ArticleJournal of virology2000
Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1.
Article in Journal of virology, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed, 55 citations in OpenAlex.
- Geographic variability of severe fever with thrombocytopenia syndrome virus genomes in the Miyazaki Prefecture, Japan: a cross-sectional molecular epidemiological study.Parasites & vectors · 2026Article
- SARS-CoV-2 Error Catastrophe Under Molnupiravir: Mutagenic Enhancement Enables Viral Persistence with Impaired Fitness.Viruses · 2026Article
- Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.Nature protocols · 2017Article
- Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity.Scientific reports · 2016Article
- Article
- Arboviral bottlenecks and challenges to maintaining diversity and fitness during mosquito transmission.Viruses · 2014Review
- A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918.Theoretical biology & medical modelling · 2012Article
- Vector-borne transmission imposes a severe bottleneck on an RNA virus population.PLoS pathogens · 2012Article
- Dynamics of in vitro fitness recovery of HIV-1.Journal of virology · 2011Article
- Article
- Article
- Article
- Fitness declines in Tobacco etch virus upon serial bottleneck transfers.Journal of virology · 2007Article
- Site-specific amino acid frequency, fitness and the mutational landscape model of adaptation in human immunodeficiency virus type 1.Genetics · 2006Article
- Mechanisms of genetic robustness in RNA viruses.EMBO reports · 2006Review
- The replicative fitness of primary human immunodeficiency virus type 1 (HIV-1) group M, HIV-1 group O, and HIV-2 isolates.Journal of virology · 2005Article
- Few mutations in the 5' leader region mediate fitness recovery of debilitated human immunodeficiency type 1 viruses.Journal of virology · 2005Article
- Genetic bottlenecks reduce population variation in an experimental RNA virus population.Journal of virology · 2004Article
- Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Covariation in the capsid protein of hibiscus chlorotic ringspot virus induced by serial passaging in a host that restricts movement leads to avirulence in its systemic host.Journal of virology · 2002Article
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 at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Repeated bottleneck passages result in fitness losses of RNA viruses. In the case of human immunodeficiency virus type 1 (HIV-1), decreases in fitness after a limited number of plaque-to-plaque transfers in MT-4 cells were very drastic. Here we report an analysis of entire genomic nucleotide sequences of four HIV-1 clones derived from the same HIV-1 isolate and their low-fitness progeny following 7 to 15 plaque-to-plaque passages. Clones accumulated 4 to 28 mutations per genome, with dominance of A --> G and G --> A transitions (57% of all mutations) and 49% nonsynonymous replacements. One clone-but not three sibling clones-showed an overabundance of G --> A transitions, evidencing the highly stochastic nature of some types of mutational bias. The distribution of mutations along the genome was very unusual in that mutation frequencies in gag were threefold higher than in env. Particularly striking was the complete absence of replacements in the V3 loop of gp120, confirmed with partial nucleotide sequences of additional HIV-1 clones subjected to repeated bottleneck passages. The analyses revealed several amino acid replacements that have not been previously recorded among natural HIV-1 isolates and illustrate how evolution of an RNA virus genome, with regard to constant and variable regions, can be profoundly modified by alterations in population dynamics.
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.