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

ABSTRACT: 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 co

SUBMITTER: Purdy MA 

PROVIDER: S-EPMC5678955 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature