Iranian Strains Research Articles

Crimean-Congo hemorrhagic fever cases in the North of Iran have three distinct origins.

An on-going surveillance program on Crimean-Congo haemorrhagic fever virus (CCHFV) in Iran has been launched since 2000. An outbreak of CCHF occurred in northern Iran between June and July 2015. Three cases were involved in this outbreak. One patient died after admission to hospital, and the others were treated successfully. Phylogenetic analysis showed that three sequences obtained from Iranian patients grouped within clade IV (Asia-1), clade V (Europe) and clade VI (Greece). The partial sequence of the strain Noshahr59 (KT588642) showed the highest similarity with other strains isolated from Russia, Kosovo and Turkey (Clade V, Europe). The genome sequence of the strain Chalous65 (KT588640) showed 100% homology to the strain AP29 isolated from Greece (DQ211638). The genome sequence of the strain Noshahr43 (KT588641) showed 88% similarity to the Pakistani and previously reported Iranian strains (AF527810, AJ538198, AY366379 and AY366373). These data support previous studies, which showed a distinct similarity between Iranian S segments of CCHFV strains with other strains within clade IV (Asia-1) and clade V (Europe). In addition, clade VI was detected for the first time in Iran. Moreover, strain Chalous65 with similar genetic characteristics to strain AP29 from Greece was isolated from a fatal human case.

Comparative genomic analysis of wide and narrow host range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of their pathogenicity and virulence factors

The causal agent of Asiatic citrus bacterial canker, Xanthomonas citri subsp. citri (Xcc), has three pathotypes: A, A* and Aw. A*-type strains have a restricted host range to Mexican lime and are classified into four subgroups, among which strains isolated from the Sistan-Baluchistan province in Iran have not been defined and reported anywhere else in the world. For comparative analysis, we determined the genome sequence of strain NIGEB-386 from this new A* subgroup. We also select complete genome sequences of XccA306 (type A strain), Xcaw12879 (type Aw strain) and draft genome sequences of two A* strains, XccA* LG115 (isolated from India) and XccA* JS581 (Iranian strain from other subgroups), from GenBank sequence databases. Approximately 98% of coding DNA sequences (CDSs) are shared by the three pathotype genomes and there are about 2% unique CDSs for each pathotype. XccA* NIGEB-386 and XccA* JS581 contain 28 putative Type III secretion system effectors; Xcaw12879 and XccA* LG115 contain 29; and XccA306 contains 27. Despite previous data on the presence of the AvrGf1 effector and its contribution to the host range limitation in Xcaw12879, the only effector gene is in XccA* LG115 and was not detected in two narrow host range Iranian strains. Additionally, the Lipopolysaccharide gene cluster of XccA* NIGEB-386 showed a high similarity to other host-limited strains, and significant differences with the broad host range strain, XccA306. Generally, Iranian A* strains show a close relationship together, while XccA* LG115 shares a close relationship with Xcaw12879.

Role of Plasticity Region Genes and cagE gene of cagPAI of Helicobacter pylori in Development of Gastrointestinal (GI) Diseases

Backround::Helicobacter pylori is a Gram-negative, micro aerophilic bacterium in the human stomach that is associated with the development of gastrointestinal ailments such as peptic ulcer (PU) and gastric cancer (GC). In the present study, plasticity region genes (jhp0940, jhp0945 and jhp0947) and and cagE gene of cag PAI were assessed independently and in combination for their ability to predict clinical consequences.Materials and Methods::A total of 211 strains which were isolated from patients with different gastrointestinal diseases (114 with non-atrophic gastritis, 59 with PU, and 38 with GC) were genotyped by PCR and sequencing. Data were collected and analyzed using SPSS software version 19. Logistic regression models were applied to determine relationships between the plasticity region genes and cagE of H.pylori and clinical status.Results::The cagE gene (71.1%) had the highest frequency and jhp0945 (13.7%) was the least abundant among the genes examined. The jhp0940 gene was significantly associated with GC (P = 0.0007), but not PU. On multiple logistic regression analysis, adjusted for both age and sex, the jhp0940 genotype was significantly associated with GC (odds ratio, OR = 2.8, 95%CI = 1.1–7.0; P = 0.027). The jhp0940+/ jhp0945+/jhp0947+ genotype was also linked to an increased risk of GC (OR = 50.4, 95%CI = 5.1–500.0; P = 0.0008) while no genotype correlation was found with PU in Iran (P > 0.05).Conclusions::Given the high frequency of cagE, this gene could be a suitable marker for the presence of cag PAI in Iranian strains. The jhp0940 genotype could also be a strong predictor of GC in Iran.

