Prevalence of avian influenza, Newcastle disease, and infectious bronchitis viruses in broiler flocks infected with multifactorial respiratory diseases in Iran, 2015-2016

Epidemiological distribution of respiratory viral pathogens in marketable vaccinated broiler chickens in five governorates in the Nile Delta, Egypt, from January 2022 to October 2022

Background and Aim

Respiratory viral infections significantly negatively impact animal welfare and have significant financial implications in the poultry industry. This study aimed to determine the frequency of the most economically relevant respiratory viruses that circulated in Egyptian chicken flocks in 2022.

Materials and Methods

Chickens from 359 broiler flocks in five different Egyptian governorates in the Nile Delta (Beheira, Gharbia, Giza, Monufiya, and Qalyoubia) at marketing time (33-38 days of age) were used in this study. Combined oropharyngeal and cloacal swabs and tissue samples were collected from clinically diseased or freshly dead birds suffering from respiratory disease. Avian influenza (AI)-H5, AI-H9, Newcastle disease (ND), and infectious bronchitis virus (IBV) were analyzed by reverse transcriptase polymerase chain reaction.

Results

Of the 359 flocks examined, 293 tested positive, whereas 66 were completely negative for the four viruses evaluated, with the highest positive results in Beheira. Out of 293 positive flocks, 211 were positive for a single virus, with Beheira having the highest rate, followed by Qalyoubia, Giza, and Monufiya. ND virus (NDV) was found to be the highest across all governorates, followed by IBV, AI-H9, and AI-H5. A double infection was detected in 73 flocks with either H9 or ND, or both H9 and IB could coinfect each other. The most common viral coinfections were H9 + IB, ND + IB, and ND + H9. Giza had the highest prevalence of ND + H9, H9 + IB, and ND + IB coinfection in the governorates, followed by Monufiya and Beheira. Only six out of 359 flocks were tribally infected with ND + H9 + IB in Giza, Monufiya, and Beheira governorates. On the basis of the number of flocks and the month of the year, July had the lowest number of flocks (23), while September and October had the highest number (48 flocks). Positive flock numbers were highest in October and lowest in January.

Conclusion

From January to October 2022, prevalent respiratory viral infections (H5N1, NDV, H9N2, and IBV) were detected in broiler chickens across the Delta area governorate, according to the findings of the present study. In addition, IBV and H9, either alone or in combination, significantly contributed to the respiratory infection observed in broiler chickens. Regardless of the type and origin of the vaccine used, it is not possible to protect broiler chickens from the development of the infection and the subsequent dissemination of the virus into the poultry environment. In the presence of face-infectious field virus mutations, poultry vaccinations must be regularly reviewed and updated, and poultry farms must take further biosecurity measures.

A Quick Review of the Prevalence of Important Infectious Poultry Diseases all Around the World

The poultry industry is one of the fastest growing industries in the world. Poultry breeding has developed significantly to meet the food needs of the increasing population and it is expected that this growth will continue in the coming years. Prevalent poultry diseases are of great importance as they are responsible for vast economic losses and public health concerns. They also affect the national and international trade of the poultry products. This review will provide a quick and general view of different important poultry diseases for poultry breeders, scientists and decision makers. Based on this review, Campylobacteriosis and infectious bursal disease (IBD) in the Asian continent, and Campylobacteriosis, Newcastle disease (ND) and coccidiosis in the African continent were the most prevalent diseases. In Europe, Campylobacter species and in America, Escherichia coli species are widespread in poultry meat. Infectious Bronchitis (IB) in Europe and Coccidiosis in America were high-incident.

