The genesis and evolution of H9N2 influenza viruses in poultry from southern China, 2000 to 2005

Epidemiology and evolutionary dynamics of H9N2 avian influenza virus in Bangladesh

Low pathogenicity avian influenza (LPAI) H9N2 has been enzootic in Bangladeshi poultry since 2006. H9N2 outbreaks can decrease egg production and growth and pose a risk to human health. The role of avian hosts in the persistence, evolution, and dispersion of H9N2 is poorly understood in Bangladesh. Hence, this study unveils the intricate role of major host species in virus maintenance and evolution and the temporal and seasonal patterns of H9N2 in Bangladesh from 2006 to 2023. Multinomial logistic regression analysis indicated that the circulation of H9N2 in different species and interfaces is significantly influenced by the seasons. Bayesian phylogenetic analysis of H9N2 sequences in Bangladesh revealed two distinct lineages: G1 and Eurasian. The G1 lineage split into two clusters, coexisting until 2019, at which point only one cluster persisted. Bayesian phylodynamic analysis of G1 lineage unveiled frequent bidirectional viral transitions among ducks, chickens, and quails. Chickens might be a pivotal source of H9N2 in Bangladesh, with a higher number of viral transitions from chickens to ducks and quails. Quails appear to acquire most of their viral transitions from chickens rather than ducks, suggesting that quail epizootics are primarily triggered by spillover events from chickens. Our results suggest viral circulation in commercial chickens despite vaccination. The vaccination approach should be revised, assess vaccine efficacy, and extension of vaccination to backyard chickens and quails.

Research Note: Novel reassortant avian influenza A(H9N2) Viruses in Wild Birds in Shanghai, China, 2020-2023

The H9N2 subtype of avian influenza virus poses significant challenges to global poultry and human health. During the active surveillance of avian influenza virus in wild birds in Shanghai from 2020 to 2023, a total of nine H9N2 viruses were identified. To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways. The nine H9N2 viruses were classified into seven genotypes, and some of them could contribute internal genes to recently circulating HPAI A(H5N8) and A(H5N1) viruses of clade 2.3.4.4b. These results highlight the importance of active surveillance of AIVs in wild birds to comprehend viral ecology and evaluate potential transmission risk in poultry and humans.

Random forest algorithm reveals novel sites in HA protein that shift receptor binding preference of the H9N2 avian influenza virus

A switch from avian-type α-2,3 to human-type α-2,6 receptors is an essential element for the initiation of a pandemic from an avian influenza virus. Some H9N2 viruses exhibit a preference for binding to human-type α-2,6 receptors. This identifies their potential threat to public health. However, our understanding of the molecular basis for the switch of receptor preference is still limited. In this study, we employed the random forest algorithm to identify the potentially key amino acid sites within hemagglutinin (HA), which are associated with the receptor binding ability of H9N2 avian influenza virus (AIV). Subsequently, these sites were further verified by receptor binding assays. A total of 12 substitutions in the HA protein (N158D, N158S, A160 ​N, A160D, A160T, T163I, T163V, V190T, V190A, D193 ​N, D193G, and N231D) were predicted to prefer binding to α-2,6 receptors. Except for the V190T substitution, the other substitutions were demonstrated to display an affinity for preferential binding to α-2,6 receptors by receptor binding assays. Especially, the A160T substitution caused a significant upregulation of immune-response genes and an increased mortality rate in mice. Our findings provide novel insights into understanding the genetic basis of receptor preference of the H9N2 AIV.

H9 Consensus Hemagglutinin Subunit Vaccine with Adjuvants Induces Robust Mucosal and Systemic Immune Responses in Mice by Intranasal Administration

The H9N2 subtype avian influenza viruses mainly cause respiratory symptoms, reduce the egg production and fertility of poultry, and result in secondary infections, posing a great threat to the poultry industry and human health. Currently, all H9N2 avian influenza commercial vaccines are inactivated vaccines, which provide protection for immunized animals but cannot inhibit the spread of the virus and make it difficult to distinguish between the infected animals and vaccinated animals. In this study, a trimeric consensus H9 hemagglutinin (HA) subunit vaccine for the H9N2 subtype avian influenza virus based on a baculovirus expression system was first generated, and then the effects of three molecular adjuvants on the H9 HA subunit vaccine, Cholera toxin subunit B (CTB), flagellin, and granulocyte-macrophage colony-stimulating factor (GM-CSF) fused with H9 HA, and one synthetic compound, a polyinosinic-polycytidylic acid (PolyI:C) adjuvant, were evaluated in mice by intranasal administration. The results showed that these four adjuvants enhanced the immunogenicity of the H9 HA subunit vaccine for avian influenza viruses, and that GM-CSF and PolyI:C present better mucosal adjuvant activity for the H9 HA subunit vaccine. These results demonstrate that we have developed a potential universal H9 HA mucosal subunit vaccine with adjuvants in a baculovirus system that would be helpful for the prevention and control of H9N2 subtype avian influenza viruses.

Mutual antagonism of mouse-adaptation mutations in HA and PA proteins on H9N2 virus replication

Avian H9N2 viruses have wide host range among the influenza A viruses. However, knowledge of H9N2 mammalian adaptation is limited. To explore the molecular basis of the adaptation to mammals, we performed serial lung passaging of the H9N2 strain A/chicken/Hunan/8.27 YYGK3W3-OC/2018 (3W3) in mice and identified six mutations in the hemagglutinin (HA) and polymerase acidic (PA) proteins. Mutations L226Q, T511I, and A528V of HA were responsible for enhanced pathogenicity and viral replication in mice; notably, HA-L226Q was the key determinant. Mutations T97I, I545V, and S594G of PA contributed to enhanced polymerase activity in mammalian cells and increased viral replication levels in vitro and in vivo. PA-T97I increased viral polymerase activity by accelerating the viral polymerase complex assembly. Our findings revealed that the viral replication was affected by the presence of PA-97I and/or PA-545V in combination with a triple-point HA mutation. Furthermore, the double- and triple-point PA mutations demonstrated antagonistic effect on viral replication when combined with HA-226Q. Notably, any combination of PA mutations, along with double-point HA mutations, resulted in antagonistic effect on viral replication. We also observed antagonism in viral replication between PA-545V and PA-97I, as well as between HA-528V and PA-545V. Our findings demonstrated that several antagonistic mutations in HA and PA proteins affect viral replication, which may contribute to the H9N2 virus adaptation to mice and mammalian cells. These findings can potentially contribute to the monitoring of H9N2 field strains for assessing their potential risk in mammals.

