Phylogenetic relationships of Iranian infectious hematopoietic necrosis virus of rainbow trout (Oncorhynchus mykiss) based on the glycoprotein gene

Genome-wide association analysis of the resistance to infectious hematopoietic necrosis virus in two rainbow trout aquaculture lines confirms oligogenic architecture with several moderate effect quantitative trait loci

Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV), which can cause substantial mortality and economic losses in rainbow trout aquaculture and fisheries enhancement hatchery programs. In a previous study on a commercial rainbow trout breeding line that has undergone selection, we found that genetic resistance to IHNV is controlled by the oligogenic inheritance of several moderate and many small effect quantitative trait loci (QTL). Here we used genome wide association analyses in two different commercial aquaculture lines that were naïve to previous exposure to IHNV to determine whether QTL were shared across lines, and to investigate whether there were major effect loci that were still segregating in the naïve lines. A total of 1,859 and 1,768 offspring from two commercial aquaculture strains were phenotyped for resistance to IHNV and genotyped with the rainbow trout Axiom 57K SNP array. Moderate heritability values (0.15-0.25) were estimated. Two statistical methods were used for genome wide association analyses in the two populations. No major QTL were detected despite the naïve status of the two lines. Further, our analyses confirmed an oligogenic architecture for genetic resistance to IHNV in rainbow trout. Overall, 17 QTL with notable effect (≥1.9% of the additive genetic variance) were detected in at least one of the two rainbow trout lines with at least one of the two statistical methods. Five of those QTL were mapped to overlapping or adjacent chromosomal regions in both lines, suggesting that some loci may be shared across commercial lines. Although some of the loci detected in this GWAS merit further investigation to better understand the biological basis of IHNV disease resistance across populations, the overall genetic architecture of IHNV resistance in the two rainbow trout lines suggests that genomic selection may be a more effective strategy for genetic improvement in this trait.

Characterization and pathogenicity analysis of a newly isolated strain of infectious hematopoietic necrosis virus

Rainbow trout is one of the fastest-growing aquaculture species and infectious hematopoietic necrosis virus (IHNV) is endemic throughout almost all rainbow trout farms in China nowadays. In this study, IHNV GS21 was identified as the causative pathogen, which resulted in massive mortality of rainbow trout occurring in northwest China. GS21 isolate was propagated in Chinook salmon embryonic cell line (CHSE-214) and induced apparent cytopathic effects (CPE) at 3 days post-infection (dpi). Phylogenetic analysis revealed that GS21 isolate was clustered with other reported Chinese isolates within the J genogroup. Moreover, the complete cDNA sequence of GS21 isolate was obtained and it possesses more than 98 % of ANI values and 89 % of DDH values with other Chinese IHNV isolates. The detailed sequence analysis of G gene revealed the distinct amino acid substitutions of G230, G252, G270, and I277 in GS21 isolate. Furthermore, the artificially infected rainbow trout exhibited similar clinical disease symptoms as natural infection did. The cumulative mortality infected by GS21 isolate of 104 PFU/mL reached 93 % at approximately 13.5 °C. Additionally, viral loads in tissues increased first and declined then as well as the expression of immune-associated genes. Collectively, our results characterized a novel IHNV GS21 isolate that can lead to massive mortality in juvenile rainbow trout and provided a basis to define the pathogenic characteristics and evolutionary relationship of IHNV and host immune response against IHNV infection.

Infectious hematopoietic necrosis virus (IHNV) nucleoprotein amino acid residues affect viral virulence and immunogenicity in rainbow trout (Oncorhynchus mykiss)

