Effects of ultra-filtration purification of infectious bursal disease virus on immune responses and cytokine activation in specific pathogen free chickens.

Purification is an important step in the production of viral vaccines that strongly affects product recovery and subsequent immune responses. The present study was carried out with the aim of improving the purification of infectious bursal disease virus (IBDV) by the tangential flow filtration (TFF) method. Then, the effect of the purified virus on the induction of immune responses against IBDV in specific pathogen free (SPF) chickens was investigated. The IBD07IR strain was propagated in embryonated SPF eggs. The virus was purified using a 100 kDa cassette. The quality of the recovered viruses was evaluated by titration. A total number of 60 SPF chickens were randomly divided into three groups (n = 20) and received the concentrated viral antigen, commercial live IBDV vaccine and phosphate-buffered saline at the age of 3 weeks by eye drop method. The bursa of Fabricius was examined histopathologically for possible changes. Sera were collected at 1-week intervals from day 0 until the end of 6 weeks after vaccination. The IBDV-specific antibody levels, induction of cell-mediated immunity and mRNA expression levels of cytokines were evaluated. The results showed that despite a relative raise in virus titer from 7.66 to 8.17 embryo infectious dose (EID)50 mL-1 following purification, both the purified IBDV and commercial vaccine are able to induce strong immune responses against the virus. Within a context of egg-based IBDV vaccine production, a single-step TFF can be applied for the relatively purification. This platform requires a further study in the selection of multiple membranes to optimize the operating conditions and final product.

Down-regulating CD19 surface markers expression correlates with infectious bursal disease virus replication.

The infectious bursal disease virus (IBDV) causes an acute and highly contagious immunosuppressive response in young chickens by targeting B lymphocytes in immune organs. Changes in regulatory T-cell ratio and apoptosis have been demonstrated during IBDV infection in these cells. The possible change in CD19 expression as the precursor of B cells after IBDV replication was detected in this study. Raji cells were infected with an IBDV isolate at MOIs of 1.0 and 3.0. The viral kinetics were determined using the characteristic virus-induced CPE, cell viability, and infectious titer. Induction of apoptosis and also changes in the CD19 expression within the virus infection were assessed by flow cytometry. The Raji cells were found to be susceptible to IBDV infection by producing marked CPEs dependent on MOI. The infectivity titers were determined in intra- and extracellular samples at the defined hours. The kinetics of early IBDV replication in Raji cells were nearly identical for both MOIs, but a significant difference in the infectivity titer was observed at 48 hpi. The quick apoptotic events were observed to be significantly higher in MOI 3.0, which was correlated with the lower virus titer. A significant CD19 expression change in the IBDV-infected Raji cells was revealed. The results suggested that Raji cells mimic the IBDV replication in lymphoid organs and the virus replication is related to CD19 expression frequencies in the lymphoid cells.

A Combination of Recombinant HA1-and Nucleoprotein-Based Chitosan Nanoparticles Induces Early and Potent Immune Responses Against the H9N2 Influenza Virus.

The effectiveness of inactivated H9N2 influenza vaccines is doubtful due to changes in antigenic regions of the virus hemagglutinin (HA) protein. One strategy for the development of the efficacious vaccine is the use of nanoparticles that display more immunogenic regions of the influenza virus. In this study, chitosan (CS)-based nanoparticles were developed as a delivery system for intranasal immunization using recombinant H9N2 virus HA1 and nucleoprotein (NP), for the induction of humoral and cellular responses. CS-HA1 and CS-NP nanoparticles were prepared by the ionic gelation method and characterized for their physicochemical properties and shape. The immunogenicity and the protective efficacy were evaluated by measuring antibody titers, T cell proliferation response, CD4+/CD8+ ratio, and quantitative real-time RT-PCR following intranasal administration of the prepared nanoparticles alone or in combination in chickens compared to an inactivated H9N2 vaccine. The average size, surface charge, and spherical structure of the synthesized nanoparticles showed high quality. Serologic analysis revealed that the immunization of inactivated vaccine groups resulted in strong influenza antibodies, which were significantly (p < 0.05) higher compared to the other groups. The vaccinated chickens with CS-HA1+CS-NP developed higher specific anti-influenza antibodies than in those vaccinated with each of rHA1 and rNP. Administration of a combination of the protein-based nanoparticles has stimulated the activation of both CD4+ and CD8+T cells and induced a significantly higher T cell proliferation. The viral shedding was significantly lower in CS-HA1+CS-NP and inactivated vaccine groups compared with other challenged groups. The data demonstrate the potential of CS-HA1+CS-NP nanoparticles for eliciting specific influenza antibodies and conferring protection in chickens.