Molecular identification of formae specialis and racial identity in Iranian strains of Fusarium oxysporum f. sp. lycopersici: detection of avirulence genes

قارچ Fusarium oxysporum f. sp. lycopersici (Fol) عامل پژمردگی آوندی و یکی از مهم ترین عوامل بیماری زای گیاهی در ایران است. تاکنون چهار ژن مقاومت تک ژنی در گوجه فرنگی شناسایی شده اند که در تعیین نژاد این بیمارگر به کار گرفته می شوند. در مقابل ژن های غیربیماری-زایی Avr1، Avr2و Avr3 در نژادهای FOL شناسایی شده اند که در این بین Avr2 فقط در فرم اختصاصی FOL حضور دارد. از این رو سه ژن فوق می توانند نشانگرهای مناسبی جهت تشخیص فرم تخصصی و هویت نژادی در این عامل بیماری زا باشند. این فرضیه در جدایه هایی از کشورهای مختلف مورد بررسی قرار گرفته، ولیکن تاکنون در جدایه های ایرانی بررسی نشده است. هم چنین مطالعات قبلی نشان داده اند که یک جهش نقطه ای در Avr3 می تواند سبب افزایش توان بیماری زایی FOL در ارقام حساس گوجه فرنگی گردد. در این تحقیق به منظور شناسایی فرم تخصصی و هویت نژادی، ژن های Avr در مجموعه ای از جدایه های ایرانی مورد مطالعه قرار گرفت. نتایج حاصل نشان داد که این روش سنجش ملکولی در تفکیک جدایه های غیربیماری زا از جدایه های بیماری زا با توان بیماری زایی پایین بسیار موثر است. هم چنین براساس نتایج حاصل اکثر جدایه های مورد بررسی دارای ژنوتیپ غیربیماری زایی مشابه با نژاد یک بودند. علاوه براین به منظور بررسی این نکته که آیا تنوع آللی در Avr3 می تواند جدایه هایی با توان بیماری زایی مختلف را از یک دیگر تفکیک نماید، ژن فوق در جدایه هایی با توان بیماری زایی بالا و پایین تعیین توالی گردید. نتایج حاصل نشان داد که در جدایه-های ایرانی ارتباطی میان توان بیماری زایی آن ها و تنوع آللی در Avr3 وجود ندارد.

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

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.

Deep divergence and evidence for translocations between Iranian and European populations of the alfalfa weevil (Coleoptera: Curculionidae) based on mitochondrial DNA

AbstractThe alfalfa weevil (Hypera postica(Gyllenhal): Coleoptera: Curculionidae) is an invasive pest of alfalfa (Medicago sativaLinnaeus; Fabaceae) in the Holarctic region. Across the wide geographic distribution of the species different local adaptions have been observed. Further, several distinct mitochondrial lineages have been discovered, which have been treated as western and Egyptian/eastern strains. However, our knowledge of the biogeography ofH. posticais largely limited to North American and Japanese populations. We sampled the species from four locations in Iran and two countries in Europe (Poland and Czech Republic) and sequenced the mitochondrial COI gene to detect patterns of mitochondrial DNA divergence among Iranian and European strains. We detected two groups separated by a deep molecular split, even justifying the distinction of two molecular operational taxonomic units. Joint analyses with previously published sequences suggest that the European samples may represent the western strain, whereas both the western and Egyptian/eastern strains can be found in Iran. This distribution of genetic lineages may be the result of human-mediated translocations. The directionality, however, cannot be inferred. Our data suggest that translocations may have led to the coexistence of multipleH. posticalineages in some parts of the world,e.g., Iran. We discuss these findings against the background of the current taxonomy ofH. postica.

