Molecular epidemiology of respiratory viruses in commercial chicken flocks in Pakistan from 2014 through to 2016

A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan

OBJECTIVES

The study aimed to examine how management practices, farming setup and breed influence disease outbreaks. It also sought to investigate the frequency and types of antimicrobials used, as well as the relationship between antimicrobial usage and disease occurrences.

METHODS

We conducted a survey of 140 poultry farms [Broiler farms = 66; Layer farms = 36; Local (Desi and its crosses) farms = 38] across major poultry producing regions of Pakistan. The gathered information covered demographics as well as the farming associated parameters including size, type of the farms, management practices, breeds raised, disease outbreak and antimicrobials use.

RESULTS

Using contingency analyses and log binomial regression models, we identified Broiler control sheds at high risk of disease. Diseases such as Avian Influenza, Newcastle Disease, and Fowl Typhoid were frequently reported and their outbreaks were associated with low cleaning frequency, high stocking density, bedding material using rice husk, and canola as a major feed ingredient. Farmer education was associated with a decrease in disease outbreak. Antimicrobial use was associated with farming experience, farm size, type and breed.

CONCLUSION

High disease incidence is associated with management practices and breed types across various farm setups. Experienced Broiler farmers often report disease outbreaks and use antimicrobials more frequently. Educated farmers, however, experience fewer outbreaks and can better regulate antimicrobial usage.

A multi-dimensional validation strategy of pharmacological effects of Radix Isatidis Mixtures against the co-infection of Mycoplasma gallisepticum and Escherichia coli in poultry

Natural drugs possess exceptional pharmacological properties, yet their development is often hindered by a lack of clarity regarding the mechanisms of their pharmacological actions. Building on our previous research, we employed a co-infection model with Mycoplasma gallisepticum (MG) and Escherichia coli (E. coli) to investigate the pharmacological action of Radix Isatidis Mixtures (RIM). To further demonstrate the various mechanisms underlying the pharmacological effects of RIM, we conducted a validation study focusing on gene expression, protein interactions, metabolic pathways, and molecular docking. Through a multi-omics joint analysis network, we identified key targets and metabolites associated with co-infection and conducted targeted verification experiments with RIM aqueous extracts. The experimental results indicated that, compared to the co-infection group, the RIM treatment group significantly modulated the expression of select genes and proteins, particularly MMP2 and TLR4, with a high level of statistical significance (p < 0.01). At the metabolic level, the treatment group exhibited significantly reduced expression levels of Dopamine and γ-Aminobutyric acid. Notably, the molecular docking results highlighted compounds with the most favorable binding affinities: Salvianolic acid A (-10.1 kcal/mol), Licorice (-9.3 kcal/mol), and Isoglycyrrhiza (-8.7 kcal/mol). In conclusion, our multi-level experiments demonstrated that RIM possesses the characteristics of multi-pathway and multi-target treatment for co-infection.

Introduction of Avian metapneumovirus subtype A to the United States: molecular insights and implications

Avian metapneumovirus (aMPV) poses a significant threat to the poultry industry worldwide, primarily affecting turkeys and chickens. The recent detection of aMPV-A and -B subtypes in the United States marks a significant shift after a prolonged period free of aMPV following the eradication of the previously circulating subtype C. Hence, the demand for molecular diagnostic tests for aMPV has arisen due to their limited availability in the US market. In this study, we present the molecular characterization based on the complete genome sequence of aMPV subtype A, which was detected in the US for the first time. Four RT-qPCR positive samples were subjected to next-generation sequencing analysis, resulting in the assembly of one complete and one near-complete genome sequences. Phylogenetic analysis revealed that the isolated strains clustered within the aMPV-A subtype and were most closely related to recent Mexican strains. A detailed amino acid analysis identified unique mutations in the G gene of the US isolates compared to Mexican strains. Additionally, we compared the performance, cross-reactivity, and limit of detection of our revised aMPV subtype-specific RT-qPCR test with two commercial kits, demonstrating similar detection and subtyping capabilities. These findings highlight the importance of accurate diagnostic methods for disease management in the poultry industry, provide valuable insights into the epidemiology of aMPV, and underscore the need for continued vigilance and surveillance to mitigate its impact on poultry production.

Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya

Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross-sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral-pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired-end reads with an average of 200 nucleotides were generated from the cloacal and oral-pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral-pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral-pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus.

