Avian Respiratory Coinfection and Impact on Avian Influenza Pathogenicity in Domestic Poultry: Field and Experimental Findings

The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases

Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

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.

Molecular detection of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks

Respiratory tract infections are of serious concern to the poultry industry. The present study was aimed to delineate the extent of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks. A total of 146 poultry flocks of Haryana and Rajasthan, India, suspected for chronic respiratory disease (CRD) were screened for avian mycoplasmas, Newcastle disease virus (NDV), infectious bronchitis virus (IBV), and avian pathogenic Escherichia coli (APEC) by conventional polymerase chain reaction (PCR) assays. A total of 49.31% (72/146) flocks were found positive for Mycoplasma infection. Of the Mycoplasma-positive flocks, 80.55% (58/72) represented pathogenic avian mycoplasmas (MG and/or MS), while 19.44% (14/72) flocks were positive for commensal avian mycoplasmas (other than MG and MS). A correlation was deduced between avian mycoplasmosis and bacterial and/or viral co-infections. The results revealed that 17.24% (10/58) flocks had only avian mycoplasmosis infection. However, in the remaining flocks, the avian mycoplasmosis was associated either with APEC infection [17.24% (10/58)], IBV infection [43.10% (25/58)], or both APEC and IBV infections [22.41% (13/58)], respectively. Further epidemiological studies on respiratory avian mycoplasmosis associated concurrent infections with other pathogens are recommended to assess circulating strains, risk factors, and economic losses.

Evaluation of inactivated avian influenza virus and Newcastle disease virus bivalent vaccination program against newly circulated H5N8 and NDV strains

Avian influenza virus (AIV) and Newcastle disease virus (NDV) are respiratory illness syndromes that have recently been detected in vaccinated flocks and are causing major financial losses in the chicken farming industry. The objective was to evaluate the efficacy of Valley Vac H5Plus NDVg7 vaccine in protecting chickens against the H5N8 and NDV strains that have recently been circulating in comparison with the efficacy of the commercially available bivalent H5+ND7 vaccine. In contrast to the H5+ND7 vaccine, which was made of genetically distinct H5N8/2018 clade 2.3.4.4b genotype group (G5), H9N2/2016, H5N1/2017, and genetically comparable NDV genotype VII 1.1/2019 of the recently circulating challenge viruses, the Valley Vac H5Plus NDVg7 vaccine consisted of the recently isolated (RG HPAI H5N1 AIV/2015 Clade 2.2.1.2, RG HPAIV H5N8/2020 Clade 2.3.4.4b genotype group 6 (G6), and NDV genotype VII 1.1/2012) which were genetically similar to challenged strains. To determine the effectiveness of the Valley Vac H5Plus NDVg7 vaccine, a total of 70-day-old commercial chicks were divided into 7 groups of 10 birds each. Groups (G1 and G4) received Valley Vac H5Plus NDVg7 vaccine. Groups (G2 and G5) groups received commercial H5+ND7 vaccine. While groups (G3 and G6) were kept nonvaccinated, and group (G7) was kept as a nonchallenged and nonvaccinated. After 3-wk post vaccination (WPV), groups G1, G2, and G3 were challenged with A/Duck/ Egypt/SMG4/2019(H5N8) genotype G6. On the other hand, groups G4, G5, G6 were challenged with NDV/EGYPT/18629F/2018 genotype VII 1.1 with an intranasal injection of 0.1 mL. Antibody titer was calculated at the first 3 wk after vaccination, and the viral shedding titer was calculated at 3-, 5-, and 7-days post challenge. Mortality and morbidity rates were monitored daily during the experiment, and for the first 10 d after the challenge, to provide an estimate of the protection rate. The results showed that a single dosage of 0.5 mL per bird of Valley Vac H5Plus NDVg7 vaccine provides 80% protection against both H5N8 and NDV, compared to the bivalent H5+ND7 vaccine, which provided 20 and 80% protection against H5N8 and NDV, respectively. In addition, 0.5 mL per bird of Valley Vac H5Plus NDVg7 vaccine produced a greater immune response against both viruses than commercial vaccination at 1 to 3 WPV with a significant difference at 1 WPV for H5N8 and a comparatively higher immune response for NDV. Furthermore, it reduced virus shedding of H5N8 on the third, fifth, seventh, and tenth days lower than H5+ND7 vaccine with a significant difference on the third day for H5N8 and relatively lower than bivalent H5+ND7 vaccine for NDV with a significant difference on the fifth day. The Valley vaccinated group demonstrated more tissue intactness compared to the commercially vaccinated group against the H5N8 challenge, however the bivalent commercially vaccinated group showed the similar level of tissue integrity against NDV. In conclusion, Valley Vac H5Plus NDVg7  that contains the  genetically similar strain to recently circulating challenged virus (H5N8 genotype G6) provided better protection with greater immune response and decreased the amount of virus shed against H5N8 genotype G6 and showed less histopathological alteration than the commercial bivalent H5+ND7 vaccine that contain genetically distinct (H5N8 genotype G5). However the Valley Vac H5Plus NDVg7 provided the same protection with relatively high immune response and  relatively decreased the amount of virus shed and showed equal tissue integrity than the commercial bivalent H5+ND7 vaccine against NDV genotype VII 1.1 that contain the same genotype of NDV genotype VII 1.1.

Trends and Challenges in the Surveillance and Control of Avian Metapneumovirus

Among the respiratory pathogens of birds, the Avian Metapneumovirus (aMPV) is one of the most relevant, as it is responsible for causing infections of the upper respiratory tract and may induce respiratory syndromes. aMPV is capable of affecting the reproductive system of birds, directly impacting shell quality and decreasing egg production. Consequently, this infection can cause disorders related to animal welfare and zootechnical losses. The first cases of respiratory syndromes caused by aMPV were described in the 1970s, and today six subtypes (A, B, C, D, and two more new subtypes) have been identified and are widespread in all chicken and turkey-producing countries in the world, causing enormous economic losses for the poultry industry. Conventionally, immunological techniques are used to demonstrate aMPV infection in poultry, however, the identification of aMPV through molecular techniques helped in establishing the traceability of the virus. This review compiles data on the main aMPV subtypes present in different countries; aMPV and bacteria co-infection; vaccination against aMPV and viral selective pressure, highlighting the strategies used to prevent and control respiratory disease; and addresses tools for viral diagnosis and virus genome studies aiming at improving and streamlining pathogen detection and corroborating the development of new vaccines that can effectively protect herds, preventing viral escapes.

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.

Common viral and bacterial avian respiratory infections: an updated review

Many pathogens that cause chronic diseases in birds use the respiratory tract as a primary route of infection, and respiratory disorders are the main leading source of financial losses in the poultry business. Respiratory infections are a serious problem facing the poultry sector, causing severe economic losses. Avian influenza virus, Newcastle disease virus, infectious bronchitis virus, and avian pneumovirus are particularly serious viral respiratory pathogens. Mycoplasma gallisepticum, Staphylococcus, Bordetella avium, Pasteurella multocida, Riemerella anatipestifer, Chlamydophila psittaci, and Escherichia coli have been identified as the most serious bacterial respiratory pathogens in poultry. This review gives an updated summary, incorporating the latest data, about the evidence for the circulation of widespread, economically important poultry respiratory pathogens, with special reference to possible methods for the control and prevention of these pathogens.

