Publications by authors named "Vahid Karimi"

24 Publications

  • Page 1 of 1

Intraocular Pressure Measurements Using Rebound Tonometry in Eight Different Species of Companion Birds.

J Avian Med Surg 2020 Dec;34(4):338-342

Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

The purpose of this study was to determine reference interval intraocular pressure (IOP) values in 8 different species of companion birds. One hundred and nineteen companion birds (238 eyes) from a captive colony were examined: 21 pigeons (; 18%), 17 African grey parrots (; 14%), 22 common mynahs (; 18%), 24 cockatiels (; 20%), 12 zebra finches (; 10%), 9 budgerigars (; 8%), 6 domestic canaries (; 5%), and 8 ring-necked parakeets (; 7%). Intraocular pressure was measured by rebound tonometry (TonoVet) avoiding induced, undesired pressure on the head, neck, or eyes. Mean IOP values varied by species. Mean (± SD) IOP values determined for each species were pigeon (5.42 ± 2.06 mm Hg), African grey parrot (4.93 ± 1.91 mm Hg), common mynah (6.22 ± 2.04 mm Hg), cockatiel (5.08 ± 1.76 mm Hg), zebra finch (5.90 ± 2.11 mm Hg), budgerigar (5.88 ± 2.31mm Hg), canary (5.83 ± 1.60 mm Hg), and ring-necked parakeet (6.25 ± 1.75 mm Hg). No statistically significant differences were found in IOP values between right and left eyes for the species studied ( > .22), with the exception of the ring-necked parakeet ( = .001). The results of this study provide representative IOP values measured using rebound tonometry in 8 different species of companion birds.
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http://dx.doi.org/10.1647/1082-6742-34.4.338DOI Listing
December 2020

Complete genome sequence of a subgenotype XXI.1.1 pigeon paramyxovirus type 1 virus (PPMV‑1) isolated from Iran in 2018 and phylogenetic analysis of a possible novel, but unassigned, PPMV-1 group isolated in 2014.

Comp Immunol Microbiol Infect Dis 2020 Dec 17;73:101565. Epub 2020 Oct 17.

Department of Poultry Diseases, RAZI Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.

Newcastle disease (ND) is one of the most serious infectious and contagious viral diseases in avian species. Recently, several ND outbreaks in pigeon caused by pigeon paramyxovirus serotype-1 (PPMV-1) have been reported from Iran, but unfortunately, phylogenetic studies have been mostly conducted on partial sequence of NDV fusion (F) gene. In addition, a complete genome data of Iranian PPMV-1 strains are not available. In the present study, a PPMV-1, named Avian avulavirus 1/pigeon/Iran/UT-EGV/2018, isolated from an infected pigeon, was subjected to whole-genome sequencing. The isolate showed an MDT of 74 h, thus categorizing it as mesogenic. The phylogenetic analysis based on the F gene sequence revealed the isolate belongs to XXI.1.1 subgenotype (min 0.9 % and max 3 %). To our knowledge, our study is the first study to publish the complete genome of a PPMV-1 from Iran. According to BLAST results, the whole genome of UT-EGV had high homology with some Russian, Egyptian and Ukrainian strains (the highest was 96.55 %). Additionally, we conducted a phylogenetic analysis on five PPMV-1 that we isolated in 2014 to find that they may belong to a completely unreported subgenotype (6 % distance when compared as a group). The information obtained from this study can be useful in preventive measures, including constructing an effective vaccine against PPMV-1 in Iran.
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http://dx.doi.org/10.1016/j.cimid.2020.101565DOI Listing
December 2020

An investigation into seasonal variations of groundwater nitrate by spatial modelling strategies at two levels by kriging and co-kriging models.

J Environ Manage 2020 Sep 30;270:110843. Epub 2020 Jun 30.

The Centre for Advanced Modelling and Geospatial Information Systems (CAMGIS), Faculty of Engineering and IT, University of Technology Sydney, NSW, 2007, Australia; Department of Energy and Mineral Resources Engineering, Choongmu-gwan, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, 05006, Republic of Korea.