Mixed selling of different poultry species facilitates emergence of public-health-threating avian influenza viruses

Live poultry markets (LPMs) are regarded as hubs for avian influenza virus (AIV) transmission in poultry and are a major risk factor in human AIV infections. We performed an AIV surveillance study at a wholesale LPM, where different poultry species were sold in separate stalls, and nine retail LPMs, which received poultry from the wholesale LPM but where different poultry species were sold in one stall, in Guangdong province from 2017 to 2019. A higher AIV isolation rate was observed at the retail LPMs than the wholesale LPM. H9N2 was the dominant AIV subtype and was mainly present in chickens and quails. The genetic diversity of H9N2 viruses was greater at the retail LPMs, where a complex system of two-way transmission between different poultry species had formed. The isolated H9N2 viruses could be classed into four genotypes: G57 and the three novel genotypes, NG164, NG165, and NG166. The H9N2 AIVs isolated from chickens and quails at the wholesale LPM only belonged to the G57 and NG164 genotypes, respectively. However, the G57, NG164, and NG165 genotypes were identified in both chickens and quails at the retail LPMs. We found that the replication and transmission of the NG165 genotype were more adaptive to both poultry and mammalian models than those of its precursor genotype, NG164. Our findings revealed that mixed poultry selling at retail LPMs has increased the genetic diversity of AIVs, which might facilitate the emergence of novel viruses that threaten public health.

Current situation and control strategies of H9N2 avian influenza in South Korea

The H9N2 avian influenza (AI) has become endemic in poultry in many countries since the 1990s, which has caused considerable economic losses in the poultry industry. Considering the long history of the low pathogenicity H9N2 AI in many countries, once H9N2 AI is introduced, it is more difficult to eradicate than high pathogenicity AI. Various preventive measures and strategies, including vaccination and active national surveillance, have been used to control the Y439 lineage of H9N2 AI in South Korea, but it took a long time for the H9N2 virus to disappear from the fields. By contrast, the novel Y280 lineage of H9N2 AI was introduced in June 2020 and has spread nationwide. This study reviews the history, genetic and pathogenic characteristics, and control strategies for Korean H9N2 AI. This review may provide some clues for establishing control strategies for endemic AIV and a newly introduced Y280 lineage of H9N2 AI in South Korea.

Protective Efficacy of Inactivated H9N2 Vaccine in Turkey Poults under Both Experimental and Field Conditions

Low pathogenic avian influenza (LPAI) H9N2 virus is one of the major poultry pathogens associated with severe economic losses in the poultry industry (broiler, layers, breeders, and grandparents' flocks), especially in endemic regions including the Middle East, North Africa, and Asian countries. This work is an attempt to evaluate the efficacy of whole inactivated H9N2 vaccine (MEFLUVAC^TM H9) in turkey poults kept under laboratory and commercial farm conditions. Here, 10,000 white turkey poults (1-day old) free from maternally derived immunity against H9N2 virus were divided into four groups; G1 involved 10 vaccinated birds kept under biosafety level-3 (BLS-3) as a laboratory vaccinated and challenged group, while G2 had 9970 vaccinated turkeys raised on a commercial farm. Ten of those birds were moved to BLS-3 for daily cloacal and tracheal swabbing to check for the absence of any life-threating disease, before conducting analyses. G3 (10 birds) served as a non-vaccinated challenged control under BSL-3 conditions, while G4 (10 birds) was used as a non-vaccinated and non-challenged control under BSL-3 conditions. Sera were collected on days 7-, 14-, 21-, and 28-post-vaccinations to monitor the humoral immune response using a hemagglutination-inhibition (HI) test. At these same intervals, cloacal and tracheal swabs were also checked for any viral infection. The challenge was conducted 28 days post-vaccination (PV) using AI-H9N2 in BSL-3 by intranasal inoculation of 6-log10 embryo infective dose₅₀ (EID₅₀). At 3-, 6-, and 10-days post-challenge, oropharyngeal swabs were taken from challenged birds to quantify viral shedding by quantitative polymerase chain reaction (qRT-PCR). The results of this study showed that vaccinated groups (G1/2) developed HI titers of 1.38, 4.38, 5.88, and 7.25 log₂ in G1 vs. 1.2, 3.8, 4.9 and 6.2 log₂ in G2 when measured at 7-, 14-, 21- and 28-days PV, respectively, while undetectable levels were recorded in non-vaccinated groups (G3/4). Birds in G3 showed 90% clinical sickness vs. 10% and 20% in G1/2, respectively, over a 10-day monitoring period following challenge. Vaccinated birds showed a significant reduction in virus shedding in terms of the number of shedders, amount of shed virus and shedding interval over the non-vaccinated challenged birds. Regarding mortality, all groups did not show any mortality, which confirms that the circulating H9N2 virus still has low pathogenicity and cannot cause mortality. However, the virus may cause up to 90% clinical sickness in non-vaccinated birds vs. 10% and 20% in laboratory- and farm-vaccinated birds, respectively, highlighting the role of the vaccine in limiting clinical sickness cases. In conclusion, under the current trial circumstances, MEFLUVAC^TM-H9 provided protective seroconversion titers, significant clinical sickness protection and significant reduction in virus shedding either in laboratory- or farm-vaccinated groups after a single vaccine dose.

Status and Challenges for Vaccination against Avian H9N2 Influenza Virus in China

In China, H9N2 avian influenza virus (AIV) has become widely prevalent in poultry, causing huge economic losses after secondary infection with other pathogens. Importantly, H9N2 AIV continuously infects humans, and its six internal genes frequently reassort with other influenza viruses to generate novel influenza viruses that infect humans, threatening public health. Inactivated whole-virus vaccines have been used to control H9N2 AIV in China for more than 20 years, and they can alleviate clinical symptoms after immunization, greatly reducing economic losses. However, H9N2 AIVs can still be isolated from immunized chickens and have recently become the main epidemic subtype. A more effective vaccine prevention strategy might be able to address the current situation. Herein, we analyze the current status and vaccination strategy against H9N2 AIV and summarize the progress in vaccine development to provide insight for better H9N2 prevention and control.

