VIRALERT project

Background

The frequency and size of viral epidemics have increased in the last decades. Great inter-connectivity undeniably facilitates infectious disease spreads across continents. Global changes are also affecting the geographic distribution of disease vectors and the interface between humans and animals, thus providing more opportunities for pathogens to jump between species.

Viral infections such as SARS-CoV-2 frequently cause a wide array of symptoms, and severe disease often constitutes only the tip of the iceberg. This may lead to a lag time between the emergence of pathogens and their detection by classical infectious disease surveillance systems relying on clinical signs.

The emergence and spread of SARS-CoV-2 illustrated the current challenges in infectious disease surveillance, management and control. But it also promoted innovations. While virus surveillance in wastewater had already been used in the context of poliovirus elimination strategies, the COVID-19 pandemic offered the opportunity to further highlight its advantage for providing a cost-effective and non-invasive picture of pathogen circulation in an entire population.

Yet, in a One Health context that recognises the interdependency of human, animal and environment health, surveillance should still go further. Wastewater mainly captures the human microbiome but leaves out animal populations. Surface water epidemiology, exploiting environmental faecal contamination as a marker of wild and domestic animal health, has been seldom explored to bridge this gap.

Aims

Building on the long-standing expertise of the Clinical and Applied Virology group of the LIH in human and animal disease surveillance and on previous collaborations between LIH and LIST in the domain of infectious disease surveillance in the environment (cfr FNR funded projects “SENSORLUX” and “CORONASTEP+”), the VIRALERT project proposed an innovative integrative approach for paving the way towards monitoring the circulation of viruses with high epidemic and pandemic potential in a non-invasive cost effective manner.

To this end, VIRALERT aimed to

• monitor an extended range of viruses in wastewater, including enteric and respiratory viruses,
• monitor population health in a post-pandemic context in which the circulation of other viruses has been affected by pandemic containment measures,
• cover wild and domestic animal health by investigating viral populations in freshwater,
• explore the potential of various technologies with differing sensitivity and specificity characteristics for the molecular detection and sequencing of influenza viruses, human and bovine respiratory syncytial viruses, seasonal human and animal coronaviruses, enteroviruses, noroviruses and mosquito-borne flaviviruses and
• take advantage of next generation sequencing (NGS) technologies to explore the possibility to detect a wider range of viruses.

In the long run, enhanced environmental surveillance will provide an additional tool to public and animal health authorities to complement existing surveillance systems and contribute to decreasing infectious disease burden.

Graphical view of the VIRALERT project overarching scheme and technologies employed (created with BioRender).

Abbreviations: RT-qPCR real-time reverse transcription polymerase chain reaction; RT-ddPCR reverse transcription digital droplet polymerase chain reaction; NGS next generation sequencing

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