Methyltransferase K-D-K-E motif influences the intercellular transmission of Newcastle disease virus

We previously demonstrated that two methyltransferase motifs, K-D-K-E and G-G-D, affect the pathogenicity of Newcastle disease virus (NDV) by regulating mRNA translation and virus transmission. Here, we compared the infectious centre area produced by the NDV strain, rSG10, and methyltransferase motifs mutant rSG10 strains in DF-1 cells. The results show that intercellular transmission was attenuated by methyltransferase motif mutations. We further determined the ability of mutant viruses to spread in cell-free and cell-to-cell situations. Cell-free transmission of rSG10-K1756A was not reduced, indicating that cell-to-cell transmission of rSG10-K1756A was decreased. Using a donor and target system, we demonstrated that NDV can spread from cell-to-cell directly. Furthermore, by comparing the protein distribution area of three strains when treated with 2% agar overlay, we found that rSG10-K1756A was defective in cell-to-cell transmission. Tunnelling nanotubes (TNTs) are an important mode for cell-to-cell transmission. Treatment of cells with cytochalasin D (CytoD) or nocodazole to inhibit the formation of TNTs, reduced protein levels in all strains, but rSG10-K1756A was the least affected. These results indicate that mutation of the K-D-K-E motif is likely to restricted the spread of NDV via TNTs. Finally, we observed that matrix protein (M) and fusion protein (F) promoted the formation of cellular extensions, which may be involved in the cell-to-cell spread of NDV. Our research reveals a novel mechanism by which methyltransferase motifs affect the cell-to-cell spread of NDV and provides insight into dissemination of paramyxoviruses.

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.

Avian Metapneumovirus Infection in Poultry Flocks: A Review of Current Knowledge

Avian metapneumovirus (aMPV) is one of the respiratory viruses that cause global economic losses in poultry production systems. Therefore, it was important to design a comprehensive review article that gives more information about aMPV infection regarding the distribution, susceptibility, transmission, pathogenesis, pathology, diagnosis, and prevention. The aMPV infection is characterized by respiratory and reproductive disorders in turkeys and chickens. The disease condition is turkey rhinotracheitis in turkeys and swollen head syndrome in chickens. Infection with aMPV is associated with worldwide economic losses, especially in complications with other infections or poor environmental conditions. The genus Metapneumovirus is a single-stranded enveloped RNA virus and contains A, B, C, and D subtypes. Meat and egg-type birds are susceptible to aMPV infection. The virus can transmit through aerosol, direct contact, mechanical, and vertical routes. The disease condition is characterized by respiratory manifestations, a decrease in egg production, growth retardation, increasing morbidity rate, and sometimes nervous signs and a high mortality rate, particularly in concurrent infections. Definitive diagnosis of aMPV is based mainly on isolation and identification methods, detection of the viral DNA, as well as seroconversion. Prevention of aMPV infection depends on adopting biosecurity measures and vaccination using inactivated, live attenuated, and recombinant or DNA vaccines.

Phylogenetic and antigenic analysis of infectious bronchitis virus isolated from commercial and backyard chickens in Pakistan, 2015-2018

Infectious bronchitis virus (IBV) is a rapidly evolving virus affecting both vaccinated and unvaccinated poultry flocks and is responsible for significant economic losses globally; hence, it is imperative to obtain a deeper understanding of this pathogen. In this study, seven IBV strains were isolated from commercial and backyard poultry flocks during 2015-2018. We obtained full-length IBV genomes of two viruses using the Illumina sequencing method, while five additional viruses were genetically characterized through full-length spike (S1) gene sequencing. Phylogenetic and distance analysis based on complete S1 gene and full-length genome sequences revealed that one IBV isolate belonged to genotype GI-1 and six viruses were clustered within genotype GI-13. Deduced amino acid sequences of GI-13 strains exhibited 31.8-37.2 % divergence with the commonly used classic vaccine strains (M41) and 2.7-12.6 % with variant vaccine strains (4/91) in Pakistan. High evolutionary distances suggest that the IBV viruses circulating in Pakistan are under continuous evolutionary pressure. Moreover, ch/IBV/Pak/AW-2/2017 was found to have originated from an intra-genotypic recombination event between the variant group (GI-23 lineage as a major parent) and variant vaccine strain (4/91-like as a minor parent) and is the first example of recombination within genotype GI-13 in Pakistan. Together, these findings provide genetic and evolutionary insights into the currently circulating IBV genotypes in Pakistan, which could help to better understand the origin, spread and evolution of IBVs, and to ascertain the importance of disease monitoring as well as re-evaluation forof currently used vaccines and vaccination programmes.

