07/07/2025  |  Camila Neumam

https://butantan.gov.br/noticias/butantan-desenvolve-sistema-de-codigo-aberto-para-monitoramento-de-virus-da-dengue-covid-19-e-influenza- 

Viral Identification Pipeline for Emergency Response (VIPER) is on GitHub and is undergoing redesigns to be able to analyze the genomes of other viruses

Researchers from the Cell Cycle Laboratory at the Butantan Institute (LCC), participants in the Center for Viral Surveillance and Serological Evaluation (CeVIVAS), have developed software for genomic surveillance of SARS-CoV-2, influenza, and dengue viruses on an open-source platform within Windows.

The Viral Identification Pipeline for Emergency Response (VIPER) was built on Windows Subsystem for Linux (WSL), a kind of “emulator” that allows the inclusion of pipelines (automated workflows) within the system and the creation of a graphical interface. The goal is to allow researchers, who are not necessarily familiar with servers such as Linux (a free, open-source operating system), to include sequenced epidemiological samples.

“Most researchers use Windows, not Linux. Leaving the pipelines there and creating a more user-friendly graphical interface simplified this complex process, while enabling users to extract data,” says Alex Ranieri, bioinformatician at the Cell Cycle Laboratory (LCC) and creator of VIPER.

The name of the system was carefully thought out by the CeVIVAS team, coordinated by Sandra Coccuzzo, director of the Butantan Scientific Development Center, and Carolina Sabbaga, technical director of the LCC, during a flight from Italy to São Paulo after the EPIDEMICS9: 9th International Conference on Infectious Disease Dynamics, held in Bologna in 2023.

“We knew it had to be something related to Butantan, preferably the name of a snake, so we came up with the name Viper, which is a snake in English, and turned it into an acronym,” says Alex Ranieri. 

To install VIPER, you only need to have Windows 10 (version 2004) or Windows 11 downloaded on your computer. Produced entirely at Butantan, the system is available in the GitHub open source repository.

Usability

VIPER began running experimentally in 2023 with the assembly of genomes and then the phylogeny of SARS-CoV-2. Thus, it began to allow the inclusion of samples from Butantan and other users and comparison with samples from other groups, which also analyze the same virus. This investigation is fundamental for the genomic surveillance of a virus. 

Alex presented the system to the management of some Central Health Laboratories (LACENs), responsible for laboratory analyses of interest in epidemiological surveillance in the country, based in all states and the Federal District. As VIPER gained robustness, it began to be used by LACENs in Minas Gerais, Paraná, Bahia, and the Federal District—both through partnerships with Butantan and in their own analyses of viral genomes.

VIPER also has a new dengue virus strain system, which was developed with significant participation from the LCC team. The dengue virus has four serotypes, and each serotype has around five genotypes, but before the creation of this system, there was no systematic classification below the genotypes. 

“We were able to classify strains in a way that allows us to identify whether a new strain has entered Brazil, where it is coming from, and where it is going. When there is a new strain, the literature says that it may have the potential to cause major outbreaks. Therefore, it is crucial to understand where it comes from and where it is going in order to control and monitor it," says Alex Ranieri.

VIPER continues to be improved, and the bioinformatics team's idea is to make it capable of analyzing the genome of any virus, not just SARS-CoV-2, influenza, and dengue. 

In addition, Alex Ranieri believes that VIPER can also be used in other areas. “I see great potential for using it not only in research but also in education, in the sense of introducing the concepts of bioinformatics to a wider audience, such as high school students,” he reflects.

Democratization of access

In 2021, the Butantan Institute created the Variant Alert Network with the aim of identifying the SARS-CoV-2 strains circulating in the state of São Paulo at the time. In 2022, the network became CeVIVAS, which currently maintains genomic surveillance of the Covid-19 virus, as well as influenza, dengue, and chikungunya viruses.

At the height of the pandemic, CeVIVAS received up to 1,500 SARS-CoV-2 samples for sequencing each week. Faced with this overload, researchers saw the need to create an interface to automate sequencing as much as possible—which would later give rise to VIPER. The team also began offering bioinformatics courses to researchers who had scientific knowledge but not computer skills, to strengthen the monitoring team and offer autonomy to LACENs.

“At first, we gathered all the codes we had to be accessed with a click to allow analysis, but we still couldn’t make them available to the public. We also invested in sequencing courses and in the competence of the teams here at Butantan, who managed to master and create protocols to deal with biological big data,” recalls Alex Ranieri.

The ease of accessing VIPER and the fact that it is open source, meaning it can be accessed by anyone, makes genomic surveillance more accessible, in the bioinformatician's view. 

“The goal is not to patent or close a program that is helping people do their work, such as LACENS and Butantan itself. We welcome this proposal to leave the code open, because the more people discover the system, the more they can give us feedback to make it better and do their work better,” he notes.

The CeVIVAS Bioinformatics team also intends to launch an artificial intelligence platform linked to VIPER to enable the creation of epidemiological bulletins.

“The proposal is to create a very dynamic ecosystem in which people understand how it works, become familiar with the concepts, and are curious about what is being done,” concludes Alex Ranieri.