The role of Newcastle Disease Virus in Broiler Chickens with High Mortality of Kerman Province

The Newcastle disease virus (NDV) is a member of the paramyxoviridea family and has great significance in the poultry production industry, which spends a huge amount of money every year on prevention and economic loss caused by this disease. A wide range of symptoms, including respiratory and nervous disorders, as well as hemorrhage lesions in the digestive system are observed in this disease. This research investigated the presence of NDV in 10 poultry farms with high mortality and respiratory symptoms in Kerman province, Iran (between January 2020 to October 2020). Tissue samples were collected from mortalities of 10 flocks in different parts of Kerman province and inoculated into embryonated eggs. The NDV was detected in the allantoic fluid by polymerization of partial F gene protein. The virus was positive in the samples of 5 flocks. The results of the phylogenetic analysis also showed that the sequence of isolates was related to genotype II (three isolates) and sub-genotype VIId (two isolates) of NDVs. It was also found that the amino acid sequences of sub-genotype VIId isolates in the 113 to 116 positions were RRQKR and in the 117 positions was the presence of F (phenylalanine). The other three isolates were grouped with B1, Clone, and LaSota vaccines, and the amino acid sequence in the cleavage site included GRQGRL. The similarity between the studied isolates was 99.6%-98.4%. In this study, virulent viruses were isolated and tracked in broiler farms that were vaccinated with live and killed vaccines. It is recommended to pay more attention to designing the vaccination program.

Replication of infectious bronchitis virus (IBV) Delmarva (DMV)/1639 variant in primary and secondary lymphoid organs leads to immunosuppression in chickens

Infectious bronchitis virus (IBV) that primarily causes respiratory infection in chickens, disseminate to multiple body systems leading to pathology, results in economic losses to poultry industry. IBV replicates in the bursa of Fabricius (BF), Harderian gland (HG), cecal tonsils (CT), and spleen. The objective of this study was to investigate the immunosuppressive effect of IBV Delmarva (DMV/1639) variant in chickens. Specific pathogen free chickens were infected with the IBV DMV/1639 variant while maintaining an age-matched uninfected control group. At predetermined time points, subsets of the infected and control chickens were observed for changes in body weights and pathological changes. The histopathological lesions were observed in the CT and BF, with minimal lesions in the thymus and spleen. The mRNA expression of pro-inflammatory mediators suggested immunomodulation by IBV, favoring viral replication. Further studies are warranted to observe the functional impact of the IBV DMV/1639 variant's replication in immune organs.

Identification of an additional N-glycosylation site and thermostable mutations within the hemagglutinin-neuraminidase gene of the Newcastle disease virus belonging to the VII.1.1 sub-genotype

Newcastle disease virus (NDV) is considered one of the most devastating avian viral patho-gens affecting the avian population, and it causes a significant economic burden on the poultry industry worldwide. The study aimed to gain deeper understanding of the molecular and phylogenetic analyses of the complete hemagglutinin-neuraminidase (HN) coding region among NDV isolates. The samples were obtained from different parts of Iran from July 2017 to February 2020, were used for phylogenic analysis in this study. The results confirmed the predominance of sub-genotype VII.1.1, previously known as sub-genotype VIIL, which is circulating in commercial broiler farms of Iran. Identification of (a) an additional N-glycosylation site (NIS) at position 144; (b) mutations S315P and I369V which are related to increasing the viral thermostability; (C) cysteine residues at positions 123; (d) amino acid substitutions in the HN antigenic sites, especially the mutations I514V and E347Q, as well as the other mutant within HN binding sites of the VII.1.1 sub-genotype, suggests the idea that this new sub-genotype of NDV may possess a high level of pathogenicity and virulence compared to other NDV sub-genotypes. In conclusion, the results indicate the presence of an additional NIS at position 144, which may alter the virulence of the isolates. Furthermore, the presence of the thermostable mutations (S315P and I369V) and the other amino acid substitutions among the VII.1.1 sub-genotype isolates may have an impact on the vaccine immunity against this new NDV sub-genotype.