بررسی in silico پلیمرفیسم ژن Ta9 در سویه S15 رده سلولی شیزونت تیلریا آنولاتا واکسن ایران و جدایه‌های بومی

Bovine theileriosis is a tick-borne disease caused by obligate intracellular parasites related to the genus Theileria . Cellular immune responses protect cattle against pathogens through the activation of immune cells. Nowadays, live, attenuated vaccine of Theileria annulata (T. annulata ) is being produced in Iran and is recommended for active cattle immunization. Detection of the immunogenic antigens and epitopes recognized by CD8+ T Lymphocytes is vital for the development of recombinant and subunit vaccines. Herein, sequences of the genes encoding Ta9, which is an important antigen recognized by bovine CD8+ T cells specific for T. annulata, in Iranian S15 vaccine strains, several Iranian isolates, as well as reference Ta9 DNA sequences registered in GeneBank were compared through polymerase chain reaction (PCR). The obtained data from DNA sequences were analyzed by using Nucleotide, Blast n, BioEdit and IEDB softwares . The results showed high level of variation in nucleotides and amino acids level. The observed polymorphism in Ta9 gene sequences of Iranian vaccine strains and some isolates from Iran demonstrated that this antigen contains polymorphic sequences and is active along with the specific major histocompatibility complex (MHC) of the host. Polymorphic sequences and specific epitopes of Ta9 gene for CD8+ T cell provides an explanation for incomplete protection observed after inoculation of heterologous parasites in vaccinated cattle. These results have important implications for the application of Ta9 antigen for developing novel subunit vaccines.

Occurrence and Characterization of the Bacterial Spot Pathogen Xanthomonas euvesicatoria on Pepper in Iran

AbstractWe report in this study for the first time the occurrence of bacterial spot of pepper in Iran and both phenotypic and genetic characterization of its causal agent, Xanthomonas euvesicatoria. Pepper plants grown in 15 of 30 surveyed private gardens and commercial fields were infected by the pathogen in Marand County, East Azerbaijan Province, north‐western Iran. The obtained strains of X. euvesicatoria had different amylolytic and pectolytic activities compared with those reported for this species elsewhere. Pathogenicity tests showed that strains isolated from diseased pepper are able to infect tomato, in addition to pepper. Host range of the pathogen was assessed on eight annual plant species including crops and weeds by measuring the population dynamics. The host range assessment showed that in addition to pepper and tomato, known hosts of X. euvesicatoria, the Iranian strains were able to colonize a number of new hosts such as nightshade and common bean. In contrast, none of them were able to build up their population on cowpea, eggplant, bindweed and zucchini. All X. euvesicatoria strains obtained in this study were sensitive to copper sulphate and streptomycin at concentrations higher than 20 and 50 mg/l, respectively. Phylogenetic analyses of the strains using the sequences of gyrB and hrpB genes confirmed their species as X. euvesicatoria. Given a direct commercial trade of fresh solanaceous vegetables between Iran and Turkey, it is hypothesized that the pathogen entered north‐western Iran from eastern parts of Turkey through infected plant materials. Finally, the role of prevention – based on the use of healthy planting materials and resistant and/or tolerant plant varieties – to contain the potential disease epidemics is discussed.

Molecular detection of Crimean-Congo haemorrhagic fever virus in ticks collected from infested livestock populations in a New Endemic Area, South of Iran.

Crimean-Congo haemorrhagic fever (CCHF) is a viral zoonotic disease with potentially fatal systemic effects on man. We aimed to determine the presence of CCHF virus among collected ticks from domestic livestock from October 2012 to September 2013. A total of 1245 hard and soft ticks were collected from naturally infested ruminants in Marvdasht County, Fars Province, south of Iran. Nine tick species and one unidentified species in four disparate genera were detected. A total of 200 ticks were randomly selected and analysed by reverse transcription-polymerase chain reaction (RT-PCR) for the presence of CCHF virus genome. The viral genome was detected in 4.5% (9 samples) of the studied tick population. The infected ticks belonged to the species of Hyalomma marginatum' Hyalomma anatolicum and Rhipicephalus sanguineus. The viruses detected in these three tick species were clustered in the same lineage as Matin and SR3 strains in Pakistan and some other Iranian strains. These results indicate that the ticks were wildly infected with a genetically closely related CCHF virus in the region. Regular controls and monitoring of livestock to reduce the dispersion of ticks and providing information to those involved in high-risk occupations are urgently required.

