A research team from the Institute for Integrative Systems Biology (I2SysBio), located at the University of Valencia Science Park (PCUV), together with other Spanish centers, has created software to analyze the evolution of SARS-CoV-2 in patients suffering chronic infections by this virus, which can last for many months. The tool, VIPERA (Viral Intra-Patient Evolution Reporting and Analysis), has been described in the journal Virus Evolution, and evaluates the evolution of serial samples during infection through the report it automatically generates
It is an intuitive and scalable tool that facilitates access to the most advanced evolutionary analyses: it allows any professional to track the different populations of the virus within the same patient and study its adaptive changes associated with its transmissibility, pathogenicity or the administration of treatments. The Department of Clinical Microbiology of the Hospital Clínic de Barcelona, the CIBER of Infectious Diseases (CIBERINFEC), the Institute of Biomedicine of Valencia (IBV-CSIC) and the CIBER of Epidemiology and Public Health (CIBERESP) have also participated in the project.
"After validating the software with known datasets, we have successfully applied it to a new case, and have managed to reveal interesting population dynamics and evidence of adaptive evolution. In the future, we want to apply VIPERA to the study of other organisms that sustainably affect the same patient, such as HIV or bacteria like Mycobacterium tuberculosis," explains Mireia Coscollá, a researcher at the Institute for Integrative Systems Biology (I2SysBio), located at the University of Valencia Science Park (PCUV).
“After validating the software with known datasets, we have successfully applied it to a new case, and have managed to reveal interesting population dynamics and evidence of adaptive evolution. In the future, we want to apply VIPERA to the study of other organisms that sustainably affect the same patient, such as HIV or bacteria like Mycobacterium tuberculosis”, Mireia Coscollá, researcher at the I2SysBio
The importance of this work lies in the fact that it analyzes chronic infections, which are more pathogenic or transmissible, as a potential source of new SARS-CoV-2 variants of concern. "With the report generated, it is possible to analyze how the virus evolves throughout the infection," explains Miguel Álvarez Herrera, researcher at I2SysBio and first author of the article.
Until now there was no tool that integrated and standardized the analysis of the intra-patient evolution of SARS-CoV-2. VIPERA is simple to use and generates an easily interpretable report. In addition, it is open source and scalable. "By applying this tool, we have analyzed a chronic infection in depth, revealing the appearance of mutations associated with immune escape and variants of concern," highlights Jordi Sevilla, co-first author of the article.
“By applying this tool, we have analyzed a chronic infection in depth, revealing the appearance of mutations associated with immune escape and variants of concern”, Jordi Sevilla, co-first author of the article
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