Nitrate pollution of groundwater through spatial models is investigated in this paper by using a sample of nitrate values at monitoring wells using the data from four seasons of a year, in which data are sparse. Two spatial modelling strategies are formulated at two levels, in which Strategy 1 comprises: three variations of kriging-based models (ordinary kriging, simple kriging and universal kriging), which are constructed at Level 1 to predict nitrate concentrations; and a Multiple Co-Kriging (MCoK) model is used at Level 2 to enhance the accuracy of the predictions. Strategy 2 is also at two levels but employs Indicator Kriging (IK) at Level 1 as a probabilistic spatial model to predict areas at risk of exceeding two thresholds of 37.5 mg/L and 50 mg/L of nitrate concentration, and Multiple Co-Indicator Kriging (MCoIK) at Level 2 for a better accuracy. The improvements at Level 2 for both strategies are remarkable and hence they are used to gain an insight into inherent problems. The results of a study delineate areas with excessive nitrate concentrations, which are in the vicinity of urban areas and hence reflect poor planning practices since the 1990s. The results further reveal the patterns on sensitivities to seasonal variations driven by aquifer recharge and strong dilution processes in spring times; and on the role of pumpage impacting aquifers giving rise to possible hotspots of nitrate concentrations.
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http://dx.doi.org/10.1016/j.jenvman.2020.110843DOI Listing
September 2020

Including 793/B type avian infectious bronchitis vaccine in 1-day-old chicken increased the protection against QX genotype.

Trop Anim Health Prod 2019 Mar 29;51(3):629-635. Epub 2018 Oct 29.

Iranian Veterinary Organization, Tehran, Iran.

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 (10 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.
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http://dx.doi.org/10.1007/s11250-018-1730-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088605PMC
March 2019

Seroprevalence and genotyping of avian infectious bronchitis virus detected from Iranian unvaccinated backyard chickens.

Iran J Microbiol 2018 Feb;10(1):65-71

Department of Health and Management of Poultry Diseases, Iranian Veterinary Organization, Tehran, Iran.

Background And Objectives: Different epidemiological studies have found that backyard chickens are a reservoir for poultry diseases. Most backyard chicken flocks have a poor level of biosecurity, which increases the risk of spread of diseases. In recent years, the number of backyard chickens has been on the rise in Iran. However, the health status of backyard flocks is still poorly documented. Thus, this study aimed at examining the seroprevalence of antibodies against infectious bronchitis virus (IBV) and molecular surveillance and genotyping of IBV among backyard chickens (without vaccination history) in Mazandaran province, North of Iran, 2014.

Materials And Methods: A total of 460 blood samples of unvaccinated backyard chickens in the mentioned area were tested for antibodies against IBV using commercial ELISA. Also, cecal tonsils were collected from 75 chickens in the same area. Real time RT-PCR (for detection) and RT-PCR and sequencing spike gene were performed.

Results: The seropositivity rate was 54.5%. In addition, we detected 793/B, Variant 2, and QX in the backyard flocks and performed phylogenetic studies on them. The phylogenetic study revealed that the detected genotypes had high homology with IBV strains that were infected broilers, pullets, and layers in Iran.

Conclusion: There is a need for continuous monitoring of IBV among avian species to complete the epidemiological map and work on the pathogenesis of Iranian IBV strains in Iranian backyard chickens.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6004632PMC
February 2018

Prevalence of avian metapneumovirus subtype B in live bird market in Gilan province, Iran.

Vet Res Forum 2018 15;9(1):93-97. Epub 2018 Mar 15.

Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

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.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5913567PMC
March 2018

Effect of fiber inserts on gingival margin microleakage of Class II bulk-fill composite resin restorations.

Gen Dent 2018 May-Jun;66(3):58-63

This study evaluated the effect of fiber inserts combined with composite resins on enamel and dentin margin microleakage. The fiber inserts were used with high- (x-tra fil) and low-viscosity (x-tra base) bulk-fill composite resins and as well as conventional composite resins (Grandio and Grandio Flow). In 96 sound, recently extracted molars, 2 standardized Class II cavities were prepared. The teeth were randomly divided into 8 groups of 12 teeth each, based on composite resin type and presence or absence of fiber inserts: groups 1 and 2, x-tra fil with and without fiber inserts, respectively; groups 3 and 4, x-tra base with and without fiber inserts; groups 5 and 6, Grandio with and without fiber inserts; and groups 7 and 8, Grandio Flow liner (gingival floor)/Grandio (remainder of cavity) with and without fiber inserts. In all the groups, a 2-step etch-and-rinse adhesive was used. The specimens were processed in a dye penetration technique to determine microleakage percentages. Data were analyzed with analysis of variance, Tukey, and t tests. There was significantly less leakage at the enamel margins than the dentin margins. Fiber reinforcement significantly decreased enamel microleakage in all the groups, with no significant differences among the groups. Concerning dentin microleakage, there were no significant differences among the 4 groups without fiber inserts, while a significant difference was detected in groups 2 (x-tra fil plus fiber) and 8 (Grandio Flow plus fiber/Grandio). Fibers significantly improved dentin sealing in groups 2 and 8. These findings suggest that a fiber insert reinforcing bulk-fill and conventional composite resins might improve enamel sealing in shallow Class II cavi-ties. The effect of fiber reinforcement on the dentin margins of deep cavities depended on the viscosity of the composite resins; fiber reinforcement was effective for flowable bulk-fill and conventional composite resin restorations.
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December 2018

