Discovery and genomic characterization of a novel hepadnavirus from asymptomatic anadromous alewife (Alosa pseudoharengus)

Authors: RAINES, CLAYTON - Us Geological Survey (USGS); Iwanowicz, Luke; LOVY, JAN - Us Geological Survey (USGS); PHELPS, NICOLAS - University Of Minnesota; MOR, SUNIL - South Dakota State University; NG, TERRY FEI FAN - Centers For Disease Control And Prevention (CDC) - United States

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2024
Publication Date: 5/22/2024
Citation: Raines, C.D., Iwanowicz, L.R., Lovy, J., Phelps, N., Mor, S., Ng, T. 2024. Discovery and genomic characterization of a novel metahepadnavirus from clinically normal anadromous alewives (Alosa pseudoharengus). Viruses. 16(6):824. https://doi.org/10.3390/v16060824.
DOI: https://doi.org/10.3390/v16060824

Interpretive Summary: A previously undescribed virus was identified in clinically normal, migratory alewives. The complete genome was sequenced and diagnostic markers developed. These fish migrate in waters proximate to open water aquaculture operations. Understanding the disease ecology of such species enhances biopreparedness in the event of cross-species transmission.

Technical Abstract: The alewife (Alosa pseudoharangus) is an anadromous herring that inhabits waters of Northeastern North America. This prey species is critical forage species for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify novel, potentially emerging diseases of this species, we identified the full genome of a novel hepatitis B-like virus from clinically normal alewives. Infected fish were collected from the Maurice River and Great Egg Harbor River in New Jersey, USA. Sanger sequencing was used to verify genome completeness. We identified the closed, covalent circular DNA genome (3146 nt) of a previously undescribed hepadnavirus. with the characteristic hepadnavirus open reading frames and genomic organization. Phylogenetic analysis of the polymerase protein places this virus in the clade of metahepadnaviruses. Electron microscopy of liver lysate did not yield viral particles, and there was no evidence of cellular pathology associated with viral infection in other sampled organ tissue. We developed a SYBR green-based qPCR assay and screened river herring from different aquatic habitats. We sequenced an additional genome from a qPCR positive sample that was 99.4% identical. Single nucleotide polymorphisms were observed between the two genomes that included 7/9 and 12/8 synonomous vs nonsynonymous mutations across the polymerase and surface protein open reading frames, respectively. Compared to other described hepadnaviruses, sequence conservation of the core, polymerase and surface proteins was less than 50%. Phylogenetic analysis of the polymerase protein places this virus in the clade of metahepadnaviruses. Similar to other metahepadnaviruses, the Alosa pseudoharengus hepatitis B virus (ApHBV) described here does not have an X protein homologue common to the orthohepadnaviruses. While it is not clear if this virus is associated with a disease of significant consequence to this species, alewives are migratory interjurisdictional fishes of management concern. Identification of microbial agents using de novo sequencing and other advanced technologies is a critical aspect of understanding disease ecology for informed population management.