ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2010
Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus.
Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed, 8 citations in OpenAlex.
- Within-host nucleotide diversity of virus populations: insights from next-generation sequencing.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2015Review
- Application of next-generation sequencing technologies in virology.The Journal of general virology · 2012Review
- Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes.Genome biology and evolution · 2012Article
- Epitope-specific CD8+ T lymphocytes cross-recognize mutant simian immunodeficiency virus (SIV) sequences but fail to contain very early evolution and eventual fixation of epitope escape mutations during SIV infection.Journal of virology · 2011Article
- Conflicting selection pressures on T-cell epitopes in HIV-1 subtype B.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2011Article
- Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences.Journal of virology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Deep pyrosequencing of a CD8+TL epitope from the Tat protein of simian immunodeficiency virus (SIV) from four infected rhesus macaques carrying the restricting MHC allele (Mamu-A*01) for that epitope, revealed that natural selection favoring escape mutations led to an increase in the frequency of haplotypes in the epitope region that differed from the inoculum. After 20 weeks of infection, a new sequence haplotype in the epitope region had increased to a frequency greater than 50% in each of the four monkeys (range 57.9-98.9%); but the predominant haplotype was not the same in all four monkeys. Thus, even under strong selection favoring escape from CD8+TL recognition, the random nature of mutation itself is the primary factor affecting which escape mutation is likely to become predominant within an individual host. The relationship between the frequency of the inoculum haplotype in the epitope region and time post-infection approximated a simple hyperbola. On this assumption, the expected ratio of the frequencies at the inoculum at two times t(1) and t(2), f(i)(t(2))/f(i)(t(1)), will be given by t(1)/t(2). Because standard phylogenetic methods for reconstructing ancestral sequences failed to predict the inoculum sequence correctly, we used this relationship to predict the inoculum sequence with 100% accuracy, given data on haplotype frequencies at different time periods.
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.