ArticleVirus evolution2021
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool.
Article in Virus evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 768 papers.
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Who cites it
768 citing papers in PubMed.
- Trial
- Longitudinal characterization of mixed-genotype SARS-CoV-2 infections in a military cohort reveals compartmentalized viral populations.Microbiology spectrum · 2026Article
- A generalized lineage nomenclature for viral genomic epidemiology.Nature microbiology · 2026Article
- Review
- A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.Scientific reports · 2026Article
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Artificial Intelligence in Infectious Diseases and Clinical Microbiology.Infectious diseases & clinical microbiology · 2026Review
- SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.Microbial genomics · 2026Article
- The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California.PLOS digital health · 2026Article
- Serological Predictors of Protection from Infection Upon Household Exposure to SARS-CoV-2.European journal of immunology · 2026Article
- Leveraging synthetic and genetic data to improve epidemic forecasting.PLoS computational biology · 2026Article
- SARS-CoV-2 Surveillance in Free-Ranging Wildlife in New England and Virginia, United States, 2022-2025.Viruses · 2026Article
- Within-host SARS-CoV-2 diversity in immunocompromised patients during acute infection.Journal of virology · 2026Article
- SARS-CoV-2 Delta variant re-emerges in US farmed mink and free-ranging white-tailed deer in 2022-2023.Nature communications · 2026Article
- Review
- Coronavirus protein interaction mapping in bat and human cells reveals network rewiring governing immune evasion and zoonotic potential.Cell host & microbe · 2026Article
- Combinatorial analysis of clinical and genomic data used to assess the association between SARS-CoV-2 mutations and disease severity.PNAS nexus · 2026Article
- From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens.Genes · 2026Article
- Citywide indoor air sampling mirrors wastewater and clinical case surveillance of respiratory viruses.Nature communications · 2026Article
- Article
708 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The response of the global virus genomics community to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards the 'real-time' generation and sharing of SARS-CoV-2 genomic data. The rapid growth in virus genome data production has necessitated the development of new analytical methods that can deal with orders of magnitude of more genomes than previously available. Here, we present and describe Phylogenetic Assignment of Named Global Outbreak Lineages (pangolin), a computational tool that has been developed to assign the most likely lineage to a given SARS-CoV-2 genome sequence according to the Pango dynamic lineage nomenclature scheme. To date, nearly two million virus genomes have been submitted to the web-application implementation of pangolin, which has facilitated the SARS-CoV-2 genomic epidemiology and provided researchers with access to actionable information about the pandemic's transmission lineages.
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