8205292
Das S, Frank MK. Strategies for scaling up SARS-CoV-2 molecular testing capacity. Clin Lab Med. 2022;42:261–82. https://doi.org/10.1016/j.cll.2022.02.006 .
doi: 10.1016/j.cll.2022.02.006
pubmed: 35636826
pmcid: 8901375
Tomberg BJ, Schwetz TA, Pérez-Stable EJ, Hodes RJ, Woychik RP, Bright RA, et al. Rapid scaling up of Covid-19 diagnostic testing in the United States — the NIH RADx initiative. N Engl J Med. 2020;383:1071–7. https://doi.org/10.1056/NEJMsr2022263 .
doi: 10.1056/NEJMsr2022263
Coronavirus (COVID-19): scaling up our testing programmes. https://www.gov.uk/government/publications/coronavirus-covid-19-scaling-up-testing-programmes/coronavirus-covid-19-scaling-up-our-testing-programmes . Accessed 16 Mar 2023.
Raymenants J, Geenen C, Budts L, Thibault J, Thijssen M, DeMulder H, et al. Indoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium. Nat Commun. 2023;14:1332.
doi: 10.1038/s41467-023-36986-z
pubmed: 36898982
pmcid: 10005919
Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–9. https://doi.org/10.1038/s41586-020-2008-3 .
doi: 10.1038/s41586-020-2008-3
pubmed: 32015508
pmcid: 7094943
Meurisse M, Lajot A, Dupont Y, Lesenfants M, Klamer S, Rebolledo J, et al. One year of laboratory-based COVID-19 surveillance system in Belgium: main indicators and performance of the laboratories (March 2020–21). Arch Public Health. 2021;79:188. https://doi.org/10.1186/s13690-021-00704-2 .
doi: 10.1186/s13690-021-00704-2
pubmed: 34706768
pmcid: 8548266
Stellrecht KA, Cimino JL, Wilson LI, Maceira VP, Butt SA. Panther Fusion® respiratory virus assays for the detection of influenza and other respiratory viruses. J Clin Virol. 2019;121: 104204. https://doi.org/10.1016/j.jcv.2019.104204 .
doi: 10.1016/j.jcv.2019.104204
pubmed: 31743836
pmcid: 7172166
Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25:23–30. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045 .
doi: 10.2807/1560-7917.ES.2020.25.3.2000045
Quick J (2023) nCoV-2019 sequencing protocol V.1. https://www.protocols.io/view/ncov-2019-sequencing-protocol-bp2l6n26rgqe/v1 . Accessed 9 May 2023.
Cuypers L, Dellicour S, Hong SL, Potter BI, Verhasselt B, Vereecke N, et al. Two years of genomic surveillance in Belgium during the SARS-CoV-2 pandemic to attain country-wide coverage and monitor the introduction and spread of emerging variants. Viruses. 2022;14:2301. https://doi.org/10.3390/v14102301 .
doi: 10.3390/v14102301
pubmed: 36298856
pmcid: 9612291
Cuypers L, Bode J, Beuselinck K, Laenen L, Dewaele K, Janssen R, et al. Nationwide harmonization effort for semi-quantitative reporting of SARS-CoV-2 PCR test results in Belgium. Viruses. 2022;14:1294. https://doi.org/10.3390/v14061294 .
doi: 10.3390/v14061294
pubmed: 35746765
pmcid: 9230955
Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. J Open Source Softw. 2021;6:3773.
doi: 10.21105/joss.03773
Nextclade: clade assignment, mutation calling and quality control for viral genomes. https://clades.nextstrain.org . Accessed 5 Oct 2022.
O‘Toole A, Scher E, Underwood A, Jackson B, Hill V, McCrone JT, et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol. 2021;7:veab064. https://doi.org/10.1093/ve/veab064 .
doi: 10.1093/ve/veab064
pubmed: 34527285
Pangolin COVID-19 Lineage Assigner. https://pangolin.cog-uk.io/ . Accessed 5 Oct 2022.
Khare S, Gurry C, Freitas L, Schultz MB, Bach G, Diallo A, et al. GISAID’s role in pandemic response. China CDC Week. 2021;3:1049–51.
doi: 10.46234/ccdcw2021.255
Federal Public Service of Health, Food chain safety and Environment; 3 December 1999. – Royal Decree for the licensing of clinical pathology laboratories by the Minister of Public Health. http://www.ejustice.just.fgov.be/eli/besluit/1999/12/03/1999024072/staatsblad . Accessed 24 Jan 2023.
ISO 15189:2012 - Medical laboratories - Requirements for quality and competence. https://www.iso.org/standard/56115.html . Accessed 24 Jan 2023.
Federal Public Service of Economy, S.M.E.s, Self-Employed and Energy; 31 January 2006. - Royal Decree establishing the BELAC accreditation system of conformity assessment bodies. http://www.ejustice.just.fgov.be/eli/besluit/2006/01/31/2006011052/staatsblad . Accessed 25 Jan 2023.
Werkgroep Praktijkrichtlijn, Commissie voor Klinische biologie. Praktijkrichtlijn voor het opzetten van een kwaliteitshandboek in de erkende laboratoria voor klinische biologie werkzaam binnen het kader van het Erkenningsbesluit. https://www.sciensano.be/sites/default/files/praktijkrichtlijn_klinische_biologie.pdf . Accessed 15 Sep 2022.
Quality Control for Molecular Diagnostics (QCMD). SARS-CoV-2 EQA Programme. https://www.qcmd.org/#fragment-2 . Accessed 15 Sep 2022.
