Spillover Virus Projects
We use the term 'spillover viruses' to denote viruses that typically circulate in animal reservoirs but have the potential to cross species barriers and infect humans, leading to outbreaks of zoonotic disease. These viruses are of significant public health concern due to their unpredictable emergence and the severe diseases they can cause in humans.
The GLUE projects within this category focus on tracking viral diversity, adaptation, and spread. By providing standardized datasets, comparative genomic tools, and integrative analysis frameworks, these projects aim to enhance surveillance, risk assessment, and response strategies for spillover events.
Spillover virus-focused GLUE projects developed in the Gifford lab. Please note this list contains projects grouped under other, additional categories:
- Rabies virus: RABV-GLUE
- Lassa virus: Lassa-GLUE
- Influenza Viruses: Flu-GLUE
- SARS-CoV2: CoV-GLUE
- Chikungunya virus: CHIKV-GLUE
- Dengue virus: Dengue-GLUE
- Yellow fever virus: YFV-GLUE
- West Nile virus: WNV-GLUE
- Zika virus: Zika-GLUE
Rabies virus (RABV) is a neglected zoonotic disease that causes around 59,000 human deaths each year, with a near 100% mortality rate after the onset of symptoms. The virus is a member of the Lyssavirus genus, within the Rhabdoviridae family, which is characterised by a single stranded, negative-sense RNA genome. Infection with RABV can occur in all species of mammal, but up to 99% of human rabies cases arise from bites from infected domestic dogs. Vaccinating dogs to interrupt transmission is therefore paramount, and a major focus of the 'Zero by 30' global strategy to eliminate human deaths from dog-mediated rabies by 2030.
RABV-GLUE aims to leverage new and existing RABV sequences in order to improve our understanding of the epidemiology and pathology of RABV.
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Analysis tool: provides genotyping, analysis and visualisation of submitted FASTA sequences.
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Comprehensive Database: RABV sequences and metadata from NCBI, updated daily and arranged into major and minor clades.
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Phylogenetic Structure: The data in RABV-GLUE is organized in a phylogenetically-structured manner, allowing users to explore evolutionary relationships easily.
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Automated Updates: RABV-GLUE provides an automatically-updated collection of RABV sequence data, ensuring users have access to the latest information for their analyses.
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Rich Annotations: Annotated reference sequences enable rigorous comparative genomic analysis related to conservation, adaptation, structural context, and genotype-to-phenotype associations.
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Automated Genotyping: RABV-GLUE can perform automated genotyping of RABV sequences (including subgenomic sequences) using GLUE's maximum likelihood clade assignment (MLCA) algorithm, as described here.
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Web user interface: The RABV-GLUE-WEB extension project defines a web user interface that supports online browsing of the RABV-GLUE sequence database, and provides web access to an in-built sequence analysis tool (provides genotyping, analysis and visualisation of submitted FASTA sequences).
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Exploratory and operational: The GLUE framework allows sequence-based resources to be used for exploratory work in a research setting, as well as operational work in a public or animal health setting.
| Virus | Rabies virus (RABV) |
|---|---|
| Development Period | 2016-2022 |
| Lead Developers | Josh Singer |
| Main Objectives | Surveillance, Outbreak Response, Genotyping |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Project | GitHub |
| Online Access | University of Glasgow CVR |
| Status | Mature. Not currently being developed |
| User Guide | GitHub Wiki (Under Construction) |
- NCBI-RABV-GLUE: Adds all GenBank sequences.
Lassa virus (LASV) is an arenavirus responsible for Lassa fever, a viral hemorrhagic illness endemic in West Africa. Lassa fever is a priority disease for public health organizations such as the World Health Organization (WHO) due to its epidemic potential and the high mortality rates associated with severe cases. Regular outbreaks place considerable strain on healthcare systems in affected regions, and the potential for Lassa virus to spread beyond endemic areas (through travel) raises global health concerns.
Lassa-GLUE was initially developed as part of a collaborative effort between research groups at the University of Glasgow and the University of Leuven. However, progress on the project was impacted by the emergence of SARS-CoV-2, which shifted research priorities. Although Lassa-GLUE has yet to be deployed in an active research context, it remains a relatively mature GLUE project with substantial foundational work completed.
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Comprehensive Database
Integrates LASV genome feature definitions, genome-length reference sequences, multiple sequence alignments, and standardized metadata for all LASV lineages, providing a robust foundation for comparative genomics. -
M49 Schema Extension
Includes an M49 schema extension for standardized country and region annotations, enhancing data consistency.
| Virus | Lassa virus |
|---|---|
| Development Period | 2019-2020 |
| Lead Developers | Robert J. Gifford |
| Main Objectives | Surveillance, Outbreak Response |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Online Access | None |
| Offline Access | GitHub |
| Status | Mature. Not currently being developed |
| User Guide | None Yet |
GLUE by Robert J. Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.