ORIGINAL_ARTICLE Background and Aims: Avian Influenza (AI) H9N2 subtype was first reported to infect turkeys in the United States in 1966 and has been panzootic in Europe and Asia. The impact of avian influenza caused by H9N2 viruses in Iran is now significantly more severe than in previous years. Methods: Sequence analysis and phylogenetic study of the complete coding region Polymerase A (PA) gene of H9N2 subtype of avian influenza virus isolates (outbreaks of 1999-2009) in Iran were studied. Results: Sequence and phylogenetic analysis revealed a large number of similar substitution mutations and close evolutionary relation among sequences of PA. Based on analysis of AminoAcid sequences Iranian H9N2 isolates have some substitution that found in human and mouse adapted isolates. It is raised concern that H9N2 Isolates has trend to infect mammalian host. In Phylogenetic analysis Iranian isolates cluster in unknown Indian-Middle East cluster. However, the early isolate of H9N2 (11T strain) in Iran classified in DK-1 lineage. Conclusion: The results show, Iranian avian influenza H9N2 isolates have undergone extensive genetic reassortment which led to emergence of a new genotype. Interestingly, continuous monitoring of viral genetic changes throughout the years is warranted to monitor variations of Influenza viruses in the field. http://journal.isv.org.ir/article-1-71-en.pdf 2014-11-07 1 6 10.21859/isv.5.3.1 Avian Influenza (AI) H9N2 subtype Iran Phylogenetic Study F Tayefeh-Fazel-Khalkhali 1 Science and Research Branch, Islamic Azad University, Tehran, Iran AUTHOR M Soleimani 2 TASNIM Biotechnology Research Center, AJA University of Medical Sciences, Tehran, Iran AUTHOR K Majidzadeh-A 3 Iranian Centers for Breast Cancer (ICBC); Academic Center for Education, Culture and Research (ACECR), Tehran, Iran AUTHOR A Ghalyanchi-Langeroudi 4 Departments of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR MR Zolfaghari 5 Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran AUTHOR V Karimi 6 Departments of Clinical Sciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR

ORIGINAL_ARTICLE Background and Aims: Genotyping assay has been accepted as a guidance in the therapeutic management of Human Immunodeficiency virus 1 (HIV-1). But, it is not commonly used in our country due to its high running cost. The aim of this study is evaluate an in-house genotyping resistance test (GRT) for HIV-1. Methods: HIV-1 RNA of 20 samples were extracted from plasma and RT Nested- PCR was performed and the final products were sequenced. Stanford HIV Sequence Database was used for genotyping and interpretation of resistance data. Results: Subtype A was the dominant viral subtype in these patients. Also the results of drug resistance interpretation showed that drug-naïve patients are susceptible to drugs and for patients taking the drugs 66.6% susceptible for AZT, 50% high- level resistance for 3TC, 66.6% low- level resistance for ABC, 66.6% susceptible for TDF, 50% high- level resistance for NVP and 50% high- level resistance for EFV. Conclusion: Our method is able to amplify and sequence HIV-RNA from plasma samples from a random selection of patients encompassing different subtypes. The results of this study may have important consequences for survey and clinical management of patients with AIDS in Iran. http://journal.isv.org.ir/article-1-72-en.pdf 2014-11-07 7 11 10.21859/isv.5.3.7 Human Immunodeficiency Virus Type 1 Subtypes Genotyping Drug Resistance K Baesi 1 Research Center of Virus and Vaccine, Baqiatallah University of Medical Sciences, Tehran, Iran AUTHOR E Saberfar 2 Research Center of Virus and Vaccine, Baqiatallah University of Medical Sciences, Tehran, Iran AUTHOR M Haji-Abdolbaghi 3 Iranian Research Center for HIV/AIDS (IRCHA), Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran AUTHOR Z Goodarzi 4 Research Center of Virus and Vaccine, Baqiatallah University of Medical Sciences, Tehran, Iran AUTHOR

ORIGINAL_ARTICLE Background and Aims: Newcastle disease virus (NDV) infection have been established in at least 241species of birds representing 27 of the 50 orders of the class.NDV isolate were obtained from infected ostrich flock during the outbreaks of ND in Iran 2012. The F gene fragment which codes the main functional region of the F protein was obtained by RT-PCR and sequenced. Methods: From the pathotype prediction based on the cleavage site of the fusion protein, this isolate was placed into the velogenic group with the motif 112 RRQKRF 117. Results: Phylogenetic analysis based on a partial F gene sequence showed that the isolates from ostrich cluster together with concurrent isolates from poultry in Iran within the sub genotype VIId, which is the predominant pathogen involved currently in Newcastle disease outbreaks in poultry worldwide. Conclusion: This study adds to the understanding of the ecology of NDV in ostrich and emphasizes the need for constant surveillance in times of an ongoing and expanding epidemic of NDV. This finding is essential for improving the disease control strategies and development of vaccines for ND. http://journal.isv.org.ir/article-1-73-en.pdf 2014-11-07 12 17 10.21859/isv.5.3.12 Newcastle disease Struthio camelus Iran Phylogenetic study A Ghalyanchi-Langeroudi 1 Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR H Hosseini 2 Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran AUTHOR O Madadgar 3 Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR V Karimi 4 Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR A Shahraeini‏ 5 DVM, Tehran, Iran AUTHOR MM Ghafari 6 Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran AUTHOR

