Protection of animals against devastating RNA viruses using CRISPR-Cas13s.

The intrinsic nature of CRISPR-Cas in conferring immunity to bacteria and archaea has been repurposed to combat pathogenic agents in mammalian and plant cells. In this regard, CRISPR-Cas13 systems have proved their remarkable potential for single-strand RNA viruses targeting. Here, different types of Cas13 orthologs were applied to knockdown foot-and-mouth disease virus (FMDV), a highly contagious disease of a wide variety of species with genetically diverse strains and is widely geographically distributed. Using programmable CRISPR RNAs capable of targeting conserved regions of the viral genome, all Cas13s from CRISPR system type VI (subtype A/B/D) could comprehensively target and repress different serotypes of FMDV virus. This approach has the potential to destroy all strains of a virus as targets the ultra-conserved regions of genome. We experimentally compared the silencing efficiency of CRISPR and RNAi by designing the most effective short hairpin RNAs according to our developed scoring system and observed comparable results. This study showed successful usage of various Cas13 enzymes for suppression of FMDV, which provides a flexible strategy to battle with other animal infectious RNA viruses, an underdeveloped field in the biotechnology scope.

The full genome characterization of avian encephalomyelitis virus, Iran: a vertical transmission case.

Avian encephalomyelitis (AE) is an important infectious poultry disease worldwide that is caused by avian encephalomyelitis virus (AEV). The causative virus can be transmitted both horizontally and vertically. In the present study, an AEV suspected outbreak with typical neurological signs occurred in broilers. Histopathological examination, RT-PCR assay and full genome sequencing were applied to confirm the presence of AEV. Phylogenetic analysis of the full genome sequence showed that the detected AEV strain at 7055 nucleotide length is classified in cluster I and is closely related to vaccinal USA and China originated isolates. Although, the outbreaks of AE in progeny of vaccinated breeders have been reported previously, the source of infection was unknown. Based on the results obtained in this study, the outbreaks are vaccine-originated. This study provides the first whole genome analysis of AEV from Iran and reveals that the AEV possesses a hepatitis C virus-like internal ribosome entry site.

Whole-genome characterization of avian picornaviruses from diarrheic broiler chickens co-infected with multiple picornaviruses in Iran.

Gastrointestinal symptoms in poultry are caused by several factors, such as infecting viruses. Several avian picornaviruses can cause diarrhea in these valuable animals. Poultry flocks in Iran suffer from gastrointestinal diseases, and information on picornaviruses is limited. In this study, two genera of avian picornaviruses were isolated from poultry and identified by the viral metagenomics. Fecal samples were collected from broiler chicken flocks affected with diarrhea from Gilan province Iran. The results showed that Eastern chicken flocks carried two genera of picornaviridae belonging to Sicinivirus A (SiV A) and Megrivirus C (MeV C). The Western chicken flocks carried SiV A based on whole-genome sequencing data. SiV A had type II IRES and MeV C contained a type IVB IRES 5'UTR. Phylogenetic results showed that all these three picornaviruses were similar to the Hungarian isolates. Interestingly, two different picornavirus genera were simultaneously co-infected with Eastern flocks. This phenomenon could increase and facilitate the recombination and evolution rate of picornaviruses and consequently cause this diversity of gastrointestinal diseases in poultry. This is the first report and complete genome sequencing of Sicinivirus and Megrivirus in Iran. Further studies are needed to evaluate the pathogenic potential of these picornaviruses.

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

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.

Molecular characterization of a pigeon paramyxovirus type 1 virus isolated from Eurasian collared doves in Iran, 2017.

In September 2017, an outbreak with high mortality, which showed the typical signs of ND, occurred among a flock of more than 2000 Eurasian collared doves in Konarak, southeast of Iran. A confirmed pigeon paramyxovirus type 1 strain was isolated from the brain tissues of the dead doves. The isolate, which was called Pigeon/Iran/Konarak/Barin/2017, was classified as a highly velogenic NDV. Complete genome sequencing and phylogenetic analysis showed that the isolate belonged to subgenotype XXI.2, which has never been reported from Iran before. The isolate had the highest homology (96.15%) with early 2010s Italian isolates. Further studies will be required to understand the diversity better.

Complete genome sequence of Himetobi P strain Sh.Moghaddam, isolated from the Laodelphax striatellus (small brown planthopper).

OBJECTIVE: Himetobi P virus (HiPV) is an insect virus belonging to the genus Cripavirus in the Dicistroviridae family within the Picornavirales order. Himetobi P strain. Sh.Moghaddam is the first study reported, was isolated from the Laodelphax striatellus (small brown planthopper) of an internal chicken organ in Iran. DATA DESCRIPTION: Genomic analysis showed a nucleotide identity of 93.16% with the family Dicistroviridae, genus Triatovirus, and species Himetobi P. The genome assembly comprised 9227 bp, with a 38.8% GC content. Annotation of the genome showed 2 ORF, a total of 2 genes: including 2 coding sequences (CDs) (total) and 8 Miss features. Thus, the whole-genome sequence presented in this study serves as a platform for detecting new genes that may contribute to the pathogenicity of the Himetobi P strain. Sh.Moghaddam.

Complete genome analysis of Iranian IS-1494 like avian infectious bronchitis virus.

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

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.