Pathogenicity of Genetically Similar, H5N1 Highly Pathogenic Avian Influenza Virus Strains in Chicken and the Differences in Sensitivity among Different Chicken Breeds

Modelling the transmission dynamics of H9N2 avian influenza viruses in a live bird market

H9N2 avian influenza viruses (AIVs) are a major concern for the poultry sector and human health in countries where this subtype is endemic. By fitting a model simulating H9N2 AIV transmission to data from a field experiment, we characterise the epidemiology of the virus in a live bird market in Bangladesh. Many supplied birds arrive already exposed to H9N2 AIVs, resulting in many broiler chickens entering the market as infected, and many indigenous backyard chickens entering with pre-existing immunity. Most susceptible chickens become infected within one day spent at the market, owing to high levels of viral transmission within market and short latent periods, as brief as 5.3 hours. Although H9N2 AIV transmission can be substantially reduced under moderate levels of cleaning and disinfection, effective risk mitigation also requires a range of additional interventions targeting markets and other nodes along the poultry production and distribution network.

Development of a DAS-ELISA for Gyrovirus Homsa1 Prevalence Survey in Chickens and Wild Birds in China

Gyrovirus homsa1 (GyH1) is an emerging pathogenic single-stranded circular DNA virus that leads to immunosuppression, aplastic anemia, and multisystem damage in chickens. However, the prevalence of GyH1 infection in chickens and wild birds remains unknown. Here, we developed a double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) to investigate GyH1 infection in 8 chicken species and 25 wild bird species. A total of 2258 serum samples from chickens (n = 2192) in 15 provinces, and wild birds (n = 66) in Jinan Wildlife Hospital were collected from 2017 to 2021 in China. The GyH1-positive rates in chickens and wild birds were 9.3% (203/2192) and 22.7% (15/66), respectively. GyH1 was present in all flocks in 15 provinces. From 2017 to 2021, the positive rate ranged from 7.93% (18/227) to 10.67% (56/525), and the highest positive rate was present in 2019. Upon chicken age, the highest positive rate (25.5%) was present in young chickens (14-35 days old). Moreover, the GyH1-positive rate in broiler breeders (12.6%, 21/167) was significantly higher than that in layer chickens (8.9%, 14/157). This study shows that GyH1 has spread in chicken flocks and wild birds, and the higher GyH1-positive rate in wild birds indicates the risk of spillover from wild birds to chickens. Our study expanded the GyH1 epidemiological aspects and provided a theoretical basis for GyH1 prevention.

Can Infectious Disease Control Be Achieved without Antibiotics by Exploiting Mechanisms of Disease Tolerance?

Antimicrobial use in animal agriculture may be contributing to the emerging public health crisis of antimicrobial resistance. The sustained prevalence of infectious diseases driving antimicrobial use industry-wide suggests that traditional methods of bolstering disease resistance are, for some diseases, ineffective. A paradigm shift in our approach to infectious disease control is needed to reduce antimicrobial use and sustain animal and human health and the global economy. Targeting the defensive mechanisms that promote the health of an infected host without impacting pathogen fitness, termed “disease tolerance,” is a novel disease control approach ripe for discovery. This article presents examples of disease tolerance dictating clinical outcomes for several infectious diseases in humans, reveals evidence suggesting a similarly critical role of disease tolerance in the progression of infectious diseases plaguing animal agriculture, and thus substantiates the assertion that exploiting disease tolerance mechanisms can positively impact animal and human health.

First detection of Schmallenberg virus antibody in cattle population of eastern Iran

Schmallenberg virus (SBV) is an emerging single-stranded RNA virus being classified under Simbu serogroup of Bunyaviridae family. This study aimed to detect antibodies against SBV in cattle for the first time in three eastern provinces of Iran. Blood samples were randomly collected from jugular veins of 273 cattle, from 19 farms in Razavi Khorasan, South Khorasan and Sistan and Baluchestan provinces. Separated sera were analyzed to find SBV antibody using ID vet^® SBV indirect multi-species enzyme-linked immunosorbent assay test kit. From a total of 273 serum samples analyzed for SBV presence, 12.45% (n = 34) were positive for SBV antibody. Risk factors including breed, age and geographic area showed a statistically significant relationship with the virus prevalence. In conclusion, the seroprevalence of SBV is not high; but it is considerable in the studied parts of Iran. This is the first study regarding SBV seroprevalence in cattle population of eastern Iran and further studies about the virus epidemiology are recommended.

