Fast identification and Analysis of SARS-CoV-2 variants using Viral Instant Mutation Viewer (VIMVer)

ABSTRACT

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has become one of the most studied viruses since its emergence. Two years after its outbreak, SARSCoV- 2 still represents a major public health priority as it keeps spreading at an alarming rate through the rise of many pathogenic variants. These latter can be a serious threat the more their genomic sequence diverge from the original strain, the less efficient the vaccine will remain. Therefore, it is critical for medical services to be able to determine straight out the strain they are dealing with, also as the location of the occurred genomic mutations and identify which viral protein has evolved. In this context, our main goal is to understand the nuances behind the mutations observed simultaneously in the genome and the proteome. To do so, we developed a user-friendly web-service software (Viral Instant Mutation Viewer or VIMVer) which allows an instant identification of new mutations and displayed them in both the nucleotide and protein sequences in comparison to a reference sequence (wuhan-1). Given a SARS-CoV-2 nucleotide sequence (as a newly sequenced genome), our software will instantly extract, analyse and visualize mutations on the genome and the proteome with the proper numbering and positioning. Additionally, the output is linked to Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin COVID-19) (2), which will thus allow an automatic identification of the Lineage or its position in relation to known lineage. We believe this tool will help many in their daily process to analyse their data. The source code is released under public licence and can be adapted for further development.