Coronavirus: Taskforce testing breidt testcapaciteit testing gevoelig uit. Verschillende labo’s en bedrijven trekken samen aan de kar. http://www.philippedebacker.com/coronavirus-taskforce-testing-breidt-testcapaciteit-testing-gevoelig-uit-verschillende-labos-en-bedrijven-trekken-samen-aan-de-kar/ . Accessed 25 Jan 2023.
Van Vooren S, Grayson J, Van Ranst M, Dequeker E, Laenen L, Janssen R, et al. Reliable and scalable SARS-CoV-2 qPCR Testing at a high sample throughput: lessons learned from the Belgian initiative. Life. 2022;12:159. https://doi.org/10.3390/life12020159 .
doi: 10.3390/life12020159
pubmed: 35207446
pmcid: 8879918
Rabenau HF, Kessler HH, Kortenbusch M, Steinhorst A, Raggam RB, Berger A. Verification and validation of diagnostic laboratory tests in clinical virology. J Clin Virol. 2007;40:93–8. https://doi.org/10.1016/j.jcv.2007.07.009 .
doi: 10.1016/j.jcv.2007.07.009
pubmed: 17766174
Federal Public Service Chancellery of the Prime Minister; 17 June 2016. - Public Procurement Act (1). http://www.ejustice.just.fgov.be/eli/wet/2016/06/17/2016021053/staatsblad . Accessed 26 Jan 2023.
Federal Public Service Chancellery of the Prime Minister; 18 April 2017. – Royal decree on public procurement in traditional sectors. http://www.ejustice.just.fgov.be/eli/besluit/2017/04/18/2017020322/staatsblad . Accessed 26 Jan 2023.
RAG Meeting 08/12/2020: Interpretation and Reporting of SARS-CoV-2 PCR Results. https://covid-19.sciensano.be/sites/default/files/Covid19/20201208_Advice%20RAG%20Interpretation%20and%20reporting%20of%20COVID%20PCR%20results.pdf . Accessed 4 Oct 2022.
Brown KA, Gubbay J, Hopkins J, Patel S, Buchan SA, Daneman N, et al. S-gene target failure as a marker of variant B.1.1.7 among SARS-CoV-2 isolates in the greater Toronto area, December 2020 to March 2021. JAMA . 2021;325:2115–2116. https://doi.org/10.1001/jama.2021.5607
Clark C, Schrecker J, Hardison M, Taitel MS. Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants. PLoS ONE. 2022;17:10. https://doi.org/10.1371/journal.pone.0275150 .
doi: 10.1371/journal.pone.0275150
Vanmechelen B, Logist A-S, Wawina-Bokalanga T, Verlinden J, Martí-Carreras J, Geenen C, et al (2022) Identification of the first SARS-CoV-2 lineage B.1.1.529 virus detected in Europe. Microbiol Resour Announc 2022;11:e0116121. https://doi.org/10.1128/mra.01161-21
Quick J (2023) nCoV-2019 sequencing protocol v3 (LoCost) V.3. https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bp2l6n26rgqe/v3 . Accessed 25 Jan 2023
Van Elslande J, Kerckhofs F, Cuypers L, Wollants E, Potter B, Vankeerberghen A, et al. Two separate clusters of SARS-CoV-2 delta variant infections in a group of 41 students travelling from India: an illustration of the need for rigorous testing and quarantine. Viruses. 2022;14:1198. https://doi.org/10.3390/v14061198 .
doi: 10.3390/v14061198
pubmed: 35746671
pmcid: 9229483
Wawina-Bokalanga T, Logist A-S, Sinnesael R, Van Holm B, Delforge M-L, Struyven P, et al. Genomic evidence of co-identification with Omicron and Delta SARS-CoV-2 variants: a report of two cases. Int J Infect Dis. 2022;122:212–4. https://doi.org/10.1016/j.ijid.2022.05.043 .
doi: 10.1016/j.ijid.2022.05.043
pubmed: 35605952
pmcid: 9121643
Maschietto C, Otto G, Rouzé P, Debortoli N, Bihin B, Nyinkeu L, et al. Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting. Sci Rep. 2023;13:6934. https://doi.org/10.1038/s41598-023-34088-w .
doi: 10.1038/s41598-023-34088-w
pubmed: 37117393
pmcid: 10140720
RAG Meeting 25/01/2021: Aanbevelingen voor de selectie van stalen voor de sequentiebepaling van het volledige genoom. https://covid-19.sciensano.be/sites/default/files/Covid19/20210125_RAG_Selection%20of%20samples%20for%20sequencing_NL.pdf . Accessed 15 Sep 2022.
RAG Meeting 15/03/2021: Aanbevelingen voor de selectie van stalen voor de sequentiebepaling van het volledige genoom in het kader van surveillance - update. https://covid-19.sciensano.be/sites/default/files/Covid19/20210315_Advice%20RAG_Selection%20for%20samples%20for%20sequencing%20-%20update_NL.pdf . Accessed 15 Sep 2022.
RAG meeting 30/08/2021: Aanbevelingen voor de selectie van stalen voor de sequentiebepaling van het volledige genoom in het kader van surveillance - update August 2021. https://covid-19.sciensano.be/sites/default/files/Covid19/20210830_Advice_RAG_Update%20indications%20for%20sequencing_NL.pdf . Accessed 15 Sep 2022.
RAG meeting 23/09/2022: Indications for genomic sequencing and rapid molecular tests as POC tests. https://covid-19.sciensano.be/sites/default/files/Covid19/20220923_Adice%20RAG_Genomic%20surveillance%20and%20rapid%20PCR_EN.pdf . Accessed 27 Jan 2023.
Genomic surveillance of SARS-CoV-2 in Belgium. https://www.uzleuven.be/nl/laboratoriumgeneeskunde/genomic-surveillance-sars-cov-2-belgium . Accessed 20 Sep 2022.