Inhibitory effects of cedar pine needle extract on H9N2 avian influenza virus in vitro and in vivo

H9N2 avian influenza virus causes significant economic losses to the poultry industry, due to its wide-spread prevalence and propensity to induce secondary and mixed infections. Antigenic drift limits vaccine efficacy. New anti-viral therapies are needed to complement existing control measures. At the maximum non-cytotoxic concentration (25 mg/mL), cedar pine needle extract inhibited H9N2 avian influenza virus proliferation in vitro and in vivo. Cedar pine needle extract reduced the haemagglutinin titre, inhibited H9N2 avian influenza virus nucleocapsid protein expression, and indirectly regulate type I and II interferon expression. Interleukin-6 expression increased during the pre-infection period but decreased during the mid-to-late stages of infection. Cedar pine needle extract may inhibit the proliferation of pathogens, regulate the immune response, and reduce host tissue damage and may serve as a potential target for drug development against H9N2 avian influenza virus.

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.

The relationship among avian influenza, gut microbiota and chicken immunity: An updated overview

The alimentary tract in chickens plays a crucial role in immune cell formation and immune challenges, which regulate intestinal flora and sustain extra-intestinal immunity. The interaction between pathogenic microorganisms and the host commensal microbiota as well as the variety and integrity of gut microbiota play a vital role in health and disease conditions. Thus, several studies have highlighted the importance of gut microbiota in developing immunity against viral infections in chickens. The gut microbiota (such as different species of Lactobacillus, Blautia Bifidobacterium, Faecalibacterium, Clostridium XlVa, and members of firmicutes) encounters different pathogens through different mechanisms. The digestive tract is a highly reactive environment, and infectious microorganisms can disturb its homeostasis, resulting in dysbiosis and mucosal infections. Avian influenza viruses (AIV) are highly infectious zoonotic viruses that lead to severe economic losses and pose a threat to the poultry industry worldwide. AIV is a challenging virus that affects gut integrity, disrupts microbial homeostasis and induces inflammatory damage in the intestinal mucosa. H9N2 AIV infection elevates the expression of proinflammatory cytokines, such as interferon (IFN-γ and IFNα) and interleukins (IL-17A and IL-22), and increases the proliferation of members of proteobacteria, particularly Escherichia coli. On the contrary, it decreases the proliferation of certain beneficial bacteria, such as Enterococcus, Lactobacillus and other probiotic microorganisms. In addition, H9N2 AIV decreases the expression of primary gel-forming mucin, endogenous trefoil factor family peptides and tight junction proteins (ZO-1, claudin 3, and occludin), resulting in severe intestinal damage. This review highlights the relationship among AIV, gut microbiota and immunity in chicken.

Genetic Variations among Different Variants of G1-like Avian Influenza H9N2 Viruses and Their Pathogenicity in Chickens

Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.

Investigation of Serotype Prevalence of Escherichia coli Strains Isolated from Layer Poultry in Greece and Interactions with Other Infectious Agents

Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O-serogroups such asO78, O2 and O1. E. coli has been reported to act either as a primary or secondary agent in complicating other infections. The aim of this study was to investigate the occurrence of and characterize the O-serogroups of E. coli strains isolated from commercial layer and layer breeder flocks showing macroscopic lesions of colibacillosis and increased or normal mortality in Greece. Furthermore, we attempted to assess the interaction between infectious agents such as Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), infectious bronchitis (IBV) and infectious laryngotracheitis (ILT) with E. coli infections in layer flocks with increased mortality. Our study revealed that in addition to the common serogroups (O78, O2), many other, and less common serogroups were identified, including O111. The O78, O111 and O2 serogroups were frequently detected in flocks with lesions of colibacillosis and increased mortality whereas O2, O88 and O8 were reported more commonly in birds with colibacillosis lesions but normal mortality rates. These data provide important information for colibacillosis monitoring and define preventative measures, especially by using effective vaccination programs because E. coli vaccines are reported to mainly offer homologous protection. Finally, concerning the association of the four tested infectious agents with E. coli mortality, our study did not reveal a statistically significant effect of the above infectious agents tested with E. coli infection mortality.

Spatiotemporal Dynamics, Evolutionary History and Zoonotic Potential of Moroccan H9N2 Avian Influenza Viruses from 2016 to 2021

The H9N2 virus continues to spread in wild birds and poultry worldwide. At the beginning of 2016, the H9N2 Avian influenza virus (AIV) was detected in Morocco for the first time; despite the implementation of vaccination strategies to control the disease, the virus has become endemic in poultry in the country. The present study was carried out to investigate the origins, zoonotic potential, as well as the impact of vaccination on the molecular evolution of Moroccan H9N2 viruses. Twenty-eight (28) H9N2 viruses collected from 2016 to 2021 in Moroccan poultry flocks were isolated and their whole genomes sequenced. Phylogenetic and evolutionary analyses showed that Moroccan H9N2 viruses belong to the G1-like lineage and are closely related to viruses isolated in Africa and the Middle East. A high similarity among all the 2016–2017 hemagglutinin sequences was observed, while the viruses identified in 2018–2019 and 2020–2021 were separated from their 2016–2017 ancestors by long branches. Mutations in the HA protein associated with antigenic drift and increased zoonotic potential were also found. The Bayesian phylogeographic analyses revealed the Middle East as being the region where the Moroccan H9N2 virus may have originated, before spreading to the other African countries. Our study is the first comprehensive analysis of the evolutionary history of the H9N2 viruses in the country, highlighting their zoonotic potential and pointing out the importance of implementing effective monitoring systems.

Improved Subtyping of Avian Influenza Viruses Using an RT-qPCR-Based Low Density Array: ‘Riems Influenza a Typing Array’, Version 2 (RITA-2)

Avian influenza virus (AIV) variants emerge frequently, which challenges rapid diagnosis. Appropriate diagnosis reaching the sub- and pathotype level is the basis of combatting notifiable AIV infections. Real-time RT-PCR (RT-qPCR) has become a standard diagnostic tool. Here, a total of 24 arrayed RT-qPCRs is introduced for full subtyping of 16 hemagglutinin and nine neuraminidase subtypes of AIV. This array, designated Riems Influenza A Typing Array version 2 (RITA-2), represents an updated and economized version of the RITA-1 array previously published by Hoffmann et al. RITA-2 provides improved integration of assays (24 instead of 32 parallel reactions) and reduced assay volume (12.5 µL). The technique also adds RT-qPCRs to detect Newcastle Disease (NDV) and Infectious Bronchitis viruses (IBV). In addition, it maximizes inclusivity (all sequences within one subtype) and exclusivity (no intersubtypic cross-reactions) as shown in validation runs using a panel of 428 AIV reference isolates, 15 reference samples each of NDV and IBV, and 122 clinical samples. The open format of RITA-2 is particularly tailored to subtyping influenza A virus of avian hosts and Eurasian geographic origin. Decoupling and re-arranging selected RT-qPCRs to detect specific AIV variants causing epizootic outbreaks with a temporal and/or geographic restriction is possible.

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.