Growth Parameters Evaluation and Identification of Growth Hormone Receptor Gene Polymorphisms in Various Strains of Rainbow Trout Oncorhynchus mykiss

In the present study, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and restriction fragment length polymorphism (RFLP) methods were compared to analyze the polymorphism of growth hormone receptor (GHR) gene in French, Iranian and Danish strains of Oncorhynchus mykiss. A monomorphic SSCP pattern of AA genotype in the French and Iranian strains and a dimorphic AA and AB genotype in the Danish strain were observed in 3' non-coding regions of GHR gene. In the Danish strain, the AB genotype polymorphism of the GHR gene with its very low frequency (5%) has no effect on the production trait. While, RFLP-Dde1 showed no polymorphism with genetic variation in the location of GHR. Moreover, comparing the condition factors (K) of three different rainbow trout strains showed a significant correlation between the French (1.312 ± 0.13), Iranian (1.245 ± 0.17) and Danish strains (0.763 ± 0.1), respectively (p<0.05). In particular, the French strain obtained a higher K compared to the two others. The length-weight relationship is shown by the following equations W= 0.013 × L2.921, W= 0.012 ×L3.023 and W= 0.007 × L3.176 for French, Iranian and Danish strains, respectively. With the mean (b= 2.921), the studied French strain exhibited a negative allometric growth b<3 while the Iranian (b=3.023) and the Danish (b=3.176) showed positive allometric growths. Regardless of the underlying mechanism(s) responsible for the different relationships, the results of this study suggested that the AA and AB genotypes polymorphism of the GHR gene are not associated with condition factor and environmental variables can influence condition factor and length-weight relationship of rainbow trout strains in this study.

Evaluation of genetic diversity among some commercial cultivars and Iranian wild strains of Agaricus bisporus by microsatellite markers

Agaricus bisporus (Lange) Imbach is the most widely cultivated mushroom in Iran. Lack of diversity in mushroom crops, especially where disease is concerned, creates a crucial risk for the currently grown cultivars. The aim of this study was to assess the genetic diversity among Iranian wild strains and some commercial cultivars by using microsatellite markers. Eighteen codominant microsatellite markers of A. bisporus (AbSSR) were used to distinguish 17 wild and commercial strains. All of the microsatellite markers used in this research gave clear banding patterns, and only one strain remained undistinguished. Among 106 generated alleles, the wild subgroup presented 53 alleles never found both in brown and white commercial cultivars, and 42 alleles never found in commercial brown strains. The dendrogram obtained by UPGMA clustering analysis separated A. bisporus strains into six groups. Based on our results, the high level of genetic diversity among Iranian wild strains, compared with the commercial strains, provides a new and promising source of diversity for A. bisporus breeding programs. To our knowledge this is the first relevant study of biodiversity in native Iranian populations of A. bisporus.

Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains.

BackgroundBovine coronavirus is a primary cause of neonatal calf diarrhea worldwide, and is also associated with acute diarrhea in adult cattle during the winter season. There are no reports on molecular characterization of bovine coronavirus in Ireland, and little data exists apart from serological studies.FindingsIn this study, 11 neonatal (mean age 9 days) calf BCoV strains from the south of Ireland were collected over a one year period and characterized using molecular methods. The spike gene which encodes a protein involved in viral entry, infectivity and immune response shows the most variability amongst the isolates and was subsequently selected for in depth analysis. Phylogenetic analysis of the spike gene revealed that the Irish strains clustered with novel BCoV strains from Europe in a unique clade, possibly indicating lineage partitioning. Direct analysis of alignments identified amino acid changes in the spike protein unique to the Irish clade.ConclusionThus, monitoring of bovine coronavirus in Ireland is important as the current isolates in circulation in the south of Ireland may be diverging from the available vaccine strain, which may have implications regarding future BCoV vaccine efficacy.