Efficacy of H120 and Ma5 avian infectious bronchitis vaccines in early challenge against QX strain.

Virusdisease 2018 Mar 11;29(1):123-126. Epub 2017 Dec 11.

Iranian Veterinary Organization, Tehran, Iran.

Infectious bronchitis (IB) is a highly infectious avian pathogen, which affects the respiratory tract, gut, reproductive system, and kidney of chicks of all ages. Many different serotypes of IB virus (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 strain has been detected in Iran. QX strain causes permanent damage to the oviduct if it occurs in the early life cycle and is a significant factor in layer and breeder chicken flocks. In this study, we compare the H120 and Ma5 vaccines' protection against early challenge with the QX strain in commercial chicks. one-day-old commercial chicks were divided into six groups. Groups 1 and 2 were unvaccinated groups. Groups 3 and 5 were vaccinated with the H120 vaccine (eye drop) and groups 4 and 6 were vaccinated with Ma5 (eye drop) on the 6th day (5 days after vaccination). Groups 2, 3 and 4 challenged (oculonasal) with QX strain (10^ EID50). Ciliostasis test, histopathology, and quantitative real-time RT-PCR were done at 11 days-old of age. Results showed that neither H120 nor Ma5 could induce proper cross-protection against QX early challenge, but the viral load and adverse pathological records in vaccinated chicks were less than that in the non-vaccinated groups. It can be concluded that vaccination on the first day of the life of a chick offers not full protection against the IBV QX strain but reduced the viral load and pathological damages in vaccinated chickens. Applying other forms of vaccination and using different genotypes on one-day-old chicks are suggested.
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http://dx.doi.org/10.1007/s13337-017-0414-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5877842PMC
March 2018

Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus.

Virus Res 2017 08 5;240:101-106. Epub 2017 Aug 5.

Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

Avian infectious bronchitis virus (IBV) is causing major economic losses to the poultry industry. The analysis of the S1 gene has been used to determine IBV genotype. The aim of this study was genotyping of IBVs circulating among the Iranian broiler flocks in the period between 2015 to 2017. Trachea samples from 278 broiler flocks were collected from broiler farms in eight provinces of Iran. After Real-time RT-PCR, IBV-positive samples were further characterized based on S1 gene. The results of the Real-time RT-PCR showed that 52.16% of flocks were IBV positive. Four genotypes were detected and the frequency of occurrence rates of IS-1494-like, 793/B, QX and Massachusetts IBV genotypes were 70.34%, 19.31%, 7.58% and 2.75%, respectively. Sequence analysis revealed that nucleotide identities within IS-1494-like group ranged between 98.86-100%, while each of the QX, Massachusetts and 793/B groups were 98.05-100%, 98.20-100% and 93.29-100% respectively. These results show that the IS-1494-like IBV is the dominant IBV genotype in Iran. Proper control strategies are essential to overcoming the high frequency of occurrence of IS-1494-like IBV. The phylogenetic relationship of the strains with respect to different sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in Iran.
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http://dx.doi.org/10.1016/j.virusres.2017.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114540PMC
August 2017

Co-circulation of three clusters of 793/B-like avian infectious bronchitis virus genotypes in Iranian chicken flocks.

Arch Virol 2017 Oct 8;162(10):3183-3189. Epub 2017 Jul 8.

Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

Avian infectious bronchitis (IB) is an acute and highly contagious viral disease causing severe economic losses in the poultry industry. The 793/B IB virus is an important infectious bronchitis virus (IBV) genotype currently circulating in several countries, including Iran. One hundred confirmed IBV samples (between 2014 and 2015; from 15 provinces in Iran) were selected for genotyping based on S1 sequencing. After phylogenetic analysis, it was found that 30% of the IBV isolates belonged to the 793/B genotype. Results showed that the Iranian 793/B-like IBV isolates could be divided in to three clusters: 4/91-like (50%), 1/96-like (40%), and IB88-like (10%). The sequence similarity between Iranian 793/B-like IBV isolates is 87.69%-100%. The highest identity is between the 4/91 and IB88 clusters (96.38%), and the lowest similarity is between the 1/96 and IB88 clusters (87.62%). This study provides a comprehensive analysis of 793/B-type IBV in Iran and characterization of IBV molecular epidemiology in the country.
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http://dx.doi.org/10.1007/s00705-017-3473-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086655PMC
October 2017

Pathogenicity study of Iranian genotype of avian infectious bronchitis virus (IR-1).

Vet Res Forum 2017 15;8(1):35-41. Epub 2017 Mar 15.

Department of Microbiology and Immunology; Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

Avian infectious bronchitis (IB) is a major cause of economic losses in poultry industry. The IB virus primarily affects respiratory tract, but various strains differ in their tropism for other target organs such as kidney and alimentary tract. The objective of this study was to estimate the pathogenicity of Iranian IBV variant (IR-1), which is limited exclusively to Iran. Specific pathogen free chicks were inoculated intranasally. Sera, fecal swabs and different tissue samples were collected on different days post infection (DPI). Clinical signs, gross pathology and histological changes were recorded. The viral load was quantified in the RNA extractions from different tissue samples using real-time PCR. Anti-IBV antibodies were detected in serum samples. The IgG antibody were found on 21 and 28 DPI. Severe histological lesions were observed in the trachea and lung while the lesions in kidney were appeared to be milder. Viral RNA was detected in all tested tissues from 1 DPI to the last day of the experiment. The highest viral load was measured in the trachea and feces on 1 and 5 DPI, respectively. It can be concluded the IR-1 had broad tropism for respiratory tract, digestive system, and renal tissue, reflecting its epitheliotropic nature, but it caused the most severe lesions in the respiratory tract. This was the first pathogenicity study of Iranian IR-1 IBV. Further knowledge of IBV pathogenesis provides the groundwork to inform more effective prevention practices.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413309PMC
March 2017

Prevalence of avian infectious bronchitis virus in broiler chicken farms in south of Iraq, 2014 - 2015.

Vet Res Forum 2016 15;7(4):317-321. Epub 2016 Dec 15.

Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Karaj, Iran.

Avian infectious bronchitis (IB), caused by a gammacoronavirus, is an OIE-listed (List B) disease and characterized by respiratory and renal involvements, causing high mortality, and economic loss in both layers and broilers. In comparison with other diagnostic methods, real-time polymerase chain reaction (RT-PCR) and conventional RT-PCR are potent, more sensitive and faster techniques for infectious bronchitis virus (IBV) detection. This research was conducted to detect IBV using specific primers of IB in three governorates (Basra, Thi-Qar and Muthana) in the south of Iraq. Tracheal specimens were collected from 46 IB suspected commercial broiler flocks. XCE2+ and XCE2- Primers, which amplify all IBV serotypes, were used. Primers MCE1+, BCE1+ and DCE1+ were used to amplify the specific nucleotide sequences of Massachusetts, 793/B and D274 genotypes, respectively. The results of real-time RT-PCR of this study showed that 34 (74.00%) out of 46 infected flocks were positive to IBV. The results of nested PCR showed that 50.00% and 5.89% of positive samples were belonged to genotypes 793/B and Massachusetts, respectively, and the remaining positive (44.11%) were unknown. The results indicate presence of Massachusetts and 793/B IBV strains in commercial broilers in southern Iraq.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5251354PMC
December 2016

Myxoma Immediately above the Junction of the Inferior Vena Cava and the Right Atrium: A Rare Cause of Budd-Chiari Syndrome.

J Tehran Heart Cent 2016 Jul;11(3):139-142

Nemazee Hospital, Shiraz University of Medical Sciences, Shiraz, Iran.

