Animal Virus Projects
Animal viruses encompass a diverse array of pathogens that infect wildlife and livestock, leading to significant health impacts, economic losses, and challenges in veterinary medicine and wildlife conservation. Outbreaks of viral diseases can lead to severe economic repercussions in the agriculture sector, with implications for livestock production, trade, and food supply.
Effective surveillance, vaccination, and biosecurity measures are crucial for managing animal viral diseases, with ongoing research focusing on understanding virus-host interactions, transmission dynamics, and the development of vaccines and therapeutics. Comparative genomic approaches play an important role in addressing these challenges.
Despite the significant impact of animal viruses on agriculture and wildlife, many of these viruses receive relatively little research attention and funding. As a result, genomics resources for numerous animal viruses remain limited, hindering effective surveillance and control efforts. GLUE addresses this gap by offering a flexible platform that can rapidly establish robust genomic databases and analysis tools for any chosen virus. This adaptability enables researchers to develop tailored resources, supporting the study of under-researched animal viruses and advancing our understanding of their transmission, evolution, and control.
Note: Some animal viruses also have the potential to spill over into human populations, posing emerging infectious disease risks. Here these are grouped as a distinct, but overlapping category: spillover viruses.
Animal virus-focused GLUE projects developed in the Gifford lab:
- Bluetongue virus: BTV-GLUE
- Rabies virus: RABV-GLUE
- Lassa virus: Lassa-GLUE
- Small ruminant lentiviruses (SRLVs): Lentivirus-GLUE-SRLV
Bluetongue virus (BTV) is a double-stranded RNA virus from the Reoviridae family that causes bluetongue disease, primarily affecting domestic and wild ruminants like sheep, cattle, and goats. BTV is an arbovirus, transmitted by biting midges (Culicoides species). Infection with BTV can lead to severe disease, especially in sheep, characterized by fever, swelling, and cyanosis of the tongue, resulting in high mortality rates. While cattle and goats often show subclinical infections, the economic impact of BTV outbreaks is significant due to livestock losses, trade restrictions, and veterinary costs.
BTV's genome consists of 10 RNA segments, encoding structural and non-structural proteins, and the virus's segmented nature allows for genetic reassortment, leading to the emergence of new strains. With over 27 known serotypes and the potential for reassortment, developing effective vaccines is challenging. Current control measures include vaccination, vector control, and movement restrictions. Research efforts focus on improving vaccines that target multiple serotypes and understanding the virus's transmission dynamics, particularly its interactions with insect vectors.
BTV-GLUE, developed at the University of Glasgow's Centre for Virus Research (CVR), is a bioinformatics resource designed to facilitate the study of BTV biology and evolution. The database integrates curated sequences from NCBI, reference isolates, and metadata, along with genome feature annotations, multiple sequence alignments, and phylogenetic trees. BTV-GLUE also includes an automated genotyping tool for all BTV segments, supporting both online and offline use as a toolkit for researchers. This resource aims to support the BTV research community in adopting a unified nomenclature and advancing studies on BTV strain properties and epidemiology.
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Comprehensive Database: Contains a curated collection of BTV sequences linked to isolates with detailed metadata, providing a robust foundation for comparative genomics.
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Genotyping and Visualization Tool: Supports genotyping and visualization of submitted segment 2 sequences, enabling detailed analysis and comparison within this key genomic region.
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Pre-built Multiple Sequence Alignments: Includes pre-built alignments for all 10 BTV segments, available for download in user-defined sections, to support customized genomic analyses.
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Phylogenetic Structure: Organizes BTV sequence data in a phylogenetically-structured format, allowing users to explore evolutionary relationships among BTV strains and serotypes effectively.
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Automated Genotyping: Utilizes GLUE's maximum likelihood clade assignment (MLCA) algorithm to classify BTV sequences by serotype and lineage, supporting systematic strain classification.
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Rich Annotations: Features annotated reference sequences to enable comparative analysis, focusing on conservation, structural context, and genotype-to-phenotype relationships.
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Web User Interface: The BTV-GLUE-WEB extension provides a web interface for browsing the BTV-GLUE database, along with tools for sequence analysis and visualization.
