viruses Brief Report Genomic Epidemiology and Evolution of Duck Hepatitis A Virus Enik ˝ o Fehér 1 , Szilvia Jakab 1 , Krisztina Bali 1 , Eszter Kaszab 1 , Borbála Nagy 1 , Katalin Ihász 1 , ÁdámBálint 2 , Vilmos Palya 3 and KrisztiánBányai 1,4, *   Citation: Fehér, E.; Jakab, S.; Bali, K.; Kaszab, E.; Nagy, B.; Ihász, K.; Bálint, Á.; Palya, V.; Bányai, K. Genomic Epidemiology and Evolution of Duck Hepatitis A Virus. Viruses 2021, 13, 1592. https://doi.org/10.3390/ v13081592 Academic Editor: François-Loïc Cosset Received: 17 June 2021 Accepted: 6 August 2021 Published: 11 August 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Veterinary Medical Research Institute, Hungária krt 21, H-1143 Budapest, Hungary; feher.eniko@vmri.hu (E.F.); jakab.szilvia@vmri.hu (S.J.); bali.krisztina@vmri.hu (K.B.); kaszab.eszter@vmri.hu (E.K.); nagy.borbala@vmri.hu (B.N.); ihasz.katalin@vmri.hu (K.I.) 2 Veterinary Diagnostic Directorate, National Food Chain Safety Office, Tábornok utca 2, H-1143 Budapest, Hungary; BalintAd@nebih.gov.hu 3 Ceva-Phylaxia Veterinary Biologicals Co., Ltd., H-1107 Budapest, Hungary; vilmos.palya@ceva.com 4 Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary * Correspondence: bkrota@hotmail.com Abstract: Duck hepatitis A virus (DHAV), an avian picornavirus, causes high-mortality acute disease in ducklings. Among the three serotypes, DHAV-1 is globally distributed, whereas DHAV-2 and DHAV-3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV-1 strains using extant GenBank records and genomic sequences of 10 DHAV-1 strains originating from a large disease outbreak in 2004–2005, in Hungary. Recombination analysis revealed intragenotype recombination within DHAV-1 as well as intergenotype recombination events involving DHAV-1 and DHAV-3 strains. The intergenotype recombination occurred in the VP0 region. Diversifying selection seems to act at sites of certain genomic regions. Calculations estimated slightly lower rates of evolution of DHAV-1 (mean rates for individual protein coding regions, 5.6286 × 10 −4 to 1.1147 × 10 −3 substitutions per site per year) compared to other picornaviruses. The observed evolutionary mechanisms indicate that whole-genome-based analysis of DHAV strains is needed to better understand the emergence of novel strains and their geographical dispersal. Keywords: duck hepatitis A virus; recombination; Hungary 1. Introduction Infection caused by duck hepatitis virus 1 (DHV-1 or DHV type I), recently renamed as duck hepatitis A virus (DHAV), may be fatal in up to 95% of ducklings, typically under three weeks of age [1–3]. The disease is characterized by hepatic failures (enlargement, hemorrhages and necrosis), neurological signs (ataxia, opisthotonus) and the sudden death of affected birds [1–4]. The duck industry has been heavily affected by this virus; however, the disease can be efficiently prevented by vaccination [5]. DHAV belongs to the Avihepatovirus genus of the Picornaviridae family (https://talk. ictvonline.org/taxonomy/ accessed on 7 August 2021). The viral genome is a ~7.7-kilobase- long positive-sense single stranded RNA and consists of a single large open reading frame (ORF) flanked by the 5 ′ and 3 ′ non-coding regions. The polyprotein encoded by the single ORF is predicted to code for the VP0, VP3, and VP1 structural proteins and the 2A1, 2A2, 2B, 2C, 3A, 3B, 3C, and 3D non-structural proteins [6,7]. Three serotypes/genotypes (DHAV-1, DHAV-2 and DHAV-3) of DHAV have been distinguished by serological and phylogenetic analyses. Outbreaks of DHAV-1 have been reported in many parts of the world, whereas DHAV-2 and DHAV-3 seemed to be geographically restricted to East and South Asia, although a DHAV-3 outbreak has recently been reported in Egypt (Figure 1)[1,2,6–18]. Viruses 2021, 13, 1592. https://doi.org/10.3390/v13081592 https://www.mdpi.com/journal/viruses