Differential Transcriptomic Response of Rainbow Trout to Infection with Two Strains of IPNV

The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.

Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection

BACKGROUND

Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation's food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens.

RESULTS

A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value < 0.05. Yet, only 9 upregulated and 13 downregulated uni-genes had BLAST hits against the Non-redundant and Swiss-Prot databases. The genome ontology enrichment keywords of these DEGs were associated with immune response, cell signalling and apoptosis. Consequently, the Weighted Gene Correlation Network Analysis R tool was used to predict the functional annotation of the remaining unknown uni-genes with no significant BLAST hits. Interestingly, the functions of the three upregulated uni-genes were predicted to be related to innate immune response, while the five downregulated uni-genes were predicted to be related to cell surface functions. These results further elucidated and supported the current molecular knowledge regarding the pathophysiology of chicken's bursal infected with IBDV.

CONCLUSION

Our data revealed the commonly up- and downregulated novel uni-genes identified to be immune- and extracellular binding-related, respectively. Besides, these novel findings are valuable contributions in improving the current existing integrative chicken transcriptomics annotation and may pave a path towards the control of viral particles especially towards the suppression of IBD and other infectious diseases in chickens.

Role of MicroRNAs in Host Defense against Infectious Bursal Disease Virus (IBDV) Infection: A Hidden Front Line

Infectious bursal disease (IBD) is an acute, highly contagious and immunosuppressive avian disease caused by infectious bursal disease virus (IBDV). In recent years, remarkable progress has been made in the understanding of the pathogenesis of IBDV infection and the host response, including apoptosis, autophagy and the inhibition of innate immunity. Not only a number of host proteins interacting with or targeted by viral proteins participate in these processes, but microRNAs (miRNAs) are also involved in the host response to IBDV infection. If an IBDV–host interaction at the protein level is taken imaginatively as the front line of the battle between invaders (pathogens) and defenders (host cells), their fight at the RNA level resembles the hidden front line. miRNAs are a class of non-coding single-stranded endogenous RNA molecules with a length of approximately 22 nucleotides (nt) that play important roles in regulating gene expression at the post-transcriptional level. Insights into the roles of viral proteins and miRNAs in host response will add to the understanding of the pathogenesis of IBDV infection. The interaction of viral proteins with cellular targets during IBDV infection were previously well-reviewed. This review focuses mainly on the current knowledge of the host response to IBDV infection at the RNA level, in particular, of the nine well-characterized miRNAs that affect cell apoptosis, the innate immune response and viral replication.

Genome-Wide Association Analysis for Resistance to Infectious Pancreatic Necrosis Virus Identifies Candidate Genes Involved in Viral Replication and Immune Response in Rainbow Trout (Oncorhynchus mykiss)

Infectious pancreatic necrosis (IPN) is a viral disease with considerable negative impact on the rainbow trout (Oncorhynchus mykiss) aquaculture industry. The aim of the present work was to detect genomic regions that explain resistance to infectious pancreatic necrosis virus (IPNV) in rainbow trout. A total of 2,278 fish from 58 full-sib families were challenged with IPNV and 768 individuals were genotyped (488 resistant and 280 susceptible), using a 57K SNP panel Axiom, Affymetrix. A genome-wide association study (GWAS) was performed using the phenotypes time to death (TD) and binary survival (BS), along with the genotypes of the challenged fish using a Bayesian model (Bayes C). Heritabilities for resistance to IPNV estimated using genomic information, were 0.53 and 0.82 for TD and BS, respectively. The Bayesian GWAS detected a SNP located on chromosome 5 explaining 19% of the genetic variance for TD. The proximity of Sentrin-specific protease 5 (SENP5) to this SNP makes it a candidate gene for resistance against IPNV. In case of BS, a SNP located on chromosome 23 was detected explaining 9% of the genetic variance. However, the moderate-low proportion of variance explained by the detected marker leads to the conclusion that the incorporation of all genomic information, through genomic selection, would be the most appropriate approach to accelerate genetic progress for the improvement of resistance against IPNV in rainbow trout.

Differential activation of intraepithelial lymphocyte-natural killer cells in chickens infected with very virulent and vaccine strains of infectious bursal disease virus

To gain insights into the role of CD3^-/28.4⁺ intraepithelial lymphocytes-natural killer (CD3^-/28.4⁺IEL-NK) cells during infectious bursal disease virus (IBDV) infection, characterisation of the cells was performed following infection with different strains of the virus. In vitro treatment with IL-18 or ionomycin/PMA successfully stimulated and activated the cells via a significant increase in the expression of CD69, B-Lec, CHIR-AB1 and NK-lysin. Similarly, chickens infected with the vaccine strain of IBDV also up-regulated the expression of CD69, B-Lec, CHIR-AB1 and NK-lysin in CD3^-/28.4⁺ IEL-NK cells up to 3 days post infection (dpi) and down-regulated the expression of the inhibitory receptor B-NK at 3 dpi. On the contrary, infection with the very virulent IBDV (vvIBDV) strain lead to a reduced activation of the cells by down-regulating the expression of the CD69, CHIR-AB1 and NK-lysin especially at 1 dpi. These findings altogether demonstrate the differential activation of CD3^-/28.4⁺IEL-NK cells in chicken following infection with the vaccine or very virulent strains of IBDV. The study therefore provides an important clue into the differential pathogenesis of IBDV infection in chicken. Further studies are however required to determine the functional importance of these findings during IBDV vaccination and infection.