Modulation of Immune Responses Against HA1 Influenza Vaccine Candidate by B-lymphocyte Stimulator Cytokine in Mice.

Utilizing subunit vaccines is one of the strategies to address influenza infection. Recent innovations have focused on high doses of vaccine antigens and immune enhancers or adjuvant to induce more robust and long-lasting immune responses. Here, an effect of the B cell-activating factor receptor (BAFF-R) to increase the magnitude and durability of immune responses of the recombinant HA1 (rHA1) protein against the H1N1 influenza virus was studied. The HA1 protein and the effector domain of BAFF-R were expressed in the pET-28a (+) vector. Eight-week-old BALB/c mice were equally grouped into five groups (n=20). The 15 and 25 µg/µL of rHA1 were mixed with 2 µg/µL of rBAFF-R and injected three times for vaccinated groups. Three control groups were received normal saline and two concentrations of rHA1. The ability of rBAFF-R in eliciting HA-specific antibody response and stimulating T lymphocyte proliferation to induce the cell-mediated immunity was assayed. Induction of protection was evaluated following the challenge with PR8 strain. Analysis of immune responses showed that the co-administration of rBAFF-R with rHA1 boosted HI responses to the antigen in mice, whilst it was not able to promote the T cell proliferation responses against influenza. Compared to rHA1alone, the rBAFF-R/rHA1 generated efficient protection for the animals. There were no significant differences in eliciting the immune responses in mice immunized with the lower dose of rHA1 than that with the higher dose. The data indicate the rBAFF-R can enhance the primary and memory immune responses to protect against influenza infection.

Evaluation of cellular and humoral immune response in chickens immunized with flagellin-adjuvanted inactivated newcastle disease virus.

The aim of the present study was to evaluate the potential effect of flagellin as adjuvant in Newcastle disease virus (NDV) vaccine on the cellular and humoral immunity in chickens. Fifty-six specific pathogen-free chickens were assigned to seven groups of eight chickens and immunized twice with a two-week interval, intramuscularly. Group 1, received phosphate buffered saline as control (C), groups 2, 3, 4, 5, 6 and 7 were immunized with inactivated NDV [Ag], Ag + full FliC protein [AgF], Ag + truncated Flic protein [AgT], Ag + native Flic protein [AgN], commercial NDV vaccine [Vac] and Vac + N [VacN], respectively. After 45 days, spleen and bursa of Fabricius samples were collected and analyzed by flow cytometry and responses in control/vaccinated chickens were studied by immunophenotyping. Humoral response was also, evaluated by ELISA during the experiment. Results showed that immunized chickens with Ag + flagellin proteins had significantly higher frequency of circulating CD3+, CD4+ and CD8+ T cells in bursa of Fabricius in AgF, AgT and AgN, respectively, compared with other groups. Similar results were observed for spleen; however, the highest frequency of circulating CD3+, CD4+ and CD8+ T cells belonged to AgT and AgF, respectively. ELISA results showed that all flagellin-adjuvanted groups had higher antibody titers than other groups with the highest antibody response in VacN. It can be concluded that flagellin may induce both humoral and cellular immune responses against ND and is suggested for use as an efficient adjuvant.

Tween 80 improves the infectivity of BCL1 cell-adapted infectious bursal disease virus.