Effect of the Interaction between Viral PB2 and Host SphK1 on H9N2 AIV Replication in Mammals

The H9N2 avian influenza virus (AIV) is currently widespread worldwide, posing a severe threat to the poultry industry and public health. Reassortment is an important way for influenza viruses to adapt to a new host. In 2007, the PB2 gene of H9N2 AIV in China was reassorted, and the DK1-like lineage replaced the F/98-like lineage, forming a dominant genotype of G57. This genotype and its reassortants (such as H7N9, H10N8 and H5N6) showed higher mammalian adaptation, and caused increased human infections. However, the adaptive mechanisms of the DK1-like lineage PB2 gene remain unclear. Here, we confirmed that the PB2 lineage of the H9N2 AIV currently prevalent in China still belongs to the DK1-like lineage and, compared with the previously predominant F/98-like lineage, the DK1-like lineage PB2 gene significantly enhances H9N2 AIV to mammalian adaptation. Through transcriptomic analysis and qRT–PCR and western blot experiments, we identified a host factor, sphingosine kinase 1 (SphK1), that is closely related to viral replication. SphK1 inhibits the replication of DK1-like PB2 gene H9N2 AIV, but the ability of SphK1 protein to bind DK1-like PB2 protein is weaker than that of F/98-like PB2 protein, which may contribute to H9N2 AIV containing the DK1-like PB2 gene to escape the inhibitory effect of host factor SphK1 for efficient infection. This study broadens our understanding of the adaptive evolution of H9N2 AIV and highlights the necessity to pay close attention to the AIV that contains the adaptive PB2 protein in animals and humans.

Improved Whole Gamma Irradiated Avian Influenza Subtype H9N2 Virus Vaccine Using Trehalose and Optimization of Vaccination Regime on Broiler Chicken

Gamma (γ)-radiation can target viral genome replication and preserve viral structural proteins compared to formalin inactivation. Thus, a stronger immunity could be induced after the inoculation of the irradiated virus. In this study, γ-irradiated low-pathogenic avian influenza virus-H9N2 (LPAIV-H9N2) was used to immunize the broiler chicken in two formulations, including γ-irradiated LPAIV-H9N2 with 20% Trehalose intranasally (IVT.IN) or γ-irradiated LPAIV-H9N2 plus Montanide oil adjuvant ISA70 subcutaneously (IV+ISA.SC) in comparison with formalin-inactivated LPAIV-H9N2 vaccine intranasally (FV.IN) or formalin-inactivated LPAIV-H9N2 plus ISA70 subcutaneously (FV+ISA.SC). Two vaccination regimes were employed; the first one was primed on day 1 and boosted on day 15 (early regime), and the second one was primed on day 11 and boosted on day 25 (late regime). A challenge test was performed with a live homologous subtype virus. Virus shedding was monitored by quantifying the viral load via RT-qPCR on tracheal and cloacal swabs. Hemagglutination inhibition (HI) antibody titration and stimulation index (SI) of the splenic lymphocyte proliferation were measured, respectively, by HI test and Cell Proliferation assay. Cytokine assay was conducted by the RT-qPCR on antigen-stimulated spleen cells. The results of the HI test showed significant increases in antibody titer in all vaccinated groups, but it was more evident in the IVT late vaccination regime, reaching 5.33 log₂. The proliferation of stimulated spleen lymphocytes was upregulated more in the IVT.IN vaccine compared to other vaccines. The mRNA transcription levels of T-helper type 1 cytokines such as interferon-gamma (IFN-γ) and interleukin 2 (IL-2) were upregulated in all vaccinated groups at the late regime. Moreover, IL-6, a pro-inflammatory cytokine was upregulated as well. However, upregulation was more noticeable in the early vaccination than the late vaccination (p< 0.05). After the challenge, the monitoring of virus shedding for the H9 gene represented an extremely low viral load. The body weight loss was not significant (p > 0.05) among the vaccinated groups. In addition, the viral load of <10^0.5 TCID₅₀/ml in the vaccinated chicken indicated the protective response for all the vaccines. Accordingly, the IVT vaccine is a good candidate for the immunization of broiler chicken via the intranasal route at late regime.

Emerging threat and vaccination strategies of H9N2 viruses in poultry in Indonesia: A review

Avian influenza virus subtype H9N2 was first documented in Indonesia in 2017. It has become prevalent in chickens in many provinces of Indonesia as a result of reassortment in live bird markets. Low pathogenic avian influenza subtype H9N2 virus-infected poultry provides a new direction for influenza virus. According to the latest research, the Indonesian H9N2 viruses may have developed through antigenic drift into new genotype, posing a significant hazard to poultry and public health. The latest proof of interspecies transmission proposes that, the next human pandemic variant will be avian influenza virus subtype H9N2. Manipulation and elimination of H9N2 viruses in Indonesia, constant surveillance of viral mutation, and vaccines updates are required to achieve effectiveness. The current review examines should be investigates/assesses/report on the development and evolution of newly identified H9N2 viruses in Indonesia and their vaccination strategy.

Emerging threats and vaccination strategies of H9N2 viruses in poultry in Indonesia: A review

Avian influenza virus subtype H9N2 was first documented in Indonesia in 2017. It has become prevalent in chickens in many provinces of Indonesia as a result of reassortment in live bird markets. Low pathogenic avian influenza subtype H9N2 virus-infected poultry provides a new direction for the influenza virus. According to the latest research, the Indonesian H9N2 viruses may have developed through antigenic drift into a new genotype, posing a significant hazard to poultry and public health. The latest proof of interspecies transmission proposes that the next human pandemic variant will be the avian influenza virus subtype H9N2. Manipulation and elimination of H9N2 viruses in Indonesia, constant surveillance of viral mutation, and vaccine updates are required to achieve effectiveness. The current review examines should be investigates/assesses/report on the development and evolution of newly identified H9N2 viruses in Indonesia and their vaccination strategy.