Analysis of Amino Acid Changes in NS Protein of Influenza A/(H3N2) Virus in Iranian Isolates

Aim: Roles of NS gene of influenza A virus in virulence and replication are well established but extent of its variation in seasonal influenza A (H3N2) viruses in Iran is not well known. Materials &amp; methods: NS gene of 37 (A/H3N2) virus isolates were sequenced and analyzed for information on genetic changes. Results: Data analysis of NS1 protein revealed two amino acid substitutions E26K and Q193R in almost all strains. Substitutions in T58P in 27.0%, A86S in 13.5% and each of V11G, M81I and P85T in 2.7% Iranian strains were also observed. Mutations in NS2/NEP protein were observed in K36E, Q101L and F107S. Conclusion: Many mutations were observed for the first time in Iranian strains. Their function remains to be determined.

Pathogenicity and mycotoxin chemotypes of Iranian Fusarium culmorum isolates on durum wheat, and comparisons with Italian and Syrian isolates

Fusarium isolates obtained from Iran and Italy were identified by morphological characters and confirmed by using species-specific PCR assays. The genetic chemotyping for each strain, as a preliminary assessment for trichothecene production, was defined using PCR. Subsequently, artificial infection on durum wheat (cv. Normanno) was carried out in the greenhouse to study the pathogenicity and aggressiveness of Iranian, Italian and Syrian F. culmorum strains, the causal agent of crown and root rot of wheat. All F. culmorum strains from Iran and Italy belonged to the 3-acetyl-deoxynivalenol (3Ac-DON) chemotype, while F. culmorum strains from Syria, previously characterized, belonged to the 3Ac-DON and nivalenol (NIV) chemotypes. All of the strains were pathogenic and caused typical Fusarium crown rot (FCR) symptoms. Italian and Iranian strains showed similar mean aggressiveness levels (19.1 and 18.7% respectively), while the mean aggressiveness level for Syrian strains was 11.8%. There were statistically significant differences among the strains. Two Italian strains, F383 and F1126, had the greatest level of aggressiveness while FC9 (Italian) and F961 (Syrian) were the least aggressive strains. No significant differences relating to agro-ecological origin were detected among Iranian, Italian and Syrian strains. This is the first genetic chemotyping characterization and comparison of F. culmorum strains, isolated from different agro-ecological countries, Iran, Syria (Middle East) and Italy (Europe), which has estimated their potential for producing mycotoxins, and the aggressiveness levels of F. culmorum for development of FCR. These results support the increasing concerns about the risk of FCR in many wheat producing countries, particularly in Iran and Syria.

Antioxidant capacity of several Iranian, wild and cultivated strains of the button mushroom.

The white button mushroom, Agaricus bisporus, is the most commonly grown mushroom in Iran; however, there is a significant shortage of research on its antioxidant activity and other medicinal properties. The aim of this study was to evaluate antioxidant capacity of the methanolic extracts from four cultivated strains and four Internal Transcribed Spacer (ITS)-identified, Iranian wild isolates of A. bisporus. Evaluations were made for total phenols, flavonoids and anthocyanins, and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity. Overall, results showed that all the wild isolates exhibited significantly lower DPPH-derived EC50, compared to the cultivated strains (p < 0.05). A relatively high relationship was observed between total phenols and flavonoids or anthocyanins (r2 > 0.60). However, these constituents could not statistically differentiate the group of wild samples from the cultivated ones, and there was low correlation with the DPPH-derived EC50s (r2 < 0.40). In conclusion, comparisons showed that wild isolate 4 and cultivated strains A15 and H1 had higher antioxidant capacity than the others (p < 0.05). This result identifies these mushrooms as good candidates for further investigation.

EPIYA motiefs of cagA and upper gastrointestinal diseases.