This study compared the N protein sequences of genotype J with other genotypes of IHNV to select amino acid residues that may be related to the change in viral virulence. The recombinant viruses containing different mutation sites were rescued by alanine scanning mutagenesis and the reverse genetic system. The nine recombinant virus strains obtained in this work were named rIHNV-N₈₅, rIHNV-N₁₀₂, rIHNV-N₁₄₆, rIHNV-N₃₈₀, rIHNV-N_85-102-146, rIHNV-N_85-102-380, rIHNV-N_85-146-380, rIHNV-N_102-146-380, and rIHNV-N_{85-102-146-380}. Pathogenicity and immunity assays were performed to determine the role of virulence sites. The result of the pathogenicity test showed that the survival rates of rIHNV-N₈₅, rIHNV-N₁₀₂, rIHNV-N_85-102-146, and rIHNV-N_85-102-380 groups were 52.5%, 55%, 67.5%, and 57.5%, while the survival rate of wild-type (wt) IHNV HLJ-09 group was only 10%. The replication ability of recombinant viruses with substitutions at positions 85 and 102 was significantly inhibited in vivo and in vitro. The qRT-PCR result indicated that the cytokines of IFN1, IL-8, and IL-1β expression levels were increased in rIHNV-N₈₅, rIHNV-N₁₀₂, rIHNV-N_85-102-146, and rIHNV-N_85-102-380 groups. In addition, these four recombinant viruses could cause the rainbow trout to produce anti-IHNV-specific antibodies immunoglobulin M (IgM) earlier, confirming that 85 and 102 amino acid residues of N protein affected the virulence and immunogenicity of IHNV. All these results suggest that mutations of the N protein virulence sites reduce virulence while retaining immunogenicity. This also provides a new idea for studying the virulence mechanism of rhabdoviruses and preparing attenuated vaccines.

Molecular Epidemiology of Novirhabdoviruses Emerging in Iranian Trout Farms

Novirhabdoviruses cause large epizootics and economic losses of farmed trout. In this study, we surveyed Viral hemorrhagic septicemia virus and Infectious hematopoietic and necrosis virus (VHSV and IHNV) through both monitoring and investigation of clinical outbreaks reported by farmers in the regions with major rainbow trout production in Iran from 2015 to 2019. RT-PCR assays of the kidney samples and cell culture (EPC/FHM cells) samples confirmed the presence of the viruses, with 9 VHSV and 4 IHNV isolates, in both endemic and new areas of Iran. Sequence analysis of the G gene revealed that VHSV isolates belonged to genogroup Ia, and IHNV isolates were clustered into genogroup E, both typical for isolates from European countries. A haplotype analysis based on non-homologous amino acids of the G gene supports the emergence of two lineages of IHNV from clade 1 (E-1), as well as VHSV clade 2 (Ia-2) of the European genogroups, confirming that VHSV and IHNV isolates in Iran, have originated from Europe possibly via imported eggs.

Transcriptome analysis based on RNA-seq of common innate immune responses of flounder cells to IHNV, VHSV, and HIRRV

Viral hemorrhagic septicemia virus (VHSV) and hirame rhabdovirus (HIRRV) belong to the genus Novirhabdovirus and are the causative agents of a serious disease in cultured flounder. However, infectious hematopoietic necrosis virus (IHNV), a prototype of the genus Novirhabdovirus, does not cause disease in flounder. To determine whether IHNV growth is restricted in flounder cells, we compared the growth of IHNV with that of VHSV and HIRRV in hirame natural embryo (HINAE) cells infected with novirhabdoviruses at 1 multiplicity of infection. Unexpectedly, we found that IHNV grew as well as VHSV and HIRRV. For successful growth in host cells, viruses modulate innate immune responses exerted by virus-infected cells. Our results suggest that IHNV, like VHSV and HIRRV, has evolved the ability to overcome the innate immune response of flounder cells. To determine the innate immune response genes of virus-infected HINAE cells which are commonly modulated by the three novirhabdoviruses, we infected HINAE cells with novirhabdoviruses at multiplicity of infection (MOI) 1 and performed an RNA sequencing-based transcriptome analysis at 24 h post-infection. We discovered ~12,500 unigenes altered by novirhabdovirus infection and found that many of these were involved in multiple cellular pathways. After novirhabdovirus infection, 170 genes involved in the innate immune response were differentially expressed compared to uninfected cells. Among them, 9 genes changed expression by more than 2-fold and were commonly modulated by all three novirhabdoviruses. Interferon regulatory factor 8 (IRF8), C-X-C motif chemokine receptor 1 (CXCR1), Toll/interleukin-1 receptor domain-containing adapter protein (TIRAP), cholesterol 25-hydroxylase (CH25H), C-X-C motif chemokine ligand 11, duplicate 5 (CXCL11.5), and Toll-like receptor 2 (TLR2) were up-regulated, whereas C-C motif chemokine receptor 6a (CCR6a), interleukin-12a (IL12a), and Toll-like receptor 1 (TLR1) were down-regulated. These genes have been reported to be involved in antiviral responses and, thus, their modulation may be critical for the growth of novirhabdovirus in flounder cells. This is the first report to identify innate immune response genes in flounder that are commonly modulated by IHNV, VHSV, and HIRRV. These data will provide new insights into how novirhabdoviruses survive the innate immune response of flounder cells.

