A cloud-based software for the surveillance of SARS-CoV-2 variants

Image source: Unsplash/Quinten Braem

Viral mutation is a naturally occurring phenomenon leading to the emergence of variants that can have different characteristics. Today, a number of SARS-CoV-2 variants are circulating worldwide. Some of these variants are under particular scrutiny because of their impact on the pandemic (increased infectiousness or severity of infection, possible vaccine escape). Genomic surveillance of mutant circulation is therefore essential for public health.

Launched worldwide, the new application is intended to identify SARS-CoV-2 variants using samples from positive patients. Automatically updated each week, the platform identifies variants based on international nomenclatures (PANGO and NextStrain) including any new variant of concern (VOC) as defined by the World Health Organization and the US Centers for Disease Control and Prevention. Episeq SARS-CoV-2 is compatible with three major sequencing platforms (Illumina, Oxford Nanopore, Thermo Fisher) and easy to use by any microbiology lab without bioinformatics knowledge or computing resources, bioMérieux states.

The application permits the export of viral genome assemblies and mutations in order to facilitate reporting to national public health authorities and for epidemiology studies. “Microbiologists today deal with extensive data sets and need to translate these into meaningful information that impacts clinical decisions and public health actions. Episeq SARS-CoV-2 responds entirely to that challenge. It enables the in-depth analysis of complex viral genetic sequencing data without any need for specific bioinformatics competencies or major hardware investments.” noted Mark Miller, Executive Vice President, Chief Medical Officer.

Drawing on its expertise in microbiology and informatics, bioMérieux has developed the genomic cloud-based computing platform that supports laboratories in the utilization of next generation sequencing (NGS) technologies and interpretation of its outcome. Multiple NGS- and cloud-based software modules are being developed on this platform. “bioMérieux’s strategy is to leverage the tremendous potential of diagnostics data to support the fight against infectious diseases. Hence, we decided earlier this year to draw on our broad and deep expertise in the fields of data science, software development and bioinformatics in order to develop an easy-to-use application to serve our customers using next generation sequencing to identify SARS-CoV-2 variants.” said Pierre Boulud, Chief Operating Officer, Clinical Operations.

Source: bioMérieux

24.06.2021

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