Non-ionic surfactants have the ability to alter the cell membrane's permeability for enhancing virus replication. The impact of non-ionic surfactant Tween 80 (TW80) on the infectivity of infectious bursal disease virus (IBDV) was studied in BCL1 cells. The toxicity of different concentrations of TW80 for BCL1 cells was determined for five-time passages. The confluent monolayer of BCL1 was infected by IBDV and subsequently passaged. The adaptation was confirmed by virus titration and RT-PCR assay. Replication kinetics of the cell-adapted IBDV was evaluated in pre-treatment and simultaneous treatment with TW80 at 0.01% concentration. The IBDV infectivity patterns were determined by virus titration, FRAP assay, and transmission electron microscopy. Sequence analysis, RNA secondary structure, and potential N-glycosylation site were conducted for IBDV VP2. Despite the similar cytopathic effects found in both TW80-treated cells and similar ROS levels, the IBDV titer was higher in TW80 pre-treated cells compared to the simultaneous treatment one. Such an increase in IBDV titer did not associate with changes in the VP2 sequence and RNA secondary structure. The possible antioxidant capacity of TW80 can attenuate the ROS damage and improve the cell viability, thereby improving IBDV infectivity.

Comparison of flagellin and an oil-emulsion adjuvant in inactivated Newcastle disease vaccine in stimulation of immunogenic parameters.

The present study was designed to investigate the potential application of native (N) and recombinant (truncated modified [tmFliC] and full-length [flFliC]) flagellin proteins along with inactivated Newcastle disease virus (NDV). Fifty six SPF chickens were immunized twice with PBS (control), inactivated NDV (Ag), inactivated NDV/flFliC (AgF), inactivated NDV/tmFliC (AgT), inactivated NDV/N (AgN), commercial vaccine containing Montanide (Vac) and Vac/N (VacN), with a two-week interval. Blood was collected weekly and spleens were harvested after chickens were sacrificed. Interleukin-6 (IL-6) and tumor necrotic factor-α (TNF-α) gene expression in peripheral blood mononuclear cells were analyzed by Real-Time PCR. Antibody response was assessed by haemagglutination inhibition (HI). Cellular activity was quantified by MTT assay. Results showed that the most IL-6 and TNF-α gene expression was observed in AgF group (P < 0.01). The lowest gene expression among vaccinated groups was observed in Ag group for IL-6 and Ag and Vac group for TNF-α. The highest HI titer was observed in Vac, VacN, AgF and AgT groups. The AgF group showed the highest cellular activity (P < 0.01). In conclusion, flagellin-adjuvanted groups showed a pro-inflammatory effect and acted similarly to or better than the Vac group. Hence, flagellin can be proposed as a potential adjuvant for ND vaccine.

Isolation, identification and chemical inactivation of infectious laryngotracheitis virus for use as a vaccine candidate.

Infectious laryngotracheitis (ILT) is a poultry respiratory disease associated with considerable mortality in chicken and decreasing egg production. Vaccination along with biosecurity measures are considered as the main strategy for ILT control. This study was aimed to evaluate the potency of an inactive ILT vaccine candidate derived from a local ILTV isolate. The isolated virus was characterized and treated with various chemicals and their concentrations. The virus infectivity was entirely abolished by treatment of 3 mM binary ethylene imine following 16 h incubation. The immune response of inactivated ILTV suspension with adjuvans was evaluated in both SPF chickens (experiment-I) and Hyline pullets (experiment-II). Efficacy of the inactivated and live ILT vaccines combination was compared. The results of experiment-I showed that the inactivated antigen induced specific antibody titers against ILTV. In experiment-II, despite the increase in serum antibody level administration of the inactivated antigen alone did not offer sufficient protection. The full protection was found in chickens that received the combination regimen. We conclude that simultaneous administration of the inactivated and live ILT vaccines was efficient for induction of immunity against ILTV. Keywords: infectious laryngotracheitis virus; vaccine; inactivation; immune response.