Bursal transcriptome profiling of different inbred chicken lines reveals key differentially expressed genes at 3 days post-infection with very virulent infectious bursal disease virus

Infectious bursal disease is a highly contagious disease in the poultry industry and causes immunosuppression in chickens. Genome-wide regulations of immune response genes of inbred chickens with different genetic backgrounds, following very virulent infectious bursal disease virus (vvIBDV) infection are poorly characterized. Therefore, this study aims to analyse the bursal tissue transcriptome of six inbred chicken lines 6, 7, 15, N, O and P following infection with vvIBDV strain UK661 using strand-specific next-generation sequencing, by highlighting important genes and pathways involved in the infected chicken during peak infection at 3 days post-infection. All infected chickens succumbed to the infection without major variations among the different lines. However, based on the viral loads and bursal lesion scoring, lines P and 6 can be considered as the most susceptible lines, while lines 15 and N were regarded as the least affected lines. Transcriptome profiling of the bursa identified 4588 genes to be differentially expressed, with 2985 upregulated and 1642 downregulated genes, in which these genes were commonly or uniquely detected in all or several infected lines. Genes that were upregulated are primarily pro-inflammatory cytokines, chemokines and IFN-related. Various genes that are associated with B-cell functions and genes related to apoptosis were downregulated, together with the genes involved in p53 signalling. In conclusion, bursal transcriptome profiles of different inbred lines showed differential expressions of pro-inflammatory cytokines and chemokines, Th1 cytokines, JAK-STAT signalling genes, MAPK signalling genes, and their related pathways following vvIBDV infection.

Sexual maturation in Atlantic salmon induces a constitutive Mx protein production and influences the infectious pancreatic necrosis virus carrier-status

The aim of this study was to demonstrate for the first time that sexual maturation induces a constitutive increase in Mx gene expression and protein production in Atlantic salmon. This could explain the reduction in IPNV prevalence previously observed in broodfish at the time of ova/milt stripping. For this purpose, Mx transcript and protein levels were analysed in different tissues/samples and compared between mature broodfish (female and male) and immature parr.

Differential Expression Profile of Chicken Embryo Fibroblast DF-1 Cells Infected with Cell-Adapted Infectious Bursal Disease Virus

RNA-Seq was used to unveil the transcriptional profile of DF-1 cells at the early stage of caIBDV infection. Total RNAs were extracted from virus-infected cells at 0, 6 and 12 hpi. RNA-Seq datasets of respective samples mapped to 56.5–57.6% of isoforms in the reference genome Galgal4.73. At 6 hpi, 23 isoforms underwent an elevated expression, while 128 isoforms were up-regulated and 5 were down-regulated at 12 hpi in the virus-infected group. Besides, 10 isoforms were exclusively expressed in the virus-infected cells. Though no significant change was detected in cytokine and interferon expression levels at the first 12 hours of infection, modulations of the upstream regulators were observed. In addition to the reported regulatory factors including EIF2AK2, MX, OAS*A, GBP7 and IFIT, IBDV infection also triggered a IFIT5-IRF1/3-RSAD5 pathway in the DF-1 cells which potentially restricted the viral replication cycle in the early infection stage. Over-expression of LIPA and CH25H, together with the suppression of STARD4, LSS and AACS genes implied a modulation of membrane fluidity and lipid raft arrangement in the infected cells. Alternative splicing of the EFR3 homolog A gene was also through to be involved in the lipid membrane regulation, and these cumulative responses projected an inhibition of viral endocytosis. Recognition of viral RNA genomes and intermediates was presumably enhanced by the elevated levels of IFIH1, DHX58 and TRIM25 genes which possess properties on detecting viral dsRNA. On the other hand, the caIBDV arrested the host's apoptotic process by inducing the expression of apoptosis inhibitors including NFKBIA/Z, TNFAIP2/3 and ITA at the first 12 hours of infection. In conclusion, the differential expression landscape demonstrated with RNA-Seq provides a comprehensive picture on the molecular interactions between host cells and virus at the early stage of infection.

Interferon regulatory factor-1 (IRF-1) is involved in the induction of phosphatidylserine receptor (PSR) in response to dsRNA virus infection and contributes to apoptotic cell clearance in CHSE-214 cell

The phosphatidylserine receptor (PSR) recognizes a surface marker on apoptotic cells and initiates engulfment. This receptor is important for effective apoptotic cell clearance and maintains normal tissue homeostasis and regulation of the immune response. However, the regulation of PSR expression remains poorly understood. In this study, we determined that interferon regulatory factor-1 (IRF-1) was dramatically upregulated upon viral infection in the fish cell. We observed apoptosis in virus-infected cells and found that both PSR and IRF-1 increased simultaneously. Based on a bioinformatics promoter assay, IRF-1 binding sites were identified in the PSR promoter. Compared to normal viral infection, we found that PSR expression was delayed, viral replication was increased and virus-induced apoptosis was inhibited following IRF-1 suppression with morpholino oligonucleotides. A luciferase assay to analyze promoter activity revealed a decreasing trend after the deletion of the IRF-1 binding site on PSR promoter. The results of this study indicated that infectious pancreatic necrosis virus (IPNV) infection induced both the apoptotic and interferon (IFN) pathways, and IRF-1 was involved in regulating PSR expression to induce anti-viral effects. Therefore, this work suggests that PSR expression in salmonid cells during IPNV infection is activated when IRF-1 binds the PSR promoter. This is the first report to show the potential role of IRF-1 in triggering the induction of apoptotic cell clearance-related genes during viral infection and demonstrates the extensive crosstalk between the apoptotic and innate immune response pathways.

Infectious bursal disease virus influences the transcription of chicken γc and γc family cytokines during infection

Infectious bursal disease virus (IBDV) infection causes immunodeficiency in chickens. To understand cell-mediated immunity during IBDV infection, this study perform a detailed analysis of chicken γ_c chain (chCD132) and γ_c family cytokines, including interleukins 2, 4, 7, 9, and 15. The mouse anti-chCD132 monoclonal antibody (mAb) was first generated by the E.coli-expressed γ_c protein. Immunofluorescence assay further showed that γ_c was a protein located with the anti-chCD132 mAb on the surface of chicken's splenic mononuclear cells. Real-time quantitative RT-PCR revealed that the chCD132 mRNA transcript was persistently downregulated in embryo fibroblasts, spleen and thymus of chickens infected with IBDV. Correspondingly during IBDV infection, the transcription of five γ_c family cytokines was downregulated in the thymus and presented an imbalance in the spleen. Fluorescence-activated cell sorting analyses also indicated that the percentage of CD132⁺CD8⁺ T cells linearly decreased in the bursa of IBDV-infected chickens. These results confirmed that IBDV infection disturbed the in vivo balance of CD132 and γ_c family cytokine expression and that IBDV-induced immunodeficiency involved cellular networks related to the γ_c family.

