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Introduction: Trichomonas gallinae (T. gallinae) infects numerous species of birds worldwide. Many antiprotozoal drugs have been utilized for therapeutic purposes. Herbal plants extracts do not result in drug resistance or tissue residue; therefore, they are a dependable and safe substitute for treating trichomoniasis. The current study, the antitrichomonal properties of three herbal plants (Quercus infectoria, Artemisia annua, and Allium sativum) were compared to those of metronidazole in pigeons. Materials and methods: In this experiment, 32 pigeons were used, each of which was divided into four groups with four replicates. All groups were experimentally infected with T. gallinae except for group D. Group A was treated with a herbal mixture (80% Quercus infectoria extract, 11% Artemisia annua extract, and 9% Allium sativum extract [standardized to 8% total tannic acid]; Coccyphyt-L®; Makian Dam Pars Science-Based Company), while Group B was given metronidazole. The positive control group C was experimentally infected but not treated with T. gallinae, while group D remained healthy throughout the experiment. The experiment consisted of a performance index, weight gain, wet mount, and biochemical and hematological examination. Results: Compared to metronidazole, the treatment with a herbal mixture significantly reduced the pathogenic effects of Trichomonas spp. After a week of treatment, chickens in group A were nearly healthy and, in some respects, superior to those in the metronidazole treatment group. Conclusion: In conclusion, the antiprotozoal properties of the aforementioned herbal mixture suggest its use as an alternative antitrichomonal agent to chemotherapeutic drugs in trichomoniasis treatment.

Coccidiosis is a critical disease in the poultry industry worldwide. Producers apply different strategies to control and prevent this disease. Herbal drugs are suitable remedies for reducing losses associated with coccidiosis in poultry. The present study aimed to evaluate the effectiveness of an herbal mixture in preventing coccidiosis. A total of 160 broiler chickens were divided into four treatment groups, with five replicates for each. Experimental infection of all groups, except group D, was carried out with mixed Eimeria species (E. tenella, E. necatrix, E. brunetti, and E. maxima) on day 14. Broiler chickens in group A were given an herbal mixture (75% Quercus infectoria, 16% Artemisia annua, and 9% Allium sativum) as feed additives during the rearing period, and group B was treated with Monensin. No treatment was applied to group C after the chickens were experimentally infected with mixed Eimeria spp. Group D was used as the negative control since chickens in this group were not infected or sick during the experiment. Body weight gain, feed conversion ratio (FCR), mortality rate, intestinal lesion scoring, and oocyst count per gram (OPG) were evaluated in this study. The results of the present study revealed that the highest mean body weight was gained in group D, followed by chickens in group A. The best FCR results were attributed to chickens in group D, followed by group B. In this study, both drugs decreased mortality rate, intestinal lesion scores, and OPG in the treated chickens. In conclusion, this herbal mixture can reduce coccidial lesions. Keywords: Broiler, Coccidiosis, Herbal mixture, Prevention

Caliciviruses are (+) RNA viruses with a worldwide distribution and wide host range, including humans and birds. The family caliciviridae consists of eleven genera, two of which, bavovirus and nacovirus, are found in chickens affected by stunting syndrome. In this study, for the first time the presence of calicivirus in Iranian broiler flocks was investigated by viral metagenomics method. Fecal samples were collected from broiler chicken farms affected with diarrhea from Gilan province Iran. Our results showed that some of the diseased chickens carried a genus of calicivirus belonging to bavovirus. The complete 7824 nt genome of this bavovirus, named UT Shahhosseini1 2018, was sequenced and characterized. Phylogenetic analysis revealed that our calicivirus shared 87% similarity to the closest strains, including the German calicivirus chicken/V0021/Bayern/2004, suggesting that the avian- derived strain belongs to the bavoviruses. Conserved motifs shared between bavoviruses further confirmed this finding. Phylogenetic analysis of nonstructural (NS) and VP proteins also revealed similar values. This is the first report and first complete genome sequence of bavovirus in Iran. However, further studies are needed to obtain a better epidemiological picture of the abundance avian-origin caliciviruses of in Iranian bird populations, including poultry. The pathogenic potential of these caliciviruses to affect poultry production should also be investigated.