The Immunogenicity of a Novel Chimeric Hemagglutinin-Neuraminidase-Fusion Antigen from Newcastle Disease Virus by Oral Delivery of Transgenic Canola Seeds to Chickens.

Newcastle disease (ND) is considered as one of the most devastating infectious diseases targeting domestic birds and has considerable threat to the commercial poultry production. Two surface glycoproteins, hemagglutinin-neuraminidase (HN) and fusion (F), act as antigens in the virus structure and also play important roles in infecting host cells. In the current study, the expression of the chimeric HN-F protein in canola seeds and its immunogenicity in chickens were investigated. The HN-F gene was cloned downstream of the fatty acid elongase 1 (FAE1) promoter in the binary expression vector, pBI1400-HN-F, and introduced into rapeseed (Brassica napus L.) using Agrobacterium-mediated transformation. The amount of the HN-F glycoprotein was estimated up to 0.18% and 0.11% of the total soluble protein (TSP) in transgenic seeds and leaves of canola, respectively. Confirmatory analyses of 36 transgenic lines revealed that the HN-F gene was integrated into the genome. Subsequently, HN-F protein could be expressed and accumulated in the seed tissue. Specific pathogen-free (SPF) chickens immunized orally with recombinant HN-F showed a significant rise in specific and hemagglutination inhibition (HI) antibodies 35 to 42 days post the first administration. The results implied the potential of transgenic canola seed-based expression for oral delivery of NDV immunogenic glycoproteins.

TIR-TLR7 as a Molecular Adjuvant: Simultaneous Enhancing Humoral and Cell-Mediated Immune Responses Against Inactivated Infectious Bursal Disease Virus.

Despite the robust induction of humoral immune responses, a limitation of many adjuvants is their weak stimulation of cellular immunity. The development of synthetic gene-encoding adjuvants for simultaneous induction of both humoral and cell-mediated immune responses is under study. In this study, we examined the impact of toll/interleukin-1 receptor (TIR) domain of toll-like receptor 7 (TLR7) as molecular adjuvants on potency of inactivated infectious bursal disease (IBD) vaccines. A total of 60 specific pathogen-free week-old chicks were randomized grouped to receive either TIR-TLR7-adjuvanted IBD-inactivated vaccine or inactivated IBD antigen along with an unvaccinated control. Serum antibody titers were measured to estimate the humoral immunity, as well as lymphocyte proliferation activity for cellular immune responses. The protection was estimated after challenge with a very virulent IBD virus (IBDV) strain at 4 weeks postvaccination. The results indicated that one dose of IBD/TIR-TLR7 vaccine induced specific antibody responses, whereas a lower response after administration of inactivated IBD antigen was observed. The stimulation of splenocytes results indicated that the TIR-TLR7 adjuvanted IBD vaccine is capable of modulating cell-mediated immune response in treated chickens. A full protection against IBDV infection was achieved by injection of one dose IBD/TIR-TLR7 vaccine in the challenge trial. This study demonstrated that codelivery of TIR-TLR7 with inactivated IBD antigen resulted in simultaneous enhancing immune responses against IBD.

Interfering With Lipid Raft Association: A Mechanism to Control Influenza Virus Infection By Sambucus Nigra.

Sambucus nigra (elder) are broadly used species to treat microbial infections. The potential antiviral activity and mechanism action of elder fruit (EF) in human epithelium cell (A549) cultures infected with H9N2 influenza virus were determined. The effect of various concentrations of EF on influenza virus replication was examined by using virus titration, quantitative real time RT-PCR, fusion and lipid raft assays following two treatment procedures: A) pre-treated H9N2 virus with each concentration of EF extract and transfection of A549 cell cultures, and B) each concentrations of EF was added to H9N2 virus infected-cell cultures following virus adsorption. In both treatments with lower doses of EF increased viral titer as well as synthesized viral nucleoprotein as indicating the herb had no inhibitory effects on virus replication. In (B) trial with higher doses, 40 and 80 µg/mL of EF, a significant decrease in virus titer and viral protein synthesis were shown in EF treated cells indicating the herb affect either entry of viruses or inhibition virus particle release. The results suggest that EF treatment of the influenza virus infected-human epithelial cells may involve in lipid raft association which function as platform for formation of viral membrane fusion and budding. Differencesin treatment time and dose of EF extract in infected cells with influenza virus have a marked effect on the efficacy of the herb.