Antigenic Evolution Characteristics and Immunological Evaluation of H9N2 Avian Influenza Viruses from 1994–2019 in China

The H9N2 subtype avian influenza viruses (AIVs) have been circulating in China for more than 20 years, attracting more and more attention due to the potential threat of them. At present, vaccination is a common prevention and control strategy in poultry farms, but as virus antigenicity evolves, the immune protection efficiency of vaccines has constantly been challenged. In this study, we downloaded the hemagglutinin (HA) protein sequences of the H9N2 subtype AIVs from 1994 to 2019 in China—with a total of 5138 sequences. The above sequences were analyzed in terms of time and space, and it was found that h9.4.2.5 was the most popular in various regions of China. Furthermore, the prevalence of H9N2 subtype AIVs in China around 2006 was different. The domestic epidemic branch was relatively diversified from 1994 to 2006. After 2006, the epidemic branch each year was h9.4.2.5. We compared the sequences around 2006 as a whole and screened out 15 different amino acid positions. Based on the HA protein of A/chicken/Guangxi/55/2005 (GX55), the abovementioned amino acid mutations were completed. According to the 12-plasmid reverse genetic system, the rescue of the mutant virus was completed using A/PuertoRico/8/1934 (H1N1) (PR8) as the backbone. The cross hemagglutination inhibition test showed that these mutant sites could transform the parental strain from the old to the new antigenic region. Animal experiments indicated that the mutant virus provided significant protection against the virus from the new antigenic region. This study revealed the antigenic evolution of H9N2 subtype AIVs in China. At the same time, it provided an experimental basis for the development of new vaccines.

H9N2 influenza virus spillover into wild birds from poultry in China bind to human-type receptors and transmit in mammals via respiratory droplets

H9N2 influenza virus has been reported worldwide for several decades, and it has evolved into multiple genotypes among domestic poultry. However, the study involving ecology and evolution of low pathogenic avian influenza virus H9N2 in wild birds in China is limited. Here, we carried out surveillance of avian influenza virus H9N2 in wild birds along with the East Asian-Australian migratory flyway in China in 2017. To estimate the prevalence of H9N2 avian virus in wild birds, information on exposure of wild bird populations to H9N2 viruses using serology, in addition to virology, would greatly improve monitoring capabilities. In this study, we also present serological data of H9N2 among wild birds in China during 2013-2016. We report the identification of poultry-derived H9N2 isolates from asymptomatic infected multispecies wild birds such as Common kestrel (Falco tinnunculus), Northern goshawk (Accipiter gentilis), Little owl (Athene noctua) and Ring-necked Pheasant (Phasianus colchicus) in North China in June 2017. Phylogenetic analysis demonstrated that Tianjin H9N2 isolates belong to the G81 and carry internal genes highly homologous to human H10N8 and H7N9. The isolates could directly infect mice without adaptation but were restricted to replicate in the respiratory system. Glycan-binding preference analyses suggested that the H9N2 isolates have acquired a binding affinity for the human-like receptor. Notably, results from transmission experiment in guinea pigs and ferrets demonstrated the wild birds-derived H9N2 influenza virus exhibits efficient transmission phenotypes in mammalian models via respiratory droplets. Our results indicate that the H9N2 AIVs continued to circulate extensively in wild bird populations and migratory birds play an important role in the spread and genetic diversification of H9N2 AIVs. The pandemic potential of H9N2 viruses demonstrated by aerosol transmission in mammalian models via respiratory droplets highlights the importance of monitoring influenza viruses in these hosts.

Sequence characteristics and phylogenetic analysis of H9N2 subtype avian influenza A viruses detected from poultry and the environment in China, 2018

H9N2 subtype avian influenza A virus (AIV) is a causative agent that poses serious threats to both the poultry industry and global public health. In this study, we performed active surveillance to identify H9N2 AIVs from poultry (chicken, duck, and goose) and the environment of different regions in China, and we phylogenetically characterized the sequences. AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) showed that 5.43% (83/1529) samples were AIV positive, and 87.02% (67/77) of which were H9N2 AIVs. Phylogenetic analysis revealed that all H9N2 field viruses belonged to the Y280-like lineage, exhibiting 93.9-100% and 94.6-100% of homology in the hemagglutinin (HA) gene and 94.4-100% and 96.3-100% in the neuraminidase (NA) gene, at the nucleotide (nt) and amino acid (aa) levels, respectively. All field viruses shared relatively lower identities with vaccine strains, ranging from 89.4% to 97.7%. The aa sequence at the cleavage site (aa 333-340) in HA of all the isolated H9N2 AIVs was PSRSSRG/L, which is a characteristic of low pathogenic avian influenza virus (LPAIV). Notably, all the H9N2 field viruses harbored eight glycosylation sites, whereas a glycosylation site 218 NRT was missing and a new site 313 NCS was inserted. All field viruses had NGLMR as their receptor binding sites (RBS) at aa position 224-229, showing high conservation with many recently-isolated H9N2 strains. All H9N2 field isolates at position 226 had the aa Leucine (L), indicating their ability to bind to sialic acid (SA) α, a 2-6 receptor of mammals that poses the potential risk of transmission to humans. Our results suggest that H9N2 AIVs circulating in poultry populations that have genetic variation and the potential of infecting mammalian species are of great significance when monitoring H9N2 AIVs in China.

