Molecular Diagnosis of Infectious Hematopoietic Necrosis and Viral Hemorrhagic Septicemia

Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus

Introduction: Viral hemorrhagic septicemia virus (VHSV) is the most lethal pathogen in aquaculture, infecting more than 140 fish species in marine, estuarine, and freshwater environments. Viral hemorrhagic septicemia virus is an enveloped RNA virus that belongs to the family Rhabdoviridae and the genus Novirhabdovirus. The current study is designed to infer the worldwide Viral hemorrhagic septicemia virus isolates' genetic diversity and evolutionary dynamics based on G-gene sequences. Methods: The complete G-gene sequences of viral hemorrhagic septicemia virus were retrieved from the public repositories with known timing and geography details. Pairwise statistical analysis was performed using Arlequin. The Bayesian model-based approach implemented in STRUCTURE software was used to investigate the population genetic structure, and the phylogenetic tree was constructed using MEGA X and IQ-TREE. The natural selection analysis was assessed using different statistical approaches, including IFEL, MEME, and SLAC. Results and Discussion: The global Viral hemorrhagic septicemia virus samples are stratified into five genetically distinct subpopulations. The STRUCTURE analysis unveiled spatial clustering of genotype Ia into two distinct clusters at K = 3. However, at K = 5, the genotype Ia samples, deposited from Denmark, showed temporal distribution into two groups. The analyses unveiled that the genotype Ia samples stratified into subpopulations possibly based on spatiotemporal distribution. Several viral hemorrhagic septicemia virus samples are characterized as genetically admixed or recombinant. In addition, differential or subpopulation cluster-specific natural selection signatures were identified across the G-gene codon sites among the viral hemorrhagic septicemia virus isolates. Evidence of low recombination events elucidates that genetic mutations and positive selection events have possibly driven the observed genetic stratification of viral hemorrhagic septicemia virus samples.

Universal reverse-transcriptase real-time PCR for infectious hematopoietic necrosis virus (IHNV)

Infectious hematopoietic necrosis virus (IHNV) is an acute pathogen of salmonid fishes in North America, Europe and Asia and is reportable to the World Organization for Animal Health (OIE). Phylogenetic analysis has identified 5 major virus genogroups of IHNV worldwide, designated U, M, L, E and J; multiple subtypes also exist within those genogroups. Here, we report the development and validation of a universal IHNV reverse-transcriptase real-time PCR (RT-rPCR) assay targeting the IHNV nucleocapsid (N) gene. Properties of diagnostic sensitivity (DSe) and specificity (DSp) were defined using laboratory-challenged steelhead trout Oncorhynchus mykiss, and the new assay was compared to the OIE-accepted conventional PCR test and virus isolation in cell culture. The IHNV N gene RT-rPCR had 100% DSp and DSe and a higher estimated diagnostic odds ratio (DOR) than virus culture or conventional PCR. The RT-rPCR assay was highly repeatable within a laboratory and highly reproducible between laboratories. Field testing of the assay was conducted on a random sample of juvenile steelhead collected from a hatchery raceway experiencing an IHN epizootic. The RT-rPCR detected a greater number of positive samples than cell culture and there was 40% agreement between the 2 tests. Overall, the RT-rPCR assay was highly sensitive, specific, repeatable and reproducible and is suitable for use in a diagnostic setting.

Accurate detection and quantification of the fish viral hemorrhagic Septicemia virus (VHSv) with a two-color fluorometric real-time PCR assay

Viral Hemorrhagic Septicemia virus (VHSv) is one of the world's most serious fish pathogens, infecting >80 marine, freshwater, and estuarine fish species from Eurasia and North America. A novel and especially virulent strain - IVb - appeared in the Great Lakes in 2003, has killed many game fish species in a series of outbreaks in subsequent years, and shut down interstate transport of baitfish. Cell culture is the diagnostic method approved by the USDA-APHIS, which takes a month or longer, lacks sensitivity, and does not quantify the amount of virus. We thus present a novel, easy, rapid, and highly sensitive real-time quantitative reverse transcription PCR (qRT-PCR) assay that incorporates synthetic competitive template internal standards for quality control to circumvent false negative results. Results demonstrate high signal-to-analyte response (slope = 1.00±0.02) and a linear dynamic range that spans seven orders of magnitude (R(2) = 0.99), ranging from 6 to 6,000,000 molecules. Infected fishes are found to harbor levels of virus that range to 1,200,000 VHSv molecules/10(6) actb1 molecules with 1,000 being a rough cut-off for clinical signs of disease. This new assay is rapid, inexpensive, and has significantly greater accuracy than other published qRT-PCR tests and traditional cell culture diagnostics.

The use of a one-step real-time reverse transcription polymerase chain reaction (rRT-PCR) for the surveillance of viral hemorrhagic septicemia virus (VHSV) in Minnesota

Viral hemorrhagic septicemia virus (VHSV) is a highly contagious and pathogenic virus of fish. The virus infects more than 70 fish species worldwide, in both fresh and salt water. A new viral strain (VHSV-IVb) has proven both virulent and persistent, spreading throughout the Great Lakes of North America and to inland water bodies in the region. To better understand the geographic distribution of the virus, we used a modified real-time reverse transcription polymerase chain reaction (rRT-PCR) assay for high-throughput testing of fish for VHSV. The assay was shown to be twice as sensitive as the gold standard, virus isolation, and did not cross react with other viruses found in fish. In addition, the diagnostic turnaround time was reduced from 28 to 30 d for virus isolation to 2-4 d for rRT-PCR. To demonstrate the usefulness of the rRT-PCR assay, 115 high-priority water bodies in Minnesota were tested by both methods from April 2010 to June 2011. All survey sites tested negative for VHSV by both methods. The survey results have informed fisheries managers on the absence of VHSV in Minnesota and have better prepared them for the eventual arrival of the disease. In addition, the results demonstrate the value of this rRT-PCR as a surveillance tool to rapidly identify an outbreak so that it can be controlled in a timely manner.