CAvant® WO-60 as an Effective Immunological Adjuvant for Avian Influenza and Newcastle Disease Vaccine

Despite the immunogenicity of vaccines currently used in poultry, several pathogens, including avian influenza virus (AIV) and Newcastle disease virus (NDV), cause enormous economic losses to the global poultry industry. The efficacy of vaccines can be improved by the introduction of effective adjuvants. This study evaluated a novel water-in-oil emulsion adjuvant, CAvant® WO-60, which effectively enhanced both the immunogenicity of conserved influenza antigen sM2HA2 and inactivated whole H9N2 antigen (iH9N2). CAvant® WO-60 induced both humoral and cell-mediated immunity in mice and provided 100% protection from challenge with 10 LD50 of A/Aquatic bird/Korea/W81/2005 (H5N2) and A/Chicken/Korea/116/2004 (H9N2) AIV. Importantly, immunization of chickens with iH9N2 plus inactivated NDV LaSota (iNDV) bivalent inactivated vaccine emulsified in CAvant® WO-60 induced seroprotective levels of antigen-specific antibody responses. Taken together, these results suggested that CAvant® WO-60 is a promising adjuvant for poultry vaccines.

Antigenic and molecular characterization of low pathogenic avian influenza A(H9N2) viruses in sub-Saharan Africa from 2017 through 2019

Sub-Saharan Africa was historically considered an animal influenza cold spot, with only sporadic highly pathogenic H5 outbreaks detected over the last 20 years. However, in 2017, low pathogenic avian influenza A(H9N2) viruses were detected in poultry in Sub-Saharan Africa. Molecular, phylogenetic, and antigenic characterization of isolates from Benin, Togo, and Uganda showed that they belonged to the G1 lineage. Isolates from Benin and Togo clustered with viruses previously described in Western Africa, whereas viruses from Uganda were genetically distant and clustered with viruses from the Middle East. Viruses from Benin exhibited decreased cross-reactivity with those from Togo and Uganda, suggesting antigenic drift associated with reduced replication in Calu-3 cells. The viruses exhibited mammalian adaptation markers similar to those of the human strain A/Senegal/0243/2019 (H9N2). Therefore, viral genetic and antigenic surveillance in Africa is of paramount importance to detect further evolution or emergence of new zoonotic strains.

New Insights into the Host-Pathogen Interaction of Mycoplasma gallisepticum and Avian Metapneumovirus in Tracheal Organ Cultures of Chicken

Respiratory pathogens are a health threat for poultry. Co-infections lead to the exacerbation of clinical symptoms and lesions. Mycoplasma gallisepticum (M. gallispeticum) and Avian Metapneumovirus (AMPV) are two avian respiratory pathogens that co-circulate worldwide. The knowledge about the host-pathogen interaction of M. gallispeticum and AMPV in the chicken respiratory tract is limited. We aimed to investigate how co-infections affect the pathogenesis of the respiratory disease and whether the order of invading pathogens leads to changes in host-pathogen interaction. We used chicken tracheal organ cultures (TOC) to investigate pathogen invasion and replication, lesion development, and selected innate immune responses, such as interferon (IFN) α, inducible nitric oxide synthase (iNOS) and IFNλ mRNA expression levels. We performed mono-inoculations (AMPV or M. gallispeticum) or dual-inoculations in two orders with a 24-h interval between the first and second pathogen. Dual-inoculations compared to mono-inoculations resulted in more severe host reactions. Pre-infection with AMPV followed by M. gallispeticum resulted in prolonged viral replication, more significant innate immune responses, and lesions (p < 0.05). AMPV as the secondary pathogen impaired the bacterial attachment process. Consequently, the M. gallispeticum replication was delayed, the innate immune response was less pronounced, and lesions appeared later. Our results suggest a competing process in co-infections and offer new insights in disease processes.

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.

Temporal Dynamics of Influenza A(H5N1) Subtype before and after the Emergence of H5N8

Highly pathogenic avian influenza (HPAI) viruses continue to circulate worldwide, causing numerous outbreaks among bird species and severe public health concerns. H5N1 and H5N8 are the two most fundamental HPAI subtypes detected in birds in the last two decades. The two viruses may compete with each other while sharing the same host population and, thus, suppress the spread of one of the viruses. In this study, we performed a statistical analysis to investigate the temporal correlation of the HPAI H5N1 and HPAI H5N8 subtypes using globally reported data in 2015-2020. This was joined with an in-depth analysis using data generated via our national surveillance program in Egypt. A total of 6412 outbreaks were reported worldwide during this period, with 39% (2529) as H5N1 and 61% (3883) as H5N8. In Egypt, 65% of positive cases were found in backyards, while only 12% were found in farms and 23% in live bird markets. Overall, our findings depict a trade-off between the number of positive H5N1 and H5N8 samples around early 2017, which is suggestive of the potential replacement between the two subtypes. Further research is still required to elucidate the underpinning mechanisms of this competitive dynamic. This, in turn, will implicate the design of effective strategies for disease control.

Avian Paramyxovirus Type 1 in Egypt: Epidemiology, Evolutionary Perspective, and Vaccine Approach

Avian orthoavulavirus 1, formerly known as avian paramyxovirus type-1 (APMV-1), infects more than 250 different species of birds. It causes a broad range of clinical diseases and results in devastating economic impact due to high morbidity and mortality in addition to trade restrictions. The ease of spread has allowed the virus to disseminate worldwide with subjective virulence, which depends on the virus strain and host species. The emergence of new virulent genotypes among global epizootics, including those from Egypt, illustrates the time-to-time genomic alterations that lead to simultaneous evolution of distinct APMV-1 genotypes at different geographic locations across the world. In Egypt, the Newcastle disease was firstly reported in 1947 and continued to occur, despite rigorous prophylactic vaccination, and remained a potential threat to commercial and backyard poultry production. Since 2005, many researchers have investigated the nature of APMV-1 in different outbreaks, as they found several APMV-1 genotypes circulating among various species. The unique intermingling of migratory, free-living, and domesticated birds besides the availability of frequently mobile wild birds in Egypt may facilitate the evolution power of APMV-1 in Egypt. Pigeons and waterfowls are of interest due to their inclusion in Egyptian poultry industry and their ability to spread the infection to other birds either by presence of different genotypes (as in pigeons) or by harboring a clinically silent disease (as in waterfowl). This review details (i) the genetic and pathobiologic features of APMV-1 infections in Egypt, (ii) the epidemiologic and evolutionary events in different avian species, and (iii) the vaccine applications and challenges in Egypt.

Surveillance on respiratory diseases reveals enzootic circulation of both H5 and H9 avian influenza viruses in small-scale commercial layer farms of Bangladesh

Poultry production in Bangladesh has been experiencing H5N1 highly pathogenic avian influenza (HPAI) and H9N2 low pathogenic avian influenza (LPAI) for the last 14 years. Vaccination of chickens against H5 HPAI is in practice since the end of 2012. Subsequently, the official reporting of HPAI outbreaks gradually decreased. However, the true extent of circulation of avian influenza virus (AIV) in commercial poultry production is not clear. To explore this, we conducted active surveillance in 422 small-scale commercial layer farms in 20 villages of Mymensingh and Tangail districts of Bangladesh during 2017 and 2018 for the presence of diseases with respiratory signs. A total of 88 farms with respiratory disease problems were identified and investigated during the surveillance. In addition, 22 small-scale commercial layer farms in the neighbouring areas with respiratory disease problem were also investigated on request from the farmers. Pooled samples of oropharyngeal swabs from live birds or respiratory tissues from dead birds of the farm suffering from respiratory disease problem were tested for molecular detection of avian influenza virus (AIV), Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), Mycoplasma gallisepticum and Avibacterium paragallinarum. A total of 110 farms (88 in the surveillance site and 22 in the neighbouring region) were investigated, and one or more respiratory pathogens were detected from 89 farms. AIV was detected in 57 farms often concurrently with other pathogens. Among these 57 farms, H5, H9, both H5 and H9 or non-H5 and non-H9 AIV were detected in 28, 9, 13 or 7 farms, respectively. Birds of most of the H5 AIV-positive farms did not present typical clinical signs or high mortality. Twenty such farms were observed longitudinally, which had only 1.05%-5.50% mortality but a marked drop in egg production. This widespread circulation of H5 AIV along with H9 AIV and other pathogens in small-scale commercial layer farms, often with low mortality, reaffirms the enzootic circulation of AIV in Bangladesh, which may escape syndromic surveillance focused on unusual mortality only. To reduce public health risks, strengthening of the control programme with comprehensive vaccination, enhanced biosecurity, improved surveillance and outbreak response is suggested.

