Discovery of a Novel Hepatovirus (Phopivirus of Seals) Related to Human Hepatitis A Virus

Abstract

Describing the viral diversity of wildlife can provide interesting and useful insights into the natural history of established human pathogens. In this study, we describe a previously unknown picornavirus in harbor seals (tentatively named phopivirus) that is related to human hepatitis A virus (HAV). We show that phopivirus shares several genetic and phenotypic characteristics with HAV, including phylogenetic relatedness across the genome, a specific and seemingly quiescent tropism for hepatocytes, structural conservation in a key functional region of the type III internal ribosomal entry site (IRES), and a codon usage bias consistent with that of HAV.

Importance: Hepatitis A virus (HAV) is an important viral hepatitis in humans because of the substantial number of cases each year in regions with low socioeconomic status. The origin of HAV is unknown, and no nonprimate HAV-like viruses have been described. Here, we describe the discovery of an HAV-like virus in seals. This finding suggests that the diversity and evolutionary history of these viruses might be far greater than previously thought and may provide insight into the origin and pathogenicity of HAV.

FIG 1

Maximum-likelihood phylogenetic reconstruction of the picornaviruses, based on peptide 3D amino acid sequences. The model used was LG (34) complete deletion, gamma distributed with invariant sites (G+I). The tree shows that phopivirus is most closely related to HAV. Relationships are consistent when repeated for other peptides. Scale indicates number of amino acid substitutions per site per year. Bootstrap values are shown at nodes.

FIG 2

Schematic of the phopivirus genome, with predicted polyprotein cleavage sites, and sequence identities across the genome to HAV, avian encephalomyelitis virus (AEV), and seal aquamavirus A1 (SeAV-A1). The picornavirus genome consists of a single open reading frame (ORF) which produces a polyprotein that is cleaved into the structural (P1) and non-structural (P2 and P3) proteins.

FIG 3

Phopivirus viral loads for all 12 positive animals identified in this study. Viral loads were determined by qPCR and are expressed as genome copy numbers per 250 ng. Pg, Phoca groenlandicus (harp seal); Pv, Phoca vitulina (harbor seal); *, tissue not available for testing.

FIG 4

Harbor seal infected liver tissue. (Top) Two liver sections from animal NEAQ-11-295-Pv, stained with hematoxylin; left-hand image includes bile duct (A), hepatic vein (B), and hepatic artery (C). No inflammation is observed in the infected tissue. (Bottom) Distribution of phopivirus in liver using fluorescent in situ hybridization (FISH), with higher-magnification insets demonstrating clear cytoplasmic infection.

FIG 5

Structural comparison of the type III IRES, domain IV (which corresponds to nucleotides 320 to 570 of the phopivirus 5′ UTR). Highlighted nucleotides represent pairings where complementary mutations have been selected in order to preserve structural integrity. (A) HAV. (B) Phopivirus.