Evolutionary pressures rendered by animal husbandry practices for avian influenza viruses to adapt to humans

Commercial poultry operations produce and crowd billions of birds every year, which is a source of inexpensive animal protein. Commercial poultry is intensely bred for desirable production traits, and currently presents very low variability at the major histocompatibility complex. This situation dampens the advantages conferred by the MHC’s high genetic variability, and crowding generates immunosuppressive stress. We address the proteins of influenza A viruses directly and indirectly involved in host specificities. We discuss how mutants with increased virulence and/or altered host specificity may arise if few class I alleles are the sole selective pressure on avian viruses circulating in immunocompromised poultry. This hypothesis is testable with peptidomics of MHC ligands. Breeding strategies for commercial poultry can easily and inexpensively include high variability of MHC as a trait of interest, to help save billions of dollars as a disease burden caused by influenza and decrease the risk of selecting highly virulent strains.

Dual Host and Pathogen RNA-Seq Analysis Unravels Chicken Genes Potentially Involved in Resistance to Highly Pathogenic Avian Influenza Virus Infection

Highly pathogenic avian influenza viruses (HPAIVs) cause severe systemic disease and high mortality rates in chickens, leading to a huge economic impact in the poultry sector. However, some chickens are resistant to the disease. This study aimed at evaluating the mechanisms behind HPAIV disease resistance. Chickens of different breeds were challenged with H7N1 HPAIV or clade 2.3.4.4b H5N8 HPAIV, euthanized at 3 days post-inoculation (dpi), and classified as resistant or susceptible depending on the following criteria: chickens that presented i) clinical signs, ii) histopathological lesions, and iii) presence of HPAIV antigen in tissues were classified as susceptible, while chickens lacking all these criteria were classified as resistant. Once classified, we performed RNA-Seq from lung and spleen samples in order to compare the transcriptomic signatures between resistant and susceptible chickens. We identified minor transcriptomic changes in resistant chickens in contrast with huge alterations observed in susceptible chickens. Interestingly, six differentially expressed genes were downregulated in resistant birds and upregulated in susceptible birds. Some of these genes belong to the NF-kappa B and/or mitogen-activated protein kinase signaling pathways. Among these six genes, the serine protease-encoding gene PLAU was of particular interest, being the most significantly downregulated gene in resistant chickens. Expression levels of this protease were further validated by RT-qPCR in a larger number of experimentally infected chickens. Furthermore, HPAIV quasi-species populations were constructed using 3 dpi oral swabs. No substantial changes were found in the viral segments that interact with the innate immune response and with the host cell receptors, reinforcing the role of the immune system of the host in the clinical outcome. Altogether, our results suggest that an early inactivation of important host genes could prevent an exaggerated immune response and/or viral replication, conferring resistance to HPAIV in chickens.

Different Sensitivity of Japanese Native-Bred Chickens to H5 Subtypes of Highly Pathogenic Avian Influenza Viruses

The aim of this study was to investigate the sensitivity of three breeds of Japanese native chickens, commercial broilers, and specific-pathogen-free (SPF) white leghorns to three strains of the H5 subtype of highly pathogenic avian influenza viruses (HPAIVs). Chickens were experimentally inoculated with doses of 10², 10⁴, and 10⁶ 50% egg infective dose of A/mandarin duck/Miyazaki/22M-765/2011 (duck-11), A/chicken/Miyazaki/7/2014 (chicken-14), and A/chicken/Kumamoto/1-2C/2016 (chicken-16). The 50% chicken lethal dose of each virus, mean death time, and viral shedding patterns were compared. The Japanese native chickens showed varied susceptibility to the three H5 HPAIV isolates. Although two of the breeds showed some degree of resistance to duck-11 and chicken-14, all three were more sensitive to chicken-16 than commercial broiler chickens. We have shown that Japanese native chickens do not necessarily have resistance to HPAIV and that the pathogenic characteristics of HPAIVs are quite different between native and commercial chickens.