Co-infection of Salmonella enteritidis with H9N2 avian influenza virus in chickens

Salmonella and avian influenza virus are important pathogens affecting the poultry industry and human health worldwide. In this experimental study, we evaluated the consequences of co-infection of Salmonella enteritidis (SE) with H9N2 avian influenza virus (H9N2-AIV) in chickens. Four groups were included: control group, H9N2-AIV group, H9N2-AIV + SE group, and SE group. Infected chickens were intranasally inoculated with H9N2-AIV at 21 days of age and then orally administered SE on the same day. The birds were monitored for clinical signs, mortality rates, and alterations in body weight. Sera, intestinal fluids, oropharyngeal, and cloacal swabs, and tissue samples were collected at 2, 6, 10, and 14 days post-infection (dpi). Significant increases in clinical signs and mortality rates were observed in the H9N2-AIV + SE group. Moreover, chickens with co-infection showed a significant change in body weight. SE faecal shedding and organ colonization were significantly higher in the H9N2-AIV + SE group than in the SE group. H9N2-AIV infection compromised the systemic and mucosal immunity against SE, as evidenced by a significant decrease in lymphoid organ indices as well as systemic antibody and intestinal immunoglobulin A (IgA) responses to SE and a significant increase in splenic and bursal lesion scores. Moreover, SE infection significantly increased shedding titres and duration of H9N2-AIV. In conclusion, this is the first report of co-infection of SE with H9N2-AIV in chickens, which leads to increased pathogenicity, SE faecal shedding and organ colonization, and H9N2-AIV shedding titre and duration, resulting in substantial economic losses and environmental contamination, ultimately leading to increased zoonoses.

The Airway Pathobiome in Complex Respiratory Diseases: A Perspective in Domestic Animals

Respiratory infections in domestic animals are a major issue for veterinary and livestock industry. Pathogens in the respiratory tract share their habitat with a myriad of commensal microorganisms. Increasing evidence points towards a respiratory pathobiome concept, integrating the dysbiotic bacterial communities, the host and the environment in a new understanding of respiratory disease etiology. During the infection, the airway microbiota likely regulates and is regulated by pathogens through diverse mechanisms, thereby acting either as a gatekeeper that provides resistance to pathogen colonization or enhancing their prevalence and bacterial co-infectivity, which often results in disease exacerbation. Insight into the complex interplay taking place in the respiratory tract between the pathogens, microbiota, the host and its environment during infection in domestic animals is a research field in its infancy in which most studies are focused on infections from enteric pathogens and gut microbiota. However, its understanding may improve pathogen control and reduce the severity of microbial-related diseases, including those with zoonotic potential.

Comparison of genomic and antigenic properties of Newcastle Disease virus genotypes II, XXI and VII from Egypt do not point to antigenic drift as selection marker

Newcastle disease (ND), caused by avian orthoavulavirus type-1 (NDV), is endemic in poultry in many regions of the world and causes continuing outbreaks in poultry populations. In the Middle East, genotype XXI, used to be present in poultry in Egypt but has been replaced by genotype VII. We investigated whether virus evolution contributed to superseding and focussed on the antigenic sites within the hemagglutinin-neuraminidase (HN) spike protein. Full-length sequences of an NDV genotype VII isolate currently circulating in Egypt was compared to a genotype XXI isolate that was present as co-infection with vaccine-type viruses (II) in a historical virus isolated in 2011. Amino acid differences in the HN glycoprotein for both XXI and VII viruses amounted to 11.7% and 11.9%, respectively, compared to the La Sota vaccine type. However, mutations within the globular head (aa 126-570), bearing relevant antigenic sites, were underrepresented (a divergence of 8.8% and 8.1% compared to 22.4% and 25.6% within the protein domains encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1-125) for genotypes XXI and VII, respectively). Nevertheless, reaction patterns of HN-specific monoclonal antibodies inhibiting receptor binding revealed differences between vaccine-type viruses and genotype XXI and VII viruses for epitopes located in the head domain. Accordingly, compared to Egyptian vaccine-type isolates and the La Sota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes of HN were found. However, the same alterations in neutralization sensitive epitopes were present in old genotype XXI as well as in newly emerged genotype VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest that factors other than antigenic differences within the HN protein account for facilitating the spread of genotype VII versus genotype XXI viruses in Egypt.

Neuraminidase-associated plasminogen recruitment enables systemic spread of natural avian Influenza viruses H3N1

Repeated outbreaks due to H3N1 low pathogenicity avian influenza viruses (LPAIV) in Belgium were associated with unusually high mortality in chicken in 2019. Those events caused considerable economic losses and prompted restriction measures normally implemented for eradicating high pathogenicity avian influenza viruses (HPAIV). Initial pathology investigations and infection studies suggested this virus to be able to replicate systemically, being very atypical for H3 LPAIV. Here, we investigate the pathogenesis of this H3N1 virus and propose a mechanism explaining its unusual systemic replication capability. By intravenous and intracerebral inoculation in chicken, we demonstrate systemic spread of this virus, extending to the central nervous system. Endoproteolytic viral hemagglutinin (HA) protein activation by either tissue-restricted serine peptidases or ubiquitous subtilisin-like proteases is the functional hallmark distinguishing (H5 or H7) LPAIV from HPAIV. However, luciferase reporter assays show that HA cleavage in case of the H3N1 strain in contrast to the HPAIV is not processed by intracellular proteases. Yet the H3N1 virus replicates efficiently in cell culture without trypsin, unlike LPAIVs. Moreover, this trypsin-independent virus replication is inhibited by 6-aminohexanoic acid, a plasmin inhibitor. Correspondingly, in silico analysis indicates that plasminogen is recruitable by the viral neuraminidase for proteolytic activation due to the loss of a strongly conserved N-glycosylation site at position 130. This mutation was shown responsible for plasminogen recruitment and neurovirulence of the mouse brain-passaged laboratory strain A/WSN/33 (H1N1). In conclusion, our findings provide good evidence in natural chicken strains for N1 neuraminidase-operated recruitment of plasminogen, enabling systemic replication leading to an unusual high pathogenicity phenotype. Such a gain of function in naturally occurring AIVs representing an established human influenza HA-subtype raises concerns over potential zoonotic threats.

