ArticleBMC genomics2022
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers, 1 of them a synthesis that pooled it.
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Who cites it
93 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Clinical effects of ursodeoxycholic acid in COVID-19 infection: a systematic review and dose-response meta-analysis.Frontiers in pharmacology · 2026Pooled it
- A SARS-CoV-2 variant‑adjusted threshold of protection model for monoclonal antibody pre-exposure prophylaxis against COVID-19.Nature communications · 2025Trial
- Safety, tolerability, and efficacy of intranasally-administered detoxified LTh(αK) in mild-to-moderate COVID-19 patients: A randomized, double-blinded, placebo-controlled phase 2 study.Human vaccines & immunotherapeutics · 2024Trial
- Can self-testing be enhanced to hasten safe return of healthcare workers in pandemics? Random order, open label trial using two manufacturers' SARS-CoV-2 lateral flow devices concurrently and nested viral culture study.BMC infectious diseases · 2024Trial
- Breakthrough SARS-CoV-2 Infections in the PROVENT Prevention Trial Were Not Associated With AZD7442 (Tixagevimab/Cilgavimab) Resistant Variants.The Journal of infectious diseases · 2023Trial
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Characterization of recombinant genomes of the omicron variant of SARS-CoV-2 between 2022 and 2023 in the department of Antioquia, ColombiaBiomedica : revista del Instituto Nacional de Salud · 2026Article
- Article
- Genomic surveillance of SARS-CoV-2 variants in hospitalized patients: a cohort study from the metropolitan area of valle de Aburrá, ColombiaBiomedica : revista del Instituto Nacional de Salud · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Virus variant quantification with Orthanq.BMC bioinformatics · 2026Article
- Extended Grammar of Systematized Nomenclature of Medicine - Clinical Terms for Semantic Representation of Clinical Data: Methodological Study.Journal of medical Internet research · 2026Article
- Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants.Journal of virology · 2025Article
- Five Years of COVID-19 in Tocantins, Brazil: Epidemiology, Vaccination Impact, and SARS-CoV-2 Genomic Dynamics (2020-2025).Viruses · 2025Article
- SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2025Article
- Spike mutations that affect the function and antigenicity of recent KP.3.1.1-like SARS-CoV-2 variants.bioRxiv : the preprint server for biology · 2025Article
- Clustering-based methodology for comparing multi-characteristic epidemiological dynamics with application to COVID-19 epidemiology in Europe.Royal Society open science · 2025Article
- Review
- SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein.Briefings in bioinformatics · 2025Article
- Worldwide SARS-CoV-2 Omicron variant infection: Emerging sub-variants and future vaccination perspectives.Journal of the Formosan Medical Association = Taiwan yi zhi · 2025Review
33 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
backgroundMore than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status.
resultsAlthough many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a "lineage set", which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence.
conclusionsWe find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.
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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.