Avian influenza transmission risk along live poultry trading networks in Bangladesh

Live animal markets are known hotspots of zoonotic disease emergence. To mitigate those risks, we need to understand how networks shaped by trading practices influence disease spread. Yet, those practices are rarely recorded in high-risk settings. Through a large cross-sectional study, we assessed the potential impact of live poultry trading networks’ structures on avian influenza transmission dynamics in Bangladesh. Networks promoted mixing between chickens sourced from different farming systems and geographical locations, fostering co-circulation of viral strains of diverse origins in markets. Viral transmission models suggested that the observed rise in viral prevalence from farms to markets was unlikely explained by intra-market transmission alone, but substantially influenced by transmission occurring in upstream network nodes. Disease control interventions should therefore alter the entire network structures. However, as networks differed between chicken types and city supplied, standardised interventions are unlikely to be effective, and should be tailored to local structural characteristics.

Knock-in of the duck retinoic acid-inducible gene I (RIG-I) into the Mx gene in DF-1 cells enables both stable and immune response-dependent RIG-I expression

Waterfowls, such as ducks, are natural hosts of avian influenza virus (AIV) and can genetically limit the pathogenicity. On the other hand, some AIV strains cause severe pathogenicity in chickens. It is suggested that differences in the pathogenicity of AIV infection between waterfowls and chickens are related to the expression of retinoic acid-inducible gene I (RIG-I), a pattern recognition receptor that chickens evolutionally lack. Here, we knocked-in the duck RIG-I bearing the T2A peptide sequence at the 3′ region of the Mx, an interferon-stimulated gene (ISG), in chicken embryo fibroblast cells (DF-1) using the precise integration into target chromosome (PITCh) system to control the duck RIG-I expression in chickens. The expression patterns of the duck RIG-I were then analyzed using qPCR. The knocked-in DF-1 cells expressed RIG-I via the stimulation of IFN-β and poly(I:C) in a dose-dependent manner. Moreover, poly(I:C) stimulation in the knocked-in DF-1 cells upregulated RIG-I-like receptor (RLR) family signaling pathway-related genes IFN-β, OASL, and IRF7. The IFN-β-dependent expression of RIG-I and upregulation of IFN-β in the poly(I:C) stimulation demonstrated a positive-feedback loop via RIG-I, usually evident in ducks. Overall, this novel strategy established RIG-I-dependent immune response in chickens without overexpression of RIG-I and disruption of the host genes.

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RIG-I activates the innate immune response-related genes such as type I interferons.

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Loss of chicken RIG-I accounts for the pathogenicity of the avian influenza virus.

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This strategy controls RIG-I by host gene promoter activation via gene targeting.

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The knocked-in DF-1 cells express RIG-I upon IFN-β and poly (I:C) stimulation.

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A RIG-I-dependent immune response was observed without overexpression.

PA-X is an avian virulence factor in H9N2 avian influenza virus

Influenza A viruses encode several accessory proteins that have host- and strain-specific effects on virulence and replication. The accessory protein PA-X is expressed due to a ribosomal frameshift during translation of the PA gene. Depending on the particular combination of virus strain and host species, PA-X has been described as either acting to reduce or increase virulence and/or virus replication. In this study, we set out to investigate the role PA-X plays in H9N2 avian influenza viruses, focusing on the natural avian host, chickens. We found that the G1 lineage A/chicken/Pakistan/UDL-01/2008 (H9N2) PA-X induced robust host shutoff in both mammalian and avian cells and increased virus replication in mammalian, but not avian cells. We further showed that PA-X affected embryonic lethality in ovo and led to more rapid viral shedding and widespread organ dissemination in vivo in chickens. Overall, we conclude PA-X may act as a virulence factor for H9N2 viruses in chickens, allowing faster replication and wider organ tropism.

Transmission experiments support clade-level differences in the transmission and pathogenicity of Cambodian influenza A/H5N1 viruses

Influenza A/H5N1 has circulated in Asia since 2003 and is now enzootic in many countries in that region. In Cambodia, the virus has circulated since 2004 and has intermittently infected humans. During this period, we have noted differences in the rate of infections in humans, potentially associated with the circulation of different viral clades. In particular, a reassortant clade 1.1.2 virus emerged in early 2013 and was associated with a dramatic increase in infections of humans (34 cases) until it was replaced by a clade 2.3.2.1c virus in early 2014. In contrast, only one infection of a human has been reported in the 6 years since the clade 2.3.2.1c virus became the dominant circulating virus. We selected three viruses to represent the main viral clades that have circulated in Cambodia (clade 1.1.2, clade 1.1.2 reassortant, and clade 2.3.2.1c), and we conducted experiments to assess the virulence and transmissibility of these viruses in avian (chicken, duck) and mammalian (ferret) models. Our results suggest that the clade 2.3.2.1c virus is more "avian-like," with high virulence in both ducks and chickens, but there is no evidence of aerosol transmission of the virus from ducks to ferrets. In contrast, the two clade 1 viruses were less virulent in experimentally infected and contact ducks. However, evidence of chicken-to-ferret aerosol transmission was observed for both clade 1 viruses. The transmission experiments provide insights into clade-level differences that might explain the variation in A/H5N1 infections of humans observed in Cambodia and other settings.

