Development of a graphical bioinformatics tool for viral taxonomic level demarcation

• Grant number: 23/17992-8
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: March 01, 2024
• End date: December 31, 2024
• Field of knowledge: Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
• Principal Investigator: Arthur Gruber
• Grantee: Igor Custodio dos Santos
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

Viruses exhibit a much greater diversity than that observed in cellular organisms. The classic classification proposed by David Baltimore more than 50 years ago was based on the routes of transmission of information from viral genomes, and despite the enormous advancement of knowledge, this classification still represents an important conceptual foundation. However, the taxonomy of viruses is still disorganized, with taxonomic attribution rules often based on different criteria and inconsistent between different groups of viruses. Only in 2023, the International Committee on Taxonomy of Viruses (ICTV) decided to finish the utilization of phage morphology and create a hierarchical classification with 15 taxonomic levels. Given the enormous advancement in viral genome sequencing, especially from metagenomic samples, the development of tools for the taxonomic classification of viral sequences has become fundamental. Currently, there already exist a relatively large set of applications with different methodological approaches, which allow to classify viruses in more specialized taxonomic levels such as species, genus and family. The big challenge, however, remains being the classification of more basal taxonomic levels such as order, class, phylum and kingdom, for those cases where a virus does not fit in the most specialized level. For the more basal categories, a promising methodology is the share level of structural domains of proteins, since along the evolution, proteins can conserve their functional domains through 3D structure, even though the primary sequences are very divergent. The development of a simple and integrated tool, using different metrics and displaying a graphical output in a heatmap plot would be very useful for the easy visualization of viral groups. The utilization of different distance metrics such as the nucleotide, protein, maximum likelihood (based on an evolutionary model) and structural distance, all integrated in a unique tool, is totally novel and can represent an important contribution to the scientific community of virology, aiming at the demarcation of taxonomic ranks and the classification of viruses. In this project, we aim to develop this integrated tool for the analysis and graphical visualization of biological distance data using primary sequences and 3D structures of proteins. We intend to validate this tool using genome data of dsRNA viruses of the Totiviridae and Amalgaviridae families, and of bacteriophages of the class Caudoviricetes.