ORIGINAL_ARTICLE Background and Aims: Tomato yellow leaf curl virus (TYLCV) is one of the most destructive viruses of tomato that leads to reduced tomato yield up to 100% in tropical and subtropical regions. In this study, the complete sequence of TYLCV isolate from Hormozgan province, Iran and its recombination evsent was determined. Methods: TYLCV infected tomato was collected from Hormozgan province. Total DNA was extracted from infected tomato and whiteflies and used as template for amplification by PCR. Analyses of sequences data were done by Clustal W method and GeneDoc software and then phylogenic tree and bootstrapping was prepared by the Maximum likelihood method by Clustal X with 100 replication. Amino acids analysis was carried out by neighbor joining method and RDP3 with 1000 replication. Results: A 670 bp fragment was amplified by using the specific primer for TYLCV and was then sequenced. Based on the 670 bp sequence, new primers were designed to amplify and characterize the next part in TYLCV circular genomeA 670 bp fragment was amplified by using the specific primer for TYLCV and was then sequenced. Based on the 670 bp sequence, new primers were designed to amplify and characterize the next part in TYLCV circular genome. Conclusion: Gene analysis showed that the genome includes six ORFs with 94% identity relatives which were most close to TYLCV-Kahnooj. It also showed that this isolate has an additional part of sequences in the rep gene that has not been found in the other strains of TYLCV. http://journal.isv.org.ir/article-1-74-en.pdf 2014-11-07 18 27 10.21859/isv.5.3.18 Identification nucleotide sequence Tomato disease TYLCV A Azizi 1 Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran AUTHOR M Shams-Bakhsh 2 Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran AUTHOR J Mozafari 3 National Plant Gene bank of Iran, Seed & Plant Improvement Institute, Mahdasht Road, Karaj, Iran AUTHOR R Montazeri-Hedesh 4 Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran AUTHOR

ORIGINAL_ARTICLE Background and Aims: Plant certification programs need reliable, fast, cheap and sensitive methods for detection of systemic pathogens with special interest in virus and viroid detection. Reverse transcriptase-polymerase chain reaction (RT-PCR) has been documented as an alternative assay for certification of plant propagating materials. The main object of the present study was the optimization of a multiplex RT-PCR assay for simultaneous detection of Citrus tristeza virus (CTV) and Hop stunt viroid (HSVd), the casual agents of citrus tristeza and cachexia, together with the plant mRNA as an internal control for citrus certification in the country. Materials and Methods: Total RNA was extracted from healthy CTV- and HSVd- infected citrus tissues and subjected to cDNA synthesis by M-MuLV H- reverse transcriptase, followed by optimization of simplex, diplex and multiplex RT-PCR (s-, d-, and mRT-PCR). Amplified fragments were further sequenced for evaluation of the accuracy of the assays. Results: CTV, HSVd and the plant internal control (Nad 5 gene) were successfully amplified in all assays and the sequence information revealed the accuracy of all assays in citrus certification programs. Conclusion: Results from the developed s-, d-, and mRT-PCR assays revealed these detection methods as excellent candidates for citrus certification. http://journal.isv.org.ir/article-1-75-en.pdf 2014-11-07 28 33 10.21859/isv.5.3.28 Citrus Tristeza Disease Multiplex RT-PCR Assay Cachexia Disease M Naderpour 1 Seed and Plant Certification Research Institute, Karaj, Iran AUTHOR L Sadeghi 2 Seed and Plant Certification Research Institute, Karaj, Iran AUTHOR Z Nouri 3 Department of Biotechnology, Faculty of Agriculture, Science and Research Unit, Islamic Azad University, Tehran, Iran AUTHOR A Kavand 4 Seed and Plant Certification Research Institute, Karaj, Iran AUTHOR

ORIGINAL_ARTICLE Background and Aims: Primary infections of rubella and human cytomegalovirus (HCMV) can lead to severe complications in pregnancy. The screening of Rubella and HCMV in pregnant women is not routinely carried out in Iran. This cross sectional study aimed to investigate the seroprevalence of HCMV and rubella infections in neonates with and without congenital defects. Materials and Methods: This study was carried out in four provinces of Iran including Mazandaran, Hormozgan, Yazd, and Kerman. Demographic data were collected through questioners and samples were taken from umbilical cord bloods of 182 and 387 neonates with and without congenital defects, respectively. To detect HCMV and rubella infections we measured IgG and IgM antibodies using ELISA and HI which were used for measurement of anti-rubella total antibodies. Results: The prevalence of anti-HCMV IgG antibody was found to be around 90%, while 7.14% of neonates with congenital defects were positive for anti-HCMV IgM antibody compared to 2.84% of control group (p< 0.05). Anti-rubella total antibody was found in 85% and rubella IgM seropositivity rate was 0.5%. Conclusion: Although not for rubella, the significant correlation found between HCMV IgM positivity and congenital defects highlights the importance of these infections during pregnancy. Routine screening for rubella and HCMV should be introduced for pregnant women in our setting. Although mass rubella vaccination program is introduced in our system since 2004, preventive measures should be taken to decrease the mortality and morbidity related to primary HCMV infections. http://journal.isv.org.ir/article-1-76-en.pdf 2014-11-07 34 39 10.21859/isv.5.3.34 Rubella congenital malformations maternal antibodies neonates SM Marashi 1 Virology center, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran AUTHOR H Tabatabaei 2 Virology center, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran AUTHOR M Mahmoodi 3 Epidemiology Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran AUTHOR R Nategh 4 Virology center, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran AUTHOR T Mokhtari-Azad 5 Virology center, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran AUTHOR