ArticleMolecular biology and evolution2012
Slow fitness recovery in a codon-modified viral genome.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 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
39 citing papers in PubMed.
- Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.Bulletin of mathematical biology · 2026Article
- Codon usage modulates the relationship between the burden and yield of protein overexpression.Journal of biological engineering · 2025Article
- Article
- Heat adaptation of phage T7 under an extended genetic code.Virus evolution · 2021Article
- Scalable live-attenuated SARS-CoV-2 vaccine candidate demonstrates preclinical safety and efficacy.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2021Review
- Rescue of codon-pair deoptimized respiratory syncytial virus by the emergence of genomes with very large internal deletions that complemented replication.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines.Frontiers in microbiology · 2021Review
- Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence.Nucleic acids research · 2020Article
- Transcript degradation and codon usage regulate gene expression in a lytic phage.Virus evolution · 2019Article
- Optimizing the dynamics of protein expression.Scientific reports · 2019Article
- Attenuation of Human Respiratory Viruses by Synonymous Genome Recoding.Frontiers in immunology · 2019Review
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- Generation and comparative genomics of synthetic dengue viruses.BMC bioinformatics · 2018Article
- Transmissible Viral Vaccines.Trends in microbiology · 2018Review
- Viral attenuation by engineered protein fragmentation.Virus evolution · 2018Article
- Arresting Evolution.Trends in genetics : TIG · 2017Review
- Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis.BMC genomics · 2017Article
- Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization.G3 (Bethesda, Md.) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Extensive synonymous codon modification of viral genomes appears to be an effective way of attenuating strains for use as live vaccines. An assumption of this method is that codon changes have individually small effects, such that codon-attenuated viruses will be slow to evolve back to high fitness (and thus to high virulence). The major capsid gene of the bacterial virus T7 was modified to have varying levels of suboptimal synonymous codons in different constructs, and fitnesses declined linearly with the number of changes. Adaptation of the most extreme design, with 182 codon changes, resulted in a slow fitness recovery by standards of previous experimental evolution with this virus, although fitness effects of substitutions were higher than expected from the average effect of an engineered codon modification. Molecular evolution during recovery was modest, and changes evolved both within the modified gene and outside it. Some changes within the modified gene evolved in parallel across replicates, but with no obvious explanation. Overall, the study supports the premise that codon-modified viruses recover fitness slowly, although the evolution is substantially more rapid than expected from the design principle.
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.