Pre-treatment with chicken IL-17A secreted by bioengineered LAB vector protects chicken embryo fibroblasts against Influenza Type A Virus (IAV) infection

The recent advances in our understanding of the host factors in orchestrating qualitatively different immune responses against influenza Type A virus (IAV) have changed the perception of conventional approaches for controlling avian influenza virus (AIV) infection in chickens. Given that infection-induced pathogenicity and replication of influenza virus largely rely on regulating host immune responses, immunoregulatory cytokine profiles often determine the disease outcomes. However, in contrast to the function of other inflammatory cytokines, interleukin-17A (IL-17A) has been described as a 'double-edged sword', indicating that in addition to antiviral host responses, IL-17A has a distinct role in promoting viral infection. Therefore, in the present study, we investigated the chicken IL-17A mediated antiviral immune effects on IAVs infection in primary chicken embryo fibroblasts cells (CEFs). To this end, we first bioengineered a food-grade Lactic Acid Producing Bacteria (LAB), Lactococcus lactis (L. lactis), secreting bioactive recombinant chicken IL-17A (sChIL-17A). Next, the functionality of sChIL-17A was confirmed by transcriptional upregulation of several genes associated with antiviral host responses, including granulocyte-monocyte colony-stimulating factor (GM-CSF) (CSF3 in the chickens), interleukin-6 (IL-6), interferon-α (IFN-α), -β and -γ genes in primary CEFs cells. Consistent with our hypothesis that such a pro-inflammatory state may translate to immunoprotection against IAVs infection, we observed that sChIL-17A pre-treatment could significantly limit the viral replication and protect the primary CEFs cells against two heterotypic IAVs such as A/turkey/Wisconsin/1/1966(H9N2) and A/PR/8/1934(H1N1). Together, the data presented in this work suggest that exogenous application of sChIL-17A secreted by modified LAB vector may represent an alternative strategy for improving antiviral immunity against avian influenza virus infection in chickens.

G1-like PB2 gene improves virus replication and competitive advantage of H9N2 virus

H9N2 subtype avian influenza virus has dramatically evolved and undergone extensive reassortment since its emergence in early 1990s in China. The genotype S (G57), emerging in 2007 with the substitution of F98-like PB2 and M gene by G1-like ones, has become the overwhelming predominant genotype for the past 11 years since 2010. Here, we found that virus with G1-like PB2 were more efficient in protein expression and in infectious virus production than that with F98-like PB2 gene. By coinfected MDCK cells with the reassortant virus, more survival opportunity for viruses with G1-like PB2 than that of F/98-like was observed. Besides, in animal experiments, we found that the G1-like PB2 increases virus infectivity, replication, and virus shedding of H9N2 in chickens. Our results suggested that the substitution of G1-like PB2 play important role in promoting the fitness of genotype S H9N2 virus in China.

Double mutations in the H9N2 avian influenza virus PB2 gene act cooperatively to increase viral host adaptation and replication for human infections

Avian H9N2 influenza viruses in East Asia are genetically diversified and multiple genotypes (A-W) have been established in poultry. Genotype S strains are currently the most prevalent strains, have caused many human infections and pose a public health threat. In this study, human adaptation mutations in the PB2 polymerase in genotype S strains were identified by database screening. Several PB2 double mutations were identified that acted cooperatively to produce higher genotype S virus polymerase activity and replication in human cells than in avian cells and to increase viral growth and virulence in mice. These mutations were chronologically and phylogenetically clustered in a new group within genotype S viruses. Most of the relevant human virus isolates carry the PB2-A588V mutation together with another PB2 mutation (i.e. K526R, E627V or E627K), indicating a host adaptation advantage for these double mutations. The prevalence of PB2 double mutations in human H9N2 virus isolates has also been found in genetically related human H7N9 and H10N8 viruses. These results suggested that PB2 double mutations in viruses in the field acted cooperatively to increase human adaptation of the currently prevalent H9N2 genotype S strains. This may have contributed to the recent surge of H9N2 infections and may be applicable to the human adaptation of several other avian influenza viruses. Our study provides a better understanding of the human adaptation pathways of genetically related H9N2, H7N9 and H10N8 viruses in nature.

Pathogenicity of H9N2 low pathogenic avian influenza viruses of different lineages isolated from live bird markets tested in three animal models: SPF chickens, Korean native chickens, and ducks

Since its first appearance in 1996, H9N2 avian influenza virus (AIV) of the Y439 lineage persisted in Korean live bird markets (LBMs) until the last documented occurrence in 2018. However, in June 2020, the avian influenza surveillance program detected a novel H9N2 AIV belonging to the Y280 lineage, which has zoonotic potential, in a Korean native chicken (KNC) from a LBM. In this study, we infected KNCs and ducks (the 2 major species held at LBMs), as well as SPF chickens, with Y280-lineage H9N2 AIV LBM261/20 and Y439-equivalent LBM294/18 to compare pathogenicity and transmissibility. In SPF chickens, LBM261/20 replicated mostly in the respiratory tract and spread rapidly among birds. By contrast, LBM294/18 replicated preferentially in the gastrointestinal tract and transmitted more slowly than LBM261/20. LBM261/20 replicated for a longer time in KNCs than in SPF chickens, and only in the respiratory tract; by contrast, LBM294/18 was detected in the oropharynx and cloaca. Ducks did not shed either virus or seroconvert. Taken together, the data suggest that the scheme used to monitor the newly introduced H9N2 AIV of the Y280 lineage needs to be modified to place emphasis on oropharyngeal sampling. Such changes will facilitate better disease control and protect public health.

Neurovirulence of avian influenza virus is dependent on the interaction of viral NP protein with host factor FMRP in the murine brain

Avian influenza viruses (AIVs) are zoonotic viruses that exhibit a range infectivity and severity in the human host. Severe human cases of AIVs infection are often accompanied by neurological symptoms, however, the factors involved in the infection of the central nervous system (CNS) are not well known. In this study, we discovered that avian-like sialic acid (SA)-α2, 3 Gal receptor is highly presented in mammalian (human and mouse) brains. In the generation of a mouse-adapted neurotropic H9N2 AIV (SD16-MA virus) in BALB/c mice, we identified key adaptive mutations in its hemagglutinin (HA) and polymerase basic protein 2 (PB2) genes that conferred viral replication ability in mice brain. The SD16-MA virus showed binding affinity for avian-like SA-α2, 3 Gal receptor, enhanced viral RNP polymerase activity, increased viral protein production and transport that culminated in elevated progeny virus production and severe pathogenicity. We further established that host Fragile X Mental Retardation Protein (FMRP), a highly expressed protein in the brain that physically associated with viral nucleocapsid protein (NP) to facilitate RNP assembly and export, was an essential host factor for the neuronal replication of neurotropic AIVs (H9N2, H5N1 and H10N7 viruses). Our study identified a mechanistic process for AIVs to acquire neurovirulence in mice.IMPORTANCE Infection of the CNS is a serious complication of human cases of AIVs infection. The viral and host factors associated with neurovirulence of AIVs infection are not well understood. We identified and functionally characterized specific changes in the viral HA and PB2 genes of a mouse-adapted neurotropic avian H9N2 virus responsible for enhanced virus replication in neuronal cells and pathogenicity in mice. Importantly, we showed that host FMRP was a crucial host factor that was necessary for neurotropic AIVs (H9N2, H5N1 and H10N7 viruses) to replicate in neuronal cells. Our findings have provided insights into the pathogenesis of neurovirulence of AIV infection.

