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

Cuypers, Lize; Dellicour, Simon; Hong, Samuel L.; Potter, Barney; Verhasselt, Bruno; Vereecke, Nick; Lambrechts, Laurens; Durkin, Keith; Klamer, Sofieke; Bayon-Vicente, Guillaume; Vael, Carl; Ariën, Kevin K.; Mendonça, Ricardo De; Soetens, Oriane; Michel, Charlotte; Bearzatto, Bertrand; Naesens, Reinout; Gras, Jérémie; Vankeerberghen, Anne; Matheeussen, Veerle; Martens, Geert A.; Obbels, Dagmar; Lemmens, Ann; Poel, Bea Van den; Even, Ellen Van; Rauw, Klara De; Waumans, Luc; Degosserie, Jonathan; Maes, Piet; André, Emmanuel; Baele, Guy

doi:10.3390/v14102301

Cited by 10 publications

(27 citation statements)

References 40 publications

(53 reference statements)

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“…In all samples for which typing by VOC RT‐qPCR and/or WGS was possible, the Alpha variant (Pango lineage B.1.1.7) was detected. This is in accordance with the epidemiologic situation in Belgium during that period, with Alpha being the dominant variant, representing between 80% and 85% of circulating strains 27 …”

Section: Resultssupporting

confidence: 89%

“…Using our multiplex RT‐qPCR assay, we were unable to distinguish between Omicron BA.1 and BA.2 nor between Omicron BA.4 and BA.5. The signature mutations detected in the wastewater samples of the WWTP of Leuven are in accordance with the baseline surveillance data on circulating variants in Belgium, published by the Belgian National reference lab 27 …”

Section: Resultssupporting

confidence: 84%

“…The viral RNA levels in the city sewage mostly followed the same trend as the number of positive cases in Leuven. Since the start of the pandemic, seven COVID waves have occurred in Belgium up to September 2022, caused by consecutive variants of the virus 23,27 . All but the first wave are covered by our wastewater sampling and are reflected in the wastewater viral loads (Figure 3A).…”

Section: Resultsmentioning

confidence: 99%

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Monitoring of SARS‐CoV‐2 concentration and circulation of variants of concern in wastewater of Leuven, Belgium

Rector

Bloemen

Thijssen

et al. 2023

Journal of Medical Virology

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Wastewater surveillance plays an important role in the management of the coronavirus disease 2019 (COVID‐19) pandemic all over the world. Using different wastewater collection points in Leuven, we wanted to investigate the use of wastewater surveillance as an early warning system for an uprise of infections and as a tool to follow the circulation of specific variants of concern (VOCs) in particular geographic areas. Wastewater samples were collected from local neighborhood sewers and from a large regional wastewater treatment plant (WWTP) in the area of Leuven, Belgium. After virus concentration, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA was quantified by real‐time quantitative polymerase chain reaction (RT‐qPCR) and normalized with the human fecal indicator pepper mild mottle virus (PMMoV). A combination of multiplex RT‐qPCR assays was used to detect signature mutations of circulating VOCs. Fecal virus shedding of SARS‐CoV‐2 variants was measured in feces samples of hospitalized patients. In two residential sampling sites, a rise in wastewater SARS‐CoV‐2 concentration preceded peaks in positive cases. In the WWTP, viral load peaks were seen concomitant with the consecutive waves of positive cases caused by the original Wuhan SARS‐CoV‐2 strain and subsequent VOCs. During the Omicron BA.1 wave, the wastewater viral load increased to a lesser degree, even after normalization of SARS‐CoV‐2 concentration using PMMoV. This might be attributable to a lower level of fecal excretion of this variant. Circulation of SARS‐CoV‐2 VOCs Alpha, Delta, Omicron BA1/BA.2, and BA.4/BA.5 could be detected based on the presence of specific key mutations. The shift in variants was noticeable in the wastewater, with key mutations of two different variants being present simultaneously during the transition period. Wastewater‐based surveillance is a sensitive tool to monitor SARS‐CoV‐2 circulation levels and VOCs in larger regions. In times of reduced test capacity, this can prove to be highly valuable. Differences in excretion levels of various SARS‐CoV‐2 variants should however be taken into account when using wastewater surveillance to monitor SARS‐CoV‐2 circulation levels in the population.

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Section: Resultssupporting

confidence: 89%

Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Monitoring of SARS‐CoV‐2 concentration and circulation of variants of concern in wastewater of Leuven, Belgium

Rector

Bloemen

Thijssen

et al. 2023

Journal of Medical Virology

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“…It is essential that information be timely exchanged between systems collecting data and information related to different sectors, in order to alert authorities to unusual disease outbreaks so that they can take appropriate action. At the global level, countries around the world intensified their efforts in the establishment of advanced systems for genomic surveillance such as the Belgian genomic surveillance consortium [ 42 ], the The Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (COG-UK) [ 43 ], the FAO EMPRES-i [ 44 ] and the GLEWS [ 45 ], and serve as early Warning One Health systems able to deal with pandemic threats.…”

Section: Discussionmentioning

confidence: 99%

One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy

Lorenzo¹,

Mangone²,

Colangeli³

et al. 2023

One Health

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“…Most countries have tried to control new waves of infection by implementing public health measures with the aim of avoiding the flooding of healthcare facilities, thus ensuring access to healthcare for people in need of essential treatment. In this context, it was essential to develop an efficient surveillance network allowing the early detection of new circulating variants and their transmission in the population 7 , 8 . Whole genome sequencing not only helps scientists study the virus and develop vaccines but is also the key tool for establishing strong surveillance networks.…”

Section: Introductionmentioning

confidence: 99%

Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting

Maschietto

Otto

Rouzè

et al. 2023

Sci Rep

Self Cite

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Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.

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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

Cited by 10 publications

References 40 publications

Monitoring of SARS‐CoV‐2 concentration and circulation of variants of concern in wastewater of Leuven, Belgium

Monitoring of SARS‐CoV‐2 concentration and circulation of variants of concern in wastewater of Leuven, Belgium

One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy

Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting

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