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Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Serdari, Dora
; 
Kostaki, Evangelia-Georgia
; 
Paraskevis, Dimitrios
; 
Stamatakis, Alexandros
; 
Kapli, Paschalia
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2019-10-25
Submitted Date
2019-04-17
Subject Terms
Biodiversity
Computational Biology
Taxonomy
Virology
Infectious Diseases
Virus
DNA-barcoding
Species delimitation
Phylogeny
HBV
HCV
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Abstract
Background: The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods: Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion: We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.
Citation
Serdari D, Kostaki E, Paraskevis D, Stamatakis A, Kapli P. 2019. Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV. PeerJ 7:e7754 https://doi.org/10.7717/peerj.7754
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PeerJ
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PeerJ
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http://hdl.handle.net/10141/623350
DOI
10.7717/peerj.7754
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Journal Article
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Copyright 2019 Serdari et al. Distributed under Creative Commons CC-BY 4.0. The linked file is the published version of the article.
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2167-8359
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2167-8359
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openAccess
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