In a significant stride towards enhancing genomic surveillance, researchers from the Cell Cycle Laboratory of the Butantan Institute (LCC), who are also part of the Center for Viral Surveillance and Serological Evaluation (CeVIVAS), have developed an innovative software solution known as VIPER. Standing for Viral Identification Pipeline for Emergency Response, this tool is designed to facilitate the genomic monitoring of critical viruses such as SARS-CoV-2, Influenza, and Dengue. What sets VIPER apart is its user-friendly design on a platform that is open-source and runs within the Windows environment.
VIPER: A Game-Changer in Genomic Surveillance
VIPER was meticulously crafted to operate on Windows Subsystem for Linux (WSL), which acts as an emulator allowing the integration of automated workflows, known as pipelines, into the Windows system while providing a graphical interface. This approach simplifies the complex process of genomic data analysis, making it accessible to researchers who might not be well-versed in Linux servers. The software’s development was spearheaded by bioinformatician Alex Ranieri from the LCC, who envisioned a system that could be easily navigated and utilized by a broader range of scientists.
The name VIPER was cleverly coined during a flight from Italy to São Paulo by the CeVIVAS team, led by the Butantan Institute’s Scientific Development Center Director, Sandra Coccuzzo, and LCC Technical Director, Carolina Sabbaga. Inspired by the English word for a type of snake, ‘viper’, they created an acronym that aptly represents the software’s purpose.
Installing and Using VIPER
To get started with VIPER, users need only to have Windows 10 (version 2004) or Windows 11 installed on their computers. The software, developed entirely at the Butantan Institute, is freely available on GitHub, a repository for open-source code.
In 2023, VIPER began its experimental phase, focusing on the assembly of SARS-CoV-2 genomes and phylogenetic analysis. Its capability to incorporate samples from various sources, including those from the Butantan Institute and external users, allows for comprehensive comparison and investigation, which are essential for effective genomic surveillance.
Expanding Usability and Impact
The software has been embraced by several Central Health Laboratories (LACENs) across Brazil, including those in Minas Gerais, Paraná, Bahia, and the Federal District. These laboratories are responsible for epidemiological surveillance and have found VIPER to be an invaluable tool in their analyses.
One of VIPER’s standout features is its implementation of a new lineage system for the dengue virus. This classification system enables the identification of new lineages, their origins, and destinations, which is crucial for controlling and monitoring potential outbreaks.
Looking ahead, the VIPER team aims to expand the software’s capabilities to analyze the genomes of any virus, not limited to SARS-CoV-2, influenza, and dengue. Moreover, Ranieri sees potential in using VIPER as an educational tool to introduce bioinformatics concepts to a wider audience, including high school students.
Democratizing Access to Genomic Surveillance
CeVIVAS was established in 2022 as an evolution of the Variants Alert Network created in 2021 to track SARS-CoV-2 strains in São Paulo. Facing a deluge of 1,500 samples weekly during the pandemic’s peak, the researchers recognized the need for an automated solution, leading to the development of VIPER.
By making VIPER open-source and easily accessible, the Butantan Institute is democratizing genomic surveillance. The software’s non-commercial nature ensures that it remains a tool for aiding public health efforts rather than being locked behind patents or paywalls.
Future Developments
The CeVIVAS bioinformatics team plans to integrate an artificial intelligence platform with VIPER to automate the generation of epidemiological bulletins. This initiative aims to create a dynamic ecosystem where users can understand the functionality, engage with the concepts, and contribute to the system’s improvement.
Source: Butantan
