ArticleMolecular phylogenetics and evolution2008
An exploratory algorithm to identify intra-host recombinant viral sequences.
Article in Molecular phylogenetics and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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.
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Who cites it
26 citing papers in PubMed, 34 citations in OpenAlex.
- Delayed Expression of PD-1 and TIGIT on HIV-Specific CD8 T Cells in Untreated HLA-B*57:01 Individuals Followed from Early Infection.Journal of virology · 2020Trial
- Diversity and Genetic Reassortment of Keystone Virus in Mosquito Populations in Florida.The American journal of tropical medicine and hygiene · 2023Article
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- Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution.medRxiv : the preprint server for health sciences · 2021Article
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- Evolution of Neuroadaptation in the Periphery and Purifying Selection in the Brain Contribute to Compartmentalization of Simian Immunodeficiency Virus (SIV) in the Brains of Rhesus Macaques with SIV-Associated Encephalitis.Journal of virology · 2016Article
- Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission.Retrovirology · 2015Article
- Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques.Journal of virology · 2015Article
- Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing.Journal of virology · 2014Article
- Reduced evolutionary rates in HIV-1 reveal extensive latency periods among replicating lineages.Retrovirology · 2014Article
- Longitudinal analysis of intra-host simian immunodeficiency virus recombination in varied tissues of the rhesus macaque model for neuroAIDS.The Journal of general virology · 2013Article
- The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective.Infectious disease reports · 2013Review
- Phylogenetic analysis reveals a high prevalence of Sporothrix brasiliensis in feline sporotrichosis outbreaks.PLoS neglected tropical diseases · 2013Article
- Article
- Combination of immune and viral factors distinguishes low-risk versus high-risk HIV-1 disease progression in HLA-B*5701 subjects.Journal of virology · 2012Article
- Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital.PloS one · 2012Article
- Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species.BMC evolutionary biology · 2011Article
- Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a bayesian framework.Molecular biology and evolution · 2011Article
- HIV-1 molecular epidemiology in Guinea-Bissau, West Africa: origin, demography and migrations.PloS one · 2011Article
- Multiple independent lineages of HIV-1 persist in breast milk and plasma.AIDS (London, England) · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Since recombination leads to the generation of mosaic genomes that violate the assumption of traditional phylogenetic methods that sequence evolution can be accurately described by a single tree, results and conclusions based on phylogenetic analysis of data sets including recombinant sequences can be severely misleading. Many methods are able to adequately detect recombination between diverse sequences, for example between different HIV-1 subtypes. More problematic is the identification of recombinants among closely related sequences such as a viral population within a host. We describe a simple algorithmic procedure that enables detection of intra-host recombinants based on split-decomposition networks and a robust statistical test for recombination. By applying this algorithm to several published HIV-1 data sets we conclude that intra-host recombination was significantly underestimated in previous studies and that up to one-third of the env sequences longitudinally sampled from a given subject can be of recombinant origin. The results show that our procedure can be a valuable exploratory tool for detection of recombinant sequences before phylogenetic analysis, and also suggest that HIV-1 recombination in vivo is far more frequent and significant than previously thought.
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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.