First description of natural concomitant infection of avian nephritis virus and infectious bronchitis virus reveals exacerbated inflammatory response and renal damage in broiler chicks

We describe the first report on spontaneous Avian Nephritis Virus (ANV) and Infectious Bronchitis Virus (IBV) concurrent infection in broiler chicks. On necropsy, the kidneys were found swollen with its parenchyma and ureters stuffed with urate flakes. Histopathologically, the renal tubular damage and inflammatory response were severe in concurrently infected birds compared to the cases infected only with ANV, which had direct correlation with significantly (p < 0.001) increased expression of IL-1 β, IL-4, IL-12, IL-13, iNOS and IFN-γ transcripts in the kidneys of concurrently infected birds. Relative decrease in IFN-β transcript levels in the concurrently infected birds indicates suppression of antiviral response; the iNOS level was manifold increased which can be attributed to the enhanced macrophage response. Nucleotide sequencing of S1-spike glycoprotein gene of IBV and RNA dependent RNA polymerase gene of ANV confirmed etiologies as Igacovirus of Gammacoronavirus and ANV-2 of Avastrovirus 2, respectively. Both ANV and IBV virus affect kidneys. Our findings suggested that concurrent infections of these two viruses might have enhanced the transcripts of Th1, Th2 and proinflammatory cytokines with reduced IFN-β transcripts resulting in decreased host innate antiviral mechanisms leading to exacerbated renal lesions. Future experimental co-infection studies could throw more lights on pathology and pathogenesis during concurrent infections of ANV and IBV in poultry.

Experimental infection of domestic geese (Anser anser var. domesticus) with H5N8 Gs/GD and H7N1 highly pathogenic avian influenza viruses

Prior to the emergence of the Asian-origin H5 Goose/Guangdong/1/96 (Gs/GD) lineage, highly pathogenic avian influenza viruses (HPAIV) had rarely caused high mortalities in domestic geese. In 2016/2017 European epidemics, H5N8 Gs/GD clade 2.3.4.4 Group B produced an unprecedented number of outbreaks in waterfowl holdings. In this study, the pathogenesis of H5N8 HPAIV in comparison with H7N1 HPAIV, and the role of domestic geese in the epidemiology of these viruses, were evaluated. Local and commercial geese (Anser anser var. domesticus) were intranasally inoculated with 10⁵ ELD₅₀ of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored daily during 15 days. H5N8 was highly virulent to domestic geese, reaching 100% mortality by 10 days post-infection. Systemic microscopic necrotizing lesions associated with widespread AIV-antigen were detected by IHC techniques, the central nervous system being the most severely affected. High viral loads, measured by qRT-PCR, were present in all samples collected: oral and cloacal swabs, plasma tissues, and moderate levels in pool water. Domestic geese were also susceptible to H7N1 infection, as demonstrated by seroconversion and detection of viral RNA in tissues and plasma in some geese, but all lacked clinical signs. Viral shedding was confirmed in only some geese and was restricted to the oral route, but levels were high and still detected at the end of the study. Overall, H7N1 presents a lower lethality and shedding than H5N8 in geese; however, the viral shedding indicates that these species could play a role in the epidemiology of Gs/GD and other lineages of HPAIVs. RESEARCH HIGHLIGHTS H5N8 Gs/GD clade 2.3.4.4 Group B is highly virulent to domestic geese. The severity of H5N8 is associated with multisystemic replication. H7N1 can infect domestic geese but is avirulent to this species. Domestic geese could play a role in the epidemiology of Gs/GD HPAIVs.

Nitrate Is Crucial for the Proliferation of Gut Escherichia coli Caused by H9N2 AIV Infection and Effective Regulation by Chinese Herbal Medicine Ageratum-Liquid

H9N2 avian influenza virus (AIV) infection in chickens is often accompanied by secondary bacterial infection, but the mechanism is unclear. The aim of the present study was to reveal that mechanism and explore non-antibiotic treatment. 16s rRNA sequencing and metabonomics were performed in the intestinal contents of chickens infected with H9N2 AIV or H9N2 AIV and fed with ageratum-liquid (AL) to reveal the metabolite that promote intestinal Escherichia coli (E. coli) proliferation caused by H9N2 AIV, as well as to determine the regulatory effect of AL. It was found that H9N2 AIV infection led E. coli to become the dominant gut microbe and promoted E. coli translocation from the intestinal tract to the visceral tissue through the damaged intestinal barrier. H9N2 AIV infection induces inflammation in the intestinal mucosa and promotes the secretion and release of nitrate from the host intestinal epithelium. In addition, nitrate promoted E. coli proliferation in the inflamed intestinal tract following H9N2 AIV infection. Furthermore, Chinese herbal medicine AL can restore intestinal homeostasis, inhibit the production of nitrate in the intestinal epithelium and effectively prevent the proliferation and translocation of E. coli in the intestines. This is the first report on the mechanism of E. coli secondary infection induced by H9N2 AIV, where herbal medicine AL was shown to have a good preventive effect on the secondary infection.

Co-inections of domestic and wild birds with avian influenza and Newcastle disease viruses: implications for control and genetic mutations

Co-infections of birds' upper respiratory tract by avian pathogens are common and cause increasing economic losses. This study determines co-infection status of avian influenza (AI) and Newcastle disease (ND) in birds in two Nigerian states with different highly pathogenic avian influenza (HPAI) records and where modified stamping out policy contained the virus for seven years after which the virus resurged with higher infectivity in 2015. A cross-sectional study sampling 910 apparently healthy domestic and 90 wild birds from wild habitats, commercial poultry farms, households and live bird markets (LBMs) was conducted. Cloacal and tracheal swabs were tested for AI H5 and ND viruses using conventional reverse transcriptase polymerase chain reaction (RT-PCR). Overall detection rates of 3% and 18% for AI and ND were obtained. There was an equivalence of 8.5% ND detection rate in poultry and wild birds in the two states. Co-infection (0.2%) of a local chicken from a live bird market (LBM) and crown crane (Balearica regulorum) from a household to AI H5 and ND viruses occurred, respectively. Exposure of birds to AI and ND was significantly detected in apparently healthy domestic and wild birds. The probability of these viruses exchanging genetic materials to resurge with increasing virulence is foreseen. Therefore, routine AI and ND control measures should incorporate virus surveillance and instituting appropriate preventive measures in domestic and wild birds held in households, commercial farms and LBMs.

GIS-augmented survey of poultry farms with respiratory problems in Haryana

Among various infectious diseases of poultry, diseases of the respiratory tract are responsible for considerable economic losses. The present study was conducted to evaluate some of the risk factors, which included locations of farm, ventilation facilities, number of farms in 1 km² area, agro-climatic zone, and age of flock in relation to respiratory problem in Haryana, India. One hundred poultry flocks with respiratory problems were identified and selected for conducting the survey. The "ODK Collect" app installed on a smartphone was used to capture coordinates of the farms. The collected data was accessed through http://odkproject-iirs.appspot.com/ . The location of farms was mapped with the help of QGIS. All the three parameters, viz., morbidity, mortality (p < 0.001), and case fatality rate (CFR) (p = 0.045), were significantly higher in birds of age 0-2 weeks. Natural ventilation was the most common facility observed in the present study (51/100). Maximum morbidity and mortality were observed in small flocks (< 10,000), whereas maximum CFR was observed in medium-sized flocks (> 10,000-30,000), and there was a significant difference in morbidity, mortality, and CFR. Further, there was a significant difference between agro-climatic zones with respect to morbidity and mortality (p < 0.001). It can be concluded that age, flock size, and agro-climatic conditions have an impact on intensity of diseases especially respiratory diseases. Therefore, special precautions should be taken for young flock. Flock size should be adequate, and such management practices should be adopted that are suitable for particular climatic conditions.

