They create software that evaluates how SARS-CoV-2 evolves throughout the infection

VALENCIA, 21 Mar. (EUROPA PRESS) -

A research team from the Institute of Integrative Systems Biology - I2SysBio, a joint center of the University of Valencia and the Higher Council for Scientific Research - and other Spanish centers has created software that allows analyzing the evolution of SARS-CoV. 2 within patients who suffer chronic infections from this virus, which can last many months.

The tool, called 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 generates automatically.

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 their adaptive changes associated with their transmissibility, pathogenicity or the administration of treatments. . The Department of Clinical Microbiology of the Hospital Clínic of Barcelona, ​​the CIBER of Infectious Diseases (Ciberinfec), the Institute of Biomedicine of València (IBV-CSIC) and the CIBER of Epidemiology and Public Health (Ciberesp) have also participated in the project.

"After validating the software with known data sets, we have successfully applied it to a new case, and we 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 such as Mycobacterium tuberculosis," explains Mireia Coscollá, I2SysBio researcher, in a statement.

The importance of this work lies in the fact that it analyzes chronic, more pathogenic or transmissible infections, as a potential source of new variants of SARS-CoV-2 of concern. "With the report generated, we can analyze how the virus evolves throughout the infection," comments Miguel Álvarez Herrera, I2SysBio researcher and first signatory of the article.

Until now, there was no tool that integrated and standardized the analysis of the intrapatient evolution of SARS-CoV-2. Using VIPERA is simple and generates an easily interpretable report. Additionally, 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 signatory of the article.

This work is part of the project CNS2022-135116, which has been funded by the European Union NextGenerationEU/PRTR, the Ministry of Science and Innovation, the Generalitat Valenciana, the European Research Council, the Ministry of Industry and Competitiveness, and by the Funds FEDER. The computational work was carried out in Garnatxa, the high-performance computing (HPC) cluster of the Institute of Integrative Systems Biology (I2SysBio).