VARIANT Web Server for Viral Mutation Analysis
Figure 1: Overview of the VARIANT web server for genome- and protein-level viral mutation analysis. The VARIANT web server supports both single- and multi-segment viral genomes and offers single or batch decoding modes. The workflow begins with user pre-configuration and input of reference genome and proteome sequences (FASTA Format) along with aligned viral genomes (MSA Format). The server performs mutation decoding at both the nucleotide (genome-level) and amino acid (protein-level) resolution, supporting standard mutation types such as substitutions, insertions, and deletions, as well as co
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Paper title: VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels Abstract: A comprehensive analysis of viral mutations is essential for understanding viral evolution, disease epidemiology, diagnosis, drug resistance, etc. However, challenges remain in capturing complex mutation patterns and supporting diverse viral families with varying genome architectures. To address these needs, we present VARIANT, an web server for mutational analysis of RNA viral genomes and associated viral products across both single- and multi-segment virus genomes. The server takes as input a viral reference genome, a reference protein sequence, and/or multiple sequence alignment, and automatically provides full annotation of mutation types, including standard categories such as point mutations (missense, silent, and nonsense), insertions, deletions, or frameshift events in both coding and non-coding regions. In addition, VARIANT detects three biologically significant mutation patterns that are overlooked by conventional software/packages: ``row mutations'' (consecutive substitutions within a window of 3 nts), ``hot mutations'' (two non-consecutive substitutions within a window of 3 nts), and potential programmed ribosomal frameshifting (PRF) regions. The server currently contains automatic analysis of major viral pathogens, including SARS-CoV-2, HIV-1, Influenza H3N2, Ebola virus, and Chikungunya virus. It also allows users to analyze customized viruses. Users can track VARIANT analysis progress in real time, visualize mutation distributions, and download structured result Passages referencing this figure: previously published techniques [ 23 , 17 ] and is implemented in Python with a modular architecture that separates user interaction, mutation processing, and the result output into distinct components. It is implemented via Railway and uses the FastAPI framework to support asynchronous task execution, real-time progress tracking, and structured file management. The typical VARIANT workflow (see Figure 1 ) begins with three required input files from users: 1) a reference genome in FASTA format, 2) a corresponding reference proteome (amino acid sequences), and 3) a multiple sequence alignment (MSA) file of viral genomes aligned to the reference. Users can either select a pre-configured virus (e.g., SARS-CoV-2, HIV-1, Influenza H3N2, Chikungunya, Zaire Ebola) or upload custom virus referenc s for streamlined data management. The web interface is fully automated and allows users to monitor the analysis pipeline in real time. Once users click the ”Generate All Visualizations”, the interactive visualizations are provided to further interpret the results, such as genome-wide mutation barcode maps, mutation rate statistics on each protein, row/hot mutation spots, and potential PRF sites. Figure 1: Overview of the VARIANT web server for genome- and protein-level viral mutation analysis. The VARIANT web server supports both single- and multi-segment viral genomes and offers single or batch decoding modes. The workflow begins with user pre-configuration and input of reference genome and proteome sequences (FASTA Format) along with aligned viral genomes (MSA Format). The server perfor
