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

Clayton D. Raines; Jan Lovy; Nicolas B.D. Phelps; Sunil Mor; Terry Ng; Luke R. Iwanowicz

doi:10.3390/v16060824

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

Clayton D. Raines·Jan Lovy·Nicolas B.D. Phelps·Sunil Mor·Terry Ng·Luke R. Iwanowicz

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Abstract

The alewife ( Alosa pseudoharengus) is an anadromous herring that inhabits waters of northeastern North America. This prey species is a critical forage for piscivorous birds, mammals, and fishes in estuarine and oceanic ecosystems. During a discovery project tailored to identify potentially emerging pathogens of this species, we obtained the full genome of a novel hepadnavirus (ApHBV) from clinically normal alewives collected from the Maurice River, Great Egg Harbor River, and Delaware River in New Jersey, USA during 2015–2018. This previously undescribed hepadnavirus contained a circular DNA genome of 3146 nucleotides. Phylogenetic analysis of the polymerase protein placed this virus in the clade of metahepadnaviruses (family: Hepadnaviridae ; genus: Metahepadnavirus ). There was no evidence of pathology in the internal organs of infected fish and virions were not observed in liver tissues by electron microscopy. We developed a Taqman-based quantitative (qPCR) assay and screened 182 individuals collected between 2015 and 2018 and detected additional qPCR positives (n = 6). An additional complete genome was obtained in 2018 and it has 99.4% genome nucleotide identity to the first virus. Single-nucleotide polymorphisms were observed between the two genomes, including 7/9 and 12/8 synonymous vs nonsynonymous mutations across the polymerase and surface proteins, respectively. While there was no evidence that this virus was associated with disease in 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.

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Source-reported bounding extent: 39.47832891534992° to 41.012795334894605° latitude; -75.45013476920779° to -73.8900761754575° longitude. This indicates report coverage, not an exact sampling location. View area on OpenStreetMap.

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Clayton D. Raines, Jan Lovy, Nicolas B.D. Phelps, Sunil Mor, Terry Ng, Luke R. Iwanowicz. 2024-05-22. Discovery and genomic characterization of a novel hepadnavirus from asymptomatic anadromous alewife (Alosa pseudoharengus). https://doi.org/10.3390/v16060824

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