Quantitative genetics of disease resistance in vaccinated and unvaccinated Atlantic salmon (Salmo salar L.)

Furunculosis (Aeromonoas salmonicida) is an important disease in Atlantic salmon (Salmo salar) farming. Vaccination and selective breeding for increased resistance to the disease on the basis of challenge tests of unvaccinated fish are used as complementary prophylactic methods. An important issue is whether genetic predisposition to infection is consistent across vaccinated and unvaccinated fish. Hence, the main objective of this study was to determine the magnitude of the genetic associations (correlations) between resistance to furunculosis in vaccinated and unvaccinated fish, and to estimate the magnitude of the correlation of resistance to furunculosis with resistance to the viral diseases infectious pancreatic necrosis (IPN) and infectious salmon anaemia (ISA). Sub-samples of unvaccinated and vaccinated salmon from 150 full-sib families were subjected to separate cohabitation challenge tests. Substantial genetic variation was found in resistance to furunculosis in both the unvaccinated (heritabilities of 0.51 ± 0.05) and vaccinated (0.39 ± 0.06) fish. However, the genetic correlation between resistance to furunculosis in the two groups was low (0.32 ± 0.13), indicating a weak genetic association between resistance in the two groups. Hence, the current selection strategy on the basis of challenge tests of unvaccinated fish is likely to produce low genetic improvement in resistance to furunculosis under field conditions, where fish are vaccinated with an effective vaccine. Evidence was found of significantly favourable genetic associations of resistance to furunculosis in unvaccinated (but less so for vaccinated) fish with resistance to both IPN and ISA (unvaccinated fish), indicating that vaccination 'mask' genetic associations between resistance to different diseases.

Stage-specific expression of TNFα regulates bad/bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in Birnavirus-infected fish cells

Infectious pancreatic necrosis virus (IPNV) can induce Bad-mediated apoptosis followed by secondary necrosis in fish cells, but it is not known how these two types of cell death are regulated by IPNV. We found that IPNV infection can regulate Bad/Bid-mediated apoptotic and Rip1/ROS-mediated necrotic death pathways via the up-regulation of TNFα in zebrafish ZF4 cells. Using a DNA microarray and quantitative RT-PCR analyses, two major subsets of differentially expressed genes were characterized, including the innate immune response gene TNFα and the pro-apoptotic genes Bad and Bid. In the early replication stage (0–6 h post-infection, or p.i.), we observed that the pro-inflammatory cytokine TNFα underwent a rapid six-fold induction. Then, during the early-middle replication stages (6–12 h p.i.), TNFα level was eight-fold induction and the pro-apoptotic Bcl-2 family members Bad and Bid were up-regulated. Furthermore, specific inhibitors of TNFα expression (AG-126 or TNFα-specific siRNA) were used to block apoptotic and necrotic death signaling during the early or early-middle stages of IPNV infection. Inhibition of TNFα expression dramatically reduced the Bad/Bid-mediated apoptotic and Rip1/ROS-mediated necrotic cell death pathways and rescued host cell viability. Moreover, we used Rip1-specific inhibitors (Nec-1 and Rip1-specific siRNA) to block Rip1 expression. The Rip1/ROS-mediated secondary necrotic pathway appeared to be reduced in IPNV-infected fish cells during the middle-late stage of infection (12–18 h p.i.). Taken together, our results indicate that IPNV triggers two death pathways via up-stream induction of the pro-inflammatory cytokine TNFα, and these results may provide new insights into the pathogenesis of RNA viruses.

[Inhibition of infectious bursal disease virus replication in chicken embryos by miRNAs delivered by recombinant avian adeno-associated viral vector]

OBJECTIVE

We studied the inhibition of infectious bursal disease virus (IBDV) replication in chicken embryos by recombinant avian adeno-associated virus (AAAV)-delivered VP1- and VP2-specific microRNAs (miRNAs).

METHODS AND RESULTS

We co-transfected AAV-293 cells with the VP1- or VP2 gene-specific miRNA expression vector pAITR-RFPmiVP1 or AITR-RFPmiVP2E, AAAV packaging vector pcDNA-ARC and adenovirus helper vector pHelper, resulting in recombinant virus rAAAV-RFPmiVP1 or rAAAV-RFPmiVP2E. We also generated the recombinant viruses rAAAV-RFP (without miRNA expression cassette) and rAAAV-RFPmiVP2con (expressing control miRNA) using the same method as the control purpose. Electron microscopy showed that the recombinant viruses had a typical morphology of AAV. We confirmed the presence of miRNA expression cassette in the recombinant viral genomes by using PCR. Our poly (A)-tailed RT-PCR showed correct expression of the miRNAs in the rAAAV-transduced DF-1 cells. We inoculated the recombinant viruses individually into 8-day-old SPF chicken embryos and then challenged them using Lukert strain IBDV on day 2 after inoculation. Our IBDV titration assay showed that the 50% tissue culture infectious dose (TCID50) of rAAAV-RFP- or rAAAV-RFPmiVP2con-inoculated group was 8.0 log10, whereas the TCID50 of rAAAV-RFPmiVP1-inoculated group decreased to 1.0 and 0.8 log10 on day 3 and 6 after challenge, respectively. Similarly, the TCID50 of rAAAV-RFPmiVP2E-inoculated group decreased to 1.5 and 2.0 log10, respectively.

CONCLUSION

These data suggest that rAAAV can transduce efficiently chicken embryos and the expressed VP1- and VP2-specific miRNAs can inhibit the replication of IBDV efficiently.

