Genome-based Approaches to Diagnosis and Phylogenetic Analysis in the Epidemiology of Aquatic Animal Viruses : 수생동물바이러스 역학을 위한 유전체 기반 진단 및 계통분석

다국어 초록 (Multilingual Abstract)

Global aquaculture faces persistent and escalating threats of viral pathogens. Low-titer or latent infections often escape routine checks and later manifest as production losses through mortality and subclinical effects such as growth retardation and prolonged grow-out. This thesis applies a genome-based molecular surveillance framework to three priority viruses—Decapod hepandensovirus 1 (DHPV) in shrimp, Japanese eel endothelial cells-infecting virus (JEECV) in eels, and Megalocytivirus in finfish—to show how whole-genome sequencing, comparative phylogenomics, and molecular diagnostics, interpreted with traceable metadata, can turn otherwise invisible circulation into a practical basis for disease control.
Chapter I characterizes a newly emerged DHPV genotype from Korean Penaeus vannamei farms based on polymerase chain reaction (PCR) screening and complete genome analysis. The 6,173 nt genome retains the canonical Densovirinae organization with three major ORFs encoding NS1, NS2, and VP, but shows markedly reduced nucleotide identities to nine reference DHPV genomes, especially in VP. Furthermore, phylogenies based on the whole genome and each ORF consistently place the new DHPV genome on a distinct branch, supporting the emergence of a novel genotype. PCR screening of field samples from multiple farms detected DHPV in shrimp, pond water, feces, and cohabiting crustaceans, indicating an environmental and non-shrimp reservoir. These results highlight an overlooked risk to the world’s most dominant shrimp species.
Chapter II investigates JEECV epidemiology in Korean eel aquaculture and its relationship with Anguillid herpesvirus 1 (AngHV-1). Targeted farm screening conducted between 2021 and 2024 showed frequent detection of JEECV and AngHV-1, and repeated coinfection. A complete circular JEECV genome from Anguilla bicolor provides the first Korean whole genome sequence and shows high conservation among JEECV isolates, whereas the large T-antigen-like gene remains clearly distinct from Polyomaviridae homologues, supporting the unique taxonomic position of JEECV. Building on these data, the new TaqMan quantitative PCR (qPCR) outperformed conventional PCR in sensitivity, enabling detection at lower copy numbers. Quantitative results, interpreted with coinfection status, support proportionate responses such as enhanced observation, movement holds, or adjusted harvest timing.
Chapter III extends surveillance to borders by screening imported ornamental fish for Megalocytivirus. Samples comprised ten imported ornamental fish species from eight declared origins. A structured survey of liver pools used a two‑step protocol: an initial general MCP‑targeted Megalocytivirus PCR for screening, followed by genotype‑specific assays for red sea bream iridovirus (RSIV), infectious spleen and kidney necrosis virus (ISKNV), and turbot reddish body iridovirus (TRBIV). Megalocytivirus was detected in a subset of pools from diverse origins and host species, and all positive pools were identified as ISKNV. Phylogenetic analysis of representative MCP sequences placed all isolates within ISKNV Clade 1. These findings indicate that imported ornamental fish can carry high‑consequence Megalocytivirus lineages into Korea and support including ISKNV, in addition to RSIV, in border sanitary measures and import risk analysis.
Taken together, the chapters outline an evidence‑based workflow that links case confirmation with population‑level surveillance. Genome‑informed qPCR assays reveal diversity, refine gene maps, and support stable target design, while integration with animal movement and basic metadata clarifies where and how viruses circulate. In shrimp, detection of DHPV in non‑shrimp organisms and environmental samples points to micro‑ecosystem reservoirs that warrant management beyond the host stock. In eels, overlapping endothelial tropism and potential immunomodulation during JEECV and AngHV‑1 coinfection help explain severe vascular disease and emphasize surveillance of pathogen complexes. In ornamental fish, repeated ISKNV detections across mixed consignments argue for sustained sequence‑based monitoring to guide targeted interventions. Overall, the thesis demonstrates that proactive, quantitative, genome‑based molecular surveillance is feasible in routine settings and offers an operational pathway that links diagnostics, phylogeny, and metadata to align stocking, movement, and harvest decisions with viral risk in modern aquaculture.

목차 (Table of Contents)

• Literature review 1
• 1. Aquatic animal health 2
• 1.1. Viral disease in aquaculture 2
• 1.2. Global trade causes recurrent losses 2
• 1.3. Early molecular detection of disease 3
• 1.4. Rationale for focusing on Decapod hepandensovirus 1 (DHPV), Japanese eel endothelial cells-infecting virus (JEECV), and Megalocytivirus 4
• 2. Decapod hepandensovirus 1 (DHPV) overview 5
• 2.1. Genotype diversity of DHPV 5
• 2.2. Genome-based assay using conserved NS and variable VP 6
• 3. Japanese eel endothelial cells-infecting virus (JEECV) overview 6
• 3.1. Atypical genome organization of JEECV 6
• 3.2. Ongoing taxonomic discussion 7
• 3.3. Diagnostic considerations and surveillance implications 8
• 4. Megalocytivirus pagrus 1 overview 9
• 4.1. Family Iridoviridae in aquaculture 9
• 4.2. Ornamental fish trade pathway and transboundary risk 10
• 4.3. Detection and surveillance at import nodes 10
• Chapter I. Genomic characterization and phylogeny of a newly emerged Decapod hepandensovirus 1 genotype 12
• 1. Introduction 13
• 2. Materials and methods 14
• 2.1. Sample collection and DNA extraction 14
• 2.2. Whole genome sequencing and assembly 17
• 2.3. Genome comparison and phylogeny 18
• 3. Results 20
• 3.1. Complete genome of the Korean nDHPV 20
• 3.2. Comparative genomics and phylogeny 23
• 4. Discussion 32
• Chapter II. Farm-level epidemiology of Japanese eel endothelial cells-infecting virus and Real-time surveillance 35
• 1. Introduction 36
• 2. Materials and methods 37
• 2.1. Sample collection, DNA extraction, and initial screening 37
• 2.2. Complete genome sequence of JEECV and its annotations 42
• 2.3. Phylogenetic analysis of JEECV 42
• 2.4. Design of JEECV and AngHV-1 qPCR and assay performance 46
• 3. Results 46
• 3.1. Farm-level detection of JEECV and AngHV-1 46
• 3.2. WGS recovery and genomic features of JEECV 47
• 3.3. Pairwise comparison and phylogenetic relationship of JEECV sequences 50
• 3.4. Assay performance of the newly developed TaqMan qPCR 50
• 4. Discussion 53
• Chapter III. Molecular detection and phylogenetic characterization of Megalocytivirus in imported ornamental fish 56
• 1. Introduction 57
• 2. Materials and methods 60
• 2.1. Ornamental fish sample collection 60
• 2.2. Detection of Megalocytivirus genome by PCR 61
• 2.3. MCP gene sequencing and phylogenetic analysis 61
• 3. Results 65
• 3.1. Prevalence of Megalocytivirus in imported ornamental fish samples 65
• 3.2. Sequencing of the MCP gene and phylogenetic analysis of representative ISKNV isolates 69
• 4. Discussion 73
• General conclusions 76
• References 79
• Abstract 94
• Abstract in Korean 98