ArticleRetrovirology2013
Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture.
Article in Retrovirology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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
52 citing papers in PubMed, 82 citations in OpenAlex.
- Attenuation without protective immunogenicity: effects of codon-pair deoptimization on foot-and-mouth disease virus serotype O in swine.Scientific reports · 2026Article
- Evolution shapes and conserves genomic signatures in viruses.Communications biology · 2024Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Article
- Article
- Article
- Evaluation and Determination of a Suitable Passage Number of Codon Pair Deoptimized PRRSV-1 Vaccine Candidate in Pigs.Viruses · 2023Article
- Codon Pair Deoptimization (CPD)-Attenuated PRRSV-1 Vaccination Exhibit Immunity to Virulent PRRSV Challenge in Pigs.Vaccines · 2023Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation.Vaccines · 2022Article
- Compositional biases in RNA viruses: Causes, consequences and applications.Wiley interdisciplinary reviews. RNA · 2022Review
- Synthetically recoded virus sCPD9 - A tool to accelerate SARS-CoV-2 research under biosafety level 2 conditions.Computational and structural biotechnology journal · 2022Review
- Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases.Computational and structural biotechnology journal · 2022Review
- Synonymous Codon Pair Recoding of the HIV-1Cells · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Association of Zinc Finger Antiviral Protein Binding to Viral Genomic RNA with Attenuation of Replication of Echovirus 7.mSphere · 2021Article
- Review
- Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines.Frontiers in microbiology · 2021Review
- Review
- Impact of Synonymous Genome Recoding on the HIV Life Cycle.Frontiers in microbiology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHuman immunodeficiency virus type 1 (HIV-1) has a biased nucleotide composition different from human genes. This raises the question of how evolution has chosen the nucleotide sequence of HIV-1 that is observed today, or to what extent the actual encoding contributes to virus replication capacity, evolvability and pathogenesis. Here, we applied the previously described synthetic attenuated virus engineering (SAVE) approach to HIV-1.
resultsUsing synonymous codon pairs, we rationally recoded and codon pair-optimized and deoptimized different moieties of the HIV-1 gag and pol genes. Deoptimized viruses had significantly lower viral replication capacity in MT-4 and peripheral blood mononuclear cells (PBMCs). Varying degrees of ex vivo attenuation were obtained, depending upon both the specific deoptimized region and the number of deoptimized codons. A protease optimized virus carrying 38 synonymous mutations was not attenuated and displayed a replication capacity similar to that of the wild-type virus in MT-4 cells and PBMCs. Although attenuation is based on several tens of nucleotide changes, deoptimized HIV-1 reverted to wild-type virulence after serial passages in MT-4 cells. Remarkably, no reversion was observed in the optimized virus.
conclusionThese data demonstrate that SAVE is a useful strategy to phenotypically affect the replicative properties of HIV-1.
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.