Chemokine transcription in rainbow trout (Oncorhynchus mykiss) is differently modulated in response to viral hemorrhagic septicaemia virus (VHSV) or infectious pancreatic necrosis virus (IPNV)

Chemokines not only act as chemoattractants for immune cells, but also exert immunomodulatory actions, thus modulating the immune functions of their target cells. In rainbow trout (Oncorhynchus mykiss), twenty-four chemokines have been identified to date. Even though their sequences have been reported, their biological role has been scarcely elucidated and the role that these chemokines have on the antiviral response in fish has been poorly studied. In this sense, in the current work, we have determined the levels of expression of several of these rainbow trout chemokines (CXCd, gammaIP, CK1, CK3, CK5B, CK6, CK7A, CK9 and CK12) in head kidney and spleen during the course of a viral infection using two different viruses, viral hemorrhagic septicaemia virus (VHSV) and infectious pancreatic necrosis virus (IPNV), comparing them to the levels induced by poly I:C. We also determined the effects that the two viruses and poly I:C provoked on the levels of expression of these chemokines in vitro in head kidney leucocytes. Overall, VHSV was capable of modulating gammaIP, CXCd, CK1, CK3, CK5B, CK6 and CK12, while IPNV induced a very different chemokine profile and affected CK1, CK5B, CK6, CK7A, CK9 and CK12. On the other hand, a viral mimic such as poly I:C was capable of up-regulating gammaIP, CXCd, CK1, CK3, CK5B, CK7A and CK12. As more information becomes available concerning the immune role and target cells that these chemokines have on rainbow trout, we would be able to better interpret the importance of these differences in the pathogenicity of these two viruses.

Atlantic salmon IPS-1 mediates induction of IFNa1 and activation of NF-kappaB and localizes to mitochondria

The striking difference in evolution of type I IFN genes of fish and mammals poses the question of whether these genes are induced through similar or different signalling pathways in the two vertebrate groups. Previous work has shown that expression of both Atlantic salmon (Salmo salar) IFNa1 and mammalian IFN-beta genes is dependent on IRF and NF-kappaB elements in their promoters. In mammals, IFN-beta transcription is induced through the RIG-I/MDA5 pathway where the adaptor protein IPS-1 plays a key role in the signal transduction. In this work we show that an Atlantic salmon homologue of IPS-1 (AsIPS-1) mediates activation of the salmon IFNa1 promoter and an NF-kappaB driven promoter. AsIPS-1 shares only 18% identity in amino acid sequence with human IPS-1, but possesses the CARD, proline-rich and transmembrane domains found in mammalian IPS-1. Overexpression of AsIPS-1 resulted in induction of an antiviral state in the cells apparently due to induction of IFN. Deletion of the CARD and transmembrane domains of AsIPS-1 abolished its ability to activate the IFNa1 promoter and the NF-kappaB driven promoter, and thus its ability to induce an antiviral state. AsIPS-1 is located to mitochondria similar to human IPS-1. Taken together, IPS-1 plays a key role in the induction of Atlantic salmon IFNa1, which appears to be the first and major IFN induced in host cells upon recognition of viral dsRNA.

Detection and confirmation of a major QTL affecting resistance to infectious pancreatic necrosis (IPN) in Atlantic salmon (Salmo salar)

Infectious pancreatic necrosis (IPN) is a viral disease currently presenting a major problem to the aquaculture of Atlantic salmon (Salmon salar), during both the freshwater and seawater stages of production. Genetic variation in resistance to IPN has previously been demonstrated and the purpose of this study was to determine whether this variation includes loci of major effect. The initial QTL detection methodology utilized the limited recombination seen in male salmon to detect QTL in ten large full-sib families, using a genome-wide scan of two to three markers per linkage group. QTL were then positioned by adding additional markers to the significant linkage groups in a female-based analysis. The most significant QTL was mapped to LG 21, and further confirmation of the LG 21 QTL is provided in an analysis of the QTL flanking markers in an additional nine full-sib families from the same population. The size of QTL effect is such that the QTL flanking markers can be immediately applied in marker-assisted selection programmes to improve the resistance of salmon populations to IPN, thus reducing mortality due to the disease.

Strong genetic influence on IPN vaccination-and-challenge trials in Atlantic salmon, Salmo salar L

Two series of experimental challenge trials were performed for evaluation of multivalent oil-adjuvanted vaccines with and without an infectious pancreatic necrosis virus (IPNV) antigen component. In both the trial series, Atlantic salmon were hatched, reared, vaccinated and subjected to temperature and light manipulation to induce smoltification. When ready for sea the fish were transported to the VESO Vikan experimental laboratory for bath or cohabitant challenge with IPNV. In the first series, four vaccination and bath challenge trials involving 2-year classes of experimental fish were conducted. In the second series, three groups of eyed eggs of Atlantic salmon allegedly differing in their innate resistance to IPNV were used (Storset, Strand, Wetten, Kjøglum & Ramstad 2007). Hatching, rearing and smoltification were synchronized for each group, and fish from each genetic group were randomly allocated IPN vaccine, reference vaccine or saline before being placed into parallel tanks for bath or cohabitant challenge. In the first series of trials, IPN-specific mortality commenced on day 10-12 after bath challenge. Replicates showed similar results. In trials 1 and 2 belonging to the same experimental fish year class, the average cumulative control mortality reached 60.6% and 79.5%, respectively, whereas in trials 3 and 4 belonging to the following year class the control mortality was consistently below 50%. In the second series of trials, the experimental fish originating from allegedly IPN susceptible parents consistently showed the highest cumulative mortality among the unvaccinated controls (>75%) whereas smolts derived from allegedly IPNV resistant parents showed only 26-35% control mortality. The IPN-vaccinated fish experienced significantly improved survival vs. the fish immunized with reference vaccine, with RPS values above 75% in the IPN susceptible strain. In the IPN resistant strain, the protection outcomes were variable and in part non-significant. The outcome of both the trial series suggests that control mortalities above 50% are necessary to reliably demonstrate specific protection with IPN vaccines.

Expression and immunogenic comparison of VP2 and VP3 from marine birnavirus

The coding regions for the major epitopes of structural protein VP2 (vp2e) and structural protein VP3 were amplified from marine birnavirus (MABV) cDNA and efficiently expressed as glutathione S-transferase (GST) fusion proteins in Escherichia coli. Polyclonal antibodies against VP2e and VP3 were raised in rabbits and fish using the purified proteins of GST/VP2e and GST/VP3. The rabbit anti-serum against VP3 was more sensitive than the rabbit anti-VP2e serum in detecting virus in MABV-infected fish, while fish anti-VP2e serum showed a stronger neutralization response than fish anti-VP3 serum.