To the Editor In the April issue, Gastroenterology and Hepatology From Bed to Bench published a paper that focuses on the prevalence of EPIYA motiefs of cagA in Iranian patients and correlation with gastrointestinal disorders. Recently published research indicates that 56% of H. pylori isolated from Iranian patients carry cagA(1). It is not surprising that many H. pylori strains are cagA negative, but it should be noticed that the role of cagA in gastrointestinal cancers is still unclear. One of the first studies about EPIYA motifes is done by Shokrzadeh et al (2). Their study screened 190 patients, among them 141 patients (74.2%) were proven to be infected with H. pylori and 92 (73.6%) were positive for the cagA gene. To analyze the 3′-end variable region of the cagA gene in H. pylori isolated from Iranian population, they performed nucleotide sequencing of the cagA variable regions. Shokrzadeh et al. reported that 3' region of the cagA gene in Iranian strains is Western type. Although they had more samples of cagA positive H. pylori strains in comparison to that of the current study, they could not find any significant differences between EPIYA types and clinical outcomes. While the new research claim that the correlation between the presence of H. pylori EPIYA cagA motifs in the upper gastrointestinal diseases and clinical outcomes. Another study by our team (3) had similar results and could not find an association between the cagA status and clinical outcomes such as cancers in Iranian patients, which was in agreement with other studies in Iran (4, 5, 6,7). One more point that should be considered is about the western type of cagA EPIYA repeats or East Asian type repeats. The cagA gene is reported to be sub-typed based on the number of sequences of the repeat region in the 3′ region of the cagA gene (8, 9), and the cagA gene with multiple repeats and/or East Asian type repeats are reported to be more virulent than with fewer repeats and/or Western type repeats (8, 10). Another interesting point is about the prevalence of cagA, in published studies. The results showed that the prevalence of cagA-positive H. pylori in Shiraz is as high as in western countries. However, according to Baghaei et al. study we can add at this point that the reported prevalence is also similar to the eastern countries. Baghaei K et al, reported that among 231 H.pylori-positive patients, 154 (66.7%) patients were infected with the cagA-positive strains that is similar to the current studies and other countries such as Colombia, Cuba, china and neighbors of Iran, such as Turkey, Saudi and Iraq. Regarding the fact that Iranian cagA motiefs are western type, they cannot be really in related with severe gastrointestinal disorders like cancers. So it does not seem to be a reliable conclusion because of low samples size. However our previous studies with more cagA positive strains did not find any correlation between cagA repeats and cancer. Therefore, further studies will be necessary to investigate whether the cagA sub-typing is involved in the development of clinical outcomes among the Iranian population.

Analysis of the intactness of Helicobacter pylori cag pathogenicity island in Iranian strains by a new PCR-based strategy and its relationship with virulence genotypes and EPIYA motifs

Variants of the Helicobacter pylori cag pathogenicity island (cagPAI) and certain virulence genotypes have been proposed to be associated with different gastric disorders. In the present study, we designed a new PCR-based strategy to investigate the intactness of cagPAI in Iranian patients using highly specific primer sets spanning the cagPAI region. The possible relationship between the cagPAI status of the strains and clinical outcomes was also determined. We also characterized virulence genotypes (cagL, cagA, vacA, babA2 and sabA) and variants of CagA EPIYA motifs in these strains. H. pylori was detected in 61 out of 126 patients with various gastroduodenal diseases. The cagL, cagA, vacA s1m1, vacA s1m2, vacA s2m2, babA2, and sabA genotypes were detected in 96.7%, 85.2%, 29.5%, 45.9%, 24.6%, 96.7%, and 83.6% of the strains, respectively. Among the 52 cagA-positive strains, EPIYA motifs ABC, ABCC, ABCCC, and mixed types were orderly detected in the 39, 7, 1, and 5 strains. The cagPAI positivity included both intact and partially deleted, with the overall frequencies of 70.5% and 26.2%, respectively. The majority of the strains from patients with PUD (87.5%), gastric erosion (83.3%) and cancer (80%) presented an intact cagPAI, while a lower frequency of cagPAI intactness was detected in gastritis patients (61.1%). However, no significant relationship was found between the possession of intact cagPAI and clinical outcomes. Furthermore, we found that cagA and vacA s1m1 genotypes were significantly correlated with intact cagPAI (P=0.015 and P=0.012). A significant correlation was also found between EPIYA-ABC and intact cagPAI (P=0.010). The proposed PCR-based scheme was found to be useful for determining the intactness of cagPAI. Our findings also indicate that the cagPAI appears to be intact and rather conserved in majority of Iranian strains. Finally, our study proposed that H. pylori strains with partially deleted cagPAI were less likely to cause severe diseases in comparison with those carrying intact cagPAI.