The Budd-Chiari syndrome (BCS) is a rare disorder caused by the obstruction of the hepatic veins or the inferior vena cava (IVC) at the suprahepatic level. This syndrome is developed by either hepatic vein thrombosis or mechanical venous obstruction and leads to centrilobular hepatic congestion with the subsequent development of fibrosis and cirrhosis. Intracardiac tumors have been rarely reported as a cause of the BCS. These tumors usually originate from the atrial septum. Very rarely, they arise either from the junction of the IVC and the right atrium or from the Eustachian valve. There are a few case reports in the literature where atrial tumors have caused the BCS. In these cases, the tumors were malignant, and the patients died shortly after being diagnosed. We describe a 71-year-old female patient who presented with a 3-month history of abdominal pain and protrusion. On physical examination, blood pressure and pulse rate were normal. Jugular venous pressure was about 10 cm. Cardiac examination revealed a systolic murmur, grade IV/VI, in the left sternal border without radiation. Echocardiography showed a large mass (about 6×4 cm) in the right atrium with close contact to the origin of the IVC, obstructing it. Cardiac magnetic resonance imaging, with and without gadolinium, also confirmed the diagnosis. The patient underwent surgery, and the myxoma was removed. The tumor was a large solid mass, 5×4 cm in size, which originated immediately above the entrance of the IVC. The patient is in good condition 1 year afterward. We emphasize that atrial myxomas should be considered in the differential diagnosis of tumors that cause chronic BCS.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5148816PMC
July 2016

Genetic analysis of H9N2 avian influenza viruses circulated in broiler flocks: a case study in Iraq in 2014-2015.

Virus Genes 2017 Apr 12;53(2):205-214. Epub 2016 Nov 12.

Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Islamic Republic of Iran.

H9N2 avian influenza viruses (AIVs) have been recorded in Eurasian for several years. Since 2004-2005, the disease has become endemic in Iraq, causing serious economic losses in the poultry industry. The hemagglutinin (HA) and neuraminidase (NA), two out of eight protein-coding genes, play an important role during the early stage of infection and hinder virus assembling. Little is known about the genetic information of the H9N2 viruses currently circulating in Iraq; thus, gene sequences of six AIVS of the H9N2 subtype have been detected and analyzed in the period of 2014-2015 from different outbreaks of broiler flocks in five provinces situated in the middle and southern parts of Iraq. Genetic comparison of the partial sequences of HA gene indicated that all Iraqi viruses are related to each other and could be divided into two subgroups. Viruses of the first and the second subgroups demonstrated a high similar identity with Pakistani and Iranian viruses, respectively. The nucleotide sequences of the NA protein of the all studied Iraqi viruses were very similar (95.2-100% identity), and shared high nucleotide sequence identity with Iranian, Pakistani, and Lebanese strains. All six recent viruses possessed histidine, alanine, and leucine at positions 183, 190, and 226, respectively, which are the key residues in receptor-binding sites. The Iraqi viruses were closely related to viruses of G1-like lineage isolated from poultry flocks of Iran and Pakistan, suggesting that possible epidemiological links could be derived from a common origin. Further investigations are required and should include the viral isolation and full-length molecular characterization of H9N2 AIVs in this area.
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http://dx.doi.org/10.1007/s11262-016-1407-xDOI Listing
April 2017

The effect of Allium sativum (Garlic) extract on infectious bronchitis virus in specific pathogen free embryonic egg.

Avicenna J Phytomed 2016 Jul-Aug;6(4):458-267

Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

Objective: Garlic is a plant has been used as a flavor, and anti-microbial and anti-diarrheal agent. Infectious bronchitis virus (IBV) is a coronavirus. The available vaccines against IBV cannot cover new variants. This study evaluated the inhibitory effects of garlic extract on IBV.

Materials And Methods: The constituents of garlic extract were detected by gas chromatography. This study was done in four groups of embryonic SPF eggs; first group was used for virus titration; second group received the mixture of different virus titration and constant amount of garlic extract; third group received 10(-3) titration of virus and after 8 hr received garlic extract and the last group received different dilutions of garlic extract.

Results: Based on our results, in the second group, IBV vaccine strain (4/91) at all titration and M41 in 10(-2) and 10(-3) titration and in the third group both variants of virus the embryonic Index (EI) was significantly increased.

Conclusion: The garlic extract had inhibitory effects on IBV in the chickens embryo.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4967842PMC
August 2016

Genotyping of infectious bronchitis viruses from broiler farms in Iraq during 2014-2015.

Arch Virol 2016 May 18;161(5):1229-37. Epub 2016 Feb 18.

Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Karaj, Iran.

Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region.
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http://dx.doi.org/10.1007/s00705-016-2790-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086866PMC
May 2016

Molecular characterization of infectious bronchitis viruses isolated from broiler chicken farms in Iran, 2014-2015.

