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A novel Bayesian method for detection of APOBEC3-mediated hypermutation and its application to zoonotic transmission of simian foamy viruses
- Source :
- PLoS Computational Biology, Vol 10, Iss 2, p e1003493 (2014), PLoS Computational Biology
- Publication Year :
- 2014
- Publisher :
- Public Library of Science (PLoS), 2014.
-
Abstract
- Simian Foamy Virus (SFV) can be transmitted from non-human primates (NHP) to humans. However, there are no documented cases of human to human transmission, and significant differences exist between infection in NHP and human hosts. The mechanism for these between-host differences is not completely understood. In this paper we develop a new Bayesian approach to the detection of APOBEC3-mediated hypermutation, and use it to compare SFV sequences from human and NHP hosts living in close proximity in Bangladesh. We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo.<br />Author Summary Simian Foamy Virus (SFV) is a very common retrovirus in monkeys. When an infected monkey bites a human it can transmit the virus to the human; however, there are no documented cases of human to human transmission. There also appear to be significant differences between infection in monkey and human hosts. The reason for these differences in the two hosts is not completely understood. In this paper we show that a family of host defense enzymes called APOBEC3 may prevent replication of SFV in humans. They do this by changing the genome of the virus so that it cannot replicate. Although this same process also happens in monkeys, it appears to happen less than in humans, and the changes that the monkey APOBEC3 enzymes make are less likely to prevent the virus from replicating. We are able to make these inferences by seeing characteristic types of mutations in a collection of virus DNA sequences sampled in Bangladesh. We develop new statistical methodology to do this analysis.
- Subjects :
- viruses
Simian foamy virus
APOBEC-3G Deaminase
Simian
Virus Replication
Macaque
Cytosine Deaminase
Zoonoses
APOBEC Deaminases
Biology (General)
APOBEC3G
Genetics
Bangladesh
0303 health sciences
Ecology
biology
Transmission (medicine)
Statistics
030302 biochemistry & molecular biology
virus diseases
Innate Immunity
humanities
3. Good health
Computational Theory and Mathematics
Modeling and Simulation
Host-Pathogen Interactions
Codon, Terminator
RNA, Viral
Research Article
Sequence analysis
QH301-705.5
Immunology
Somatic hypermutation
Microbiology
03 medical and health sciences
Cellular and Molecular Neuroscience
Species Specificity
Cytidine Deaminase
Virology
biology.animal
Animals
Humans
Biology
Molecular Biology
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Models, Genetic
Immunity
Computational Biology
Bayes Theorem
biochemical phenomena, metabolism, and nutrition
biology.organism_classification
Viral replication
Mutation
Macaca
Mathematics
Retroviridae Infections
Subjects
Details
- Language :
- English
- ISSN :
- 15537358
- Volume :
- 10
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....9a95643940b2954cb0fd17ec3f3d91a1