ArticlePatterns (New York, N.Y.)2021
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.
Article in Patterns (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches.Molecular biology and evolution · 2024Article
- Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach.Viruses · 2024Article
- The race to understand immunopathology in COVID-19: Perspectives on the impact of quantitative approaches to understand within-host interactions.Immunoinformatics (Amsterdam, Netherlands) · 2023Review
- Characterization of SARS-CoV-2 Mutational Signatures from 1.5+ Million Raw Sequencing Samples.Viruses · 2022Article
- Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin.International journal of biological macromolecules · 2022Article
- Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic.Nature reviews. Genetics · 2022Review
- Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data.iScience · 2022Article
- Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19.Scientific reports · 2022Article
- Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage.Frontiers in cellular and infection microbiology · 2022Article
- Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.Virus evolution · 2022Article
- Mapping Genetic Events of SARS-CoV-2 Variants.Frontiers in microbiology · 2022Article
- Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure.Scientific reports · 2021Article
- Jumper enables discontinuous transcript assembly in coronaviruses.Nature communications · 2021Article
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
- SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.Genome research · 2021Article
- Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity.iScience · 2021Article
- Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.PLoS pathogens · 2021Article
- Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck.bioRxiv : the preprint server for biology · 2021Article
- Biosensors for Point Mutation Detection.Frontiers in bioengineering and biotechnology · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce VERSO, a two-step framework for the characterization of viral evolution from sequencing data of viral genomes, which is an improvement on phylogenomic approaches for consensus sequences. VERSO exploits an efficient algorithmic strategy to return robust phylogenies from clonal variant profiles, also in conditions of sampling limitations. It then leverages variant frequency patterns to characterize the intra-host genomic diversity of samples, revealing undetected infection chains and pinpointing variants likely involved in homoplasies. On simulations, VERSO outperforms state-of-the-art tools for phylogenetic inference. Notably, the application to 6,726 amplicon and RNA sequencing samples refines the estimation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution, while co-occurrence patterns of minor variants unveil undetected infection paths, which are validated with contact tracing data. Finally, the analysis of SARS-CoV-2 mutational landscape uncovers a temporal increase of overall genomic diversity and highlights variants transiting from minor to clonal state and homoplastic variants, some of which fall on the spike gene. Available at: https://github.com/BIMIB-DISCo/VERSO.
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