Infectivity and pathobiology of H7N1 and H5N8 high pathogenicity avian influenza viruses for pigeons (Columba livia var. domestica)

Avian influenza (AI) is one of the most important viral diseases in poultry, wildlife and humans. Available data indicate that pigeons play a minimum role in the epidemiology of AI. However, a degree of variation exists in the susceptibility of pigeons to highly pathogenic AI viruses (HPAIVs), especially since the emergence of the goose/Guangdong H5 lineage. Here, the pathogenesis of H5N8 HPAIV in comparison with a H7N1 HPAIV and the role of pigeons in the epidemiology of these viruses were evaluated. Local and urban pigeons (Columba livia var. domestica) were intranasally inoculated with 10⁵ ELD₅₀ of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored during 14 days. Several pigeons inoculated with H5N8 or H7N1 seroconverted. However, clinical signs, mortality, microscopic lesions and viral antigen were only detected in a local pigeon inoculated with H5N8 HPAIV. This pigeon presented prostration and neurological signs that correlated with the presence of large areas of necrosis and widespread AIV antigen in the central nervous system, indicating that the fatal outcome was associated with neurological dysfunction. Viral RNA in swabs was detected in some pigeons inoculated with H7N1 and H5N8, but it was inconsistent, short-term and at low titres. The present study demonstrates that the majority of pigeons were resistant to H5N8 and H7N1 HPAIVs, despite several pigeons developing asymptomatic infections. The limited viral shedding indicates a minimum role of pigeons as amplifiers of HPAIVs, regardless of the viral lineage, and suggests that this species may represent a low risk for environmental contamination. RESEARCH HIGHLIGHTS H7N1 and H5N8 HPAIVs can produce subclinical infections in pigeons. The mortality caused by H5N8 HPAIV in one pigeon was associated with neurological dysfunction. Pigeons represent a low risk for environmental contamination by HPAIVs.

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.

Pathobiology of the highly pathogenic avian influenza viruses H7N1 and H5N8 in different chicken breeds and role of Mx 2032 G/A polymorphism in infection outcome

Chickens are highly susceptible to highly pathogenic avian influenza viruses (HPAIVs). However, the severity of infection varies depending of the viral strain and the genetic background of the host. In this study, we evaluated the pathogenesis of two HPAIVs (H7N1 and H5N8) and assessed the susceptibility to the infection of local and commercial chicken breeds from Spain. Eight chicken breeds were intranasally inoculated with 10⁵ ELD₅₀ of A/Chicken/Italy/5093/1999 (H7N1) or A/Goose/Spain/IA17CR02699/2017 (H5N8 clade 2.3.4.4. B) and monitored during 10 days. Chickens were highly susceptible to both HPAIVs, but H7N1 was considerably more virulent than H5N8 as demonstrated by the highest mortality rates and shortest mean death times (MDT). Both HPAIVs produced severe necrosis and intense viral replication in the central nervous system, heart and pancreas; however, the lesions and replication in other tissues were virus-dependent. High levels of viral RNA were detected by the oral route with both viruses. In contrast, a low number of H5N8-inoculated chickens shed by the cloacal route, demonstrating a different pattern of viral shedding dependent of the HPAIV. We found a high variation in the susceptibility to HPAIVs between the different chicken breeds. The birds carrying the genotype AA and AG at position 2032 in chicken Mx gene presented a slightly higher, but not significant, percentage of survival and a statistically significant longer MDT than GG individuals. Our study demonstrated that the severity of HPAI infection is largely dependent of the viral isolate and host factors, underlining the complexity of HPAI infections.

