Used paper tissues for pathogen identification in acute respiratory infection. (preprint)

We investigated the potential of used paper tissues as a non-invasive sampling method for the diagnosis of acute respiratory infections. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. The collection of used paper tissues could therefore be useful in epidemiological surveillance for SARS-CoV-2 and other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses and Streptococcus pneumoniae.

Epidemiological surveillance of respiratory pathogens in wastewater in Belgium (preprint)

ABSTRACT Background Detailed information on the circulation of respiratory viruses in the community is crucial to gain better understanding of the burden of respiratory infections on society. Methods By using an in-house respiratory panel for simultaneous detection of 29 respiratory pathogens (22 viruses and 7 bacteria/fungi), we explored the possibility to use wastewater sampling to monitor the circulation of respiratory pathogens at population level. Results We were able to detect all respiratory viruses included in the panel (influenza A, respiratory syncytial virus (RSV), human metapneumovirus (HMPV), parainfluenza viruses (PIV) 1-4, adenovirus (Adv), human bocavirus (HBoV), enterovirus/rhinovirus (EV/RV), enterovirus D68 (EV-D68), parechovirus (HPeV), human coronaviruses (HCoV)-NL63, -229E, -OC43, -HKU-1 and -SARS, cytomegalovirus (CMV) and herpes simplex virus (HSV)-1 and -2), except for influenza B and HCoV MERS which were not circulating in Belgium during the two year study period. An upsurge of EV-D68 infections in Europe in September 2021 was clearly reflected in the wastewater samples. For the viruses where epidemiological data on virus circulation in Belgium were available, these matched the wastewater data. The wastewater pretreatment that was used, optimized for viral enrichment, was as such not suited for the surveillance of bacteria and fungi. Conclusions Community circulation levels of respiratory viruses were well reflected in wastewater samples, indicating that wastewater-based epidemiology can be a valuable tool in the epidemiology and management of respiratory infections.

Sequencing from leftover material of stored rapid Ag Tests (Ag-RDTs): a gamechanger in genomic surveillance? (preprint)

ABSTRACT Archived lateral flow antigen-detection rapid diagnostic tests (Ag-RDTs), used in the diagnosis of COVID-19, were successfully used to extract viral nucleic acids for subsequent RT-qPCR and sequencing by Sanger or Nanopore whole genome sequencing (WGS). The method was successfully applied with different brands of SARS-CoV-2 Ag-RDTs, but also with Ag-RDTs for detection of influenza, rotavirus and adenovirus 40/41. The buffer used in the Ag-RDT had an important influence on the RNA yield from the test stripand the efficiency of subsequent sequencing. Our finding that the test strip in rapid Ag tests is suited to preserve viral genomic material, even for months at room temperature, and therefore can serve as source material for genetic characterization, could improve global coverage of genomic surveillance for SARS-CoV-2 as well as for other viruses.

Environmental circulation of adenovirus 40/41 and SARS-CoV-2 in the context of the emergence of acute hepatitis of unknown origin (preprint)

The recent surge of hepatitis of unknown origin in children is hypothesized to be caused by adenovirus 41 and/or SARS-CoV-2 infections. A relatively high proportion of patients testing positive for these viruses concomitantly with the development of acute hepatitis supports this hypothesis. To formally incriminate these viral infections as causative agents of hepatitis, both a plausible physiopathological pathway and supporting epidemiological dynamics in the community need demonstration. In this study, we measured the level of circulation of adenovirus 40/41 and SARS-CoV-2 in the general population of the city of Leuven in Belgium using wastewater monitoring between December 2020 and May 2022 and indoor air sampling in day care centers between November 2021 and May 2022. We also retrospectively analyzed medical records of 12.672 children attending a tertiary hospital draining the same region between January 2019 and April 2022. Our results demonstrate a recent but modest increase in hepatitis of unknown origin concomitant with a surge of circulating adenovirus 41 and SARS-CoV-2 in the general population, including in children under 5.

Detection Of SARS-CoV-2 Variants Of Concern In Wastewater Of Leuven, Belgium (preprint)

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.

Comprehensive immunovirological and environmental screening reveals risk factors for fatal COVID-19 during post-vaccination nursing home outbreaks (preprint)

COVID-19 vaccination has resulted in excellent protection against fatal disease, including in the elderly. However, risk factors for post-vaccination fatal COVID-19 are largely unknown. We comprehensively studied three large nursing home outbreaks (20-35% fatal cases) by combining SARS-CoV-2 aerosol monitoring, whole-genome phylogenetic analysis, and immunovirological profiling by digital nCounter transcriptomics. Phylogenetic investigations indicated each outbreak stemmed from a single introduction event, though with different variants (Delta, Gamma, and Mu). SARS-CoV-2 was detected in aerosol samples up to 52 days 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 signatures and reanalysis of single-cell RNAseq data highlights the unique 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.

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

SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020. One year after the first epidemiological wave hit the country data analyses reveled the temporal and variant distribution of SARS-CoV-2 and its implication with Belgian epidemiological measures. In this study, 766 complete SARS-CoV-2 genomes of samples originating from the first epidemiological were sequenced to characterize the temporal and geographic distribution of the COVID-19 pandemic in Belgium through phylogenetic and variant analysis. Our analysis reveals the presence of the major circulating SARS-CoV-2 clades (G, GH and GR) and lineages circulating in Belgium at that time. Moreover, it contextualizes the density of SARS-CoV-2 cases over time with non-intervention measures taken to prevent the spread of SARS-CoV-2 in Belgium, specific international case imports and the functional implications of the most representative non-synonymous mutations present in Belgium between February to June 2020.