ArticleVirus evolution2023
Fitness effects of mutations to SARS-CoV-2 proteins.
Article in Virus evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 94 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
94 citing papers in PubMed, 107 citations in OpenAlex.
- The other immune landscape of SARS-CoV-2 evolution.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants.bioRxiv : the preprint server for biology · 2026Article
- Transmission of mutated SARS-CoV-2 variants is favored by relatively prolonged infections due to delayed immunity.bioRxiv : the preprint server for biology · 2026Article
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- SARS-CoV-2 Delta variant-specific ORF3a mutations destabilize lysosomal homeostasis to trigger lysosomal damage-mediated cell death.Communications biology · 2026Article
- Serum Escape Landscape of SARS-CoV-2 Omicron JN.1 and XEC RBD Under COVID-19 Vaccine Breakthrough Immunity in China.Microorganisms · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- Coronavirus protein interaction mapping in bat and human cells reveals network rewiring governing immune evasion and zoonotic potential.Cell host & microbe · 2026Article
- Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication.Antimicrobial agents and chemotherapy · 2026Article
- Epistasis and background dependence in the evolution of Omicron variants of the SARS-CoV-2 spike protein.Molecular biology and evolution · 2026Article
- Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence.bioRxiv : the preprint server for biology · 2026Article
- Extensive evolution and T cell escape by SARS-CoV-2 in a 2.5-year persistent infection of an immunocompromised host.iScience · 2026Article
- The role of receptor binding and immunity in SARS-CoV-2 fitness landscape: A modeling study.iScience · 2026Article
- Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection.bioRxiv : the preprint server for biology · 2026Article
- Coupling high-throughput protease enzymology with viral replication reveals biochemical constraints of viral fitness.bioRxiv : the preprint server for biology · 2026Article
- Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection.Virus evolution · 2026Article
- Characterization of the heterogeneity in SARS-CoV-2 fitness dynamics via graph representation learning.PLoS computational biology · 2026Article
- Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies.Virus evolution · 2026Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
- Update of
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here, we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.
Indexed as
Identifiers
What Socratic 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 Socratic graph.