ArticlePloS one2011
Differential trends in the codon usage patterns in HIV-1 genes.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 44 citations in OpenAlex.
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- Genealogical Diversity of Endogenous Retrovirus in the Jawless Fish Genome.Journal of microbiology and biotechnology · 2023Article
- Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.Viruses · 2023Article
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- Molecular adaptations during viral epidemics.EMBO reports · 2022Review
- Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host.International journal of molecular sciences · 2022Article
- Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses.Genes & genomics · 2022Article
- Expression of transgenes enriched in rare codons is enhanced by the MAPK pathway.Scientific reports · 2020Article
- Analysis of sequence diversity and selection pressure in HIV-1 clade C gp41 from India.Virusdisease · 2020Article
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
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- Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus.Evolutionary bioinformatics online · 2018Article
- A new and updated resource for codon usage tables.BMC bioinformatics · 2017Article
- Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study.AIDS research and therapy · 2017Article
- Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate.Journal of virology · 2014Article
- Pattern of the evolution of HIV-1 enν gene in Côte d׳Ivoire.Bioinformation · 2014Article
- A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily.TheScientificWorldJournal · 2014Article
- Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus.Virology journal · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.
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