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SARS-CoV-2 Variants Monitoring in Wastewater

The SARS-COV-2 virus (SARS2), the causative agent for COVID-19, mutates as it adapts to different evolutionary pressures. From the analysis undertaken so far it appears that new variants are becoming more infective, but fortunately there is similar disease severity. However, it is difficult to predict what new viruses will emerge and critical for this project it is important to know when they first appear in Scotland and how they then spread. The goal of this project was not to identify new variants. The UK, through the COG consortium, are leading efforts to identify new Variants of Concern (VoC). Instead, this project aimed to develop methods for detection of these new variants to provide real-time data to Public Health Scotland and related agencies to monitor and respond to new variants. In addition to detecting new variants, this project attempted to quantify the amount of SARS2 in wastewater compared to human markers, for example crAssphage.

A summary of the methology development can be found here. Additionally, the data obtained from the team and analysed with the support of Biomathematics & Statistics Scotland (BioSS), has been used in the “Coronavirus (Covid-19): modelling the epidemic in Scotland” governmental reports to assist with epidemic monitoring. BioSS report

The variants research team

The research team with the expertise to deliver the ‘Variants’ component of this project is led by Prof. Nick Gilbert and are based at the MRC Human Genetics Unit, University of Edinburgh (UOE). They have broad experience in molecular biology techniques, including next generation sequencing. Importantly, the ‘Variants’ team started screening for SARS2 as a node for NHS Lothian in Summer 2020, and since have developed and implemented methodologies for screening saliva for SARS2 as part of a project called TestEd which is supported by a £1.8M UKRI grant. TestEd both screens for SARS2 but has also developed PCR assays to identify alpha, beta, gamma and delta variants.