ArticlePLoS pathogens2022
Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination.
Article in PLoS pathogens, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- Adaptation of wild-type rabies virus on vaccine producing cell line and its quantification by peroxidase-based immunostaining.Archives of virology · 2026Article
- Comprehensive genomic analysis of rabies virus in India reveals distinct lineages and evolutionary stability.Virus genes · 2026Article
- Differences in codon usage between host-species-specific rabies virus clades are driven by non-GC3 nucleotide composition.Virus evolution · 2026Article
- Genomic characterization of a dog-mediated rabies outbreak in El Pedregal, Arequipa, Peru.PLoS neglected tropical diseases · 2025Article
- Integrated Community-Based Reporting and Field Diagnostics for Improved Rabies Surveillance in Rural Laikipia, Kenya.Zoonoses and public health · 2025Article
- Typing Arctic and Africa-2 clades of rabies virus using clade-defining single nucleotide polymorphisms.Archives of microbiology · 2025Article
- MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens.Database : the journal of biological databases and curation · 2025Article
- Re-emergence of Oropouche virus as a novel global threat.Current research in microbial sciences · 2025Review
- Craft: a machine learning approach to dengue subtyping.Bioinformatics advances · 2025Article
- Combining genomics and epidemiology to investigate a zoonotic outbreak of rabies in Romblon Province, Philippines.Nature communications · 2024Article
- Identification of clade-defining single nucleotide polymorphisms for improved rabies virus surveillance.New microbes and new infections · 2024Article
- Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus.PLoS pathogens · 2024Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.PLoS biology · 2024Article
- Genomic Characterization of a Dog-Mediated Rabies Outbreak in El Pedregal, Arequipa, Peru.bioRxiv : the preprint server for biology · 2024Article
- Geographic Distribution of Rabies Virus and Genomic Sequence Alignment of Wild and Vaccine Strains, Kenya.Emerging infectious diseases · 2024Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.medRxiv : the preprint server for health sciences · 2024Article
- Genetic analyses of rabies virus glycoprotein and nucleoprotein gene sequences reveal the emergence of multiple lineages in animals in Arkhangai province, a central region of Mongolia.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2023Article
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8 authors.
Funding
Abstract
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.