Arch Virol 2016 Jan 14;161(1):53-62. Epub 2015 Oct 14.

Iranian veterinary Organization, Tehran, IRAN.

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.
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http://dx.doi.org/10.1007/s00705-015-2636-3DOI Listing
January 2016

Full-length characterization and phylogenetic analysis of hemagglutinin gene of H9N2 virus isolated from broilers in Iran during 1998-2007.

Comp Clin Path 2013 21;22(3):321-330. Epub 2012 Jan 21.

1Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

H9N2 avian influenza A viruses (AIV) have become panzootic in Eurasia over the last decade and are endemic in Iran since 1998, and inactivated vaccine has been used in chickens to control the disease. The hemagglutinin (HA), one of eight protein-coding genes, plays an important role during the early stage of infection. To study their evolution and zoonotic potential, we conducted an in silico analysis of H9N2 viruses that have infected broiler in Tehran Province, Iran between 1998 and 2007. The complete coding region of HA genes from nine H9N2 subtypes isolated from chicken flocks in Tehran Province during 1998-2007 was amplified and sequenced. Sequence analysis and phylogenetic studies of H9N2 subtype viruses on the basis of data of 9 viruses in this study and 30 selected strains are available in the GenBank. Sequence and phylogenetic analyses revealed a large number of similar substitution mutations and close evolutionary relation among sequences of HA. The isolates possessed two types of amino acid motif -R-S-S-R/G-L- and -R-S-N-R/G-L- at the cleavage site of HA. The results showed that all nine representative H9N2 isolates belong to low pathogenic AIVs since none of the amino acid sequences at the cleavage site of the HA of the isolates possessed the basic motif required for highly pathogenic viruses (R-X-R/K-R). Six out of these nine isolates possessed leucine at position 226, which prevails in the sequences found in human strains. Phylogenetic analysis showed that all our isolates belonged to the G1-like sublineage. Also, these isolates showed some degree of homology with other H9N2 isolates, e.g., 89.46-93.93.39% with qu/HK/G1/97 and 93.39-98.39% with pa/Narita/92A/98. The available evidence indicates that HA genes of H9 influenza virus circulating in Iran during the past years were not well conserved. Our finding emphasizes the importance of reinforcing AIV surveillance, especially after the emergence of high pathogenicity in poultry in Iran.
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http://dx.doi.org/10.1007/s00580-012-1405-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087803PMC
January 2012

Comparison and phylogenetic analysis of the ISS gene in two predominant avian pathogenic E. coli serogroups isolated from avian colibacillosis in Iran.

Res Vet Sci 2013 Feb 30;94(1):5-8. Epub 2012 Jul 30.

Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

The ISS (increased serum survival) gene and its protein product (ISS) of avian pathogenic Escherichia coli (APEC) are important characteristics of resistance to the complement system. The aims of this study were to clone, sequence and characterize sequence diversity of the ISS gene between two predominant serogroups in Iran and among those previously deposited in Genbank. The ISS gene of 309 bp from the APEC χ1390 strain was amplified by PCR, cloned and sequenced using pTZ57R/T vector. The ISS gene from the χ1390 strain has 100% identity among different serogroups of APEC in different geographical regions throughout the world. Phylogenetic analysis shows two different phylogenic groups among the different strains. Strong association of nucleotide sequences among different E. coli strains suggests that it may be a conserved gene and could be a suitable antigen to control and detect avian pathogenic E. coli, at least in our region. Currently, our group is working on the ISS protein as candidate vaccine in SPF poultry.
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http://dx.doi.org/10.1016/j.rvsc.2012.07.010DOI Listing
February 2013

Assessment of immunity against avian colibacillosis induced by an aroA mutant containing increased serum survival gene in broilers.

Braz J Microbiol 2012 Jan 1;43(1):363-70. Epub 2012 Jun 1.

Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran , Tehran , Iran.

