AutoMuVariant: Automated mutation variant surveillance for accurate COVID-19 variant monitoring and tracking

Flomics Biotech S.L.

Presentation Video

Final Video

In the beginning of 2021, the European Commission sent a communication to all EU members highlighting the importance of monitoring the known and novel COVID-19 variants occurring in Europe. They recommended member states to sequence at least 5-10% of all positive cases detected and emphasized the need for a standard and clear method to share their results.

Standard PCR testing can detect the presence of the viral genome but sequencing is the leading tool to monitor known variants and especially to identify newly appearing ones.
Every day, thousands of people are tested for COVID-19 using a PCR, and a high proportion of those samples are available for sequencing and variant testing. The price of amplicon sequencing, a methodology for sequencing the viral genome, is lowering every month, rating right now as low as 25 euros per sample. While the processing of these samples is often streamlined for scaling up purposes, the resultant data volume is hard to interpret and represents the most common bottleneck when planning COVID-19 sample sequencing at large scale.

Flomics proposes the use of a web-based platform for the automated analysis of sequencing data derived from COVID-19 patients. The input for this platform is the raw sequencing data obtained from the sequencing platform and with only a few clicks the analyses are launched and the data interpreted. Within 30 minutes, the clients obtain a full report on the abundance of the COVID-19 genome detected, the location, type and significance of the mutations detected as well as information necessary for virus variant identification in terms of phylogeny.

This simple approach enables population-wide surveillance through both longitudinal/spatial monitoring as well as through the analysis of more complex samples such as residual waters. Our tool provides important insights to track the transmission routes of the virus globally, fast-tracking development and approval of vaccines against new variants.
INNO4COV-19 Platform financial aid we will help us meet project objectives and accelerate our journey to the market (reaching TRL 9). Additionally, by benefitting from tailored support and guidance offered by the Platform, we will be better positioned to cement our trajectory towards an established biotech company specialized in population-wide surveillance from sequencing samples. Finally, we would greatly benefit from the media exposure that only an international platform like this could help us achieve.