The tracheal virome of broiler chickens with respiratory disease complex in Iran: the metagenomics study

Background and Objectives: Avian respiratory disease complex (RDC) is one of the most detrimental economic diseases that affected different parts of the world. Various pathogens cause the disease, but the most significant viral pathogens include avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) are the most prevalent. To detect these pathogens, various methods have been discovered in the last decades. Detection and characterization of viruses by metagenomics methods have improved our knowledge about the role of virome in the avian complex respiratory disease. Materials and Methods: This research investigates the viral pathogen populations that mostly participate in emerging these diseases using the NGS method RNA-sequencing. In surveillance of ten broiler farms from different cities with respiratory symptoms, trachea samples were collected to determine the pathogenic virome causing the disease. Results: In this metagenomics analysis, nine viral families were identified, comprising 72.82% of RNA viruses, 24.32% of RT viruses, and 2.86% of DNA viruses. RNA viruses had the highest contribution to the respiratory disease complex instead of disease, including paramyxoviridae, orthomyxoviridae, coronaviridae, and picornaviridae viruses. Other viruses from the RNA viruses and DNA virus families were also identified in addition to these results. Conclusion: This research suggests that studies of pathogenic viromes in different diseases can help monitor different diseases and predict their future occurrence

MOLECULAR CHARACTERIZATION AND PHYLOGENETIC ANALYSIS OF AVIAN POX VIRUS ISOLATED FROM PET BIRDS AND COMMERCIAL FLOCKS, IN IRAN

Avian pox (AP) is a viral disease with a wide host range. The aim of the study was molecular identification and characterization of field isolated pox virus from pet birds and commercial flocks in Iran, by polymerase chain reaction (PCR). Scab materials of skin and mucosal lesions were collected from five clinically affected cases. PCR was used to amplify a 578 bp fragment of the poxvirus 4b core protein. In order to determine the genetic relationships among the viruses, this conserved poxvirus genetic region was sequenced and analyzed. The Iranian Avipoxvirus isolates in this study grouped in clade A1 (commercial chicken and turkey flocks) and B1 (canary). Further studies on a larger scale need to be developed to have a better understanding of the molecular characterization of the Iranian APV strains. Key words: avian pox; phylogenetic analysis; molecular characterization; Iran   MOLEKULARNA KARAKTERIZACIJA IN FILOGENETSKA ANALIZA AVIARNEGA VIRUSA POX, IZOLIRANEGA PRI PETIH VRSTAH PTIC V KOMERICIALNIH JATAH V IRANU Povzetek: Osepnice ptic (AP, iz angl. avian pox) so virusna bolezen, ki lahko okužijo veliko različnih vrst ptic. Cilj predstavljene raziskave je bila molekularna identifikacija in karakterizacija izoliranih virusov pox, pridobljenih iz krast ljubiteljskih ptic in farmskih ptic v Iranu, s pomočjo metode PCR. Vzorci krast s področja sprememb na koži in sluznicah je bil zbran pri petih pacientih s kliničnimi znaki bolezni. S pomočjo metode PCR je bil pomnožen 578 baznih parov dolg odsek gena poxvirusa 4b. To ohranjeno območje poxvirusa je pomembno za določitev genskih razmerij med virusi, zato je bilo doloćeno zaporedje DNK za nadaljne analize. Iranska izolata Avipoxvirusa objavljena v tej študiji sta bila razvrščena v razred A1 (komercialne piščančje in puranje jate) in B1 (kanarčki). Za boljše razumevanje molekularne karakterizacije iranskih sevov virusa AP bo potrebno opraviti nadaljnje študije. Ključne besede: osepnice ptic; filogenetska analiza; molekularna karakterizacija; Iran  

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

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

Phylogenetic analysis and genotyping of Iranian infectious haematopoietic necrosis virus (IHNV) of rainbow trout (Oncorhynchus mykiss) based on the glycoprotein gene

Abstract Background Infectious haematopoietic necrosis (IHN) is known as one of the most contagious systemic viral diseases in salmonids which can lead to significant mortality rates and negative impacts on the salmonid farming industry. Infectious haematopoietic necrosis virus (IHNV) was first detected in rainbow trout (Oncorhynchus mykiss) farms in Iran in 2003. Objectives We conducted the present study to determine the detection of IHN genotypes in rainbow trout (O. mykiss) in farms in the central parts of Iran, using molecular and phylogenetic techniques. Methods Samples were collected from fries exhibiting clinical signs such as darkening of the skin, abdominal swelling, and loss of appetite. Phylogenetic analysis was performed by the neighbour‐joining method, using MEGA 5.1 software. For phylogenetic analysis and genotyping of IHNV from central parts of Iran, the sequences of the glycoprotein gene were determined for two Iranian isolates (Jahad‐UT1 and Jahad‐UT2). Results Phylogenetic analysis revealed that the detected strains (Jahad‐UT1 and Jahad‐UT2 isolates) are closely related (97.23%–100%) to European isolates within genogroup ‘E’. Conclusions This finding indicates that Jahad‐UT1 and Jahad‐UT2 isolates have been widely transferred to Iran from European countries. Moreover, the nucleotide diversity of these Iranian isolates showed a close relationship with the North American and Asian isolates, although the Iranian isolates were collected from a smaller geographical area and within a shorter time period between 2014 and 2015

Predominance of Fourth Panzootic Newcastle Disease Virus Subgenotype VII.1.1 in Iran and Its Relation to the Genotypes Circulating in the Region

Following recent Newcastle disease virus (NDV) outbreaks in Iranian poultry farms which were mostly associated with lesions of the avian gastrointestinal tract, it was speculated that the scale of the outbreaks could be attributed in part to co-circulating infectious agents or a new NDV genotype/subgenotype. This speculation was due to the isolation of a few 5th panzootic subgenotype VII.2 viruses from Iranian poultry farms in 2017. Samples from different species of commercial and domestic birds were collected from different provinces of Iran, 19 of which were selected for the current study. Phylogenetic analyses showed that the recent outbreaks have been caused by only one agent, i.e. the distinctive NDV subgenotype VII.1.1 (previously known VIIl) viruses that seem to be circulating predominantly in Iran, but have also been sporadically reported from Iraq among neighbouring countries. At most, 96.3–96.7% BLAST identity to non-Iranian VII.1.1 isolates was observed. Genetic distance values of <1% were indicative of high similarity between the isolates, but the values were approaximately 2% when the current isolates were compared to the earliest recorded Iranian VII.1.1 viruses isolated in 2010. Using Bayesian analysis, annual mutation rates of 1.7156E-3 (strict) and 1.9902E-3 (relaxed) over 11 years were obtained. In addition, we report that our laboratories have not detected any genotype XIII strains since 2011. Following up on previous reports, we concluded that currently, and except in Columbiforms, subgenotype VII.1.1 may likely be the predominant subgenotype in many bird species in Iran despite the subgenotype VII.2 being predominant in neighbouring countries

Correction to: Predominance of Fourth Panzootic Newcastle Disease Virus Subgenotype VII.1.1 in Iran and Its Relation to the Genotypes Circulating in the Region

The original version of this article contained a mistake in the co-author names “Mohammad Sotani and Esameel Allahyari”. The correct co-author names should be Mohammad Soltani and Esmaeel Allahyari