Avian coccidiosis is thought to be one of the most expensive infectious diseases in the poultry industry.Safe and alternative anti-coccidial drugs are herbal extracts because they do not result in tissue residue and drug resistance. The objective of the present study was to evaluate the anti-coccidial effect of the herbal mixture, a complex of two plants (Echinacea purpurea, Glycyrrhiza glabra) in broiler chickens in comparison with toltrazuril.One hundred twenty broiler chickens were used in this experiment and divided into 4 equally numbered groups. All the groups, except Group D, were experimentally infected with mixed Eimeria spp. (E. Tenella, E. maxima, E. necatrix and E. brunetti) on day 14. Group A treated with an herbal mixture [Glycyrrhiza glabra Extract 5% (standardised to 5.4% glycyrrhizic acid) and Echinacea purpurea Extract 2% (standardised to 4% total phenolic content based on chlorogenic acid); Coxinin-ECPositive control group had the poorest results and more mortality than other groups. Group D was not infected and was healthy all the experiment period. Treatment with herbal complex significantly reduced the negative performance and pathogenic effects associated with Eimeria spp. at a level that was comparable with toltrazuril.In summary, the anti-coccidial activity of the studied herbal complex suggests its use as an alternative anti-coccidial agent to chemotherapeutic drugs for controlling coccidiosis in poultry.-Coccidiosis is an important infectious disease that causes serious financial loss to the poultry industry. -Chemical anti-coccidial drugs and vaccines are the main control strategies to combat the disease. However, these tools have some constraints. -Herbal remedies are suitable alternatives to chemical compounds for control of losses associated with coccidiosis in poultry. -An herbal mixture (Echinacea purpurea, Glycyrrhiza glabra) has promising effects for controlling of coccidiosis in broiler chickens.

Avian coccidiosis is considered among the infectious disease of high costs in the poultry industry. Herbal extracts are safe and reliable substitute anticoccidial drugs for chemical feed additives as they don’t sequel to drug resistance and tissue remnants. The purpose of the current study was to assess the anticoccidial effect of an herbal complex of 3 plants (Artemisia Annua, Quercus infectoria, and Allium Sativum) in broiler chickens in comparison with toltrazuril anticoccidial. One hundred twenty broiler chickens were used in this experiment and divided into 4 equally numbered groups. All the groups, except group (D), were experimentally infected whit mixed Eimeria spp. (E. Tenella, E. maxima, E. necatrix and E. brunetti) on day 14. Group (A), was treated whit an herbal mixture. Group (B), was treated whit Toltrazuril. Group (C), was experimentally infected with mixed Eimeria spp. But they didn’t have any treatment, this group was our positive control, as expected, this group had the poorest results and more mortality than other groups. Group (D), wasn't infected and was healthy all the experiment period, this was our negative control. Performance indices, fecal oocyst excretion, and intestinal lesion score were determined during the experiment. Treatment with an herbal complex significantly reduced the negative performance and pathogenic effects associated with Eimeria spp. at a level that was comparable with toltrazuril. In summary, the anticoccidial activity of the mentioned herbal complex recommends its use as an alternative anticoccidial agent to chemotherapeutic drugs for controlling coccidiosis.