Genetic Evolution Characteristics of Genotype G57 Virus, A Dominant Genotype of H9N2 Avian Influenza Virus

This study aimed to investigate the genetic evolution of the H9N2 avian influenza virus (AIV). Whole genome phylogenetic trees were constructed based on 306 H9N2 avian influenza strains collected in China from 2014 to 2019. The results showed that eight gene sequences were clustered separately according to their dominant clades, and a total of 10 genotypes were identified (seven of which were novel types). Among them, G57 genotype was confirmed as the most prevalent genotype with a frequency of 94%. In China, the G57 genotype of H9N2 first emerged in 2007, and then became the most common genotype in 2013. Therefore, the nucleotide substitution rates of G57 genotype in HA and NA genes collected from 2007 to 2019 were estimated, and the positive selection pressure sites in the same data set were measured. Taking 2013 as the boundary, the time period was divided into two periods: 2007-2012 and 2013-2019. From 2007 to 2012, multiple genotypes coexisted and could bear the pressures from both nature and environment; while G57 genotype was still in the adaptation stage, subjected to less selection pressure and in the process of slow evolution. However, from 2013 to 2019, G57 became the dominant genotype, and most of the external pressure reacted on it. Moreover, G57 genotype showed better adaptability than other genotypes. From 2013 to 2019, the nucleotide substitution rates of the HA gene were increased, and the positive selection pressures on HA and NA genes were stronger compared to those from 2007 to 2012. To sum up, the absolutely dominant G57 genotype exhibited a relatively constant genotype frequency and experienced adaptive evolution and natural selection simultaneously during the monitoring period. Therefore, urgent attention and diligent surveillance of H9N2 avian influenza virus are becoming increasingly important.

A risk marker of tribasic hemagglutinin cleavage site in influenza A (H9N2) virus

Low pathogenic avian influenza A(H9N2) virus is endemic worldwide and continually recruit internal genes to generate human-infecting H5N1, H5N6, H7N9, and H10N8 influenza variants. Here we show that hemagglutinin cleavage sites (HACS) of H9N2 viruses tended to mutate towards hydrophilic via evolutionary transition, and the tribasic HACS were found at high prevalence in Asia and the Middle East. Our finding suggested that the tribasic H9N2 viruses increased the viral replication, stability, pathogenicity and transmission in chickens and the virulence of mice compared to the monobasic H9N2 viruses. Notably, the enlarged stem-loop structures of HACS in the RNA region were found in the increasing tribasic H9N2 viruses. The enlarged HACS RNA secondary structures of H9N2 viruses did not influence the viral replication but accelerated the frequency of nucleotide insertion in HACS. With the prevailing tendency of the tribasic H9N2 viruses, the tribasic HACS in H9N2 viruses should be paid more attention.

Serological evidence of avian influenza virus subtype H5 and H9 in live bird market, Myanmar

Avian Influenza (AI), caused by Alphainfluenzaviruses (AIVs), is a contagious respiratory disease in birds and mammals. AIVs have been reported in poultry worldwide and the impact of AIVs on human health is immense. In this study, a serological survey of AIV subtype H5 and H9 was conducted in a live bird market (LBM) in Yangon, Myanmar during February 2016 to September 2016. A total of 621 serum samples were collected from chickens (n = 489) and ducks (n = 132) from 48 vendors in the LBM. The samples were examined for antibodies against influenza viruses by using NP-ELISA and specific antibodies against AIV-H5N1 (Clade 2.3.4) and AIV-H9N2 (Clade 9.4.2) by using Hemagglutination Inhibition (HI) assay. The result of NP-ELISA assay showed that 12.88 % (80/621) of poultry in LBM was positive for AIV antibodies. In detail, 38.06 % (51/134) of layers, 7.08 % (8/113) of backyard chicken, 2.07 % (5/242) of broilers and 12.12 % (16/132) of ducks were AIV positive. The HI test for specific antibodies against AIV-H5N1 and AIV-H9N2 were 1.77 % (11/621) and 4.51 % (28/621), respectively. Our findings revealed the evidence of AIV-H5N1 and AIV-H9N2 exposure in both chicken and ducks in the LBM in Yangon, Myanmar. Risks of influenza infections and transmission among poultry and humans in the LBMs could not be ignored.

MXD1 regulates the H9N2 and H1N1 influenza A virus-induced chemokine expression and their replications in human macrophage

Human infection with influenza A/Hong Kong/156/97 (H5N1) avian influenza virus is associated with a high mortality rate of 60%. This virus is originated from influenza A/Quail/Hong Kong/G1/97 (H9N2/G1) avian influenza virus. Since the 1990s, four lineages of H9N2 viruses have been circulating in poultry and cause occasional infection in humans in different countries. Due to its zoonotic and genetic reassortment potential, H9N2/G1 and H5N1 viruses are believed to be the next pandemic candidates. Previous reports, including ours, showed that the virulence of avian virus strains correlates with their ability to dysregulate cytokine expression, including TNF-α, CXCL10, and related chemokines in the virus-infected cells. However, the transcriptional factors required for this cytokine dysregulation remains undefined. In light of our previous report showing the unconventional role of MYC, an onco-transcriptional factor, for regulating the antibacterial responses, we hypothesize that the influenza virus-induced cytokine productions may be governed by MYC/MAX/MXD1 network members. Here, we demonstrated that the influenza A/Hong Kong/54/98 (H1N1)- or H9N2/G1 virus-induced CXCL10 expressions can be significantly attenuated by knocking down the MXD1 expression in primary human blood macrophages. Indeed, only the MXD1 expression was up-regulated by both H1N1 and H9N2/G1 viruses, but not other MYC/MAX/MXD1 members. The MXD1 expression and the CXCL10 hyperinduction were dependent on MEK1/2 activation. By using EMSAs, we revealed that MXD1 directly binds to the CXCL10 promoter-derived oligonucleotides upon infection of both viruses. Furthermore, silencing of MXD1 decreased the replication of H9N2 but not H1N1 viruses. Our results provide a new insight into the role of MXD1 for the pathogenicity of avian influenza viruses.

