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Volume 29, Number 12—December 2023
Dispatch

Divergent Genotype of Hepatitis A Virus in Alpacas, Bolivia, 2019

Talitha Veith, L. Fabian Beltran-Saavedra, Tobias Bleicker, Marie Luisa Schmidt, José L. Mollericona, Kim Grützmacher, Rob Wallace, Jan Felix Drexler, Christian Walzer, Terry C. Jones, Christian Drosten, and Victor Max CormanComments to Author 
Author affiliations: Charité-Universitätsmedizin Berlin—corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany (T. Veith, T. Bleicker, M.L. Schmidt, J.F. Drexler, T.C. Jones, C. Drosten, V.M. Corman); Wildlife Conservation Society, La Paz, Bolivia (L.F. Beltran-Saavedra, J.L. Mollericona, R. Wallace); Wildlife Conservation Society, New York, New York, USA (L.F. Beltran-Saavedra, J.L. Mollericona, R. Wallace, C. Walzer); Museum für Naturkunde Berlin/Leibniz-Institute for Evolution and Biodiversity Science, Berlin (K. Grützmacher); Deutsche Gesellschaft für Internationale Zusammenarbeit GmbH, Bonn, Germany (K. Grützmacher); German Centre for Infection Research (DZIF), Berlin (J.F. Drexler, C. Drosten, V.M. Corman); University of Veterinary Medicine Vienna, Vienna, Austria (C. Walzer); University of Cambridge, Cambridge, UK (T.C. Jones); Labor Berlin Charité–Vivantes GmbH, Berlin (V.M. Corman)

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Figure 2

Phylogenetic analyses of alpaca HAV from Bolivia, 2019, in the context of other HAV sequences. Alpaca HAV sequences are colored by site, Ucha-Ucha in blue, Chullumpina in orange. A) Maximum-likelihood phylogenies of alpaca HAV in the context of other hepatovirus species. P1, P2, and P3 (picornavirus regions typically separated by recombination breakpoints [10]) nucleotide alignments were made using Clustal Omega 1.2 (http://www.clustal.org/omega) in Geneious Prime 2023.1.2 (https://www.geneious.com). ModelFinder, incorporated in IQ-TREE 1.6.12 (http://www.iqtree.org), was used to determine the best-fitting nucleotide substitution model (general time reversible model with a discrete gamma model with 4 rate categories, invariable sites, and empirical base frequencies) according to the Bayesian Information Criterion. IQ-TREE 1.6.12 was used to calculate the phylogenetic tree. The trees were rooted with Hepatovirus species I (P1), B (P2), and E and C (P3) respectively. Solid black circles denote ultrafast bootstrap support of >90 for the preceding branch; open circles denotes ultrafast bootstrap support between 70 and 90. GenBank accession numbers by genogroup: I, KT452658; E, KT452735; C, KT452742; B, KR703607; G, KT452730 and KT452729; H, KT452691, KT452714, and KT877158; F, KT229611, MG181943, and KT452685; D, KT452644 and KT452637; A, OQ559662, KT819575, EU140838, D00924, AB279735, AB279732, AY644670, AY644676, M14707, and AB020564. B) Maximum-likelihood phylogeny of alpaca HAV in the context of other Hepatovirus A genotypes. Complete genomes and partial genomes (asterisks) were used. The tree was calculated as in panel A, by using a transition model with AC=AT and CG=GT, with a discrete gamma model with 4 rate categories, invariable sites, and empirical base frequencies and rooting with Hepatovirus species A genotypes IV–VI. Chu-alp-11, included in this tree, tested negative in quantitative reverse transcription PCR but positive in high-throughput sequencing and pan-Hepatovirus PCR (Appendix Table). HAV, hepatitis A virus.

Figure 2. Phylogenetic analyses of alpaca HAV from Bolivia, 2019, in the context of other HAV sequences. Alpaca HAV sequences are colored by site, Ucha-Ucha in blue, Chullumpina in orange. A) Maximum-likelihood phylogenies of alpaca HAV in the context of other hepatovirus species. P1, P2, and P3 (picornavirus regions typically separated by recombination breakpoints [10]) nucleotide alignments were made using Clustal Omega 1.2 (http://www.clustal.org/omega) in Geneious Prime 2023.1.2 (https://www.geneious.com). ModelFinder, incorporated in IQ-TREE 1.6.12 (http://www.iqtree.org), was used to determine the best-fitting nucleotide substitution model (general time reversible model with a discrete gamma model with 4 rate categories, invariable sites, and empirical base frequencies) according to the Bayesian Information Criterion. IQ-TREE 1.6.12 was used to calculate the phylogenetic tree. The trees were rooted with Hepatovirus species I (P1), B (P2), and E and C (P3) respectively. Solid black circles denote ultrafast bootstrap support of >90 for the preceding branch; open circles denotes ultrafast bootstrap support between 70 and 90. GenBank accession numbers by genogroup: I, KT452658; E, KT452735; C, KT452742; B, KR703607; G, KT452730 and KT452729; H, KT452691, KT452714, and KT877158; F, KT229611, MG181943, and KT452685; D, KT452644 and KT452637; A, OQ559662, KT819575, EU140838, D00924, AB279735, AB279732, AY644670, AY644676, M14707, and AB020564. B) Maximum-likelihood phylogeny of alpaca HAV in the context of other Hepatovirus A genotypes. Complete genomes and partial genomes (asterisks) were used. The tree was calculated as in panel A, by using a transition model with AC=AT and CG=GT, with a discrete gamma model with 4 rate categories, invariable sites, and empirical base frequencies and rooting with Hepatovirus species A genotypes IV–VI. Chu-alp-11, included in this tree, tested negative in quantitative reverse transcription PCR but positive in high-throughput sequencing and pan-Hepatovirus PCR (Appendix Table). HAV, hepatitis A virus.

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