VIRUS-MVP: Frequently Asked Questions (FAQs)
General Use and Scope
1. What is VIRUS-MVP and what problem does it solve?
VIRUS-MVP is a modular, pathogen-agnostic platform for analyzing and visualizing viral genomic data. It integrates mutation annotation, lineage tracking, and literature-based functional insights for user-provided or public health surveillance datasets. Its main goal is to empower researchers and public health users to explore viral evolution and variant impacts using a toolkit they can run locally or on the cloud.
2. Which viruses are currently supported by default?
The public instance supports SARS-CoV-2 and Mpox (MPOX). Development branches are available for RSV and Influenza, and the toolkit can be adapted to other viruses through a configuration-based setup.
3. Is VIRUS-MVP intended to replace tools like Nextstrain or Outbreak.info?
No. VIRUS-MVP is designed to complement existing tools. While tools like Nextstrain emphasize phylogenetics and global surveillance, VIRUS-MVP focuses on mutation-level functional annotation, variant tracking, and customized user data processing, including local and environmental (e.g., wastewater) samples.
Data Input and Uploading
4. What input formats does VIRUS-MVP accept?
VIRUS-MVP supports VCF, FASTA, and BAM files for mutation analysis. Metadata can be included in TSV or JSON format. Wastewater samples processed using Freyja (from aligned BAMs) can also be used for deconvolution-based input.
5. How do I upload my own data?
You can upload your data via the “Upload” section on the dashboard, which accepts VCF, FASTA, and metadata files. File naming conventions and format guidelines are now provided in the updated documentation and Help section.
6. Can I analyze wastewater or environmental sequencing data?
Yes. VIRUS-MVP supports deconvolution of mixed viral populations in wastewater using Freyja, with mutation filtering options to account for low-abundance and fragmented viral RNA. Visualizations currently show sample-level mutation profiles and will soon include lineage-stratified views.
Customization and Extension
7. Can I use VIRUS-MVP with viruses other than SARS-CoV-2 and MPOX?
Yes. The framework is pathogen-agnostic. The GitHub repository includes a guide on how to adapt the system to other viruses by configuring genome references, annotation files, and dashboard metadata using a central ad-resource.json file.
8. Is programming experience required to customize VIRUS-MVP?
While some familiarity with command-line tools is helpful, extensive helper scripts, usage examples, and configuration templates are provided to reduce technical overhead.
Technical Setup and Deployment
9. How is VIRUS-MVP deployed?
VIRUS-MVP is packaged using Docker for portability and reproducibility across environments. Instructions for Docker-based and native installation are available on GitHub.
10. Does Docker impact performance?
Docker provides portability but may incur slight performance overhead for large datasets. For high-performance settings, native installation is recommended.
Annotation and Functional Insights
11. How are functional annotations generated?
VIRUS-MVP integrates curated annotations from literature, public databases, and community input. It uses the Viriation tool, which employs NLP models (e.g., BERT) and gradient boosting to mine and summarize functional mutation impacts.
12. Do annotations include newly discovered mutations?
The system is updated regularly to incorporate emerging data. NLP pipelines support near-real-time extraction of mutation impacts from the literature to keep annotations current.
Data Export and Interoperability
13. Can I export the analysis results for use in other platforms?
Yes. You can download analysis outputs in JSON, TSV, or PDF formats. JSON exports support downstream use in tools like CovMT or Outbreak.info, and we are actively developing a REST API for broader integration.
14. Can VIRUS-MVP be integrated with other platforms?
We are developing an API for programmatic data access and plan to support standard data exchange formats (e.g., JSON, XML) to enable integration with external surveillance tools and dashboards.
Support and Community
15. Where can I report issues or request features?
You can use the GitHub issue tracker on our repository: https://github.com/cidgoh/VIRUS-MVP. Contributions, feedback, and new feature requests are welcome from the community.