ReviewPLoS pathogens2023
Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.
Review in PLoS pathogens, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
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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
22 citing papers in PubMed, 24 citations in OpenAlex.
- Inferring Patterns of Purifying, Positive, and Balancing Selection in the Coppery Titi Monkey (Plecturocebus cupreus) Utilizing a Well-Fit Evolutionary Baseline Model.Genome biology and evolution · 2026Article
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets (Callithrix jacchus) from High-Quality, Whole-Genome, Population-Level Data.Molecular biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.Virus evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.bioRxiv : the preprint server for biology · 2024Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- Temporal challenges in detecting balancing selection from population genomic data.G3 (Bethesda, Md.) · 2024Article
- Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data.Nature communications · 2024Article
- The Effects of Mutation and Recombination Rate Heterogeneity on the Inference of Demography and the Distribution of Fitness Effects.Genome biology and evolution · 2024Article
- iHDSel software: The price equation and the population stability index to detect genomic patterns compatible with selective sweeps. An example with SARS-CoV-2.Biology methods & protocols · 2024Article
- The effects of mutation and recombination rate heterogeneity on the inference of demography and the distribution of fitness effects.bioRxiv : the preprint server for biology · 2023Article
- A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2.Genome biology and evolution · 2023Article
- Innate immunity decreases pathogen diversity during infection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evaluating power to detect recurrent selective sweeps under increasingly realistic evolutionary null models.Evolution; international journal of organic evolution · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
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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.