Tracking Bat Viruses in the Atlantic Forest: Genome Sequencing and Evolutionary Insights into Zoonotic Potential

• Grant number: 25/01953-9
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: April 01, 2025
• End date: March 31, 2027
• Field of knowledge: Biological Sciences - Microbiology
• Principal Investigator: Luiz Gustavo Bentim Góes
• Grantee: Catarina Marcon Chiappetta
• Host Institution: Institut Pasteur de São Paulo (IPSP). São Paulo , SP, Brazil
• Associated research grant: 22/13054-0 - Epidemiological, evolutionary and ecological spillover-risk assessment of bat viruses from Atlantic Forest Hotspot, AP.JP

Abstract

Brazil harbors the second-largest mammal diversity in the world. At the same time, the nation has one of the highest levels of animal and agricultural production, with high levels of deforestation, which are considered to be "drivers" of the emergence of infectious diseases. In addition, Brazil is home to 15% of the world's bat diversity, recognized as one of the main hosts of origin of highly pathogenic emerging viruses. In the last decade, new viruses from different viral families capable of infecting mammals have been identified in bats, including species from the viral families: Coronaviridae, Paramixoviridae, Filoviridae, Bunyaviridae, Orthomixoviridae, Astroviridae, Arenaviridae, Rhabdoviridae, Flaviviridae, Adenoviridae, and others. Preliminary studies conducted by our group indicate that bats from AF are hosts of distinct viruses, including a great diversity of Alphacoronavirus, Betacoronavirus, Influenza virus A, Paramyxovirus, Hantavirus, and Arenavirus, all related to known pathogenic viruses. Despite the detection and preliminary phylogenetic analysis with partial gene sequences, the complete genome recovery from bat-borne viruses is still tremendously hard to be acquired. Multiple factors could hamper the full genome recovery from bat virus, including low viral load consequence of host adaptation and co-evolution, the phase of infection, the presence of molecular inhibitors, the high degree of host materials, and the degradation of virus RNA. Despite these difficulties, few protocols and molecular tools have been improved, helping the success in the recovery of virus genomes by Next-generation sequencing as the use of library capture design exclusively for specific virus groups. The main objective of this project is the full genome recovery of the arena-, hanta-, corona-, and paramyxovirus genomes detected on bats obtained from Atlantic Forest Biome. The project's first step is screening bat samples using a broad and sensitive molecular assay to detect arenaviruses, hantaviruses, coronaviruses, and paramyxoviruses. Positive samples will be used for NGS assays. Depending on the results, library capture for each target virus family will be constructed and used as a complementary step. Sanger conventional sequencing will close gaps by designing specific primers using the sequences obtained from NGS or based on the most similar virus sequence present in Genbank. These steps are essential for evolutionary analysis, co-phylogeny, and construction of pseudovirus based on the glycoprotein of each virus sequenced, making possible the preliminary analysis of the potential of spillover and emergence of specific virus detected in the Atlantic Forest biome.