First detection of infectious haematopoietic necrosis virus in farmed rainbow trout in North Macedonia

Infectious haematopoietic necrosis virus (IHNV) is the causative agent of infectious haematopoietic necrosis (IHN), a disease of salmonids responsible for great economic losses. The disease occurs in most parts of the world where rainbow trout is reared but has not been previously reported in North Macedonia. In this study, 150 pooled samples in total, each consisting of organ mix of 10 freshly killed rainbow trout Oncorhynchus mykiss, were collected from 50 trout farms by the Food and Veterinary Agency of North Macedonia as part of the annual surveillance plan for IHN and viral haemorrhagic septicaemia (VHS) control. Screening of samples was done by cell culture and real-time RT-PCR (qRT-PCR). All 150 tested samples were VHS virus (VHSV) qRT-PCR negative. Two samples from different trout farms were IHNV qRT-PCR positive. On cell culture, 1 IHNV qRT-PCR positive sample caused cytopathic effect after 2 passages on EPC cells. The virus, isolated from an asymptomatic rainbow trout fry, was identified by qRT-PCR and designated as MAKIHNV1. The phylogenetic reconstruction indicates that the isolated virus belongs to the European E genogroup, more specifically within the E-1 clade, and is similar to the German, Italian and Iranian isolates. This study has revealed for the first time the presence of IHNV in rainbow trout in North Macedonia. However, it is not possible to make interpretations about the source of infection from the phylogenetic analysis, and the origin of MAKIHNV1 remains unclear.

The L-domains in M and G proteins of infectious hematopoietic necrosis virus (IHNV) affect viral budding and pathogenicity

RNA viruses including many retroviruses encode "late-domain" motifs that can interact with host proteins to mediate viral assembly and affect viral budding and pathogenicity. For IHNV, our previous studies demonstrated that the respective interactions of the L domains of IHNV with host proteins could mediate viral assembly and budding. To our knowledge, the role of L domains of the IHNV in the budding and pathogenicity has not investigated yet. In this study, we generated two recombinant IHNV strains rIHNV-M_(PH>A4) and rIHNV-G_(PS>A4) with mutations in the L domains (PPPH to AAAA or PSAP to AARA) of IHNV by reverse genetics and explored the effect of the mutations on budding and pathogenicity of the two recombinant viruses. The RT-qPCR results showed that the production levels of the extracellular particles of rIHNV-M_(PH>A4) or rIHNV-G_(PS>A4) declined significantly, compared with those of wild-type (wt) IHNV HLJ-09. Furthermore, the challenge test showed that the survival rates of juvenile rainbow trout challenged with rIHNV-M_(PH>A4) or rIHNV-G_(PS>A4) were 90% or 87%, respectively; however, the survivability was zero in groups challenged with wtIHNV HLJ-09 or rIHNV HLJ-09 (recombinant IHNV). Additionally, the RT-qPCR results showed that the recombinant viruses induced higher expression levels of IFN1, IL-1β, and IL-8 compared with those induced by wtIHNV HLJ-09 as well as the ELISA results showed that fish vaccinated with recombinant viruses produced high levels of specific IgM antibodies, demonstrating that the two recombinant viruses may induce immune responses to resist infection by IHNV. Also, these results demonstrated for the first time that the L domains of the M and G proteins of IHNV could affect the budding and pathogenicity of IHNV, which may be beneficial in the prevention and control of IHNV infections in fish. Taken together, our study as the first research provides the foundation for effect of rhabdovirus L domains on viral budding and pathogenicity.