Detection of Low Pathogenic Avian Influenza Virus Subtype H10N7 in Poultry and Environmental Water Samples During a Clinical Outbreak in Commercial Free-Range Layers, Netherlands 2017

Wild birds are the natural reservoir of the avian influenza virus (AIV) and may transmit AIV to poultry via direct contact or indirectly through the environment. In the Netherlands, a clinically suspected free-range layer flock was reported to the veterinary authorities by the farmer. Increased mortality, a decreased feed intake, and a drop in egg production were observed. Subsequently, an infection with low pathogenic avian influenza virus was detected. This study describes the diagnostic procedures used for detection and subtyping of the virus. In addition to routine diagnostics, the potential of two different environmental diagnostic methods was investigated for detecting AIV in surface water. AIV was first detected using rRT-PCR and isolated from tracheal and cloacal swabs collected from the hens. The virus was subtyped as H10N7. Antibodies against the virus were detected in 28 of the 31 sera tested. An intravenous pathogenicity index (IVPI) experiment was performed, but no clinical signs (IVPI = 0) were observed. Post-mortem examination and histology confirmed the AIV infection. Multiple water samples were collected longitudinally from the free-range area and waterway near the farm. Both environmental diagnostic methods allowed the detection of the H10N7 virus, demonstrating the potential of these methods in detection of AIV. The described methods could be a useful additional procedure for AIV surveillance in water-rich areas with large concentrations of wild birds or in areas around poultry farms. In addition, these methods could be used as a tool to test if the environment or free-range area is virus-free again, at the end of an AIV epidemic.

Naturally Avian Influenza Virus-Infected Wild Birds Are More Likely to Test Positive for Mycobacterium spp. and Salmonella spp

Wild birds often harbor infectious microorganisms. Some of these infectious microorganisms may present a risk to domestic animals and humans through spillover events. Detections of certain microorganisms have been shown to increase host susceptibility to infections by other microorganisms, leading to coinfections and altered host-to-host transmission patterns. However, little is known about the frequency of coinfections and its impact on wild bird populations. In order to verify whether avian influenza virus (AIV) natural infection in wild waterbirds was related to the excretion of other microorganisms, 73 AIV-positive samples (feces and cloacal swabs) were coupled with 73 AIV-negative samples of the same sampling characteristics and tested by real-time PCR specific for the following microorganisms: West Nile virus, avian avulavirus 1, Salmonella spp., Yersinia enterocolitica, Yersinia pseudotuberculosis, Mycobacterium avium subspecies, Mycobacterium tuberculosis complex, and Mycobacterium spp. Concurrent detections were found in 47.9% (35/73) of the AIV-positive samples and in 23.3% (17/73) of the AIV-negative samples (P = 0.003). Mycobacterium spp. and Salmonella spp. were found to be significantly more prevalent among the AIV-positive samples than among the AIV-negative samples (42.9% vs. 22.8%; P = 0.024 and 15.2% vs. 0.0%; P = 0.0015, respectively). Prevalence of concurrent detections differed significantly among sampling years (P = 0.001), host families (P = 0.002), host species (P = 0.003), AIV subtypes (P = 0.003), and type of sample (P = 0.009). Multiple concurrent detections (more than one of the tested microorganisms excluding AIV) were found in 9.6% (7/73) of all the AIV-positive samples, accounting for 20% (7/35) of the concurrent detection cases. In contrast, in AIV-negative samples we never detected more than one of the selected microorganisms. These results show that AIV detection was associated with the detection of the monitored microorganisms. Further studies of a larger field sample set or under experimental conditions are necessary to infer causality in these trends.

Comparison of pathogenicity of subtype H9 avian influenza wild-type viruses from a wide geographic origin expressing mono-, di-, or tri-basic hemagglutinin cleavage sites

An intravenous pathogenicity index (IVPI) of > 1.2 in chickens or, in case of subtypes H5 and H7, expression of a polybasic hemagglutinin cleavage site (HACS), signals high pathogenicity (HP). Viruses of the H9N2-G1 lineage, which spread across Asia and Africa, are classified to be of low pathogenicity although, in the field, they became associated with severe clinical signs and epizootics in chickens. Here we report on a pre-eminent trait of recent H9N2-G1 isolates from Bangladesh and India, which express a tribasic HACS (motif PAKSKR-GLF; reminiscent of an HPAIV-like polybasic HACS) and compare their features to H9Nx viruses with di- and monobasic HACS from other phylogenetic and geographic origins. In an in vitro assay, the tribasic HACS of H9N2 was processed by furin-like proteases similar to bona fide H5 HPAIV while some dibasic sites showed increased cleavability but monobasic HACS none. Yet, all viruses remained trypsin-dependent in cell culture. In ovo, only tribasic H9N2 viruses were found to replicate in a grossly extended spectrum of embryonic organs. In contrast to all subtype H5/H7 HPAI viruses, tribasic H9N2 viruses did not replicate in endothelial cells either in the chorio-allantoic membrane or in other embryonic tissues. By IVPI, all H9Nx isolates proved to be of low pathogenicity. Pathogenicity assessment of tribasic H9N2-G1 viruses remains problematic. It cannot be excluded that the formation of a third basic amino acid in the HACS forms an intermediate step towards a gain in pathogenicity. Continued observation of the evolution of these viruses in the field is recommended.

Phylogeographic Dynamics of Influenza A(H9N2) Virus Crossing Egypt

Low pathogenic avian influenza (LPAI) virus of subtype H9N2 is the most frequently detected subtype among domestic poultry and is a public health concern because of its zoonotic potential. Due to the multiple and complex routes of LPAIV H9N2 between geographic regions, little is known about the spatial diffusion of H9N2 virus to, within, and from Egypt, where it is endemic among poultry since 2011. Using close to 800 publicly available hemagglutinin (HA) segment nucleotide sequences, associated location and temporal data, we conducted a Bayesian discrete phylogeographic analysis. Here, we reconstructed and traced the origin, spread and principal transmission routes of H9N2 across large geographical regions, in addition to the transmission between Egypt and the rest of the world and between different Egyptian governorates. Our analysis suggests that during the last few decades, H9N2 has been introduced back and forth continuously between the countries where it is endemic. Amongst these regions, Saudi Arabia, United Arab Emirates and Iraq act as main distribution hubs and drive the viral migration worldwide, with bi-directional and long-distance diffusions. It is noteworthy that H9N2 was introduced once to Egypt via Israel in mid 2009, and that the descendants of the Egyptian LAIVs H9N2 were back-transmitted to Israel in 2015. Additionally, governorates in middle Egypt (Giza, Fayoum and Bani Souwaif) are major hubs in the LPAIV H9N2 transmission network in Egypt. This knowledge highlights that H9N2 is both a global and a national concern and can aid in updating the surveillance program and vaccine strain selection.

Molecular survey and interaction of common respiratory pathogens in chicken flocks (field perspective)

Aim:

The present study was designed for the detection of the most prevalent respiratory infections in chicken flocks and clarifying their interaction and impact on flock health.

Materials and Methods:

A total of 359 serum samples were collected from 55 backyard chickens and tested using commercial enzyme-linked immunosorbent assay kits to determine the seroprevalence of Newcastle disease virus (NDV), infectious bronchitis virus (IBV), influenza type A, Mycoplasma gallisepticum (MG), and Mycoplasma synoviae (MS). Molecular prevalence of NDV, IBV, low pathogenic avian influenza virus (LPAIV) H9N2, MG, and MS was carried out on swab, and tissue samples collected from 55 backyard flocks and 11 commercial broiler flocks suffered from respiratory infections using polymerase chain reaction (PCR) and reverse transcription-PCR.