Identification of genes related to effects of stress on immune function in the spleen in a chicken stress model using transcriptome analysis

Stress is a physiological manifestation of the body's defense against adverse effects of external environment, but the molecular regulatory mechanism of stress effects on immune function of poultry has not been fully clarified. In this study, 7-day-old Chinese local breed Gushi cocks were used as model animal, and the stress model was successfully constructed by adding corticosterone (CORT) 30 mg/kg basic diet for 7 days. The spleen transcriptomes of the control group (B_S group) and the stress model group (C_S group) was determined by high-throughput mRNA sequencing (RNA-Seq) technology, and a total of 269 significantly differentially expressed genes (SDEGs) were obtained (Padj < 0.05, |FC| ≥ 2 and FPKM > 1). Compared with B_S group, there were 140 significantly up-regulated genes and 129 significantly down-regulated genes in C_S group. The immune/stress-related Gene Ontology (GO) terms included positive regulation of T cell mediated immunity, chemokine-mediated signaling pathway, T cell mediated immunity and so on. The SDEGs such as IL8L1, HSPA8, HSPA2, RSAD2, CCR8L and DMB1 were involved in these GO terms. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the SDEGs participated in many immune-related signaling pathways. The immune-related genes HSPA2, HSPA8, HSP90AA1, HSPH1 and HERPUD1 were enriched in Protein processing in endoplasmic reticulum pathway, IL8L1, CXCL13L2, CCR6, LEPR, CCR9 and CCR8L were enriched in Cytokine-cytokine receptor interaction pathway. The protein-protein interactions (PPI) analysis showed HSPA8, HSPA2 and IL8L1 as key core nodes had 7 interactions and may play important roles in the regulation of CORT-induced stress effects on immune function. The data onto this study enriched the genomic study of stress effects on immune function, and provided unique insights into the molecular mechanism of stress effects on immune function, and the genes identified in this study can be candidates for future research on stress response.

Genetic determinants of resistance to highly pathogenic avian influenza in chickens

Highly pathogenic avian influenza (HPAI) poses a huge threat to poultry production and also introduces an epidemiological risk in the human population. Thus far, HPAI has been controlled mainly through widespread implementation of biosecurity, and in the case of an outbreak, liquidation of flocks and establishment of protection zones. Alternative strategies for combating HPAI include the use of vaccines, genetic modification, and genetic selection for increased general and specific immunity in birds. These kinds of strategies often require identification of the genes involved in the immune response to the pathogen. Many genes have been identified as potentially associated with differences in the response to HPAI between poultry species and between individuals. Thus far, the most attention has been focused on genes taking part in regulating the innate immune response, which is responsible for preventing infection and limiting the replication and spread of the virus. The most commonly mentioned candidates for layer chickens include interferon-stimulated genes (ISGs) and RIG-I-like receptors. Proteins encoded by genes of the BTLN family, defensins, and proteins involved in apoptosis have also been associated with differences in the response to HPAI. Recent years have seen an increasing number of studies on the genetic determinants of individual differences in the response to HPAI in chickens. Data from HPAI outbreaks in the US in the spring of 2015 and Mexico in the years 2012-2016 have enabled a more precise analysis of this problem. A number of genes have been identified as associated with the immune response, but their specific role in determining the survival of birds requires further study. Preliminary results indicate that genetic determinants of resistance to HPAI are highly complex and can vary depending on the virus strain and the genetic line of birds.

Creating Disease Resistant Chickens: A Viable Solution to Avian Influenza?

Influenza A virus (IAV) represents an ongoing threat to human and animal health worldwide. The generation of IAV-resistant chickens through genetic modification and/or selective breeding may help prevent viral spread. The feasibility of creating genetically modified birds has already been demonstrated with the insertion of transgenes that target IAV into the genomes of chickens. This approach has been met with some success in minimising the spread of IAV but has limitations in terms of its ability to prevent the emergence of disease. An alternate approach is the use of genetic engineering to improve host resistance by targeting the antiviral immune responses of poultry to IAV. Harnessing such resistance mechanisms in a “genetic restoration” approach may hold the greatest promise yet for generating disease resistant chickens. Continuing to identify genes associated with natural resistance in poultry provides the opportunity to identify new targets for genetic modification and/or selective breeding. However, as with any new technology, economic, societal, and legislative barriers will need to be overcome before we are likely to see commercialisation of genetically modified birds.