Poly I:C induces Mx transcription and promotes an antiviral state against sole aquabirnavirus in the flatfish Senegalese sole (Solea senegalensis Kaup)

Mx is an interferon-induced protein that protects against viral infections. In this study the absolute number of Mx transcripts after poly I:C injection (a synthetic dsRNA) or sole aquabirnavirus (solevirus) inoculation in Senegalese sole (Solea senegalensis Kaup) has been quantified. Mx expression profiles differed clearly in both experimental conditions; the induction response was faster and more intense after poly I:C injection than after solevirus inoculation. Moreover, pre-injection of soles with poly I:C prior to solevirus infection eliminated the induction of Mx expression associated with this virus. To evaluate the possible interference of poly I:C treatments on solevirus replication, the mRNA levels of the virus capsid protein (VP2) were determined by RT-PCR. VP2 transcripts were hardly detected in poly I:C pre-injected animals from 12 to 72 h after solevirus inoculation. All these data suggest that poly I:C is able to induce an antiviral state that interferes with solevirus replication, and support the suitability of Mx expression analysis as a marker to study the defensive response against solevirus.

Bilateral effects of vaccination against infectious bursal disease and Newcastle disease in specific-pathogen-free layers and commercial broiler chickens

Different infectious bursal disease virus (IBDV) live vaccines (intermediate, intermediate plus) were compared for their immunosuppressive abilities in specific-pathogen-free (SPF) layer-type chickens or commercial broilers. The Newcastle disease virus (NDV) vaccination model was applied to determine not only IBDV-induced immunosuppression but also bilateral effects between IBDV and NDV. None of the IBDV vaccines abrogated NDV vaccine-induced protection. All NDV-vaccinated SPF layers and broilers were protected against NDV challenge independent of circulating NDV antibody levels. Sustained suppression of NDV antibody development was observed in SPF layers, which had received the intermediate plus IBDV vaccine. We observed a temporary suppression of NDV antibody development in broilers vaccinated with one of the intermediate, as well as the intermediate plus, IBDV vaccines. Different genetic backgrounds, ages, and residual maternal antibodies might have influenced the pathogenesis of IBDV in the different types of chickens. Temporary suppression of NDV antibody response in broilers was only seen if the NDV vaccine was administered before and not, as it was speculated previously, at the time the peak of IBDV-induced bursa lesions was detected. For the first time, we have demonstrated that the NDV vaccine had an interfering effect with the pathogenesis of the intermediate as well as the intermediate plus IBDV vaccine. NDV vaccination enhanced the incidence of IBDV bursa lesions and IBDV antibody development. This observation indicates that this bilateral effect of an IBDV and NDV vaccination should be considered in the field and could have consequences for the performance of broiler flocks.

Bilateral effects of vaccination against infectious bursal disease and Newcastle disease in specific-pathogen-free layers and commercial broiler chickens

Different infectious bursal disease virus (IBDV) live vaccines (intermediate, intermediate plus) were compared for their immunosuppressive abilities in specific-pathogen-free (SPF) layer-type chickens or commercial broilers. The Newcastle disease virus (NDV) vaccination model was applied to determine not only IBDV-induced immunosuppression but also bilateral effects between IBDV and NDV. None of the IBDV vaccines abrogated NDV vaccine-induced protection. All NDV-vaccinated SPF layers and broilers were protected against NDV challenge independent of circulating NDV antibody levels. Sustained suppression of NDV antibody development was observed in SPF layers, which had received the intermediate plus IBDV vaccine. We observed a temporary suppression of NDV antibody development in broilers vaccinated with one of the intermediate, as well as the intermediate plus, IBDV vaccines. Different genetic backgrounds, ages, and residual maternal antibodies might have influenced the pathogenesis of IBDV in the different types of chickens. Temporary suppression of NDV antibody response in broilers was only seen if the NDV vaccine was administered before and not, as it was speculated previously, at the time the peak of IBDV-induced bursa lesions was detected. For the first time, we have demonstrated that the NDV vaccine had an interfering effect with the pathogenesis of the intermediate as well as the intermediate plus IBDV vaccine. NDV vaccination enhanced the incidence of IBDV bursa lesions and IBDV antibody development. This observation indicates that this bilateral effect of an IBDV and NDV vaccination should be considered in the field and could have consequences for the performance of broiler flocks.

Transcriptional profiles of chicken embryo cell cultures following infection with infectious bursal disease virus

Infectious bursal disease virus (IBDV) is the causative agent of infectious bursal disease in chickens and causes a significant economic loss for the poultry industry. Little is understood about the mechanism involved in the host responses to IBDV infection. For better understanding the IBDV-host interaction, we measured steady-state levels of transcripts from 28 cellular genes of chicken embryo (CE) cell cultures infected with IBDV vaccine stain Bursine-2 during a 7-day infection course by use of the quantitative real-time RT-PCR SYBR green method. Of the genes tested, 21 genes (IRF-1, IFN 1-2 promoter, IFNAR-1, IRF-10, IFN-gamma, 2',5'-OAS, IAP-1, caspase 8, TRAIL-like, STAT-3, IL-6, IL-8, MIP-3 alpha, MHC-I, MHC-II, TVB, GLVR-1, OTF, IL-13R alpha, ST3GAL-VI and PGK) showed an increased expression. The remaining seven genes (IFNAR-2, IFN-alpha, NF-kappaB subunit p65, BLRcp38, DDX1, G6PDH and UB) showed a constant expression or only slight alteration. Apparently, the host genes involved in pro-inflammatory response and apoptosis, interferon-regulated proteins, and the cellular immune response were affected by IBDV infection, indicating involvement in the complex signaling pathways of host responses to the infection. This study thus contributes to the understanding of the pathogenesis of IBD and provides an insight into the virus-host interaction.