Evolution and biogeography of an emerging quasispecies: diversity patterns of the fish Viral Hemorrhagic Septicemia virus (VHSv)

Viral Hemorrhagic Septicemia virus (VHSv) is an RNA rhabdovirus that causes one of the most important finfish diseases, affecting over 70 marine and freshwater species. It was discovered in European cultured fish in 1938 and since has been described across the Northern Hemisphere. Four strains and several substrains have been hypothesized, whose phylogenetic relationships and evolutionary radiation are evaluated here in light of a quasispecies model, including an in-depth analysis of the novel and especially virulent new substrain (IVb) that first appeared in the North American Laurentian Great Lakes in 2003. We analyze the evolutionary patterns, genetic diversity, and biogeography of VHSv using all available RNA sequences from the glycoprotein (G), nucleoprotein (N), and non-virion (Nv) genes, with Maximum Likelihood and bayesian approaches. Results indicate that the G gene evolves at an estimated rate of μ=2.58×10(-4) nucleotide substitutions per site per year, the N gene at μ=4.26×10(-4), and Nv fastest at μ=1.25×10(-3). Phylogenetic trees from the three genes largely are congruent, distinguishing strains I-IV as reciprocally monophyletic with high bootstrap and posterior probability support. VHSv appears to have originated from a marine ancestor in the North Atlantic Ocean, diverging into two primary clades: strain IV in North America (the Northwestern Atlantic Ocean), and strains I-III in the Northeastern Atlantic region (Europe). Strain II may comprise the basal group of the latter clade and diverged in Baltic Sea estuarine waters; strains I and III appear to be sister groups (according to the G and Nv genes), with the former mostly in European freshwaters and the latter in North Sea marine/estuarine waters. Strain IV is differentiated into three monophyletic substrains, with IVa infecting Northeastern Pacific salmonids and many marine fishes (with 44 unique G gene haplotypes), IVb endemic to the freshwater Great Lakes (11 haplotypes), and a newly-designated IVc in marine/estuarine North Atlantic waters (five haplotypes). Two separate substrains independently appeared in the Northwestern Pacific region (Asia) in 1996, with Ib originating from the west and IVa from the east. Our results depict an evolutionary history of relatively rapid population diversifications in star-like patterns, following a quasispecies model. This study provides a baseline for future tracking of VHSv spread and interpreting its evolutionary diversification pathways.

Isolation of viral haemorrhagic septicaemia virus from mummichog, stickleback, striped bass and brown trout in eastern Canada

Viral haemorrhagic septicaemia virus (VHSV) was isolated from mortalities occurring in populations of mummichog, Fundulus heteroclitus, stickleback, Gasterosteus aculeatus aculeatus, brown trout, Salmo trutta, and striped bass, Morone saxatilis, in New Brunswick and Nova Scotia, Canada. The isolated viral strains produced a cytopathic effect on the epithelioma papillosum cyprini cell line. Serum neutralization indicated the virus was VHSV and sequencing identified the rhabdovirus isolates as the North American strain of VHSV. Phylogenetic analysis indicated that the isolates are closely related and form a distinguishable subgroup of North American type VHSV. To our knowledge, this is the first report of VHSV in mummichog and striped bass.

Isolation of viral haemorrhagic septicaemia virus from muskellunge, Esox masquinongy (Mitchill), in Lake St Clair, Michigan, USA reveals a new sublineage of the North American genotype

Viral haemorrhagic septicaemia virus (VHSV) was isolated from muskellunge, Esox masquinongy (Mitchill), caught from the NW portion of Lake St Clair, Michigan, USA in 2003. Affected fish exhibited congestion of internal organs; the inner wall of the swim bladder was thickened and contained numerous budding, fluid-filled vesicles. A virus was isolated using fish cell lines inoculated with a homogenate of kidney and spleen tissues from affected fish. Focal areas of cell rounding and granulation appeared as early as 24 h post-inoculation and expanded rapidly to destroy the entire cell sheet by 96 h. Electron microscopy revealed virions that were 170-180 nm in length by 60-70 nm in width having a bullet-shaped morphology typical of rhabdoviruses. The virus was confirmed as VHSV by reverse transcriptase-polymerase chain reaction. Sequence analysis of the entire nucleoprotein and glycoprotein genes revealed the virus was a member of the North American genotype of VHSV; however, the isolate was sufficiently distinct to be considered a separate sublineage, suggesting its origin may have been from marine species inhabiting the eastern coastal areas of the USA or Canada.

Detection of infectious haematopoietic necrosis virus and infectious salmon anaemia virus by molecular padlock amplification

A new method for the molecular detection of the fish pathogens, infectious haematopoietic necrosis virus (IHNV) and infectious salmon anaemia virus (ISAV), is described. By employing molecular padlock probe (MPP) technology combined with rolling circle amplification (RCA) and hyperbranching (Hbr), it is possible to detect RNA target sequence from these viruses at levels comparable with those detected by the polymerase chain reaction (PCR), but without prior reverse transcription. The use of MPP technology combined with RCA and Hbr for the detection of IHNV and ISAV in fish exhibited selectivity comparable with that of PCR while potentially reducing the time and cost required for analysis. The method described was used to detect as few as 10(4) DNA oligonucleotide targets and was sequence-specific at the single base level. Viral RNA could be detected directly, either alone or in the presence of non-viral RNA from fish tissue. This technology is applicable for detecting a variety of microbes, in addition to IHNV and ISAV, and is ideal for further integration into a biosensor platform for on-site diagnosis of pathogen infection in fish.