The molecular evolutionary characteristics of new isolated H9N2 AIV from East China and the function of vimentin on virus replication in MDCK cells

BACKGROUND

The low pathogenic H9N2 AIV caused the serious impact on the poultry industry and public safety. Our purpose was to investigate the molecular evolutionary characteristics of the new isolated H9N2 virus and investigate the intracellular target protein of H9N2 AIV replication in sensitive cells.

METHODS

AIV A/chicken/Shandong/LY1/2017 (H9N2) was isolated from the cloaca of the healthy chicken in Shandong, and the full-length eight gene segments of this isolated H9N2 AIV were amplified by RT-PCR and analyzed. MDCK cells were used as the target cell model, and VOPBA assay and LC-MS/MS were carried out to identify the virus-binding protein of H9N2 AIV. MDCK cells were pre-treated with the special antibody and siRNA, and treated with H9N2 AIV to detect the virus replication. Additionally, Vimentin-pcDNA3.0 was successfully constructed, and transinfected into MDCK cells, and then H9N2 AIV mRNA was detected with RT-PCR.

RESULTS

Phylogenetic analysis revealed that HA, NA, PB2, PB1, PA, NP and M seven genes of the isolated H9N2 AIV were derived from A/Chicken/Shanghai/F/98, while NS gene was derived from A/Duck/Hong Kong/Y439/97. The cleavage site sequence of HA gene of the isolated H9N2 AIV was a PARSSR G pattern, and the left side sequence (224 ~ 229) of receptor binding site was NGQQGR pattern, which were similar to that of A/Chicken/Shanghai/F/98. Following VOPBA assay, we found one protein of about 50KDa binding to H9N2 AIV, and the results of LC-MS/MS analysis proved that vimentin was the vital protein binding to H9N2 AIV. The pre-incubation of the specific antibody and siRNA decreased the viral RNA level in MDCK cells treated with H9N2 AIV. Furthermore, we found that over-expressed vimentin increased H9N2 AIV replication in MDCK cells.

CONCLUSIONS

These findings suggested that the isolated H9N2 AIV might be a recent clinical common H9N2 strain, and vimentin protein might be one vital factor for H9N2 AIV replication in MDCK cells, which might be a novel target for design and development of antiviral drug.

H9 Influenza Viruses: An Emerging Challenge

Influenza A viruses (IAVs) of the H9 subtype are enzootic in Asia, the Middle East, and parts of North and Central Africa, where they cause significant economic losses to the poultry industry. Of note, some strains of H9N2 viruses have been linked to zoonotic episodes of mild respiratory diseases. Because of the threat posed by H9N2 viruses to poultry and human health, these viruses are considered of pandemic concern by the World Health Organization (WHO). H9N2 IAVs continue to diversify into multiple antigenically and phylogenetically distinct lineages that can further promote the emergence of strains with pandemic potential. Somewhat neglected compared with the H5 and H7 subtypes, there are numerous indicators that H9N2 viruses could be involved directly or indirectly in the emergence of the next influenza pandemic. The goal of this work is to discuss the state of knowledge on H9N2 IAVs and to provide an update on the contemporary global situation.

Understanding the cross-talk between host and virus in poultry from the perspectives of microRNA

In poultry, viral infections (e.g., Marek's disease virus, avian leukosis virus, influenza A virus, and so on) can cause devastating mortality and economic losses. Because viruses are solely dependent on host cells to propagate, they alter the host intracellular microenvironment. Thus, understanding the virus-host interaction is important for antiviral immunity and drug development in the poultry industry. MicroRNAs are crucial posttranscriptional regulators of gene expression in a wide spectrum of biological processes, including viral infection. Recently, microRNAs have been identified as key players in virus-host interactions. In this review, we will discuss the intricacies involved in the virus-host cross-talk mediated by host and viral microRNAs in poultry (i.e., chicken and ducks), as well as recent trends and challenges in this field. These findings may provide some insights into the rapidly developing area of research regarding viral pathogenesis and antiviral immunity in poultry production.

Genetic Characteristics and Pathogenicity Analysis in Chickens and Mice of Three H9N2 Avian Influenza Viruses

H9N2 avian influenza is a remarkable disease that has circulated in domestic poultry in large regions of China and posed a serious threat to the poultry industry. The H9N2 virus can not only infect mammals directly, but also provide gene segments to generate novel, but lethal human reassortants. Therefore, it is important to study the evolution, pathogenicity, and transmission of the H9N2 virus. In this study, three H9N2 viruses isolated from chickens in different layer farms were identified. Phylogenetic analysis revealed that these H9N2 viruses were all multiple genotype reassortants, with genes originating from Y280-like, F/98-like, and G1-like viruses. Animal studies indicated that the AV1535 and AV1548 viruses replicated efficiently in the lungs, tracheas, spleens, kidneys, and brains of chickens; the viruses shed for at least 11 days post-inoculation (DPI) and were transmitted efficiently among contact chickens. The AV1534 virus replicated poorly in chickens, shed for 7 DPI, and were not transmitted efficiently among contact chickens. The AV1534 virus replicated well in mice lungs and caused about 2% weight loss. The AV1535 and AV1548 viruses were not able to replicate in the lungs of mice. Our results indicate that we should pay attention to H9N2 avian influenza virus surveillance in poultry and changes in the pathogenicity of them to mammals.

Mouse-adapted H9N2 avian influenza virus causes systemic infection in mice

BACKGROUND

H9N2 influenza viruses continuously circulate in multiple avian species and are repeatedly transmitted to humans, posing a significant threat to public health. To investigate the adaptation ability of H9N2 avian influenza viruses (AIVs) to mammals and the mutations related to the host switch events, we serially passaged in mice two H9N2 viruses of different HA lineages - A/Quail/Hong Kong/G1/97 (G1) of the G1-like lineage and A/chicken/Shandong/ZB/2007 (ZB) of the BJ/94-like lineage -and generated two mouse-adapted H9N2 viruses (G1-MA and ZB-MA) that possessed significantly higher virulence than the wide-type viruses.