The use of RT-PCR in the diagnosis and differentiation of vaccine strains of chicken infectious bronchitis and Newcastle disease

Background

Infectious diseases of young and adult birds with respiratory syndrome are a significant deterrent to the development of industrial poultry farming due to decreased productivity and significant mortality. The only effective method of combating viral diseases is timely and targeted vaccination, which largely depends on laboratory diagnostic results.

Aim

This article aims to study the real-time reverse transcription polymerase chain reaction, (RT-PCR) which has the prospect of more effective diagnosis of vaccine strains of chicken infectious bronchitis and Newcastle disease.

Methods

The fastest and most accurate method for the differential diagnosis of pathogens in an associative viral infection is RT-PCR. The method proposed in the article for selecting primers for amplification made it possible to use this method for the simultaneous interspecies differential diagnosis of two or more viral agents, significantly accelerating their diagnosis.

Results

The correlation of the nucleotide sequence obtained from sequencing to a specific virus strain is complicated by the lack of a single nomenclature mechanism for separating genetic groups.

Conclusion

The results of this study will allow easy and fast typing of sequences into known and databased virus strains and avoid further confusion in the nomenclature of genetic groups in the future.

Pathogenic bacteria associated with outbreaks of respiratory disease in Iranian broiler farms

BACKGROUND

Multi-causal respiratory infections are more commonly observed than uncomplicated cases with single agents in the commercial poultry industry. Recently, increased mortality rates associated with respiratory clinical signs have been reported in Iranian broiler farms.

OBJECTIVES

The present study aimed to determine the spectra of avian mycoplasmas (Mycoplasma gallisepticum, MG and Mycoplasma synoviae, MS) and Ornithobacterium rhinotracheale (ORT) in the broiler farms with the multi-causal respiratory disease (MCRD) from 2017 to 2020.

METHODS

Trachea and lung tissue samples were collected from 70 broiler flocks presenting increased mortality and acute respiratory disease. MG, MS, and ORT were detected by performing polymerase chain reaction with primers complementary to the 16S rRNA, vlhA, and 16S rRNA genes, respectively.

RESULTS

Genetic materials of MG, MS, and ORT were detected in five, three, and five of the 70 flocks. Based on the phylogenetic analysis of the complete mgc2 coding sequences, all MG strains formed a distinct cluster along with other Iranian MG isolates. According to the phylogenetic analysis of the partial vlhA gene of MS strains, two isolates were located along with Australian and European strains. In addition, one of them displayed an out-group association with MS isolates from Jordan. Phylogenetic analysis of Iranian ORT strains using a partial sequence of the 16S rRNA gene showed a distinct group among the other ORT strains.

CONCLUSIONS

The results indicate that MG, MS, and ORT are not predominantly responsible for the MCRD. However, continuous monitoring of poultry flocks could be significant for obtaining valuable information related to different MG, MS, and ORT strains and designing effective control strategies.

The role of the major viral pathogens in a respiratory disease outbreak of broiler flocks in Eastern Iran

Background

Infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and avian influenza virus (AIV) H9N2 are major viral pathogens in broiler respiratory disease.

Aims

Following a respiratory disease outbreak and economic losses in eastern Iran 2020-2021, we investigated the role of major viral pathogens and the implemented vaccination programs.

Methods

Thirty-six respiratory disease affected broiler flocks in South Khorasan province were sampled, molecularly tested, and coinfections were investigated. The vaccination programs were obtained and the detected IBV were genotyped.

Results

IBV, virulent NDV, and AIV H9N2 were detected in twenty-five, seven, and seven flocks, respectively. IBV+AIV, IBV+NDV, and NDV+AIV coinfections were respectively detected in six, five, and one flocks. Most IBV infected flocks (84%) had been immunized with a live IBV-Mass vaccine. All NDV infected flocks and 14.2% of AIV infected flocks had been vaccinated. IBV genotyping showed a high prevalence of variant 2 (83.3%), followed by Mass-type (12.5%), and Q1-type (4.2%). Variant 2 IB viruses were widely distributed in the province and half of them were mostly similar to the ones that had been detected in northern neighboring province, Khorasan Razavi.

