Cardé

Whole-genome Sequencing of Acipenserid Herpesvirus 2 and Identification of Potential Host Homologues

Eva M. Quijano Cardé1, Susan Yun1, Geoffrey Waldbieser2, Mark D. Fast3, Matt Griffin3, C. Titus Brown1, Esteban Soto1

1Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis CA; 2United States Department of Agriculture – Agricultural Research Service, Stoneville MS; 3Atlantic Veterinary College, University of Prince Edward Island, PE Canada; 4Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville MS

ABSTRACT

The white sturgeon (Acipenser transmontanus) is an anadromous fish native to the Pacific Coast of North America and responsible for 95% of the caviar and sturgeon meat aquaculture production in the United States. An important pathogen of white sturgeon, prevalent in broodstock populations, is Acipenserid herpesvirus 2 (AciHV-2). Both juvenile and subadult white sturgeon are susceptible to AciHV-2, resulting in a variety of clinical signs and mass mortality events. The potential for subsequent outbreaks from potentially latently infected fish as well as the poorly understood effects of the latent virus on the white sturgeon’s immune system are valuable aspects of AciHV-2 pathogenesis to elucidate. A current limiting factor in the AciHV-2 research efforts is that a complete genome is not available. Thus, the purpose of this study was to 1) assemble and annotate the complete genome of AciHV-2 and 2) identify potential host homologs that could be influencing the immune system of the white sturgeon. Four isolates were sequenced via Illumina and Nanopore technologies. The obtained assembled genomes were approximately 134Kb. Small changes among isolates were observed, with the alignment of these genomes revealing that over 98.6% of the bases are identical between any two isolates. In addition, the four isolates cluster in a similarity matrix with the published partial AciHV-2 sequence and separate from other herpesviruses. Prediction tools indicate that the four isolates share 102 open reading frames (ORFs) and have 1-3 unique predicted ORFs due to changes in their genomes. In addition, all isolates contain a terminal repeat sequence of 1,907 base pairs with only 6 base changes among the isolates. Assessment of the reads providing coverage for the terminal repeats supports the circularization of the virus during the replicative cycle. A comparison of the predicted ORFs with the white sturgeon genome revealed five homologs to be investigated. Initial assessment indicated that some of these homologs have protein kinase domains. These reference AciHV-2 genomes will serve for easier assembly of other AciHV-2 isolates, and the development of molecular tools for studying and diagnosing AciHV-2 both in vitro and in vivo.

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