Analysis of the incidence of infectious pancreatic necrosis mortality in pedigreed Atlantic salmon, Salmo salar L., populations

A total of 77,124 Atlantic salmon post-smolts, representing 197 full-sib families produced by 149 males and 197 females, experienced a field challenge from infectious pancreatic necrosis virus (IPNV), following transfer to three separate seawater sites. The first IPN mortality was observed 45 days after transfer, and the duration of the epidemic varied between 37 and 92 days among sites. Mortalities were traced to their parental families by PIT (Passive Integrated Transpondes) tag records and DNA genotyping. Full-sib family mean incidence of mortality was calculated for each family on each site. Heritabilities were estimated based on the heterogeneity of chi-square using incidence within half-sib families and the variance in incidence among full-sib families, both on the observed and underlying liability scale. The observed correlation among families across sites was used to estimate genetic correlations. The overall mortality rate was 10.8%, with only small differences between sites, ranging from 10.3% to 11.9%. Heritabilities on the liability scale were found to be moderate to strong, and ranged between 0.24 and 0.81, with a pooled estimate of 0.43, greater than is typically associated with disease traits. Genetic correlations among sites were all substantial, between 0.71 and 0.78, and indicated that a substantial component of the genetic variation displayed within sites was common to all. The results show that field challenges can yield very good genetic information on family differences in resistance, especially when replicated over sites, which may then be developed for use in selection for breeding strains of Atlantic salmon with greater resistance to IPN.

Genetic variations in maternal transfer and immune responsiveness to infectious bursal disease virus

The immune responsiveness to infectious bursal disease virus (IBDV) in four native and crossbred chicken lines was compared. ELISA IBDV antibody titers in hen serum samples, yolk from matched eggs and sera from matched 1-day-old chicks from each chicken line with an identical vaccination program were measured, and plotted. There was considerable variation between lines in the measured IBDV specific antibodies, in vaccinated parent hens and in the amounts of inherited maternally derived antibodies in both yolk and progeny chicks. Differences in ratios of the inherited antibody level from hen to 1-day-old chicks were also found among different chicken lines. Breed differences in regressions of IBDV antibody levels in yolk to that of hen or progeny chicks' sera were also found, so prediction of serum titer of hen and/or progeny chicks from yolk are varied among chicken lines.

Evaluation of the suitability of six host genes as internal control in real-time RT-PCR assays in chicken embryo cell cultures infected with infectious bursal disease virus

Infectious bursal disease virus (IBDV) can cause disease in chickens characterized by immunosuppression and high mortality. Currently, real-time RT-PCR has been used to quantitate virus-specific RNA and to better understand host response to infection. However, normalization of quantitative real-time RT-PCR is needed to a suitable internal control. We thus investigated the expression pattern of six chicken genes, including beta-actin, 28S rRNA, 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), TATA box-binding protein (TBP) and beta-2-microglobulin, in chicken embryo (CE) cell cultures following a 7-day IBDV infection. The CE cells were inoculated with various multiplicity of infection (MOI) of IBDV vaccine strain Bursine-2, the expression of genes was measured by quantitative real-time PCR-based on cDNA synthesized from either normalized (100 ng) or non-normalized (10 microl) total RNA. The results showed that beta-actin, 28S rRNA, 18S rRNA and GAPDH were the most constantly expressed genes, while TBP and beta-2-microglobulin were markedly induced during the infection course. Of these constant expressed genes, 28S rRNA and 18S rRNA are highly expressed; beta-actin intermediately expressed and GAPDH had a lower expression level in CE cell cultures. Also, beta-actin showed no significant variation in both normalized and non-normalized assays and virus dose-independent of inoculation, while other genes did. beta-Actin was further successfully used as an internal control to quantitate Bursine-2 virus-specific RNA load in CE cell cultures. Thus, beta-actin was suggested as a suitable internal control in studying gene expression as well as virus-specific RNA load in CE cell after IBDV infection.

Genetic characterization of very virulent infectious bursal disease viruses from Latin America

Very virulent infectious bursal disease viruses (vvIBDVs) were detected in phenol inactivated bursal samples obtained from Brazil, the Dominican Republic, and Venezuela. After nucleotide sequence analysis of the hypervariable region of VP2 gene, the vvIBDVs from Brazil and Venezuela exhibited all of the 14 nucleotide changes that are conserved in the European UK-661 and most other vvIBDV strains. However, the vvIBDV from the Dominican Republic presented 11 nucleotide changes that are conserved in vvIBDV strains. After phylogenetic analysis, the Latin American strains were found to be related to other vvIBDV strains from Europe, Asia, and Africa. However, Brazilian and Dominican vvIBDVs clustered in two separate subgroups, while the vvIBDVs from Venezuela were closely related to other strains from other parts of the world. By deduced amino acid sequence, the three conserved amino acid residues in vvIBDV strains (222 Ala, 256 Ile, and 294 Ile) were confirmed in the Latin American viruses, and one amino acid change (300 Ala) was unique to all vvIBDVs from the Dominican Republic. The occurrence of this change in the Dominican vvIBDVs may have an impact in their antigenic makeup. Results of this study indicate that the vvIBDVs detected in Latin America are genetically similar to IBDV strains from other parts of the world. However, vvIBDVs from Venezuela were more similar to the vvIBDV strains from Europe and Asia. Of all the samples analyzed, vvIBDVs from Brazil and the Dominican Republic exhibited more genetic changes. These changes may have emerged as a result of the different management practices and environmental conditions present in each particular geographic area.

Genetic resistance of Egyptian chickens to infectious bursal disease and Newcastle disease

Genetic resistance of native Egyptian breeds to very virulent infectious bursal disease virus (vvIBDV) and Newcastle disease virus (NDV) was investigated in two experiments. In the first experiment, birds from four breeds (Gimmizah, Sina, Dandrawi and Mandarah) were challenged with vvIBDV. The Mandarah chickens had the lowest mortalities (10%) compared to the Gimmizah, Sina and Dandrawi chickens (55%, 35%, and 55%, respectively). Antibody response, lymphocyte response to mitogen, and bursal lesions did not clearly correlate with the mortality rates. In the second experiment, the four chicken breeds were challenged with virulent NDV. The Mandarah chickens re-emerged as a resistant breed (20%, mortality), while the Sina, Dandrawi and Gimmizah breeds were highly susceptible (85%, 100% and 100% mortality, respectively). Further studies on the resistance mechanism are warranted.