During 2014-2017 Clade 2.3.4.4 H5N8 highly pathogenic avian influenza viruses (HPAIVs) have spread worldwide. In 2016, an epidemic of HPAIV H5N8 in Iran caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected and continue to experience problems. Several outbreaks were reported in 2017. One of them is related to Hooded crow (Corvus cornix) in a national park in Esfahan province in 2017. Whole genome sequencing and characterization have been done on the detected H5N8 sample. Based on HA sequencing results, it belongs to 2.3.4.4 clade, and the cleavage site is (PLREKRRKR/G). Phylogenetic analysis of the HA gene showed that the Iran 2017 H5N8 virus clustered within subgroup Russia 2016 2.3.4.4 b of group B in H5 clade 2.3.4.4 HPAIV. On the other hand, the NA gene of the virus is placed in group C of Eurasian lineage. Complete genome characterization of this virus revealed probable reassortment of the virus with East-Asian low-pathogenic influenza viruses. Furthermore, the virus possessed some phenotypic markers related to the increased potential for transmission and pathogenicity to mammals at internal segments. This study is the first full genome characterization H5N8 HPAIV in Iran. The data complete the puzzle of molecular epidemiology of H5N8 HPAIV in Iran and the region. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, that might lead to changes in virus structural and functional characteristics such as the route and method of transmission of the virus and virus infective, pathogenic and zoonotic potential.

Since 1998, Iran’s poultry industry has faced several outbreaks of low pathogenic avian influenza H9N2. Tissue samples were collected from a broiler flock with respiratory symptoms in autumn 2017. After that, virus isolation and confirmation of H9N2 using RT-PCR, sequencing, and bioinformatic analysis for all eight genes were performed. The phylogenic analysis revealed HA gene of recent Iranian isolate (A/chicken/Mashhad/UT-Barin/2017) which was clustered in G1 sublineage. In addition, all eight genes of the virus were placed with Pakistani isolates of 2015 in separate group. Based on amino acid motif KSSR in HA cleavage site, the UT-Barin is considered as low pathogenic avian influenza with eight HA and seven NA potential N-glycosylated sites. No evidence was detected regarding adamantane and neuraminidase inhibitors’ drug’s resistance. Multiple point mutations were observed in all genes that were responsible for increasing virulence of the virus for avian host and also increasing affinity to mammalian host cells.

Since 2005, H5Nx highly pathogenic avian influenza (HPAI) viruses of the Goose/Guangdong (Gs/GD) lineage have spread worldwide, affecting poultry and wild birds in Asia, Europe, Africa and North America. So far, the role of Western Asia and the Middle East in the diffusion dynamics of this virus has been poorly explored. In order to investigate the genetic diversity and the role of Iran in the transmission dynamics of the Gs/GD lineage, we sequenced the complete genome of twenty-eight H5Nx viruses which were circulating in the country between 2016 and 2018. We reported the first characterization of the HPAI H5N6 subtype of clade 2.3.4.4B in Iran and gave evidence of the high propensity of the Gs/GD H5 AIVs to reassort, describing six novel H5N8 genotypes of clade 2.3.4.4B, some of them likely generated in this area, and one H5N1 reassortant virus of clade 2.3.2.1c. Our spatial analyses demonstrated that the viruses resulted from different viral introductions from Asia and Europe and provided evidence of virus spread from Iran to the Middle East. Therefore, Iran may represent a hot-spot for virus introduction, dissemination and for the generation of new genetic variability. Increasing surveillance efforts in this high-risk area is of utmost importance for the early detection of novel emerging strains with zoonotic potential.

In this study, the prevalence and spatial distribution of Newcastle disease, infectious bronchitis, and avian influenza have been evaluated in commercial broiler farms in 31 provinces in Iran. In this survey, a total of 233 affected broiler chicken farms were sampled. The infectious bronchitis virus (alone) was detected with highest frequency in 60 farms, and separately or combined with other agents, in 110 farms; Newcastle disease virus, separately, was detected in 28 farms, and in 63 farms separately or combined with other infectious agents; and avian influenza H9N2 was detected in 22 farms separately and in 51 farms separately or concomitant with other infectious agents. The sample tested negative for all H5 serotypes. The results of the present study show that the most prevalent avian viral infectious disease contributing to respiratory syndromes in broiler farms in Iran was infectious bronchitis due to infectious bronchitis virus serotypes variant 2 and 793/B. On the other hand, combined with the alternation of dominant viruses and circulating strains, flocks are exposed to unremitting anamorphic viral infections. Thus, the permanent monitoring of cases that have occurred and the review of vaccination plans of affected flocks every year are some of the necessary measures needed for strategic control of respiratory syndrome in broilers. It is noteworthy that execution of epidemiologic examinations on the cogent factors of prevalence of this syndrome and defeat of vaccination strategy in the flocks is urgent and has to be fulfilled on the definite causes of time.