Pathobiology of Tennessee 2017 H7N9 low and high pathogenicity avian influenza viruses in commercial broiler breeders and specific pathogen free layer chickens

In March 2017, H7N9 highly pathogenic avian influenza (HPAI) virus was detected in 2 broiler breeder farms in the state of Tennessee, USA. Subsequent surveillance detected the low pathogenicity avian influenza (LPAI) virus precursor in multiple broiler breeder farms and backyard poultry in Tennessee and neighboring states. The pathogenesis of the H7N9 LPAI virus was investigated in commercial broiler breeders, the bird type mostly affected in this outbreak. Infectivity, transmissibility, and pathogenesis of the H7N9 HPAI and LPAI viruses were also studied in 4-week-old specific pathogen free (SPF) leghorn chickens. The mean bird infectious doses (BID₅₀) for the LPAI isolate was 5.6 log₁₀ mean egg infectious dose (EID₅₀) for broiler breeders and 4.3 log₁₀ EID₅₀ for SPF layer chickens, and no transmission to contact-exposed birds was observed. In both bird types, virus shedding was almost exclusively from the oropharyngeal route. These findings suggest sub-optimal adaptation for sustained transmission with the H7N9 LPAI isolate, indicating that factors other than the birds genetic background may explain the epidemiology of the outbreak. The BID₅₀ for the HPAI isolate in SPF layer chickens was more than 2 logs lower (<2 log₁₀ EID₅₀) than the LPAI isolate. Also, the HPAI virus was shed by both the oropharyngeal and cloacal routes and transmitted to contacts. Greater susceptibility and easier transmission of the H7N9 HPAI virus are features of the HP phenotype that could favor the spread of HPAI over LPAI viruses during outbreaks.

Identification of Mx gene nucleotide dimorphism (G/A) as genetic marker for antiviral activity in Egyptian chickens

Egyptian chickens, representing 2 breeds and 7 strains, were genotyped using the PCR-RFLP and sequencing techniques for detection of a non-synonymous dimorphism (G/A) in exon 14 of chicken Myxovirus resistance (Mx) gene. This dimorphic position is responsible for altering Mx protein's antiviral activity. Polymerase Chain reactions were performed using Egyptian chickens DNA and specific primer set to amplify Mx DNA fragments of 299 or 301 bp, containing the dimorphic position. Amplicons were cut with restriction enzyme Hpy81. Genotype and allele frequencies for the resistant allele A and sensitive allele G were calculated in all the tested chickens. Results of PCR-RFLP were confirmed by sequencing. The three genotypes AA, AG, GG at the target nucleotide position in Mx gene were represented in all the studied Egyptian chicken breeds and strains except Baladi strain which showed only one genotype AA. The average allele frequency of the resistant A allele in the tested birds (0.67) was higher than the sensitive G allele average frequency in the same birds (0.33). Appling PCR-RFLP technique in the breeding program can be used to select chickens carrying the A allele with high frequencies. This will help in improving poultry breeding in Egypt by producing infectious disease-resistant chickens.

Risk Factors for Avian Influenza H9 Infection of Chickens in Live Bird Retail Stalls of Lahore District, Pakistan 2009-2010

This study was conducted to identify risk factors associated with AIV infections in live bird retail stalls (LBRS) in Lahore District, Pakistan. A cross-sectional survey of LBRS was conducted from December 2009-February 2010 using two-stage cluster sampling based on probability proportional to size. A total of 280 oropharyngeal swab sample pools were collected from 1400 birds in 8 clusters and tested by qRT-PCR for the matrix (M) gene of type A influenza virus and HA gene subtypes H9, H5 and H7. Thirty-four (34) samples were positive for the M gene, of which 28 were also positive for H9. No sample was found positive for H5 or H7. Data for 36 potential risk factors, collected by questionnaire, were analyzed by survey-weighted logistic regression and prevalence odds ratios (OR) for associated risk factors were calculated. A final multivariable model identified three risk factors for H9 infection in LRBS, namely obtaining birds from mixed sources (OR 2.28, CI_95%: 1.4–3.7), keeping birds outside cages (OR 3.10, CI_95%: 1.4–7.0) and keeping chicken breeds other than broilers (OR 6.27, CI_95%: 1.7–23.2). Sourcing birds from dealers/wholesalers, keeping birds inside cages and avoiding mixing different breeds in cages could reduce the risk of H9 infections in LRBS.