Colibacillosis is an important disease in the poultry industry which causes serious economic damages. As it is suggested that vaccination is one of the means to control colibacillosis, we tried to investigate the vaccine potential of a ∆aroA derivative of an O78:K80 avian pathogenic Escherichia coli containing increased serum survival gene. 490 chicks were selected as follows: For assessment of virulence of ∆aroA mutant, 30 chicks were divided into three groups and injected with 0.5ml of PBS or bacterial suspension containing either10(7) colony forming units (CFU) of mutant or parent strains via subcutaneous route. Macroscopic lesions and mortality rate were recorded in different groups during the week after challenge. For assessment of safety and immunogenicity of the ∆aroA mutant, three groups of 20 chicks were vaccinated by aerosol administration of 250 ml of suspension containing 10(8) CFU of mutant strain at days 1 and 14, while the two other groups received PBS or wild type strain. Macroscopic lesions and mortality rate were recorded in different groups until day 21. To determine whether the vaccination is protective against challenges or not, the chickens were vaccinated at days 1 and 14 and challenged intramuscularly with either a homologous or heterologous strains at day 21. Macroscopic lesions and mortality rate were recorded in different groups during the week after challenge. The results revealed that the ∆aroA mutant was slightly virulent, however it was safe and did not cause mortality, lesions or weight loss after vaccination. Antibody responses were similar in the control and mutant groups and vaccination did not induce a significant humoral immunity. The mutant could not protect chickens against both homologous and heterologous challenges. This could be due to several factors such as the high amount of maternal antibodies in the first two weeks of life, and the vaccination procedure.
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http://dx.doi.org/10.1590/S1517-838220120001000043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768954PMC
January 2012

Characterization of class I integrons among Salmonella enterica serovar Enteritidis isolated from humans and poultry.

FEMS Immunol Med Microbiol 2012 Mar 23;64(2):237-43. Epub 2011 Nov 23.

Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.

A total of 84 Salmonella enterica serovar Enteritidis (S. Enteritidis) isolates, 42 of human and 42 of poultry origin, were characterized for antimicrobial resistance patterns and class I integrons. Among them, 58 (69%) S. Enteritidis were multidrug-resistant (MDR) and showed resistance to two or more antibiotic classes. By PCR assays and DNA sequencing, 50 (59.5%) S. Enteritidis isolates were found to carry class I integrons. Amplification of internal variable regions of class I integrons revealed five different arrays (0.75 kb only, 1 kb only, 1.3 kb only, both 1 and 1.2 kb, and both 1 and 1.3 kb). The integrons were further sequenced and the dfrA25 (0.75 kb), aadA1 (1 kb), aadA2 (1 kb), bla(PSE1) (1.2 kb) aadA6-orfD (1.3 kb) gene cassette arrays were identified. Ciprofloxacin minimum inhibitory concentration (MIC) values for the three isolates that showed resistance or reduced susceptibility via the disc diffusion method were 0.5-4 μg mL(-1), although only three isolates exhibited resistance to cefteriaxone (MIC: 128-256 μg mL(-1)) and four isolates were resistant to florfenicol (MIC: 32-128 μg mL(-1)). In conclusion, the high rates of multidrug-resistance and class I integrons found among S. Enteritidis isolates in humans and poultry in Tehran suggest that efforts are needed to confine the prevalence of MDR Salmonella isolates.
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http://dx.doi.org/10.1111/j.1574-695X.2011.00883.xDOI Listing
March 2012

Molecular genetic differentiation of avian Escherichia coli by RAPD-PCR.

Braz J Microbiol 2008 Jul 1;39(3):494-7. Epub 2008 Sep 1.

Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran , Tehran , Iran.

Escherichia coli is one of the most important bacterial avian pathogens and a common inhabitant of the gastrointestinal tract of animals. Most pathogenic E. coli can not be differentiated biochemically or by classic microbiologic methods. Molecular typing methods, particularly PCR, facilitated epidemiological and ecological studies of bacteria. Here we describe the application of a random amplified polymorphic DNA- polymerase chain reaction (RAPD-PCR) for molecular genetic differentiation of E. coli isolates in Iran. In this study 58 E. coli isolates including 4 standard strains, 3 food originated isolates, 33 avian isolates, 8 isolates form diarrheic calves and 10 isolates from unweaned diarrheic lambs were analyzed by RAPD-PCR using primer 1247(5(/)-AAG AGC CCG T-3(/)). The RAPD analysis showed that these isolates could be grouped into 33 RAPD types and avian isolates were discriminated into 29 genotypes. It was shown that the primer could not differentiate E. coli isolated from lambs. Discriminatory index for entire isolates was 0.912 and for avian isolates was 0.990. We concluded that RAPD-PCR can be used as a method for molecular differentiation of E. coli isolates.
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http://dx.doi.org/10.1590/S1517-838220080003000015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3768446PMC
July 2008