Publicação
ViruScopeDB: a comprehensive multi-omics software and database for highly infectious viruses
| dc.contributor.advisor | Carneiro, João | |
| dc.contributor.advisor | Sousa, Sérgio | |
| dc.contributor.advisor | Sá, Vítor | |
| dc.contributor.author | Lima, Ana Sofia Fafiães Pires de | |
| dc.date.accessioned | 2026-02-23T11:52:14Z | |
| dc.date.available | 2026-02-23T11:52:14Z | |
| dc.date.issued | 2025-11-07 | |
| dc.description.abstract | Highly infectious viruses, such as HIV, Ebolavirus, and SARS-CoV-2 have presented ongoing challenges to global health, leaving devastating consequences in their wake. These disruptions were not limited to the health field, as their profound economic and societal impact has been, and will continue to be, felt for decades. Effective surveillance and rapid diagnostics remain crucial to controlling their spread, yet current approaches to oligonucleotide data curation are fragmented, virus-specific, and generally highly dependent on manual approaches. To address these limitations, this thesis presents ViruScope, an automated bioinformatics tool for multi-omics data mining, in silico primer generation, validation, and scoring, together with ViruScopeDB, a centralized and continuously updated cross-viral database built on the results of the tool. The methodology integrates large-scale genomic data retrieval and alignment, literature-based extraction of experimentally validated primers (AROLit v.3), in silico primer generation and filtering (iSOP v.3), and a novel scoring framework, encompassing GC content, melting temperature, cross-species conservation, and a way to rank primers by how likely they are to not form undesirable secondary structures (No-Fold%). These modules, previously designed for specific viruses, were re-engineered into a scalable, optimized and generalized pipeline, deployed as both a command-line program and a user-friendly Shiny application, and compiled into ViruScopeDB as an openly accessible repository. Case studies conducted on Ebola datasets demonstrated the tool’s capacity to retrieve, validate, and score primers from both literature and computational approaches, producing results consistent with experimental best practices while enabling more nuanced ranking of primer candidates. Filtering by conservation scores and No-Fold% - the final and ViruScope-exclusive parameters - revealed gene and region-specific differences in conservation and stability, reinforcing the advantage in automated and scalable approaches for diagnostic tool design. By unifying data retrieval, primer design, and validation into a reproducible, automated workflow, ViruScope and ViruScopeDB provide a novel, scalable, and FAIR (Findable, Accessible, Interoperable, Reusable) solution to some of the challenges of molecular diagnostics. This work demonstrates the potential of computational pipelines to accelerate diagnostic assay development, improve cross-viral surveillance, and strengthen global preparedness for both ongoing and potential emerging viral threats. | eng |
| dc.identifier.tid | 204177812 | |
| dc.identifier.uri | http://hdl.handle.net/10400.22/31875 | |
| dc.language.iso | eng | |
| dc.relation | UIDB/04423/2020 and UIDP/04423/2020, 10.54499/LA/P/0008/2020,10.54499/UIDP/50006/2020, UIDB/04050/2020; UIDB/00319/2020; UIDB/00127/2020 | |
| dc.rights.uri | N/A | |
| dc.subject | Bioinformatic | |
| dc.subject | Virology | |
| dc.subject | Database | |
| dc.subject | PCR | |
| dc.subject | Oligonucleotide | |
| dc.title | ViruScopeDB: a comprehensive multi-omics software and database for highly infectious viruses | eng |
| dc.type | master thesis | |
| dspace.entity.type | Publication | |
| thesis.degree.name | Master’s degree in Biostatistics and Bioinformatics Applied to Health |