ArticlePLoS genetics2018
Within-patient mutation frequencies reveal fitness costs of CpG dinucleotides and drastic amino acid changes in HIV.
Article in PLoS genetics, 2018. 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 24 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.
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Who cites it
24 citing papers in PubMed, 41 citations in OpenAlex.
- Estimating HIV-1 Viremic Time From Reservoir Sequence Diversity With Uncertainty Quantification.The Journal of infectious diseases · 2026Article
- Hierarchical genotype networks and incipient ecological speciation in Q[Formula: see text] phage quasispecies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Design of an optimal combination therapy with broadly neutralizing antibodies to suppress HIV-1.eLife · 2022Article
- Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus.PLoS genetics · 2022Article
- The generative capacity of probabilistic protein sequence models.Nature communications · 2021Article
- Single-genome sequencing reveals within-host evolution of human malaria parasites.Cell host & microbe · 2021Article
- S-farnesylation is essential for antiviral activity of the long ZAP isoform against RNA viruses with diverse replication strategies.PLoS pathogens · 2021Article
- Host-virus interaction and viral evasion.Cell biology international · 2021Review
- Article
- Biased Mutation and Selection in RNA Viruses.Molecular biology and evolution · 2021Article
- Impact of Synonymous Genome Recoding on the HIV Life Cycle.Frontiers in microbiology · 2021Review
- Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2.Molecular biology and evolution · 2020Article
- Extreme Genomic CpG Deficiency in SARS-CoV-2 and Evasion of Host Antiviral Defense.Molecular biology and evolution · 2020Article
- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Drug Resistance Evolution in HIV in the Late 1990s: Hard Sweeps, Soft Sweeps, Clonal Interference and the Accumulation of Drug Resistance Mutations.G3 (Bethesda, Md.) · 2020Article
- CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms.Journal of virology · 2020Article
- Coronavirus genomes carry the signatures of their habitats.PloS one · 2020Article
- CpG-creating mutations are costly in many human viruses.Evolutionary ecology · 2020Article
- Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces.G3 (Bethesda, Md.) · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
HIV has a high mutation rate, which contributes to its ability to evolve quickly. However, we know little about the fitness costs of individual HIV mutations in vivo, their distribution and the different factors shaping the viral fitness landscape. We calculated the mean frequency of transition mutations at 870 sites of the pol gene in 160 patients, allowing us to determine the cost of these mutations. As expected, we found high costs for non-synonymous and nonsense mutations as compared to synonymous mutations. In addition, we found that non-synonymous mutations that lead to drastic amino acid changes are twice as costly as those that do not and mutations that create new CpG dinucleotides are also twice as costly as those that do not. We also found that G→A and C→T mutations are more costly than A→G mutations. We anticipate that our new in vivo frequency-based approach will provide insights into the fitness landscape and evolvability of not only HIV, but a variety of microbes.
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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.