The nephropathogenic infectious bronchitis virus (IBV) strain IS-1494 like (variant-2; GI-23) was first isolated in the Middle East (1998). Despite intensive vaccinations, IS-1494 like IBVs are still circulating in Iran (the dominant genotype) and spread to other countries. Here, the full-length genome of this Iranian IS-1494 like IBV was (Mahed) determined to understand its evolutionary relationships. The genome consists of 27,652 nucleotides, with mutations in most of the structural genes. Thirteen open reading frames (ORFs) were predicted in the Mahed isolate (5′ UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′ UTR). ORFs 4b, 4c, and 6b, which has rarely been reported, were present in the Mahed genome. According to phylogenetic analysis of the full-length genome, 1a, S2, M, E, N protein, Mahed isolate clustered with the QX type strain. Based on the partial 1b, S1, Mahed clustered with the Q1 strain. The full-length genome of Mahed isolate shared the highest sequence homology with Gray and JMK (90.06–90.07%) and was least related to the Vic-s (86.21%). These data show that evolutionary variation because of recombination in IBV plays a major role in the adaptation and origin of IBV leading to new genetic and types of the virus strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13337-018-0462-4) contains supplementary material, which is available to authorized users.

Avian influenza A virus (AIV) subtype H9N2 is the most prevalent subtype found in terrestrial poultry throughout Eurasia and has been isolated from poultry outbreaks worldwide. Tracheal tissue specimens from 100 commercial broiler flocks in Afghanistan were collected between 2016 and 2017. After real-time RT-PCR, AI-positive samples were further characterized. A part of the HA gene was amplified using RT-PCR and sequenced. The results of real-time RT-PCR showed that 40 percent of the flocks were AI positive. Phylogenetic studies showed that these H9N2 AIVs grouped within the Eurasian-lineage G1 AIVs and had a correlation with H9N2 AIV circulating in the poultry population of the neighboring countries over the past decade. Analysis of the amino acid sequence of HA revealed that the detected H9N2 viruses possessed molecular profiles suggestive of low pathogenicity and specificity for the avian-like SAα2,3 receptor, demonstrating their specificity for and adaptation to domestic poultry. The results of the current study provide great insights into H9N2 viruses circulating in Afghanistan's poultry industry and demonstrate the necessity of planning an applied policy aimed at controlling and managing H9N2 infection in Afghan poultry.

Avian infectious bronchitis (IB) is a worldwide chicken disease, caused by avian infectious bronchitis virus (IBV) which infects all commercial poultry lines. The present study was done to evaluate protection caused by two different serotype vaccines (Massachusetts and 793/B) in order to evaluate protection against challenge with IS/1494/06-like virus (variant 2-like virus), which is prevalent in the Middle East. SPF chickens were divided into four groups (n = 20). First and second group as negative control group and non-vaccinated-challenged group received no vaccine. Groups 3 and 4 received H120-H120 and H120-1/96 IBV vaccine strains at the 1st and 14th day, respectively. Twenty one days after last vaccination, non-vaccinated-challenged group and vaccinated group were challenged using variant 2-like IBV. Serum samples were collected before challenge to measure humoral immune response of chickens. Five days after challenge, the tissue samples from the trachea, lungs and kidneys were taken to evaluate cilliary activity, viral load (quantitative real-time RT-PCR), and histopathological evaluation. Clinical sign scores were also recorded after challenge. Overall, the results showed a protective efficacy of the used vaccination program. Best cross protection (69.2%) was obtained in the H120-1/96 vaccinated group. Virus replication of the challenged virus in H120-1/96 group compared with H120-H120 group showed a significant reduction of viral load in trachea (1.5×103 compared to 503) and kidneys. Clinical sign scores of the challenged groups showed significant effect of the vaccination program to reduce clinical signs. The trachea pathological scores and histopathological findings in the lungs and kidneys also confirmed better protective efficacy of vaccinated groups. In conclusion, using combination of heterologous IBV vaccine serotypes (Massachusetts and 793/B) would be a better strategy to control variant 2-like viruses, but more evaluation is needed using other circulating isolates to find the best combination of vaccines.

