ArticleNature microbiology2024
A framework for automated scalable designation of viral pathogen lineages from genomic data.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed.
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- Evolutionary history of Jamestown Canyon virus reveals complex multi-vector ecology.Current biology : CB · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology.bioRxiv : the preprint server for biology · 2026Article
- Phylogenetic insights into the transmission dynamics of arthropod-borne viruses.Nature reviews. Genetics · 2026Review
- Article
- A Pandemic-Scale Ancestral Recombination Graph for SARS-CoV-2.bioRxiv : the preprint server for biology · 2025Article
- Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).BMC bioinformatics · 2025Article
- Article
- Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2.medRxiv : the preprint server for health sciences · 2025Article
- Genetic diversity of H9N2 avian influenza viruses in poultry across China and implications for zoonotic transmission.Nature microbiology · 2025Article
- A Phylogenetic Method Identifies Candidate Drivers of the Evolution of the SARS-CoV-2 Mutation Spectrum.Molecular biology and evolution · 2025Article
- Applying prospective tree-temporal scan statistics to genomic surveillance data to detect emerging SARS-CoV-2 variants and salmonellosis clusters in New York City.International journal of epidemiology · 2025Article
- A phylogenetic method identifies candidate drivers of the evolution of the SARS-CoV-2 mutation spectrum.bioRxiv : the preprint server for biology · 2025Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.PLoS biology · 2024Article
- Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level.Emerging infectious diseases · 2024Article
- Identifying changes in viral fitness using population genetic structure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A new lineage nomenclature to aid genomic surveillance of dengue virus.medRxiv : the preprint server for health sciences · 2024Article
- Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data.GigaScience · 2024Article
- Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.
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