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.

First report of Avian metapneumovirus type B in Iraqi broiler flocks with swollen head syndrome

Background and Aim:

Swollen head syndrome (SHS) is a complex disease caused by various agents, including bacterial and viral pathogens, as well as environmental factors. Avian metapneumovirus (aMPV) is one of the most important causes of respiratory diseases and SHS in poultry and one of the most widespread viruses worldwide; however, it has not been recorded in Iraq. This study aimed at the molecular identification and subtyping of aMPV in poultry, with the objectives of investigating the prevalence of aMPV in infected broiler flocks with SHS and molecular typing using primers specific to the study of the prevalence of subtypes A, B, and C of aMPV.

Materials and Methods:

This study was performed on 67 broiler farms that reported typical SHS from September 2018 to August 2019. Swabs were collected from the trachea, infraorbital sinuses, and lung, then uploaded on FTA cards and subjected to an RNA extraction protocol.

Results:

aMPV was detected in 16 (23.8%) samples. Molecular typing using primers specific to the attachment glycoprotein (G) gene showed that all positive samples belonged to subtype B, as assessed using the real-time polymerase chain reaction technique.

Conclusion:

aMPV may be the main etiological factor causing SHS in poultry. Moreover, this was the first report of the prevalence of subtype B aMPV strains in broiler farms in Iraq.

Circulation of three genotypes and identification of unique mutations in neutralizing epitopes of infectious bronchitis virus in chickens in Bangladesh

Infectious bronchitis (IB) is a highly contagious respiratory disease caused by a gammacoronavirus that has been circulating for many years in chickens in Bangladesh, resulting in significant economic losses. The aim of this study was to detect and characterize infectious bronchitis virus (IBV) from clinical outbreaks and surveillance samples. Real-time RT-PCR was used to detect IBV in pooled lung and tracheal tissue samples (n = 78), oropharyngeal swabs (n = 19), and pooled fecal samples (n = 13) from live-bird markets. Both respiratory and nephropathogenic forms of IB were suspected at necropsy (n = 7) from clinical outbreaks. Sequencing of hypervariable regions (HVR1-2 and HVR3) of the region of the spike gene (S) encoding the S1 subunit of five isolates revealed circulation of the Mass-like, QX-like, and 4/91-like genotypes of IBV in Bangladesh. Each genotype was extremely variable, as shown by separate clustering of the viruses in a phylogenetic tree and high nucleotide (nt) sequence divergence (38.8-41.2% and 25.7-37.4% in the HVR1-2 and HVR3 sequence, respectively). The unique mutation G65E was observed in each Mass-like isolate, and Y328S was observed in each 4/91-like Bangladeshi isolate. Three neutralizing epitope sites were predicted within the HVRs that differed significantly among the three genotypes. In addition, one Bangladeshi isolate carried fixed mutations at 294F and 306Y, like other pathogenic QX-like IBVs, which could affect epitopes involved in neutralization, facilitating virus circulation among vaccinated flocks. Therefore, continuous screening and genotype characterization will be necessary to track the epidemiology of IBV and control IB infection in Bangladesh.

Arachidonic acid metabolism is elevated in Mycoplasma gallisepticum and Escherichia coli co-infection and induces LTC4 in serum as the biomarker for detecting poultry respiratory disease

Outbreaks of multiple respiratory diseases with high morbidity and mortality have been frequently reported in poultry industry. Metabolic profiling has showed widespread usage in metabolic and infectious disease for identifying biomarkers and understanding of complex mechanisms. In this study, the non-targeted metabolomics were used on Mycoplasma gallisepticum (MG) and Escherichia coli (E.coli) co-infection model in serum, which showed that Leukotriene C4 (LTC4), Leukotriene D4 (LTD4), Chenodeoxycholate, Linoleate and numerous energy metabolites were varied significantly. KEGG enrichment analysis revealed that the metabolic pathways of linoleic acid, taurine and arachidonic acid (AA) were upregulated. To further characterize the consequences of co-infection, we performed an AA metabolic network pathway with metabolic products and enzyme genes. The results showed that the expression of LTC4 increased extremely significant and accompanied with different degree of infection. Meanwhile, the AA network performed the changes and differences of various metabolites in the pathway when multiple respiratory diseases occurred. Taken together, co-infection induces distinct alterations in the serum metabolome owing to the activation of AA metabolism. Furthermore, LTC4 in serum could be used as the biomarker for detecting poultry respiratory disease.