Distribution of marine birnavirus in cultured marine fish species from Kagawa Prefecture, Japan

To determine the distribution of marine birnavirus (MABV) in cultured populations of different marine fish species, 1291 pooled tissue samples from 2672 fish belonging to 22 species and one hybrid were collected from Kagawa Prefecture, Japan, during 1999-2001. Using cell-culture MABV was isolated from three species: yellowtail, Seriola quinqueradiata Temminck & Schlegel (positive number/sample number, 10/419), amberjack, S. dumerili (Risso) (4/72), and Japanese flounder, Paralichthys olivaceus (Temminck & Schlegel) (41/481). Using PCR on MABV-negative samples, the MABV genome was detected in the same three species [yellowtail (9/409), amberjack (4/68) and Japanese flounder (93/440)] and two additional species, spotted halibut, Verasper variegatus (Temminck & Schlegel) (5/11), and goldstriped amberjack, S. lalandi Valenciennes (1/5). These MABV-positive species can be taxonomically divided into two groups: the genus Seriola and flatfish. In Japanese flounder, MABV was detected during all seasons, and the infection rate was correlated with water temperature. Aquaculture sites with MABV-positive fish were evenly distributed over the surveyed area, suggesting that MABV is widely distributed at aquaculture sites in Kagawa Prefecture. The nucleotide sequence at the variable region, the VP2/NS junction, revealed that the 39th base mutation occurs host-specifically for flatfish. Flatfish are suspected to be the main reservoir of MABV and might be responsible for establishing the infection cycle in aquaculture environments.

Effect of double-stranded RNA and interferon on the antiviral activity of Atlantic salmon cells against infectious salmon anemia virus and infectious pancreatic necrosis virus

Type I interferons (IFN) establish an antiviral state in vertebrate cells by inducing expression of Mx and other antiviral proteins. We have studied the effect of Atlantic salmon interferon-like activity (AS-IFN) and poly I:C on the Mx protein expression and antiviral activity against infectious salmon anaemia virus (ISAV) and infectious pancreatic necrosis virus (IPNV) in the Atlantic salmon cell lines SHK-1 and TO. The double-stranded RNA poly I:C is an inducer of type I IFN in vertebrates. A cell cytotoxicity assay and measurements of virus yield were used to measure protection of cells against virus infection. Maximal induction of Mx protein in TO and SHK-1 cells occurred 48 h after poly I:C stimulation and 24 h after AS-IFN stimulation. TO cells pretreated with AS-IFN or poly I:C were protected from infection with IPNV 24 to 96 h after stimulation. Poly I:C or AS-IFN induced a minor protection against ISAV infection in SHK-1 cells, but no protection was induced against ISAV in TO cells. Western blot analysis showed that ISAV induced expression of Mx protein in TO and SHK-1 cells whereas IPNV did not induce Mx protein expression. These results suggest that ISAV and IPNV have very different sensitivities to IFN-induced antiviral activity and have developed different strategies to avoid the IFN-system of Atlantic salmon. Moreover, Atlantic salmon Mx protein appears not to inhibit replication of ISAV.

Detection of infectious bursal disease virus in different lymphoid organs by single-step reverse transcription polymerase chain reaction and microplate hybridization assay

A rapid and sensitive method for the detection of infectious bursal disease virus (IBDV) RNA in different chicken lymphoid organs was developed. The method is based on a single-step reverse transcription polymerase chain reaction (RT-PCR) procedure and the enzyme-linked immunosorbent assay (ELISA) detection method of amplified products. Vaccinal IBDV strain and field isolates were used for the optimization of RT-PCR and for the determination of conditions for microplate hybridization and colorimetric detection of the amplicons. With this method, viral RNA could be detected in various stages of infection in samples of different lymphoid organs. Bursas and cecal tonsils were suitable organs for viral RNA detection at different times during IBDV infection. The RT-PCR/ELISA method can be applied for IBDV detection in routine diagnostic tests, which are not usually carried out because of the difficulties involved in isolating the virus.

Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss)

Infectious pancreatic necrosis (IPN) is a well-known acute viral disease of salmonid species. We have identified quantitative trait loci (QTLs) associated with resistance to this disease in rainbow trout. We searched for linkage among 51 microsatellite markers used to construct a framework linkage map in backcross families of rainbow trout (Oncorhynchus mykiss), produced by crossing IPN-resistant (YN-RT201) and -susceptible (YK-RT101) strains. Two putative QTLs affecting disease resistance were detected on chromosomes A (IPN R S-1) and C (IPN R/S-2), respectively, suggesting that this is a polygenic trait in rainbow trout. These markers have great potential for use in marker-assisted selection (MAS) for IPN resistance and provide the basis for cloning of IPN resistance genes. Clarification of the genetic bases of complex traits has broad implications for fundamental research, but will also be of practical benefit to fish breeding.

Selection of an infectious bursal disease virus mutant with increased immunogenicity following passage under humoral immune pressure

It is generally known that the pathogenicity of infectious bursal disease virus (IBDV) strains decreases following passage in cell culture. However, there is no information about the effect of passage under immune pressure on the phenotypic and molecular properties of IBDV. In the present study, a small plaque mutant virus with poor neutralization capability, but showing similar growth characteristics as the parental virus strain, QC2, was isolated after serial passage in Vero cells in presence of IBDV serotype 1 chicken polyclonal antiserum. This mutant virus showed reduced pathogenicity but enhanced immunogenicity compared to the parental virus. Sequence analysis of the non-coding regions of the genome revealed 4 and 3 nucleotide changes in the 3' non-coding regions of segments A and B, respectively, and none in the 5' non-coding regions. Restriction enzyme analysis of selected coding regions of the IBDV genome in both viruses revealed a loss of the PstI site in the VP2 region of the mutant virus. Selection of such mutant viruses by passaging under immune pressure may offer an improved method for developing safer and more effective attenuated vaccine strains against infectious bursal disease of chickens.