Results:

Seroprevalence of NDV, IBV, Influenza type A virus, MG, and MS in chicken backyard flocks was 56.4%, 50.9%, 12.7%, 14.5%, and 3.6%, respectively. Specific antibodies against one or more respiratory viruses and mycoplasma were detected in 36.4% of backyard flocks, indicating concurrent viral infections. The molecular survey showed that 90.9% of chicken backyard flocks were infected with common respiratory viruses (NDV, IBV, and LPAIV H9N2) while 81.8% of commercial broiler flocks were infected. The molecular prevalence rate of NDV, IBV, and LPAIV H9N2 was 46.97%, 56.1%, and 19.7% in backyard flocks, respectively. Combined viral and bacterial infection represented 40% and 63.6% of the respiratory infections, resulting in enhanced pathogenicity and increased mortalities of up to 87.5% and 27.8% in backyard and commercial flocks, respectively. Mixed infection of IBV, LPAIV H9N2, and/or Escherichia coli is the most prevalent mixed infection in broiler flocks, inducing severe clinical outcomes. Avian pathogenic E. coli was, respectively, isolated from 40% of backyard flocks and 81.82% of broiler flocks. Staphylococcus aureus was isolated from three backyard chicken flocks mixed with other respiratory pathogens with elevated mortality. Mixed infection of E. coli and MG reported in 9.1% of broiler flock. MG was detected in 14.5% of backyard flocks and 9.1% of broiler flocks while MS was detected only in 3.6% of backyard chickens mixed with E. coli, and other viruses.

Conclusion:

Our results confirm that mixed infections are more commonly prevalent and associated with dramatic exacerbation in clinical outcomes than a single infection. Bidirectional synergistic interaction between these concurrently interacted respiratory pathogens explains the severe clinical impact and high mortality rate. The high prevalence of IBV (either as a single or combined infection) with LPAIV H9N2 and/or E. coli, in spite of intensive use of commercial vaccines, increases the need for revising vaccination programs and the application of standard biosecurity measures. Backyard chickens impose a great risk and threaten commercial flocks due to the high prevalence of viral respiratory pathogens.

Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens

Infectious bronchitis virus (IBV) represents a major threat to poultry production worldwide particularly when complicated with bacterial infection. In the present study samples were collected from forty broiler farms with respiratory manifestations to characterize IBV and E. coli. Bacteriophages were isolated and enriched from sampled farms to study its efficacy to control single and mixed infections with E. coli and IBV in vivo. Twelve out of forty farms were positive for IBV. Phylogenetic analysis of partial spike protein revealed that all positive cases clustered within the GI-23 genotype. Eight out of forty farms were positive for E. coli serogroups O26, O78, O86, O114, O119, with O125 found on three farms. Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. coli. Furthermore, in mixed infections, bacteriophage treatment significantly reduced E. coli as well as IBV shedding. Groups treated with bacteriophages showed a significant reduction of E. coli shedding that gradually decreased over time, in contrast to higher and gradually increasing shedding without bacteriophage treatment. In conclusion, bacteriophage treatment significantly reduced the pathogenicity and shedding of IBVand E. coli in mixed infections.

A Recombinant La Sota Vaccine Strain Expressing Multiple Epitopes of Infectious Bronchitis Virus (IBV) Protects Specific Pathogen-Free (SPF) Chickens against IBV and NDV Challenges

Infectious bronchitis (IB) and Newcastle disease (ND) are two major infectious diseases that are a threat to the domestic poultry industry. In this study, we successfully generated a recombinant LaSota candidate vaccine strain, rNDV-IBV-T/B, which expresses a short, synthetic, previously identified IBV S1 multi-epitope cassette using the reverse genetic system. The recombinant virus was propagated in nine-day-old embryonated chicken eggs for 20 passages and genetic stability was confirmed by whole genome DNA sequencing. The recombinant virus had a hemagglutination (HA) titer of 2¹⁰, mean death time (MDT) of 118 hours, and intracerebral pathogenicity index (ICPI) of 0.05. None of these were significantly different from the parental Newcastle disease virus (NDV) LaSota strain (p > 0.05). Vaccination of white leghorn chickens at one day of age with 10⁶ EID₅₀ rNDV-IBV-T/B provided 90% protection against virulent IBV M41 challenge at three weeks of age, which was significantly higher than the protection of the control group vaccinated with phosphate-buffered saline (PBS) (p < 0.05). The ciliostasis scores of rNDV-IBV-T/B-vaccinated and LaSota-vaccinated groups were 4.2 and 37.6, respectively, which indicated that rNDV-IBV-T/B vaccination reduced the pathogenicity of IBV toward the trachea. Furthermore, real-time RT-PCR assay showed that the rNDV-IBV-T/B vaccination resulted in low levels of viral load (647.80 ± 49.65 RNA copies) in the trachea four days post-challenge, which is significantly lower than groups vaccinated with PBS (8591.25 ± 311.10 RNA copies) or LaSota (7742.60 ± 298.50 RNA copies) (p < 0.05). Meanwhile, the same dose of rNDV-IBV-T/B vaccination provided complete protection against velogenic NDV F48E9 challenge. These results demonstrate that the rNDV-IBV-T/B strain is a promising vaccine candidate to control both IB and ND simultaneously. Furthermore, epitope-based live vector vaccines provide an alternative strategy for the development of cost-effective and, broadly, cross-protective vaccines.

Genetic characterization and pathogenesis of the first H9N2 low pathogenic avian influenza viruses isolated from chickens in Kenyan live bird markets

Poultry production plays an important role in the economy and livelihoods of rural households in Kenya. As part of a surveillance program, avian influenza virus (AIV)-specific real-time RT-PCR (RRT-PCR) was used to screen 282 oropharyngeal swabs collected from chickens at six live bird markets (LBMs) and 33 backyard poultry farms in Kenya and 8 positive samples were detected. Virus was isolated in eggs from five samples, sequenced, and identified as H9N2 low pathogenic AIV (LPAIV) G1 lineage, with highest nucleotide sequence identity (98.6-99.9%) to a 2017 Ugandan H9N2 isolate. The H9N2 contained molecular markers for mammalian receptor specificity, implying their zoonotic potential. Virus pathogenesis and transmissibility was assessed by inoculating low and medium virus doses of a representative Kenyan H9N2 LPAIV isolate into experimental chickens and exposing them to naïve uninfected chickens at 2 -days post inoculation (dpi). Virus shedding was determined at 2/4/7 dpi and 2/5 days post placement (dpp), and seroconversion determined at 14 dpi/12 dpp. None of the directly-inoculated or contact birds exhibited any mortality or clinical disease signs. All directly-inoculated birds in the low dose group shed virus during the experiment, while only one contact bird shed virus at 2 dpp. Only two directly-inoculated birds that shed high virus titers seroconverted in that group. All birds in the medium dose group shed virus at 4/7 dpi and at 5 dpp, and they all seroconverted at 12/14 dpp. This is the first reported detection of H9N2 LPAIV from Kenya and it was shown to be infectious and transmissible in chickens by direct contact and represents a new disease threat to poultry and potentially to people.

