The effect of phylogenetic signal reduction on genotyping of hepatitis E viruses of the species Orthohepevirus A

The effect of phylogenetic signal reduction on genotyping of hepatitis E viruses of the species... Commonly, hepatitis E virus (HEV) sequences are genotyped phylogenetically using subgenomic sequences. This paper examines this practice with sequences from members of the species Orthohepevirus A. As the length of sequences becomes progressively shorter, the number of identical sequences in an alignment tends to increase; however, these sequences retain their genotypic identity down to 100 nucleotides in length. The best substitution models tend to become less parameterized, bootstrap support decreases, and trees created from short subgenomic fragments are less likely to be isomorphic with trees from longer subgenomic fragments or complete genome sequences. However, it is still possible to correctly genotype sequences using fragments as small as 200 nucleotides. While it is possible to correctly genotype sequences with short subgenomic sequences, the estimates of evolutionary relationships between genotypes degrade to such an extent that sequences below 1600 nucleotides long cannot be used reliably to study these relationships, and comparisons of trees from different subgenomic regions with little or no sequence overlap can be problematic. Subtyping may be done, but it requires a careful examination of the region to be used to ensure that it correctly resolves the subtypes. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Archives of Virology Springer Journals

The effect of phylogenetic signal reduction on genotyping of hepatitis E viruses of the species Orthohepevirus A

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Publisher
Springer Vienna
Copyright
Copyright © 2016 by Springer-Verlag Wien (Outside the USA)
Subject
Biomedicine; Virology; Medical Microbiology; Infectious Diseases
ISSN
0304-8608
eISSN
1432-8798
D.O.I.
10.1007/s00705-016-3135-x
Publisher site
See Article on Publisher Site

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