Highlights • An updating data about avian infectious bronchitis genotypes circulating in Iran. • First detection of D274 genotype in Iran., The coronavirus avian Infectious bronchitis virus (IBV) poses economic threats to poultry farms worldwide, affecting the performance of both meat-type and egg-laying birds. To define the evolution of recent IBVs in Iran, a genetic analysis based on hypervariable nucleotide sequences of S1 gene was carried out. Tracheal swab samples were collected from 170 Broiler flocks during 2017. Ten tracheal swabs from each flock pooled. From a total number of 170 flocks tested, 84.71% found to be positive. Phylogenetic tree analysis revealed the presence of D274 as a first time in Iran. IS/1494/06 was showed to be dominant IBV type circulating in broiler farms with a significantly higher prevalence than other four genotypes. Considering fluctuations in QX-type prevalence in recent years, continuous monitoring is necessary to reduce economic consequences in layer and broiler farms. The findings highlight the importance of using modified vaccination strategies that are adapted to the changing disease scenario.

Fowl adenoviruses D and E (FAdV-D and E) can cause inclusion body hepatitis (IBH) in commercial chicken flocks. Recently, IBH outbreaks have been increasingly reported in different regions of Iran, particularly in broiler farms. The present study was conducted to perform, for the first time, a complete genome characterization of a FAdV isolate from an IBH outbreak in Iran. Briefly, liver samples were collected from affected broiler flocks and following viral DNA extraction and confirming by PCR technique; one positive sample was selected from an affected flock to conduct a complete genome sequencing. The current FAdV, named "Fowl_Adenovirus_D_isolate_iran/UT-Kiaee_2018", was placed into FAdV-11 serotype (D species). According to the complete genome sequence analysis, UT-Kiaee had high homology with Chinese and Canadian FAdV. The partial sequence of the hexon gene revealed that UT-Kiaee shared 100% identity with previous Iranian FAdVs. The present study was the first to report full genome FAdV in Iran and complete the puzzle of molecular epidemiology of FAdV in Iran through determining the possible origin of Iranian FAdvs, which are the causative agents of recent IBH outbreaks in Iran.

Since 1998, Iran's poultry industry has faced several outbreaks of low pathogenic avian influenza H9N2. Tissue samples were collected from a broiler flock with respiratory symptoms in autumn 2017. After that, virus isolation and confirmation of H9N2 using RT-PCR, sequencing, and bioinformatic analysis for all eight genes were performed. The phylogenic analysis revealed HA gene of recent Iranian isolate (A/chicken/Mashhad/UT-Barin/2017) which was clustered in G1 sublineage. In addition, all eight genes of the virus were placed with Pakistani isolates of 2015 in separate group. Based on amino acid motif KSSR in HA cleavage site, the UT-Barin is considered as low pathogenic avian influenza with eight HA and seven NA potential N-glycosylated sites. No evidence was detected regarding adamantane and neuraminidase inhibitors' drug's resistance. Multiple point mutations were observed in all genes that were responsible for increasing virulence of the virus for avian host and also increasing affinity to mammalian host cells.

