Animal Virus Projects

Overview

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.

---

Contents

Animal virus-focused GLUE projects developed in the Gifford lab:

• Bluetongue virus: BTV-GLUE
• Rabies virus: RABV-GLUE
• Lassa virus: Lassa-GLUE

---

BTV-GLUE

Background

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.

Scope & History

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.

Features

• Comprehensive Database: Contains a curated collection of BTV sequences linked to isolates with detailed metadata, providing a robust foundation for comparative genomics.

• Genotyping and Visualization Tool: Supports genotyping and visualization of submitted segment 2 sequences, enabling detailed analysis and comparison within this key genomic region.

• 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.

• Phylogenetic Structure: Organizes BTV sequence data in a phylogenetically-structured format, allowing users to explore evolutionary relationships among BTV strains and serotypes effectively.

• Automated Genotyping: Utilizes GLUE's maximum likelihood clade assignment (MLCA) algorithm to classify BTV sequences by serotype and lineage, supporting systematic strain classification.

• Rich Annotations: Features annotated reference sequences to enable comparative analysis, focusing on conservation, structural context, and genotype-to-phenotype relationships.

• 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.

• Exploratory and Operational Applicability: Suitable for research and public health applications, supporting exploratory studies and routine genomic surveillance of BTV.

Core Project Overview

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

---