Conclusion

Single infection with variant 2 IBV was a major cause of the respiratory disease outbreak in which use of the Mass vaccine was probably not effective. The high coverage and multiple doses of vaccination against Newcastle disease possibly had reduced the prevalence of NDV. Considering the regional origin of IBV strains, strong biosecurity measures should be implemented and vaccination programs using appropriate vaccine strains should be used.

Investigation of respiratory disease outbreaks of poultry in Bangladesh using two real-time PCR-based simultaneous detection assays

For rapid and sensitive pathogen screening from field outbreaks, molecular techniques such as qPCR-based simultaneous detections are efficient. Respiratory diseases are the most detrimental diseases to the poultry industry and need to be addressed because of their major economic losses. In the current study, we have applied two different detection assays: one for simultaneous detection of avian influenza virus (AIV; M gene) and subtyping (H5, N1, H9, N2) using TaqMan probe chemistry (TaqMan multitarget) and another for simultaneous detection of Newcastle disease virus (NDV), infectious bronchitis virus (IBV), and infectious laryngotracheitis virus (ILTV) using SYBR Green chemistry (SYBR Green multitarget). Two individual qPCRs were conducted for the detection of four pathogens. Surveillance of tissue (n = 158) and oropharyngeal swab (206) samples from multiple poultry flocks during the years April 2020-July 2022 applying the TaqMan and SYBR Green multitarget qPCRs revealed that 48.9% of samples were positive for respiratory infections, of which 17.2% were positive for NDV, 25.5% were positive for AIV, 9.9% were positive for IBV, and only a single positive (0.3%) for ILTV. Among the AIV, 35% were highly pathogenic subtype H5N1 and 65% were low pathogenic subtype H9N2. Co-infections of 2-3 respiratory viruses were also accurately detected. Respiratory viral pathogens are quite common in Bangladeshi poultry and can be successfully detected using multitarget simultaneous real-time quantitative polymerase chain reaction (RT-qPCR) assays like those adopted in the current study. Increased mass surveillance, along with the molecular characterization of the circulating respiratory viruses, is crucial to control the epidemic and subsequently save the Bangladeshi poultry industry.

Concurrent Occurrence of Infectious Bursal Disease and Multicausal Respiratory Infections Caused by Newcastle Disease and Avian Metapneumovirus in Broilers

Control strategy of respiratory complex infections should address precipitating and predisposing causative agents in general and immunosuppressive agents in particular. In both clinical and subclinical forms, infectious bursal disease virus (IBDV) is one of the most immunosuppressive diseases of young chickens. This study aimed to investigate the concurrent occurrence of subclinical infectious bursal disease (IBD) and multicausal respiratory complex infections caused by Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) in broilers. In this study, 800 tissue samples (e.g., trachea, cecal tonsil, bursa of Fabricius, and spleen) and 400 sera samples were collected from broilers with confirmed respiratory signs selected from 20 broiler farms in west Azerbaijan province, Iran, from October 2018 to February 2019. Pathogens in the tissue samples were detected using RT-PCR for the VP2 gene of IBDV, F gen of NDV, and N gene of aMPV. The amplified products were sequenced afterward. At the end of the husbandry period, sera samples were used to detect antibodies against IBDV, aMPV, and NDV using ELISA and HI tests. Molecular results showed that the 45% (9/20), 30% (6/20), and 15% (3/20) of tissue samples were positive for IBDV, NDV, and aMPV, respectively. Regarding co-infection, 5% (1/20) of farm isolates were positive for IBD and ND, while 10% (2/20) of farms isolates were positive for IBD and aMPV. Co-infection of IBD, ND, and aMPV was not detected in farm isolates. Serological results indicated that the IBD co-infected flocks had almost higher (P<0.05) antibody titers against IBD; however, IBDV-NDV co-infected flocks and IBDV-aMPV co-infected flocks had lower antibody titer against NDVand aMPV, respectively. It can be concluded that lower antibody titer against ND and aMPV in IBD-ND and IBD-aMPV co-infections indicated suppressive effects of IBD on these diseases. Therefore, vaccination against IBD even in regions without clinical form of IBD is inevitable for the reduction of immunosuppressive effects of subclinical IBD on immune responses against these diseases.