Cloning of an Mx cDNA from Atlantic halibut (Hippoglossus hippoglossus) and characterization of Mx mRNA expression in response to double-stranded RNA or infectious pancreatic necrosis virus

Mx proteins are GTPases that are specifically induced by type I interferons (IFN) in vertebrates. Some mammalian Mx proteins have antiviral activity against certain RNA viruses. A 2.3-kb full-length cDNA clone of an Atlantic halibut Mx gene was isolated from a liver cDNA library. The open reading frame (ORF) predicts a 622 amino acid protein of 71.2 kDa possessing a tripartite GTP binding motif, a dynamin signature, and a leucine zipper motif, which are conserved in all known Mx proteins. The C-terminal half contains a putative bipartite nuclear localization signal. The deduced halibut Mx protein showed approximately 76% sequence identity with the Atlantic salmon and rainbow trout Mx proteins, 55% identity with the human MxA, and 48% identity with the chicken Mx protein. Based on sequence comparison of 554-bp Mx cDNA fragments, the Atlantic halibut Mx showed more relationship with the perch and turbot than the salmonid Mx genes. Halibut appears to possess at least two Mx loci, as suggested by Southern blot analysis of genomic DNA. Two halibut Mx transcripts (2.2 kb and 2.6 kb) were strongly induced in vivo by the double-stranded RNA (dsRNA) poly I:C or infectious pancreatic necrosis virus (IPNV) in all organs studied.

Development of a ssRNA internal control reagent for an infectious bursal disease virus reverse transcription/polymerase chain reaction-restriction fragment length polymorphism diagnostic assay

Infectious bursal disease virus (IBDV), family Birnaviradae, is the etiologic agent of a commercially important, globally distributed, contagious, immunosuppressive disease of young chickens. A restriction enzyme-compatible ssRNA internal control was developed for an IBDV reverse transcription/polymerase chain reaction-restriction fragment length polymorphism (RT/PCR-RFLP) diagnostic assay. An 841-bp bacteriophage-lambda DNA fragment was directionally ligated to 3' and 5' oligonucleotide linkers containing the IBDV RT/PCR target primer sequences. A pGEM-3Zf (+) transcription vector containing the internal control construct was used in an in vitro transcription reaction to produce ssRNA. After RT and PCR amplification, the transcripts produced an 882-bp cDNA product, larger than, co-amplifiable with, and free of the restriction sites used to prepare RFLP patterns of the 743-bp IBDV cDNA target product. The limit of detection of the transcripts in the RT/PCR test is 3.2 femtograms. With the internal control, a test inhibition rate of 7.7% (20/261) was determined for the IBDV RT/PCR assay. By identifying inhibited tests, the assay was improved through a reduction in the number of false-negative results.

Adaptation of very virulent infectious bursal disease virus to chicken embryonic fibroblasts by site-directed mutagenesis of residues 279 and 284 of viral coat protein VP2

The full-length RNA genomes of a chicken embryonic fibroblast (CEF)-nonpermissive, very virulent infectious bursal disease virus (IBDV) (strain HK46) were amplified into cDNAs by reverse transcription-PCR. The full-length cDNAs were sequenced and subcloned into a eukaryotic expression vector, from which point mutations were introduced into the VP2 region by site-directed mutagenesis. The wild-type and mutated plasmids were transfected directly into CEFs to examine their ability to generate CEF-permissive recombinant viruses. Substitution of amino acid residues 279 (Asp-->Asn) and 284 (Ala-->Thr) of the VP2 protein yielded a recombinant virus which was able to be passaged in CEFs, whereas the wild-type cDNAs and an amino acid substitution at residue 330 (Ser-->Arg) of the VP2 protein alone did not yield viable virus. The results indicated that mutation of other viral proteins, including VP1, VP3, VP4, and VP5, was not required for CEF adaptation of the virus. The same approach may be used to produce CEF-adapted strains from newly evolved IBDVs or to manipulate the antigenicity of the virus.

Genetic resistance to avian viruses

Viral infections of poultry can be catastrophic in terms of both welfare and economics, and although vaccines have been very successful in combating these diseases, new forms of viruses have evolved which present increasing difficulties for vaccine control. Differences in genetic susceptibility are known to exist for many of the major viral pathogens of poultry. Consequently, an increase in the level of genetic resistance provides a possible means of enhancing protection of flocks. This is particularly feasible where specific resistance genes have been identified, as in the case of avian leukosis and Marek's disease, and the development of genetic maps of the chicken has offered new possibilities for the identification of further resistance genes. It has also become clear that there are genetic differences in the response to live attenuated vaccine viruses, and new possibilities exist to manipulate the genetics of host flocks so that the effect of vaccination can be optimised.

Enhanced expression of cytokine genes in spleen macrophages during acute infection with infectious bursal disease virus in chickens

We examined the effects of infectious bursal disease virus (IBDV) on splenic T cells and macrophages. In acute IBDV infection, splenocytes responded poorly to Con A stimulation. However, when T cells were isolated from whole spleen cells, purified T cells responded normally to Con A. This result indicated that functional T cells were present in the spleen but mitogen-induced proliferation of T cells was being suppressed by other cells. Previous studies indicated that soluble factors from suppressor cells may mediate this inhibition of T cell mitogenesis. We thus examined the effects of IBDV on spleen adherent cells. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to quantitate the expression of several cytokine genes in splenic macrophages. In acute IBDV infection, splenic macrophages exhibited enhanced gene expression of type I interferon (IFN), chicken myelomonocytic growth factor (cMGF), an avian homolog of mammalian IL-6, and 9E3/CEF4, an avian homolog of mammalian IL-8. Mitogen-stimulated spleen cell cultures also produced elevated levels of nitric oxide. The elevation of cytokine gene expression by macrophages occurred transiently during the acute phase of viral infection and coincided with in vitro inhibition of T cell mitogenic response of spleen cells.