Infectious bronchitis virus (IBV) is a highly infectious pathogen, which affects the respiratory tract, reproductive system, and kidney of chickens. Many different genotypes of IBV are recognized which cause different clinical manifestations. According to the antigenic differences, different serotypes of the virus do not cross-protect. Massachusetts serotype induces the best cross-protection against other serotypes. Recently, the IBV QX genotype has been detected in Iran. QX genotype causes permanent damage to the oviduct in layer and breeder flock if it occurs in the early life cycle. In this study, we compared two vaccination program using 793/B type and Massachusetts type vaccine. One-day-old SPF chickens were divided into four groups. Groups 1 and 2 were unvaccinated groups. Group 3 was vaccinated with the H120 vaccine at day 1 and 793/B at day 14 (eye drop), and group 4 was vaccinated with H120+793/B (eye drop) on the first day and 793/B at day 14. Groups 2, 3, and 4 challenged (oculonasal) with QX genotype (104 EID50) at day 35. Five days post challenge, the sample were clollected for ciliostasis test, histopathology, and quantitative real-time RT-PCR from trachea, lung, and kidneys. Results showed that two vaccination programs created more than 80% of protection against challenge virus, but no significant difference was recorded between two programs. Based on our results, it can be concluded that vaccination with two mixed vaccines (H120+793/B) on the first day of the life of a chick does not make any difference in comparison to single vaccine (H120) in reducing of pathological damages and viral load. As long as the second vaccination against IB may not be applied properly in farm situation, applying the mixture of 793/B type vaccine with H120 at day 1 (ocular or spray) may help to increase vaccination program efficacy.

Newcastle disease (ND) is a contagious viral disease affecting numerous avian species, particularly domestic poultry, and causes devastating outbreaks. In spite of its endemicity and importance in Iran, data on the genetic characterization of ND virus (NDV) are scarce. An alarming issue that has just been raised is the occurrence of ND outbreaks with unexpected high mortality and severe clinical signs. The present study was conducted to characterize the emerging NDV genetically. An NDV strain, isolated in 2017 from commercial broilers showing severe nervous and enteric signs, was completely sequenced and found to be 15,192 nucleotides in length. The phylogenetic analysis demonstrated that the virus belonged to subgenotype VIIi, a subgenotype with potential panzootic features which has recently emerged in the Middle East and Asia. The supporting genetic pattern obtained from the complete genome, fusion and haemagglutinin gene analysis showed close relationship of the isolate with Pakistani VIIi NDVs. The analysis of the F protein showed a polybasic amino acid motif and a phenylalanine at position 117 at the cleavage site, which is a characteristic of virulent strains. The isolate showed significant differences from the previously characterized NDV strains from commercial and rural chickens in Iran. This may describe the importance of the illegal trade of pet birds from neighbouring countries leading to the emergence of new genotypes. This study introduces a newly emerging NDV VIIi subgenotype in Iran. This investigation emphasizes the necessity of effective control strategies.

Avian metapneumovirus (aMPV), also known as avian pneumovirus or turkey rhinotracheitis virus, is the causative agent of turkey rhinotracheitis and swollen head syndrome in chickens. Four aMPV subgroups (A-D) have been reported previously based on their genetic and antigenic differences. Evidence suggests that the live bird markets (LBMs) play an important role in the epidemiology of the avian viral diseases. A total number of 450 oropharyngeal samples from eight different species of birds (migratory and local) were collected from LBMs of Gilan province, Iran, from October to December 2016. The presence of aMPV was determined by reverse transcription polymerase chain reaction (RT-PCR) based on nucleoprotein gene. The aMPV was detected in 30.60% of the examined birds including chickens (37.00%), turkey (33.00%), Eurasian teal (25.00%), common blackbird (33.00%), and Eurasian woodcock (25.00%). Bioinformatics analysis and a phylogenetic tree based on partial nucleotide sequences of the N gene showed that the detected aMPVs were belonged to subtype B. This is the first report of aMPV in non-commercial birds in Iran. Knowledge of the frequency and types of infected birds with pneumoviruses allow a better understanding of the epidemiology of aMPV in Iran.