Interference between avian corona and influenza viruses: The role of the epithelial architecture of the chicken trachea

Respiratory viral infections are among the major causes of disease in poultry. While viral dual infections are known to occur, viral interference in chicken airways is mechanistically hardly understood. The effects of infectious bronchitis virus (IBV) infection on tissue morphology, sialic acid (sia) expression and susceptibility of the chicken trachea for superinfection with IBV or avian influenza virus (AIV) were studied. In vivo, tracheal epithelium of chickens infected with IBV QX showed marked inflammatory cell infiltration and loss of cilia and goblet cells five days post inoculation. Plant lectin staining indicated that sialic acids redistributed from the apical membrane of the ciliated epithelium and the goblet cell cytoplasm to the basement membrane region of the epithelium. After administration of recombinant viral attachment proteins to slides of infected tissue, retained binding of AIV hemagglutinin, absence of binding of the receptor binding domain (RBD) of IBV M41 and partial reduction of IBV QX RBD were observed. Adult chicken trachea rings were used as ex vivo model to study the effects of IBV QX-induced pathological changes and receptor redistribution on secondary viral infection. AIV H9N2 infection after primary IBV infection was delayed; however, final viral loads reached similar levels as in previously uninfected trachea rings. In contrast, IBV M41 superinfection resulted in 1000-fold lower viral titers over the course of 48 h. In conclusion, epithelial changes in the chicken trachea after viral infection coincide with redistribution and likely specific downregulation of viral receptors, with the extend of subsequent viral interference dependent on viral species.

Root-preferential expression of Newcastle virus glycoproteins driven by NtREL1 promoter in tobacco hairy roots and evaluation of oral delivery in mice

Newcastle disease virus (NDV) is a lethal virus in avian species with a disastrous effect on the poultry industry. NDV is enveloped by a host-derived membrane with two glycosylated haemagglutinin-neuraminidase (HN) and Fusion (F) proteins. NDV infection usually leads to death within 2-6 days, so the preexisting antibodies provide the most critical protection for this infection. The HN and F glycoproteins are considered the main targets of the immune system. In the present study, two constructs harboring the HN or F epitopes are sub-cloned separately under the control of a root-specific promoter NtREL1 or CaMV35S (35S Cauliflower Mosaic Virus promoter) as a constitutive promoter. The recombinant vectors were transformed into the Agrobacterium tumefaciens strain LBA4404 and then introduced to tobacco (Nicotiana tabacum L.) leaf disk explants. PCR with specific primers was performed to confirm the presence of the hn and f genes in the genome of the regenerated plants. Then, the positive lines were transformed via non-recombinant A. rhizogenes (strain ATCC15834) to develop hairy roots.HN and F were expressed at 0.37% and 0.33% of TSP using the CaMV35S promoter and at 0.75% and 0.54% of TSP using the NtREL1 promoter, respectively. Furthermore, the mice fed transgenic hairy roots showed a high level of antibody responses (IgG and IgA) against rHN and rF proteins.

