ArticlePLoS computational biology2023
Host heterogeneity and epistasis explain punctuated evolution of SARS-CoV-2.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed.
- Economic factors promoting vaccine nationalism in the face of viral evolution.PLoS computational biology · 2026Article
- Tracking Dynamics of Superspreading Through Contacts, Exposures, and Transmissions in Edge-Based Network Epidemics.Bulletin of mathematical biology · 2026Article
- Evolutionary dynamics under phenotypic uncertainty.bioRxiv : the preprint server for biology · 2026Article
- Structural Constraints Acting on the SARS-CoV-2 Spike Protein Reveal Limited Space for Viral Adaptation.Genome biology and evolution · 2026Article
- Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning.PLoS computational biology · 2026Article
- Review
- Multi-scale phylodynamic modelling of rapid punctuated pathogen evolution.PLoS computational biology · 2025Article
- Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve.Journal of the Royal Society, Interface · 2025Article
- Optimal Annual COVID-19 Vaccine Boosting Dates Following Previous Booster Vaccination or Breakthrough Infection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2025Article
- The importance of epistasis in the evolution of viral pathogens.Virus evolution · 2025Review
- High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark.Nature communications · 2024Article
- Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions.PLoS pathogens · 2024Article
- Article
- Using big sequencing data to identify chronic SARS-Coronavirus-2 infections.Nature communications · 2024Article
- A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs.Microbiology spectrum · 2023Article
Corrections and comments
- Update of
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying drivers of viral diversity is key to understanding the evolutionary as well as epidemiological dynamics of the COVID-19 pandemic. Using rich viral genomic data sets, we show that periods of steadily rising diversity have been punctuated by sudden, enormous increases followed by similarly abrupt collapses of diversity. We introduce a mechanistic model of saltational evolution with epistasis and demonstrate that these features parsimoniously account for the observed temporal dynamics of inter-genomic diversity. Our results provide support for recent proposals that saltational evolution may be a signature feature of SARS-CoV-2, allowing the pathogen to more readily evolve highly transmissible variants. These findings lend theoretical support to a heightened awareness of biological contexts where increased diversification may occur. They also underline the power of pathogen genomics and other surveillance streams in clarifying the phylodynamics of emerging and endemic infections. In public health terms, our results further underline the importance of equitable distribution of up-to-date vaccines.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.