Design of a heterosubtypic epitope-based peptide vaccine fused with hemokinin-1 against influenza viruses.

Influenza viruses continue to emerge and re-emerge, posing new threats for public health. Control and treatment of influenza depends mainly on vaccination and chemoprophylaxis with approved antiviral drugs. Identification of specific epitopes derived from influenza viruses has significantly advanced the development of epitope-based vaccines. Here, we explore the idea of using HLA binding data to design an epitope-based vaccine that can elicit heterosubtypic T-cell responses against circulating H7N9, H5N1, and H9N2 subtypes. The hemokinin-1 (HK-1) peptide sequence was used to induce immune responses against the influenza viruses. Five conserved high score cytotoxic T lymphocyte (CTL) epitopes restricted to HLA-A*0201-binding peptides within the hemagglutinin (HA) protein of the viruses were chosen, and two HA CTL/HK-1 chimera protein models designed. Using in silico analysis, which involves interferon epitope scanning, protein structure prediction, antigenic epitope determination, and model quality evaluation, chimeric proteins were designed. The applicability of one of these proteins as a heterosubtypic epitopebased vaccine candidate was analyzed.

Necrotic Response to Low Pathogenic H9N2 Influenza Virus in Chicken Hepatoma Cells.

BACKGROUND: Limited knowledge about the molecular mechanism of avian influenza H9N2 virus pathogenicity in birds as well as human hosts has limited the development of effective control against the disease. To overcome this issue detailed understanding of the infectious characteristics of the virus in host cells should be obtained. OBJECTIVES: In this study we examined the replication kinetics of H9N2 virus in a chicken hepatoma cell line to obtain insight into the pathogenesis of H9N2 viruses. MATERIALS AND METHODS: The kinetic replication of H9N2 influenza virus in chicken hepatoma and fibroblastic cells was studied in the presence and absence of supplemental trypsin. High viral titers observed in liver cells in a short time correlated with the degree of cytopathic effects. To determine whether the ultimate outcome of infection results in programmed cell death, the infected cells were observed by the cell viability assay, DNA fragmentation, caspase cascade activation, and quantified lactate dehydrogenase release. RESULTS: The degree of viability was significantly reduced in infected hepatoma cells. Observations of caspase activation and cell DNA laddering in infected cells were not indicative of apoptosis. The infected hepatoma cells released lactate dehydrogenase, which is consistent with cell death by necrosis. CONCLUSIONS: Taken together, these data reveal that cellular protease of chicken liver cells allows the replication of high yields of H9N2 virus in the absence of trypsin and also cell death in the infected cells is due to necrosis.

Evaluation of Immune Response Against Inactivated Avian Influenza (H9N2) Vaccine, by Using Chitosan Nanoparticles.

