Arbovirus Projects
Arboviruses, or arthropod-borne viruses, are a diverse group of pathogens transmitted to humans and animals through the bites of infected arthropods, such as mosquitoes and ticks. These viruses cause a range of diseases, some of which can lead to severe morbidity and mortality. The public health significance of arboviral diseases has increased due to factors like climate change, urbanization, and globalization, which have expanded the geographic range and transmission risk of these viruses.
The rising incidence of arboviral diseases underscores the need for robust surveillance and control measures to minimize their impact. Effective strategies include vector control, personal protective measures, and vaccine development—successful vaccines exist for some arboviruses, such as yellow fever. Comparative genomics tools are playing an increasingly important role in these efforts.
All arbovirus projects developed in the Gifford Lab (with the sole exception of BTV-GLUE) were developed at the Centre for Epidemic Response and Innovation (CERI) as part of its involvement in the CLIMADE consortium (Climate Amplified Diseases and Epidemics). These projects focus on genomic epidemiology, leveraging comparative genomics to aid in the prediction, tracking, and control of diseases amplified by climate change, in line with CLIMADE’s mission to address the global health challenges posed by arboviruses.
This page provides a comprehensive list of GLUE projects developed for arboviruses in the Gifford Lab:
- Dengue virus: Dengue-GLUE
- West Nile virus: WNV-GLUE
- Chikungunya virus: CHIKV-GLUE
- Yellow fever virus: YFV-GLUE
- Bluetongue virus: BTV-GLUE
Dengue virus (DENV) is a mosquito-borne RNA virus that belongs to the Flaviviridae family. It is transmitted primarily by Aedes aegypti and Aedes albopictus mosquitoes and is responsible for dengue fever, a potentially severe and life-threatening illness that occurs mainly in tropical and subtropical regions. The virus exists as four distinct serotypes (DENV-1 to DENV-4), each capable of causing disease. Infection with one serotype provides lifelong immunity to that specific serotype but not to the others, leading to the possibility of sequential infections that can result in more severe disease outcomes, such as dengue hemorrhagic fever or dengue shock syndrome. The disease burden is significant, with hundreds of millions of cases worldwide annually, making dengue a major global public health concern.
Dengue-GLUE provides a broad foundation for comparative genomics studies of dengue virus (DENV). It is the third flavivirus-focused GLUE project family developed by the Gifford Lab (after HCV-GLUE and Flaviviridae-GLUE). Extension projects are being developed at CERI with a primary focus on the molecular epidemiology aspects of DENV genomics.
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Comprehensive Database
Integrates dengue virus (DENV) genome feature definitions, genome-length reference sequences, multiple sequence alignments, and standardized metadata for all DENV lineages, providing a robust foundation for comparative genomics. -
Automated Genotyping
Uses the maximum likelihood clade assignment (MLCA) algorithm to automate genotyping of DENV sequences, including subgenomic fragments, based on recently proposed lineage nomenclature. -
M49 Schema Extension
Includes an M49 schema extension for standardized country and region annotations, enhancing data consistency. -
Variant Calling
Offers variant calling capabilities for amino acid substitutions, facilitating detailed genetic analysis.
| Property | Description |
|---|---|
| Scope | Dengue virus (serotypes 1-4) |
| Development Period | 2023-2024 |
| Lead Developers | Robert J. Gifford |
| Main Objectives | Comparative genomics, Genotyping, Molecular epidemiology |
| Data Sources | NCBI, GISAID |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Access | GitHub |
| Status | Mature. Actively being developed |
| User Guide | GitHub Wiki |
- NCBI-Dengue-GLUE: Adds all GenBank sequences.
West Nile virus (WNV) is a mosquito-borne RNA virus from the Flaviviridae family, primarily transmitted to humans through the bite of Culex mosquitoes. Birds serve as the main reservoir for the virus, with occasional spillover to humans and other mammals, particularly horses, acting as dead-end hosts. First identified in Uganda in 1937, WNV has since spread globally, with significant outbreaks occurring in North America, Europe, and parts of the Middle East. While most human infections are asymptomatic or cause mild flu-like symptoms, a small percentage of cases develop into severe neuroinvasive diseases such as encephalitis, meningitis, or acute flaccid paralysis, particularly in older adults or those with weakened immune systems.
The virus's ability to spread via bird migration and its adaptability in mosquito vectors have contributed to its wide geographic range. There is no specific treatment or vaccine for WNV in humans, so public health efforts focus on controlling mosquito populations and minimizing human exposure through surveillance, vector control measures, and public awareness campaigns. Ongoing research seeks to better understand WNV's transmission dynamics, immune interactions, and pathogenesis to improve prevention and therapeutic strategies.
