The Virus Analysis Tool (VAT) - A computational tool for the characterisation and monitoring of viruses during an acute outbreak

A main limitation of the response to novel virus outbreaks is the lack of information. While virus identification by next generation sequencing is quick, the investigation of the clinical and biological virus properties takes much longer. Moreover, methods for the early detection of novel virus strains with changed pathogenicity, transmissibility, drug sensitivity, and/ or immunogenicity are needed. Computational approaches have the potential to fill these gaps. We have created a method that identifies determinants of virus behaviour by identifying amino acid sequence positions that are differently conserved between related viruses and subsequent computational modelling of their impact on protein structure/ function. Our research has already identified substantial differences between SARS-CoV-2 and SARS-CoV. Although SARS-CoV-2 and SARS-CoV share a sequence identity of about 80%, the majority of the remaining positions are differentially conserved, which is reflected in differences in clinical behaviour, cell tropism, and drug sensitivity. Here, we will develop this approach into a webserver (the 'Virus Analysis Tool', VAT) that can be used by everyone involved in SARS-CoV-2 research and treatment. In the current outbreak, VAT will enable researchers to compare the genomic sequences of novel SARS-CoV-2 isolates to those of other SARS-CoV-2 strains and to identify novel strains rapidly, which are likely to be characterised by changes in phenotype, for example in disease severity, drug sensitivity, or immunogenicity. Hence, VAT will be a tool for the effective monitoring of the emergence of novel virus variants. VAT will also increase our preparedness for future virus outbreaks.