BACKGROUND: Influenza A is a virus that affects a wide range of animals and also human beings. Avian influenza virus (AIV) subtype H9N2 has the potential to create influenza pandemic and vaccination is a common solution for this problem. The vaccine, used for rapid intervention, should be safe to use and highly effective, after a single administration. Chitosan nanoparticles (CNP) have already been recommended as a new adjuvant for inactivated AIV H9N2 vaccine immunization. OBJECTIVES: This study aimed at the evaluation and better understanding of optimum concentration of CNP preparations and also, assessment of loading capacity of AIV into CNP, as an adjuvant in specific pathogen-free (SPF) chickens. MATERIALS AND METHODS: For measurement of vaccine-antibody response, different types of CNP were injected intramuscularly, in a single dose, to 21-day-old specific pathogen-free chickens. Chickens were monitored for the efficacy of the nanoparticles and, also, their immune response, during a follow up of 7 weeks, by using hemagglutination-inhibition (HI) test. The CNP were prepared according to modified ionic gelation method and inactivated antigen was loaded in four hemagglutinin units (HAU) concentrations. Loading capacity of nanoparticles was determined by hemagglutination (HA) method. Inactivated A/H9N2 AIV was mixed with chitosan of low molecular weight. RESULTS: The CNP did not cause any mortality or side effects, when chickens were administered the prepared vaccine. The results strongly showed that this novel vaccine significantly enhances the immunogenicity of inactivated AIV, comparing with ISA70 (SEPPIC, Puteaux, France) adjuvant that is used routinely in the Razi Serum and Vaccine Research and Production Institute, Karaj, Iran, to reduce ISA70's side effects. CONCLUSIONS: The AIV loaded into CNP vaccines induce appropriate antibody titers, after a single immunization, while requiring a low dose of antigen. The CNP also represent an interesting new platform for antigen delivery and a promising adjuvant candidate for H9N2 inactivated influenza vaccine.

Expression of Factor X in BHK-21 Cells Promotes Low Pathogenic Influenza Viruses Replication.

A cDNA clone for factor 10 (FX) isolated from chicken embryo inserted into the mammalian cell expression vector pCDNA3.1 was transfected into the baby hamster kidney (BHK-21) cell line. The generated BHK-21 cells with inducible expression of FX were used to investigate the efficacy of the serine transmembrane protease to proteolytic activation of influenza virus hemagglutinin (HA) with monobasic cleavage site. Data showed that the BHK-21/FX stably expressed FX after ten serial passages. The cells could proteolytically cleave the HA of low pathogenic avian influenza virus at multiplicity of infection 0.01. Growth kinetics of the virus on BHK-21/FX, BHK-21, and MDCK cells were evaluated by titrations of virus particles in each culture supernatant. Efficient multicycle viral replication was markedly detected in the cell at subsequent passages. Virus titration demonstrated that BHK-21/FX cell supported high-titer growth of the virus in which the viral titer is comparable to the virus grown in BHK-21 or MDCK cells with TPCK-trypsin. The results indicate potential application for the BHK-21/FX in influenza virus replication procedure and related studies.

Apoptotic response of chicken embryonic fibroblast cells to infectious bursal disease virus infections reflects viral pathogenicity.

Infectious bursal disease virus (IBDV) induces immunodeficiency in young chickens and apoptosis in chicken embryos. To understand the relation between the viral pathogenesis and the induction of cell death, chicken embryonic fibroblast (CEF) cells were infected with IBDV intermediate (im) and very virulent (vv) strains at different MOIs. The cell viability and DNA fragmentation were evaluated in infected cells. The cellular apoptotic pathway involve was investigated by determining the activities of caspase cascade. The imIBDV strain was replicated well in CEF cells and shown higher viral titers than vvIBDV. Apoptosis changes were observed only in vvIBDV-infected CEF cells at higher MOI 48 h post infection. Efflux of cytochrome c suggests that the intrinsic pathway of the apoptotic process induced by vvIBDV infection independently of virus replication. Prediction of caspase substrates cleavage sites revealed that different IBDV strains have conserved cleavage motif pattern for VP2 and VP5 viral proteins. These findings suggest the pathogenicity of IBDV strains might be involved in the induction of apoptosis in host cells.

Dose- and time-dependent apoptosis induced by avian H9N2 influenza virus in human cells.