WNV-GLUE provides a broad foundation for comparative genomics studies of West Nile virus (WNV). It was developed at CERI from May-July 2024, and represents the fifth flavivirus-focused project family developed in the Gifford Lab (after HCV-GLUE, Flaviviridae-GLUE, Dengue-GLUE, and YFV-GLUE).
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Comprehensive Database
Incorporates all WNV sequences in GenBank. -
Automated Genotyping
Uses the maximum likelihood clade assignment (MLCA) algorithm to automate genotyping of WNV sequences, including subgenomic fragments -
M49 Schema Extension
Includes an M49 schema extension for standardized country and region annotations, enhancing data consistency. -
Variant Calling
Offers variant calling capabilities for amino acid substitutions, facilitating detailed genetic analysis.
| Property | Description |
|---|---|
| Scope | West Nile virus (WNV) |
| Development Period | 2023-2024 |
| Lead Developers | Robert J. Gifford |
| Main Objectives | Comparative genomics, Genotyping, Molecular epidemiology |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Access | GitHub |
| Status | Mature. Actively being developed |
| User Guide | GitHub Wiki (Under Construction) |
Chikungunya virus (CHIKV) is a mosquito-borne RNA virus from the Togaviridae family, primarily transmitted to humans by Aedes aegypti and Aedes albopictus mosquitoes. First identified during an outbreak in Tanzania in 1952, CHIKV is now globally distributed, with significant outbreaks in Africa, Asia, the Americas, and Europe. Chikungunya fever, the disease caused by CHIKV, is characterized by sudden onset of fever, severe joint pain, muscle aches, rash, and headache. While the disease is rarely fatal, joint pain can persist for months or even years in some cases, severely affecting the quality of life for those affected.
The virus's ability to spread rapidly in areas where its mosquito vectors are present has led to recurring outbreaks in tropical and subtropical regions. There is no specific antiviral treatment or licensed vaccine for chikungunya, so public health efforts focus on vector control, personal protective measures, and early detection to reduce the spread of the virus and mitigate outbreaks.
Research is ongoing to develop vaccines and therapeutics, as well as to better understand the mechanisms behind the virus's persistent joint symptoms.
CHIKV-GLUE provides a broad foundation for comparative genomics studies of chikungunya virus (CHIKV). Its development was initiated at CERI in September 2023 and a mature version of the project was published 2 months later.
- M49 schema extension (for country/region standardization)
- Genotyping tools (MLCA-based assignment of genotypes and lineages)
- Variant calling (AA substitutions)
- Incorporates all CHIKV sequences in GenBank
| Property | Description |
|---|---|
| Scope | Chikungunya virus (CHIKV) |
| Development Period | 2023-2024 |
| Lead Developers | Robert J. Gifford |
| Main Objectives | Comparative genomics, Genotyping, Molecular epidemiology |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Access | GitHub |
| Status | Mature. Actively being developed |
| User Guide | GitHub Wiki |
Yellow fever virus (YFV) is a mosquito-borne RNA virus that belongs to the Flaviviridae family and is the causative agent of yellow fever, a severe viral hemorrhagic disease. It is primarily transmitted by Aedes aegypti mosquitoes, with monkeys serving as the main reservoir in sylvatic (jungle) cycles. The virus is endemic in tropical regions of Africa and South America, where periodic outbreaks can lead to significant mortality. Symptoms of yellow fever range from mild flu-like illness to severe jaundice, bleeding, and organ failure, with high fatality rates in severe cases. Despite the availability of a highly effective vaccine, yellow fever remains a public health threat due to low vaccination coverage, increasing urbanization, and the expanding range of mosquito vectors.
YFV-GLUE provides a broad foundation for comparative genomics studies of yellow fever virus (YFV). It represents the fourth flavivirus-focused project family developed by the Gifford Lab (after HCV-GLUE, Flaviviridae-GLUE, and Dengue-GLUE). Extension projects are being developed at CERI with a primary focus on the molecular epidemiology aspects of DENV genomics.
- M49 schema extension (for country/region standardization)
- Genotyping tools (MLCA-based assignment of genotypes and lineages)
- Incorporates all YFV sequences in GenBank
| Property | Description |
|---|---|
| Scope | Yellow Fever Virus |
| Development Period | 2023-2024 |
| Lead Developers | Robert J. Gifford |
| Main Objectives | Comparative genomics, Genotyping, Molecular epidemiology |
| Data Sources | NCBI |
| Associated Tools | BLAST+, MAFFT, RAXML |
| Offline Access | GitHub |
| Status | Mature. Actively 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.