Molecular characterisation and phylogenetic study of the fusion gene of Newcastle disease viruses isolated from broiler farms of Iran in 2018-2019

Avian orthoavulavirus, commonly known as Newcastle disease virus (NDV) has been a constant threat for the poultry industry of Iran for decades. Recently, a couple of preliminary studies on backyard and commercial chicken suggested that a major subgenotype circulating in Iran may be VII(L) subgenotype, which is now known as VII.1.1 according to the new classification system. The unique subgenotype was not reported from other parts of the world and was slightly (≥3%) different from the closest group that was VIId. The study was conducted between July 2018 and March 2019 to determine the exact NDV genotypes/subgenotypes circulating in Iranian broiler poultry farms; five-hundred and forty chickens were sampled from thirty-six broiler farms located in eighteen provinces of Iran. As other genotypes/subgenotypes such as XIII and VI.2 are circulating in neighbouring countries, border provinces were also sampled. The F gene of the NDV isolates was sequenced and phylogenetic analysis was conducted. All the isolates clustered under the VII.1.1 group. The evolutionary analysis also revealed that the distances were between 0.0 and 0.7% meaning that the Iranian NDV circulating in broiler farms were not only of VII.1.1 sub-genotype, but also genetically very identical, indicating that the routine control measures for ND in Iran were not able to prevent the circulating NDVs. Although stricter biosecurity measures have been really effective in developed countries, surveillance of NDV to determine the circulating genotypes might also help us to implement better vaccination strategies in the future.

Concurrent occurrence of infectious bursal disease and respiratory complex caused by infectious bronchitis and avian influenza (H9N2) in broilers

Infectious bursal disease (IBD) virus is considered one of the commonest immunosuppressive diseases in chickens. The aim of this study was to investigate the concurrent occurrence of subclinical IBD in respiratory complex infections caused by avian influenza (AI, H9N2) virus and infectious bronchitis (IB) virus in broilers. During this study, 800 tissue samples of the trachea, caecal tonsil, spleen, and bursa of Fabricius and 400 blood samples were collected from 20 respiratory complex infected flocks. Detection of pathogens in the tissue samples was performed by RT-PCR for amplification of the VP2 gene of IBD, HA region of AI, and S1 gene of IB viruses. The amplified products were subjected to nucleotide sequence analysis. Blood samples were also tested for the detection of antibodies against IBV by using ELISA and against AIV via using the HI test. Molecular results showed that the tissue samples were positive for field isolates of subclinical IBD (45%), IB (45%), and AI-H9N2 (25%). Co-infections of IBD and IB (30%), IBD and AI (20%), and IBD, IB, and AI (5%) were also detected. Serological results indicated that subclinical IBD infected flocks had lower (P<0.05) antibody titres against IB and AI. In conclusion, prior exposure of broilers to IBD virus increased the incidence of respiratory complex caused by IBV and AIV in broilers, and vaccination against IBD is inevitable to reduce subclinical IBD to minimise the incidence/severity of respiratory complex diseases via improving immune responses to commonly used vaccines in broilers.

Characterization of Newcastle disease virus in broiler flocks with respiratory symptoms in some provinces of Iran

BACKGROUND

Newcastle disease, is one of the most important diseases of the poultry industry, has many economic losses. The aim of this study was to isolate and determine the molecular identity of Newcastle disease virus in 40 broiler flocks with respiratory symptoms in four provinces of Iran.

METHODS AND RESULTS

Samples of farms with respiratory symptoms were collected from different regions of Isfahan, East Azerbaijan, Golestan, and Khuzestan provinces and inoculated into 9-day-old embryonated chicken eggs. The Reverse-transcription polymerase chain reaction (RT-PCR) was performed to detect the Newcastle disease virus in allantoic fluid. Of the 40 flocks, the virus was isolated and identified in 16 flocks. The PCR products of 16 isolates were sequenced, and a phylogenetic tree was drawn. Accordingly, six isolates were in genotype II and ten isolates were in subgenotype VII.1.1 (VIId) of class II.

CONCLUSION

Both genotypes were present in all four provinces. The isolates of Khuzestan province showed the greatest diversity compared to the other three provinces. The similarity of isolates belonging to genotype II in this study was observed with Pakistan, China, and Nigeria, and other isolates were similar to previous isolates in Iran. Also, the highest amino acid sequence in the F-protein cleavage site was 112RRQKR/F117 for VII.1.1 (VIId) genotype isolates and 112GRQGR/L117 for II genotype isolates.