In 2010, H5N8 highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage dramatically affected poultry and wild birds in Asia, Europe, and North America. In November 2016, HPAI H5N8 was detected in a commercial layer farm in Tehran province. The diagnosis was based on real-time reverse transcriptase PCR (RRT-PCR) and sequencing of haemaglutinin (HA) and neuraminidase (NA) genes from suspected samples. Genetic and phylogenetic analysis of the HA gene demonstrated that the Iranian HPAI H5N8 viruses belong to the HPAI H5 virus clade 2.3.4.4 and cluster within group B (Gochang-like). In particular, the highest similarity was found with the sequences of the HPAI H5N8 identified in Russia in 2016. To our knowledge, this clade has not been previously detected in Iran. Previous HPAI A (H5) epidemic in Iran occurred in 2015 and involved exclusively viruses of clade 2.3.2.1c. These findings indicate that Iran is at high risk of introduction of HPAI H5 of the A/Goose/Guangdong/1/1996 lineage from East Asia and highlight the need to maintain adequate monitoring activities in target wild and domestic bird species for HPAI early detection. This study is useful for better understanding the genetic and antigenic evolution of H5 HPAI viruses in the region and the world.

Avian influenza virus (AIV) H9N2 subtype is endemic in Iran and causes substantial economic loss to the growing poultry industry within the country. In this study, a cross-sectional analysis was carried out to determine the sero-prevalence of H9N2 in several commercial farms between the years 2014 and 2015. The comparison of the mean of serum titers and the ratio of sero-positive birds between all units were analyzed using one-way ANOVA test. In 2014, a total of 77 farms (58 turkey farms, 14 quail farms, and 5 partridge farms) and 894 birds (682 turkeys, 154 quails, and 58 partridges) were sampled while in 2015, a total of 69 farms (54 turkey farms, 8 quail farms, and 7 partridge farms) and 856 birds (675 turkeys, 105 quails, and 76 partridges) were sampled. Of that, 52 of 77 sampled farms (67.5%) and 437 of 894 samples (48.9%) were positive for H9N2 in 2014 while. Forty-one of 69 farms (59.4%) and 307 of 856 sera (35.9%) were positive in 2015. Furthermore, the mean titer of partridge farms was significantly lower than that of turkey farms (p 0.01) and the mean percentage of sero-positive turkey farms was significantly higher than partridge farms (p 0.01) in 2014. In 2015, no significant difference was observed between the mean sera titer amongst farms and percentage of sero-positive birds (p 0.05). Our results indicated that H9N2 is circulating in these farms. Since many more such farms are being established for operations, in addition to the threat of emergence and continuous reemergence of the disease in these farms, enhanced veterinary biosecurity measures on farms are required for mitigation.

Infectious bronchitis (IB) is a viral avian disease with economic importance in the world, including Iran. S1 gene sequencing has been used for molecular epidemiological studies and genotypic characterization of infectious bronchitis virus (IBV). A total of 118 IBV isolates were obtained from tissue samples from chickens with clinically suspected IB from Iranian broiler farms (eight provinces, 200 samples). The isolates were confirmed by real-time polymerase chain reaction (PCR) and characterized by sequencing the spike glycoprotein gene. The isolates formed six distinct phylogenetic groups (IS/1494/06 [Var2] like, 4/91-like, IS/720-like, QX-like, IR-1 and Mass-like) that were related to variants isolated in the region. The most frequently detected viruses were of the Var2-like (IS/1494/06-like) genotype, with an overall prevalence of 34 %. Twenty-one percent of the isolates formed a cluster together with the 4/91 IBV type, 10 % were of the QX genotype, and 8 % were of the IS/720 genotype. In addition, 4 % and 3 % of the isolates belonged to the Massachusetts and IR-1 genotype, respectively. For the first time, we have isolated and characterized IBV variants from broiler farms in different provinces of Iran. This study demonstrates a constant evolution of IBV in Iran, demonstrating the need for continuous monitoring and development of new vaccines based on indigenous viruses.