Abbreviations

MG: Mycoplasma gallisepticum; E.coli: Escherichia coli; AA: Arachidonic acid; LTC4: Leukotriene C4; CRD: chronic respiratory diseases; KEGG: Kyoto Encyclopedia of Genes and Genomes; LTs: leukotrienes; PGs: prostaglandins; NO: nitric oxide; HIS: histamine; PCA: Principal Component Analysis; PLS-DA: Partial Least Squares Discriminant Analysis; CCU: color change unit; UPLC: ultra-performance liquid chromatography; MS: mass spectrometry; DEMs: differentially expressed metabolites; ELISA: enzyme-linked immunosorbent assay; SD: standard deviation; VIP: Variable importance in the projection

Pakistan's backyard poultry farming initiative: impact analysis from a public health perspective

Commercial poultry rearing in Pakistan dates back to the 1960s. Meanwhile, backyard poultry setups have been providing meat and eggs for human consumption and supplementing the livelihood of farmers in many rural setups for ages. Different poultry rearing practices have varied approaches to feed supplementation, administration, biosafety practices, and flock size. All are important factors affecting disease spread and vulnerability. Recently, the Pakistani government announced the prime minister's Backyard Poultry Initiative under the National Agricultural Emergency program to economically develop farmers, especially women. Widespread adoption of this scheme with little to no training of inexperienced farmers may lead to the emergence of zoonotic infections in the population. The focus of the current review is to examine the probable impact of the promotion of backyard poultry farming practices by the government on the spread of zoonotic illnesses, both in the farmers and consumer population.

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.

Full-length genome sequences of the first H9N2 avian influenza viruses isolated in the Northeast of Algeria

Background

H9N2 avian influenza viruses (AIV) has a worldwide geographic distribution and affects poultry of different types of production. H9N2 AIV was first reported in the Northeast of Algeria in April 2017, following an outbreak associated with high mortality, in broiler flocks. In the present study, we report full-length genome sequences of AIV H9N2, and the detailed phylogeny and molecular genetic analyses.

Methods

Ten AIV H9N2 strains, collected in broiler flocks, were amplified in 9-day-old embryonated specific pathogen free (SPF) chicken eggs. Their full-length genomes were successfully sequenced and phylogenetic and molecular characterizations were conducted.

Results

Phylogenetic analysis showed that the isolates were monophyletic, grouped within the G-1 lineage and were very close to Moroccan and Algerian strains identified in 2016 and 2017, respectively. The low pathogenicity of the strains was confirmed by the sequence motif (335RSSR/GLF341) at the hemagglutinin (HA) cleavage site. An exclusive substitution (T197A) that had not been previously reported for H9N2 viruses; but, conserved in some pandemic H1N1 viruses, was observed. When compared to the G1-like H9N2 prototype, the studied strains showed one less glycosylation site in HA, but 2–3 additional ones in the stalk of the neuraminidase (NA). The HA protein harbored the substitution 234 L, suggesting binding preference to human-like receptors. The NA protein harbored S372A and R403W substitutions, previously detected in H9N2 from Asia and the Middle East, and especially in H2N2 and H3N2 strains that caused human pandemics. Different molecular markers associated with virulence and mammalian infections have been detected in the viral internal proteins. The matrix M2 protein possessed the S31N substitution associated with drug resistance. The non-structural 1 (NS1) protein showed the “GSEV” PDZ ligand (PL) C-terminal motif and no 80–84 deletion.

Conclusion

Characterized Algerian AIV isolates showed mutations that suggest increased zoonotic potential. Additional studies in animal models are required to investigate the pathogenicity of these H9N2 AIV strains. Monitoring their evolution in both migratory and domestic birds is crucial to prevent transmission to humans. Implementation of adequate biosecurity measures that limit the introduction and the propagation of AIV H9N2 in Algerian poultry farm is crucial.