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 of 4/91 Infectious Bronchitis Virus Leading to Studies of Pathogenesis and Host Responses in Laying Hens

Infectious bronchitis virus (IBV) initially establishes the infection in the respiratory tract and then spreads to other tissues depending on its virulence. During 2011–2018, the 4/91 IBV strain was isolated from poultry flocks affected by decreased egg production and quality in Eastern Canada. One of the Canadian 4/91 IBV isolates, IBV/Ck/Can/17-038913, was propagated in embryonated chicken eggs and molecularly characterized using whole genome sequencing. An in vivo study in laying hens was conducted to observe if IBV/Ck/Can/17-038913 isolate affects the egg production and quality. Hens were infected with IBV/Ck/Can/17-038913 isolate during the peak of egg lay, using a standard dose and routes maintaining uninfected controls. Oropharyngeal and cloacal swabs were collected at predetermined time points for the quantification of IBV genome loads. At 6 and 10 days post-infection, hens were euthanized to observe the lesions in various organs and collect blood and tissue samples for the quantification of antibody response and IBV genome loads, respectively. Egg production was not impacted during the first 10 days following infection. No gross lesions were observed in the tissues of the infected birds. The IBV genome was quantified in swabs, trachea, lung, proventriculus, cecal tonsils, kidney, and reproductive tissues. The serum antibody response against IBV was quantified in infected hens. In addition, histological changes, and recruitment of immune cells, such as macrophages and T cell subsets in kidney tissues, were measured. Overall, data show that IBV/Ck/Can/17-038913 isolate is not associated with egg production issues in laying hens infected at the peak of lay, while it demonstrates various tissue tropism, including kidney, where histopathological lesions and immune cell recruitments were evident.

Generation of ssDNA aptamers as diagnostic tool for Newcastle avian virus

Aptamers are short single-stranded DNA (ssDNA), RNA or synthetic XNA molecules, which are used as a class of affinity binders recognizing target molecules with a very high affinity and specificity. The aim of this study was to generate and characterize ssDNA aptamers for the detection of Newcastle disease virus (NDV). These aptamers were selected using systematic evolution of ligands by exponential enrichment (SELEX) in combination with quantitative high-throughput DNA sequencing. After three rounds of selections, a highly enriched ssDNA pool was sequenced, and the results were analyzed using FASTAptamer Toolkit. Sequencing reads were sorted by copy numbers and clustered into groups, according to their sequence homology. Top aptameric sequences were used to develop a sandwich enzymatic linked aptamer assay (ELAA) for rapid and sensitive detection of NDV in farm samples. The selected aptamers have an affinity within the nanomolar range, and a high specificity with no cross-reactivity towards other avian viruses. Following optimization of the sandwich ELAA method, the results demonstrated that both selected aptamers Apt_NDV01 and Apt_NDV03 with dissociation constant values of 31 nM and 78.1 nM, respectively, showed the highest specificity and affinity for NDV detection. The ELAA results were verified by quantitative real-time PCR, demonstrating strong concordance, and showing outstanding accuracy for detection of NDV in field sample. In summary, combination of SELEX with high-throughput DNA sequencing allowed rapid screening and selection of aptamers. The selected aptamers allowed recognition of NDV with high affinities. This is the first report that uses a validated sandwich ELAA for rapid and specific detection of NDV in poultry samples.