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Exploratory and Operational Applicability: Suitable for research and public health applications, supporting exploratory studies and routine genomic surveillance of BTV.
| Virus | Bluetongue virus (BTV) |
|---|---|
| Development Period | 2016-2020 |
| Lead Developer | Josh Singer |
| Main Objectives | Genotyping, Drug Resistance Analysis |
| 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 | None Yet |
Small ruminant lentiviruses (SRLVs) are a group of viruses that infect sheep and goats, causing chronic, lifelong diseases that affect various organ systems. These infections primarily spread through vertical transmission from mother to offspring via colostrum or milk, though horizontal transmission can also occur through close contact, respiratory secretions, or shared equipment---particularly in crowded conditions.
SRLVs include viruses that were initially considered separate species. Ovine maedi-visna virus (OMVV) was first isolated from sheep in Iceland in the 1950s, while caprine arthritis-encephalitis virus (CAEV) was isolated from a dairy goat in North America in 1974. It is now understood that both viruses occur in sheep and goats and represent two major genotypes (A and B) of a single virus species (SRLV). Additional genotypes, such as SRLV-C and SRLV-E, have also been identified.
These viruses target cells of the immune system, particularly macrophages and dendritic cells, leading to persistent viral replication and progressive tissue damage. Clinical signs may include pneumonia, wasting, polyarthritis, mastitis, and, in severe cases, paralysis or organ failure. Many infected animals remain asymptomatic for years, with signs typically emerging after long incubation periods. Genetic factors influence variations in disease susceptibility and symptom severity among different species and breeds.
Control measures for SRLVs rely heavily on preventive strategies, including test-and-cull programs, managing colostrum sources, and improving biosecurity practices to limit transmission. Molecular diagnostics, such as PCR and serological tests, have improved the accuracy of detection, enabling more targeted containment efforts. Genomic studies provide insights into SRLV diversity, transmission dynamics, and host adaptations, contributing to the development of tailored genotyping tools that can enhance herd management and reduce economic losses associated with SRLV infections.
Lentivirus-GLUE-SRLV, an extension to Lentivirus-GLUE, was developed at the University of Glasgow's Centre for Virus Research (CVR) to facilitate the study of SRLV diversity and evolution. This resource integrates all published SRLV sequence data with detailed metadata, including sequence-associated information (length, publication date), taxonomic details (genotype, subtype), and isolate-associated data (host species, sampling date and location, and isolation source).
Lentivirus-GLUE-SRLV supports the genotyping of SRLV sequences via Maximum Likelihood Clade Assignment (MLCA). This method allows the classification of sequences into genotypes and subtypes defined through phylogenetic analysis of full-length reference genome sequences. The resource aims to support both exploratory research and operational applications, such as monitoring viral evolution and improving disease control strategies.
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Comprehensive Database: Contains curated SRLV sequence data linked to metadata for comparative genomic studies.
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Genotyping and Visualization Tool: Facilitates the classification of SRLV sequences into genotypes and subtypes using the MLCA algorithm, enabling detailed analysis of viral diversity.
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Phylogenetic Structure: Organizes SRLV data in a phylogenetically structured format to explore evolutionary relationships effectively.
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Automated Genotyping: Leverages GLUE's MLCA algorithm for accurate and efficient classification of SRLV sequences by genotype and subtype.
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Rich Annotations: Features annotated reference sequences for investigating conservation, structural context, and genotype-to-phenotype relationships.
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Reproducible Workflows: Provides version-controlled, documented workflows to support transparent and collaborative hypothesis testing.
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Exploratory and Operational Applicability: Enables studies on SRLV origins and emergence, as well as operational applications for genomic surveillance and disease control.
| Virus | Small Ruminant Lentivirus (SRLV) |
|---|---|
| Development Period | 2012-2020 |
| Lead Developer | Robert Gifford |
| Main Objectives | Genotyping, Origins and Evolution Investigation |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Project | GitHub |
| Online Access | None at present |
| Status | Mature. |
| User Guide | Wiki |
GLUE by Robert J. Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.