In Silico Functional and Structural Characterization of H1N1 Influenza A Viruses Hemagglutinin, 2010-2013, Shiraz, Iran.

Hemagglutinin (HA) is a major virulence factor of influenza viruses and plays an important role in viral pathogenesis. Analysis of amino acid changes, epitopes' regions, glycosylation and phosphorylation sites have greatly contributed to the development of new generations of vaccine. The hemagglutinins of 10 selected isolates, 8 of 2010 and 2 of 2013 samples were sequenced and analyzed by several bioinformatic softwares and the results were compared with those of 3 vaccine isolates. The study detected several amino acid changes related to altered epitopes' sites, modification sites and physico-chemical properties. The results showed some conserved modification sites in HA structure. This study is the first analytical research on isolates obtained from Shiraz, Iran, and our results can be used to better understand the genetic diversity and antigenic variations in Iranian and Asian H1N1 pathogenic strains.

Characterization of Iranian nonaflatoxigenic strains of Aspergillus flavus based on microsatellite-primed PCR.

Out of fifty-two Iranian nonaflatoxigenic strains of Aspergillus flavus,collected from various substrates (soil and kernel) and sources (peanut, corn and pistachio), fifteen representatives were selected according to their different geographical origins (six provinces: Guilan and Golestan, Ardebil, Fars, Kerman and Semnan) and vegetative compatibility groups (VCGs, IR1 to IR15) for microsatellite-primed PCR analysis. Two inter-simple sequence repeat (ISSR) primers AFMPP and AFM13 were used to determine polymorphism and the relationship among strain isolates. A. flavus isolates were identified by their morphologies and their identities were confirmed by PCR amplification using the specific primer pair ITS1 and ITS4. The results revealed variations in the percentages of polymorphisms. In the ISSR analysis, primers AFMPP and AFM13 generated a total of 18 and 23 amplicons among the fungal strains, out of which 12 (66.7%) and 22 (95.7%) were polymorphic, respectively. Cluster analysis of the ISSR data was carried out using 1 D DNA gel image analysis. The two dendrograms obtained through these markers showed six different clusterings of testing nonaflatoxigenic A. flavus L strains, but we noticed that some clusters were different in some cases. The microsatellite-primed PCR data revealed that the Iranian nonaflatoxigenic isolates of A. flavus were not clustered according to their origins and sources. This study is the first to characterize Iranian nonaflatoxigenic isolates of A. flavususing ISSR markers.

In silico phylogenetic analysis of Vibrio cholerae isolates based on three housekeeping genes.

Vibrio cholera, a gram-negative bacterium, has been categorised into clinical and environmental species. Phylogenetic studies have been performed to investigate the relationships of the V. cholerae populations in worldwide. In this study, phylogenetic relationship between V. cholerae isolates from Iran and other regions of the world was determined, based on three housekeeping genes analysis. Results for Iranian strains showed that congruency of asd and hlyA phylogenetic trees were remarkably higher than recA tree. Iranian strains displayed 2-3%, 1-14% and 3-5% deference in asd, hlyA and recA nucleotide sequences, respectively. Sequence similarity degrees were variable between Iranian and other region's strains. Furthermore, the non-congruence in the phylogeny of the pathogenic clones in cladograms is probably due to horizontal gene transfer. Finally, results of this study suggest that monitoring of surface waters for housekeeping genes of V. cholerae in the cholera endemic areas may be valuable for forecasting the expected cholera outbreaks.