Reverse transcription recombinase-aided amplification assay combined with a lateral flow dipstick for detection of avian infectious bronchitis virus

The study was conducted to develop a specific, simple, and sensitive method for diagnosis of avian infectious bronchitis virus (IBV). In this experiment, the selected downstream primer was labeled with biotin and the 5′ end of RAA probe was labeled with FAM by reverse transcription recombinase-aided amplification (RT-RAA) combined with lateral flow dipstick (LFD). A RT-RAA-LFD assay that could be used for detection of IBV was established after optimization of RT-RAA reaction time, reaction temperature, and primer concentration. This method did not need reverse transcription of IBV template under isothermal condition (37°C), the amplification of target gene fragments could be completed within only 24 min, and the amplification products could be visually observed and determined by LFD within 3 min. The specificity test demonstrated that there was no cross reaction with the nucleic acids of other similar common pathogens. The lowest detectable limit for IBV was 10² copies/μL, and this method was 100 times more sensitive than conventional PCR (10⁴ copies/μL), as verified by sensitivity test. The results showed that RT-RAA-LFD assay with strong specificity and high sensitivity was simple and easy to operate, and could be used for rapid detection of IBV in clinical diagnosis.

Comparative clinico-pathological assessment of velogenic (sub-genotype VIIi) and mesogenic (sub-genotype VIm) Avian avulavirus 1 in chickens and pigeons

Newcastle disease (ND), caused by virulent Avian avulavirus 1 (AAvV 1), affects a wide range of avian species worldwide. Recently, several AAvVs of diverse genotypes have emerged with varying genomic and residue substitutions, and subsequent clinical impact on susceptible avian species. We assessed the clinico-pathological influence of two different AAvV 1 pathotypes [wild bird originated-velogenic strain (sub-genotype VIIi, MF437287) and feral pigeon originated-mesogenic strain (sub-genotype VIm, KU885949)] in commercial broiler chickens and pigeons. The velogenic strain caused 100% mortality in both avian species while the mesogenic strain caused 0% and 30% mortality in chickens and pigeons, respectively. Both strains showed tissue tropism for multiple tissues including visceral organs; however, minor variances were observed according to host and pathotype. The observed gross and microscopic lesions were typical of AAvV 1 infection. Utilizing oropharyngeal and cloacal swabs, a comparable pattern of viral shedding was observed for both strains from each of the infected individuals of both avian species. The study concludes a varying susceptibility of chickens and pigeons to different wild bird-originated AAvV 1 pathotypes and, therefore, suggests continuous monitoring and surveillance of currently prevailing strains for effective control of the disease worldwide, particularly in disease-endemic countries.

NDV subgenotype VII(L) is currently circulating in commercial broiler farms of Iran, 2017-2018

BACKGROUND

Based on our previous work, it was discovered that some Newcastle disease virus (NDV) isolates from backyard poultry between 2011 and 2013 in Iran formed a new separate cluster when phylogenetic analysis based on the complete F gene sequence was carried out. The novel cluster was designated subgenotype VII(L) and published.

AIM

In the current study, for further validation, we initiated a comprehensive epidemiological study to identify the dominant NDV genotype(s) circulating within the country. Collection of samples was executed between October 2017 and February 2018 from 108 commercial broiler farms which reported clinical signs of respiratory disease in their broilers.

RESULT

We report that 38 of the farms (> 35%) tested positive for NDV. The complete F gene sequences of seven of the isolates are shown as representative sequences in this study. According to the phylogenetic tree constructed, the recent broiler farm isolates clustered into the newly designated cluster VII(L) together with the older Iranian backyard poultry isolates in our previous work. All the sequences shared the same virulence-associated F cleavage site of ₁₁₂RRQKR↓F₁₁₇.

CONCLUSION

Our phylogenetic analysis suggested that the NDV subgenotype VII(L) may have been derived from subgenotype VIId, and contrary to popular belief, subgenotype VIId may not be the dominant subgenotype in Iran. Tracking of the subgenotype on BLAST suggested that the NDV subgenotype VII(L), although previously unidentified, may have been circulating in this region as an endemic virus for at least a decade. Other NDV genotypes, however, have also been reported in Iran in recent years. Hence, ongoing study is aimed at determining the exact dominant NDV genotypes and subgenotypes in the country. This will be crucial in effective mitigation of outbreaks in Iranian broiler farms.