To understand human response to avian H9N2 influenza, we investigated the effects of the viral infection on A549, HepG2, and HeLa cells at low and high MOIs. To identify virus-host interplay, expression of Mx and NP genes was measured in the cells supernatants. Cell viability and apoptosis were evaluated by MTT assay, DNA fragmentation, and florescent staining. The virus titration and NP gene transcript levels indicate lower susceptibility of HeLa cell to H9N2 replication than other cells. Although H9N2 did produce a faster CPE in HepG2, high dose of the virus induced apoptosis within early stage of A549 infection. The DNA laddering was enhanced in the cell correlated with increase in virus transcripts. The undetectable to different regulation levels of Mx gene were observed in response to H9N2 infection suggesting that an insufficient antiviral defense in the noncompetent-IFN HepG2 cell promotes efficient viral replication. These results showed that the permissivity of HepG2 for H9N2 is comparable with A549; however, liver cells are not target tissue respond to the infection. These data revealed that the H9N2 virus induced apoptosis signaling via mitochondrial pathway in human alveolar epithelial cells, indicating that the induction may be associated with a dose-dependent manner.

Impact of chicken-origin cells on adaptation of a low pathogenic influenza virus.

Understanding the growth dynamics of influenza viruses is an essential step in virus replication and cell-adaptation. The aim of this study was to elucidate the growth kinetic of a low pathogenic avian influenza H9N2 subtype in chicken embryo fibroblast (CEF) and chicken tracheal epithelial (CTE) cells during consecutive passages. An egg-adapted H9N2 virus was seeded into both cell culture systems. The amount of infectious virus released into the cell culture supernatants at interval times post-infection were titered and plaque assayed. The results as well as cell viability results indicate that the infectivity of the influenza virus was different among these primary cells. The egg-adapted H9N2 virus featured higher infectivity in CTE than in CEF cells. After serial passages and plaque purifications of the virus, a CTE cell-adapted strain was generated which carried amino acid substitutions within the HA stem region. The strain showed faster replication kinetics in cell culture resulting in an increase in virus titer. Overall, the present study provides the impact of cell type, multiplicity of infection, cellular protease roles in virus infectivity and finally molecular characterization during H9N2 virus adaptation procedure.

Phylogeny and evolution of Newcastle disease virus genotypes isolated in Asia during 2008-2011.

The full-length fusion (F) genes of 51 Newcastle disease (ND) strains isolated from chickens in Asia during the period 2008-2011 were genetically analyzed. Phylogenetic analysis showed that genotype VII of NDV still predominant in the domestic poultry of Asia. The sub-genotype VIIb circulated in the Iran and Indian sub-continent countries, whereas VIId sub-genotype existed in Far East countries. The non-synonymous to synonymous substitutions ratio was calculated 0.27 for VIId sub-genotype and 0.51 for VIIb sub-genotype indicates purifying/stabilizing selection which resulted in a low evolution rate in F gene of VIIb sub-genotype. There is evidence of localized positive selection when comparing these sub-genotypes protein sequences. Five codons in F gene of ND viruses had a posterior probability >90% using the Bayesian method, indicating these sites were under positive selection. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that although most positions were under purifying selection and can be eliminated, a few positions located in sub-genotype specific regions were subject to positive selection.

Evolutionary characterization of hemagglutinin gene of H9N2 influenza viruses isolated from Asia.

The full length hemagglutinin (HA) genes of 287 H9N2 AI strains isolated from chickens in Asia during the period 1994-2009 were genetically analyzed. Phylogenetic analysis showed that G1-like viruses circulated in the Middle East and Indian sub-continent countries, whereas other sublineages existed in Far East countries. It also revealed G1-like viruses with an average 96.7% identity clustered into two subgroups largely based on their time of isolation. The Ka/Ks ratio was calculated 0.34 for subgroup 1 and 0.57 for subgroup 2 indicates purifying/stabilizing selection, but despite this there is evidence of localized positive selection when comparing the subgroups 1 and 2 protein sequences. Five sites in HA H9N2 viruses had a posterior probability >0.5 using the Bayesian method, indicating these sites were under positive selection. These sites were found to be associated with the globular head region of HA. To identify sites under positive selection; amino acid substitution classified depends on their radicalism and neutrality. The results indicate that, although most positions in HAs were under purifying selection and can be eliminated, a few positions located in the antigenic regions and receptor binding sites were subject to positive selection.