ArticlePloS one2014
LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Influenza virus genotype to phenotype predictions through machine learning: a systematic review.Emerging microbes & infections · 2021Pooled it
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- Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment.Virus evolution · 2025Article
- Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.Nature communications · 2024Article
- A vaccine antigen central in influenza A(H5) virus antigenic space confers subtype-wide immunity.bioRxiv : the preprint server for biology · 2024Article
- Proposal for a Global Classification and Nomenclature System for A/H9 Influenza Viruses.Emerging infectious diseases · 2024Article
- Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.medRxiv : the preprint server for health sciences · 2024Article
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- Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.PLoS computational biology · 2023Article
- Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis.Influenza and other respiratory viruses · 2022Article
- Review
- Outbreak Severity of Highly Pathogenic Avian Influenza A(H5N8) Viruses Is Inversely Correlated to Polymerase Complex Activity and Interferon Induction.Journal of virology · 2020Article
- Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017.Influenza and other respiratory viruses · 2020Article
- Phylogenetic Clustering by Linear Integer Programming (PhyCLIP).Molecular biology and evolution · 2019Article
- Diversity and distribution of type A influenza viruses: an updated panorama analysis based on protein sequences.Virology journal · 2019Article
- A Dual Motif in the Hemagglutinin of H5N1 Goose/Guangdong-Like Highly Pathogenic Avian Influenza Virus Strains Is Conserved from Their Early Evolution and Increases both Membrane Fusion pH and Virulence.Journal of virology · 2018Article
- Influenza-Associated Parotitis During the 2014-2015 Influenza Season in the United States.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2018Article
- Electrostatic Variation of Haemagglutinin as a Hallmark of the Evolution of Avian Influenza Viruses.Scientific reports · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.
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