Identifying the genetic basis for resistance to avian influenza in commercial egg layer chickens

Two highly pathogenic avian influenza (HPAI) outbreaks have affected commercial egg production flocks in the American continent in recent years; a H7N3 outbreak in Mexico in 2012 that caused 70% to 85% mortality and a H5N2 outbreak in the United States in 2015 with over 99% mortality. Blood samples were obtained from survivors of each outbreak and from age and genetics matched non-affected controls. A total of 485 individuals (survivors and controls) were genotyped with a 600 k single nucleotide polymorphism (SNP) array to detect genomic regions that influenced the outcome of highly pathogenic influenza infection in the two outbreaks. A total of 420458 high quality, segregating SNPs were identified across all samples. Genetic differences between survivors and controls were analyzed using a logistic model, mixed models and a Bayesian variable selection approach. Several genomic regions potentially associated with resistance to HPAI were identified, after performing multidimensional scaling and adjustment for multiple testing. Analysis conducted within each outbreak identified different genomic regions for resistance to the two virus strains. The strongest signals for the Iowa H5N2 survivor samples were detected on chromosomes 1, 7, 9 and 15. Positional candidate genes were mainly coding for plasma membrane proteins with receptor activity and were also involved in immune response. Three regions with the strongest signal for the Mexico H7N3 samples were located on chromosomes 1 and 5. Neuronal cell surface, signal transduction and immune response proteins coding genes were located in the close proximity of these regions.

Age is not a determinant factor in susceptibility of broilers to H5N2 clade 2.3.4.4 high pathogenicity avian influenza virus

In 2014–2015, the US experienced an unprecedented outbreak of H5 clade 2.3.4.4 highly pathogenic avian influenza (HPAI) virus. The H5N2 HPAI virus outbreak in the Midwest in 2015 affected commercial turkey and layer farms, but not broiler farms. To assess any potential genetic resistance of broilers and/or age-related effects, we investigated the pathogenesis and transmission of A/turkey/Minnesota/12582/2015 (H5N2) (Tk/MN/15) virus in commercial 5-week-old broilers, 8-week-old broilers, and >30-week-old broiler breeders. The mean bird lethal dose (BLD₅₀) was 5.0 log₁₀ mean egg infectious dose (EID₅₀) for all age groups. The mean death time (MDT) was statistically not different among the three age groups, ranging between 3.2 and 4.8 days. All broilers that became infected shed high levels of virus with transmission to contacts and demonstrated severe pathology. Mortality and virus shedding results indicated that age is not a determinant factor in susceptibility of broilers to H5N2 clade 2.3.4.4 HPAI virus. Previously, the Tk/MN/15 virus had a BLD₅₀ of 3.6 log₁₀ EID₅₀ and MDT of 2 days in White Leghorn chickens and a BLD₅₀ of 5.0 log₁₀ EID₅₀ and MDT of 5.9 days in turkeys, suggesting that the broiler breed is less susceptible to Midwestern H5N2 virus than the layer breed but similarly susceptible to turkeys. Therefore, genetic resistance of broilers to infection may have accounted only partially for the lack of affected broiler farms in the Midwestern outbreaks, with other contributing factors such as fewer outside to on farm exposure to contacts, type of production management system or enhanced biosecurity.

Cytokine expression in three chicken host systems infected with H9N2 influenza viruses with different pathogenicities

SD/818 and SD/196 are H9N2 influenza virus strains isolated from chickens from the same farm at different times that exhibited similar genetic evolution. However, strain SD/818 exhibited higher pathogenicity in chickens than strain SD/196 and other H9N2 influenza virus epidemic strains from China. The expression of cytokines is an important host defence mechanism following viral infection and their intensity is a major determinant of viral pathogenicity. To elucidate the mechanism underlying the increased pathogenicity of strain SD/818 from the host's perspective, viral replication and cytokine expression were dynamically studied using real-time quantitative reverse transcription PCR in chickens infected with strain SD/818 compared with chickens infected with strain SD/196 in this study. The results showed that the replication of strain SD/818 and the expressions of IL-1β, IL-6, TNF-α, IFN-α and IFN-β induced by strain SD/818 were higher than those induced by strain SD/196 in the chicken host system. Expression of these cytokines in chickens coincided with or followed virus replication. These results suggested that high-level viral replication and pro-inflammatory cytokine expression (but not decreased type I IFN expression) were associated with the higher pathogenicity of strain SD/818 in chickens.