Identification of the optimal insertion site for expression of a foreign gene in an infectious hematopoietic necrosis virus vector

Infectious hematopoietic necrosis virus (IHNV) was developed as a vector to aid the construction of vaccines against viral diseases such as viral hemorrhagic septicemia virus, spring viremia of carp virus, and influenza virus H1N1. However, the optimal site for foreign gene expression in the IHNV vector has not been determined. In the present study, five recombinant viruses with the green fluorescence protein (GFP) gene inserted into different genomic junction regions of the IHNV genomic sequence were generated using reverse genetics technology. Viral growth was severely delayed when the GFP gene was inserted into the intergenic region between the N and P genes. Real-time fluorescence quantitative PCR assays showed that the closer the GFP gene was inserted towards the 3' end, the higher the GFP mRNA levels. Measurement of the GFP fluorescence intensity, which is the most direct method to determine the GFP protein expression level, showed that the highest GFP protein level was obtained when the gene was inserted into the intergenic region between the P and M genes. The results of this study suggest that the P and M gene junction region is the optimal site within the IHNV vector to express foreign genes, providing valuable information for the future development of live vector vaccines.

Molecular evolution and selection pressure analysis of infectious hematopoietic necrosis virus (IHNV) revealed the origin and phylogenetic relationship of Iranian isolates in recent epidemics in Iran

Infectious hematopoietic necrosis virus (IHNV) is the causative agent for a lethal salmonid disease. In this study, we surveyed the IHNV's epidemiology, diversity and the origin of infection in Iran. Phylogenetic analysis revealed that Iranian isolates belonged to one of the two lineages of E genogroup. Subsequently, a combination of phylogenetic, antigenic and structural analysis was performed to investigate the evolution of E genogroup lineages. Site-specific analysis of the viral glycoprotein showed different co-evolving and positively selected sites in each lineage. Most of these sites were mapped to the predicted antigenic patches of the glycoprotein. Further characterization revealed E lineages can be differentiated, in part, by specific mutations at positions 91 and 130, which are located in the structurally flexible regions of the glycoprotein, suggesting a key adaptative role for these sites. These data may assist in better monitoring the emerging isolates in regions infected to IHNV from E genogroup.

Molecular evolution and phylogeography of infectious hematopoietic necrosis virus with a focus on its presence in France over the last 30 years

Infectious hematopoietic necrosis virus (IHNV) is among the most important pathogens affecting the salmonid industry. Here, we investigated the molecular evolution and circulation of isolates from 11 countries or regions all over the world, with a special focus on the epidemiological situation in France. The phylogeography, time to the most recent common ancestor (TMRCA) and nucleotide substitution rate were studied using 118 full-length glycoprotein gene sequences isolated from 9 countries (5 genogroups) over a period of 47 years. The TMRCA dates back to 1943, with the L genogroup identified as the likely root (67 %), which is consistent with the first report of this pathogen in the USA. A Bayesian inference approach was applied to the partial glycoprotein gene sequences of 88 representative strains isolated in France over the period 1987-2015. The genetic diversity of these 88 sequences showed mean nucleotide and amino-acid identities of 97.1 and 97.8 %, respectively, and a d _N/d _S ratio (non-synonymous to synonymous mutations) of 0.25, indicating purifying selection. The French viral populations are divided into eight sub-clades and four individual isolates, with a clear spatial differentiation, suggesting the predominant role of local reservoirs in contamination. The atypical 'signatures' of some isolates underlined the usefulness of molecular phylogeny for epidemiological investigations that track the spread of IHNV.

Infectious hematopoietic necrosis virus (IHNV) outbreak in farmed rainbow trout in Iran: Viral isolation, pathological findings, molecular confirmation, and genetic analysis

Infectious hematopoietic necrosis virus (IHNV) is the etiological agent of a contagious disease (IHN) mainly in salmonid fish. In the present study, we isolated and identified IHNV in trout fry from Iranian trout farms with unexplained high mortality in 2016. The affected fry showed cumulative mortality of 90% with the gross pathological signs including exophthalmia and hemorrhage of the eye, skin darkening, abdominal distension, ulceration of the snout, and the visceral pallor and yellowish fluid in the intestine. Histopathological examination revealed marked necrosis in the anterior kidney, liver and spleen with the intracytoplasmic inclusion bodies in the liver sections. Also, intranuclear inclusion body and marginated chromatin were observable in the hematopoietic cells of the kidney. The homogenates tissues of infected fry induced IHNV-positive cytopathic effects (CPE) in EPC cells and confirmed by RT-PCR reactions and sequencing. Phylogenetic analysis revealed the Iranian IHNV isolates belonged to the European (E) genogroup with 100% identity to some Italian isolates. This is the first report of IHNV infection in farmed trout fry in Iran describing the viral isolation, clinical symptoms, histopathological findings, molecular confirmation, and genetic analysis suggestion of the specific country of origin.