Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

Wawina-Bokalanga, Tony; Martí-Carreras, Joan; Vanmechelen, Bert; Bloemen, Mandy; Laenen, Lies; Cuypers, Lize; Beuselinck, Kurt; Lagrou, Katrien; André, Emmanuel; Ranst, Marc Van; Maes, Piet

doi:10.1101/2021.06.29.450330

Cited by 13 publications

(10 citation statements)

References 30 publications

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“…Although without structural funding at that time, over 750 complete SARS-CoV-2 genomes of samples originating from the first epidemiological wave (March to June 2020) in Belgium were sequenced to characterize the temporal and geographic distribution of the COVID-19 pandemic in Belgium through phylogenetic and variant analysis. Wawina-Bokalanga et al [ 18 ] showed the presence of the major SARS-CoV-2 clades (G, GH and GR) and lineages circulating in Belgium at that time. The continuation of this initiative to sequence a share of the positive samples, conducted by the different sequencing centers at that time, resulted in a total of over 3700 genomes in Belgium by the end of 2020.…”

Section: Prior To the National Genomic Surveillance Initiativementioning

confidence: 99%

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

Dellicour

Hong

et al. 2022

Viruses

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An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country’s genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.

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Section: Prior To the National Genomic Surveillance Initiativementioning

confidence: 99%

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

Dellicour

Hong

et al. 2022

Viruses

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“…Whole-genome sequencing (WGS) according to a previous published protocol [30,31] was performed on the supernatant to allow classification and detailed mapping of the mutations and deletions across the SARS-CoV-2 genome.…”

Section: Preparation Of Sars-cov-2 Control Materialsmentioning

confidence: 99%

Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium

Cuypers

Bode

Beuselinck

et al. 2022

Viruses

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From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (107, 105 and 103 copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions.

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“…Complete genome sequence of SARS-CoV-2 from a wastewater sample Complete genome sequencing was performed by means of MinION sequencing (Oxford Nanopore Technologies, UK) methods are described in the paper of Wawina-Bokalanga et al [18].…”

Section: Detection Of Sars-cov-2 Variants With Rt-qpcrmentioning

confidence: 99%

Detection Of SARS-COV-2 Variants Of Concern In Wastewater Of Leuven, Belgium

Bloemen

Rector

Raymenants

et al. 2022

Preprint

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To investigate whether wastewater surveillance can be used as an early warning system to detect a rise in SARS-CoV-2 positive cases, and to follow the circulation of specific variants of concern (VOC) in particular geographical areas, wastewater samples were collected from local neighborhood sewers and from a large regional wastewater treatment plant (WWTP) in the area of Leuven, Belgium. In two residential sampling sites, a rise in viral SARS-CoV-2 copies in wastewater preceded the peaks in positive cases. In the WWTP, peaks in the wastewater viral load were seen simultaneous with the waves op positive cases caused by the original Wuhan SARS-CoV-2 strain, the Alpha variant and the Delta variant. For the Omicron BA.1 variant associated wave, the viral load in wastewater increased to a lesser degree, and much later than the increase in positive cases, which could be attributed to a lower level of fecal excretion, as measured in hospitalized patients. Circulation of SARS-CoV-2 VOCs (Alpha, Delta and Omicron) 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.We found that wastewater based surveillance is a sensitive tool to monitor SARS-CoV-2 circulation levels and VOCs in larger regions. This can prove to be highly valuable in times of reducing testing capacity. 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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Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

Cited by 13 publications

References 30 publications

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

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

Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium

Detection Of SARS-COV-2 Variants Of Concern In Wastewater Of Leuven, Belgium

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