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. 2016 Jul;22(7):1308–1310. doi: 10.3201/eid2207.151837

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This is a publication of the U.S. Government. This publication is in the public domain and is therefore without copyright. All text from this work may be reprinted freely. Use of these materials should be properly cited.

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Whole-genome phylogenetic reconstruction of representative HAVs. HAVs are grouped into 6 genotypes based on 168 bp of the C-terminal extension of the viral protein 1 gene. Baboon HAV detected in Kibale National Park, Uganda, in 2010 and 2014 (GenBank accession number KT819575) clusters with AGM-27 (3), previously the sole member of genotype V. jModeltest 2 (http://jmodeltest.org) was used to find the best-fit evolutionary model for the data, after which the maximum-likelihood tree was estimated using the heuristic search method in PAUP* (http://paup.csit.fsu.edu), with starting trees obtained by neighbor-joining, random stepwise addition, and branch swapping by tree-bisection reconnection and starting branch lengths obtained using Rogers-Swofford approximation. Bootstrap values were derived from 1,000 replicates of the heuristic search; only values >50% are shown. GenBank accession nos.: IA, EF207320; IB, M14707; II, AY644676; IIIA, FJ227135; IIIB, AB258387; V, D00924). HAV, hepatitis A virus. Scale bar indicates substitutions per site.