Respiratory disease due to mixed viral infections in poultry flocks in Egypt between 2017 and 2018: Upsurge of highly pathogenic avian influenza virus subtype H5N8 since 2018

For several years, poultry production in Egypt has been suffering from co-circulation of multiple respiratory viruses including highly pathogenic avian influenza virus (HPAIV) H5N1 (clade 2.2.1.2) and low pathogenic H9N2 (clade G1-B). Incursion of HPAIV H5N8 (clade 2.3.4.4b) to Egypt in November 2016 via wild birds followed by spread into commercial poultry flocks further complicated the situation. Current analyses focussed on 39 poultry farms suffering from respiratory manifestation and high mortality in six Egyptian governorates during 2017-2018. Real-time RT-PCR (RT-qPCR) substantiated the co-presence of at least two respiratory virus species in more than 80% of the investigated flocks. The percentage of HPAIV H5N1-positive holdings was fairly stable in 2017 (12.8%) and 2018 (10.2%), while the percentage of HPAIV H5N8-positive holdings increased from 23% in 2017 to 66.6% during 2018. The proportion of H9N2-positive samples was constantly high (2017:100% and 2018:63%), and H9N2 co-circulated with HPAIV H5N8 in 22 out of 39 (56.8%) flocks. Analyses of 26 H5, 18 H9 and 4 N2 new sequences confirmed continuous genetic diversification. In silico analysis revealed numerous amino acid substitutions in the HA and NA proteins suggestive of increased adaptation to mammalian hosts and putative antigenic variation. For sensitive detection of H9N2 viruses by RT-qPCR, an update of primers and probe sequences was crucial. Reasons for the relative increase of HPAIV H5N8 infections versus H5N1 remained unclear, but lack of suitable vaccines against clade 2.3.4.4b cannot be excluded. A reconsideration of surveillance and control measures should include updating of diagnostic tools and vaccination strategies.

Co-infections, genetic, and antigenic relatedness of avian influenza H5N8 and H5N1 viruses in domestic and wild birds in Egypt

A total of 50 poultry farms of commercial broilers (N = 39) and commercial layers (N = 11) suffered from respiratory problems and mortality during the period from January 2016 to December 2017 were investigated. Also, samples were collected from quail (N = 4), Bluebird (Sialis, N = 1), and Greenfinch (Chloris chloris, N = 1) for analysis. Respiratory viral pathogens were screened by PCR and positive samples were subjected to virus isolation and genetic identification. Antigenic relatedness of isolated avian influenza (AI) H5 subtype was evaluated using cross-hemagglutination inhibition. Results revealed that the incidence of single virus infections in commercial broilers was 64.1% (25/39), with the highest incidence for ND (33.3%) and H9N2 (20.5%), followed by H5N1 (7.7%) and H5N8 (2.7). Meanwhile, H9N2/ND mixed infection was the most observed case (7.7%). Other mixed infections H5N1/ND, H5N1/H9N2/ND, H5N1/H9N2/ND/IB, H9N2/IB, and H9N2/ILT were also observed (2.6% each). In commercial layers, H5N1 and ILT were the only detected single infections (18.1% each). Mixed H9N2/ND was the most predominant infection in layers (27.3%). Other mixed infections of H9N2/IB, H5N1/H5N8/H9N2, and H9N2/ND/IB were observed in 3 separate farms (9.1% each). The H5N8 virus was detected in one quail farm and 2 out of 3 wild bird's samples. Partial HA gene sequence analysis showed the clustering of the selected AI H5N8 within the 2.3.4.4 clade, while H5N1 clustered with the clade 2.2.1.2. Interestingly, the H5N8 isolated from chickens possessed 6 amino acids substitutions at HA1 compared to those isolated from wild birds with low antigenic relatedness to AI H5N1 clades 2.2.1 or 2.2.1.2. In conclusion, mixed viral infections were observed in both broiler and layer chickens in Egypt. The detected triple H5N1, H9N2, and H5N8 influenza co-infection raises the concern of potential AI epidemic strain emergence. The low genetic and antigenic relatedness between AI H5N1 and H5N8 viruses suggest the need for modification of vaccination strategies of avian influenza in Egypt along with strict biosecurity measures.

Viral interference between H9N2-low pathogenic avian influenza virus and avian infectious bronchitis virus vaccine strain H120 in vivo

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AIV and IBV co-infection led to decreased growth of both viruses.

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During super-infection, the second virus decreased the growth of the first virus.

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ELISA antibody titers, depending on the experimental conditions.

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Histopathological findings showed important lesions.

The interaction between a low pathogenic avian influenza virus (A/CK/TUN/145/2012), a H9N2 Tunisian isolate, and a vaccine strain (H120) of avian infectious bronchitis, administered simultaneously or sequentially three days apart to chicks during 20 days, was evaluated using ELISA antibody levels, quantitative reverse transcription–polymerase chain reaction (qRT-PCR) analyses and histopathology examination. First, the in vivo replication interference of avian influenza virus (AIV) and infectious bronchitis virus (IBV) was evaluated using qRT-PCR to detect accurately either AIV or IBV genomes or viral copy numbers during dual infections. Second, we have determined the amount of specific antibodies in sera of chick’s infected with AIV alone, IBV alone, mixed AIV + IBV, IBV then AIV or AIV IBV 3 days later using an ELISA test. Finally, histopathological analyses of internal organs from inoculated chicks were realized. Quantitative results of AIV and IBV co-infection showed that interferences between the two viruses yielded decreased viral growth. However, in the case of super-infection, the second virus, either AIV or IBV, induced a decrease in the growth of the first inoculated virus. According to our results, vaccine application was safe and do not interfere with AIV H9N2 infection, and does not enhance such infection. In conclusion, co-infection of chicks with AIV and IBV, simultaneously or sequentially, affected the clinical signs, the virus replication dynamics as well as the internal organ integrity. The results proposed that infection with heterologous virus may result in temporary competition for cell receptors or competent cells for replication, most likely interferon-mediated.

Study of the underlying mechanisms and consequences of pathogenicity differences between two in vitro selected G1-H9N2 clones originating from a single isolate

The G1-H9N2 avian influenza virus (AIV) has caused significant economic losses in the commercial poultry industry due to reduced egg production and increased mortality. The field observations have shown that H9N2 viruses circulate and naturally mix with other pathogens and these simultaneous infections can exacerbate disease. To avoid an incorrect virus characterization, due to co-infection, isolates were purified by in vitro plaque assays. Two plaque purified G1-H9N2 clones, selected on different cell types, named MDCK-and CEF-clone in regards to the cell culture used, were studied in vivo, revealing two different virulence phenotypes. Subsequently, the underlying mechanisms were studied. Specifically, the phenotypical outcome of SPF bird infection by the two clones resulted in completely different clinical outcomes. These differences in clinical outcome were used to study the factors behind this output in more detail. Further studies demonstrated that the more severe disease outcome associated with the MDCK-clone involves a strong induction of pro-inflammatory cytokines and a lack of type I interferon production, whereas the mild disease outcome associated with the CEF-clone is related to a greater antiviral cytokine response. The immunosuppressive effect of the MDCK-clone on splenocytes was further demonstrated via ChIFN-γ lack production after ex vivo mitogenic stimulation. Genome sequencing of the two clones identified only four amino acid differences including three in the HA sequence (HA-E198A, HA-R234L, HA-E502D-H9 numbering) and one in the NA sequence (NA-V33M). In the present study, valuable insights on the mechanisms responsible for AI pathogenicity and molecular mechanisms of H9N2 infections in chicken were obtained while highlighting the impact of the cells viruses are grown on their virulence.