FINDING

ZB-MA replicated systemically in mice. Genomic sequence alignment revealed 10 amino acid mutations coded by 4 different gene segments (PB2, PA, HA, and M) in G1-MA compared with the G1 virus and 23 amino acid mutations in 5 gene segments (PB1, PA, HA, M, and NS) in ZB-MA compared to ZB virus, indicating that the mutations in the polymerase, HA, M, and NS genes play critical roles in the adaptation of H9N2 AIVs to mammals, especially, the mutations of M1-Q198H and M1-A239T were shared in G1-MA and ZB-MA viruses. Additionally, several substitutions showed a higher frequency in human influenza viruses compared with avian viruses.

CONCLUSIONS

Different lineages of H9N2 could adapt well in mice and some viruses could gain the ability to replicate systemically and become neurovirulent. Thus, it is essential to pay attention to the mammalian adaptive evolution of the H9N2 virus.

The PB2 and M genes are critical for the superiority of genotype S H9N2 virus to genotype H in optimizing viral fitness of H5Nx and H7N9 avian influenza viruses in mice

Genotype S H9N2 avian influenza virus, which has been predominant in China since 2010, contributed its entire internal gene cassette to the genesis of novel reassortant influenza viruses, including H5Nx, H7N9 and H10N8 viruses that pose great threat to poultry and humans. A key feature of the genotype S H9N2 virus is the substitution of G1-like M and PB2 genes for the earlier F/98-like M and PB2 of genotype H virus. However, how this gene substitution has influenced viral adaptability of emerging influenza viruses in mammals remains unclear. We report here that reassortant H5Nx and H7N9 viruses with the genotype S internal gene cassette displayed enhanced replication and virulence over those with genotype H internal gene cassette in cell cultures as well as in the mouse models. We showed that the G1-like PB2 gene was associated with increased polymerase activity and improved nuclear accumulation compared with the F/98-like counterpart, while the G1-like M gene facilitated effective translocation of RNP to cytoplasm. Our findings suggest that the genotype S H9N2 internal gene cassette, which possesses G1-like M and PB2 genes, is superior to that of genotype H, in optimizing viral fitness, and thus have implications for assessing the potential risk of these gene introductions to generate emerging influenza viruses.

A(H9N2) influenza viruses associated with chicken mortality in outbreaks in Algeria 2017

In late 2017, increased mortality was detected in chicken farms in Algeria undergoing A(H9N2) influenza outbreaks. Analysis of viruses isolated from affected farms showed that they were monophyletic, were of the G1 hemagglutinin (HA) lineage, and were antigenically and genetically similar to viruses detected contemporaneously in other countries in Northern Africa and the Middle East. The virus was able to spread via contact transmission between ferrets but did not cause disease in intravenously inoculated chickens.

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.

New molecular evolutionary characteristics of H9N2 avian influenza virus in Guangdong Province, China

To understand the evolution of H9N2 avian influenza virus genotype and its molecular evolution rate, we systematically analyzed 72 H9N2 avian influenza virus sequences isolated from Guangdong province from 2014 to 2018. We found three genotypes (G57, G68, and G118) of the H9N2 avian influenza virus, of which G118 is a newly discovered genotype and G57 is the dominant genotype. The internal gene cassette of the G57 genotype H9N2 avian influenza virus is a stable combination that can easily transport internal genes to other novel avian influenza viruses, and the internal gene cassettes of the G68 and G118 are identical to those of G57.In addition, we estimated the nucleotide substitution rate of the HA and NA genes of the H9N2 influenza virus from 2014 to 2018.The nucleotide substitution rate of HA and NA genes showed an upward trend in 2015 and 2016. In the past two years, H9N2 avian influenza virus recombination has produced genotype G68, which disappeared in 2014 for one year. And very coincidentally, in 2015, there was a new genotype G118. We observed that the emergence of new genotypes was accompanied by a slight increase in overall nucleotide substitution rate. Therefore we hypothesize that the emergence of new genotypes could accelerate the molecular evolution rate of genes. Our research shows that the H9N2 avian influenza virus in Guangdong province has been undergoing intense evolution, demonstrating the need to strengthen influenza surveillance in the region.

Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance

Reassortment is an evolutionary mechanism by which influenza A viruses (IAV) generate genetic novelty. Reassortment is an important driver of host jumps and is widespread according to retrospective surveillance studies. However, predicting the epidemiological risk of reassortant emergence in novel hosts from surveillance data remains challenging. IAV strains persist and co-occur in the environment, promoting co-infection during environmental transmission. These conditions offer opportunity to understand reassortant emergence in reservoir and spillover hosts. Specifically, environmental RNA could provide rich information for understanding the evolutionary ecology of segmented viruses, and transform our ability to quantify epidemiological risk to spillover hosts. However, significant challenges with recovering and interpreting genomic RNA from the environment have impeded progress towards predicting reassortant emergence from environmental surveillance data. We discuss how the fields of genomics, experimental ecology and epidemiological modelling are well positioned to address these challenges. Coupling quantitative disease models and natural transmission studies with new molecular technologies, such as deep-mutational scanning and single-virus sequencing of environmental samples, should dramatically improve our understanding of viral co-occurrence and reassortment. We define observable risk metrics for emerging molecular technologies and propose a conceptual research framework for improving accuracy and efficiency of risk prediction. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.

Circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands, 2006-2016

In this study, we explore the circulation of low pathogenic avian influenza (LPAI) viruses in wild birds and poultry in the Netherlands. Surveillance data collected between 2006 and 2016 was used to evaluate subtype diversity, spatiotemporal distribution and genetic relationships between wild bird and poultry viruses. We observed close species-dependent associations among hemagglutinin and neuraminidase subtypes. Not all subtypes detected in wild birds were found in poultry, suggesting transmission to poultry is selective and likely depends on viral factors that determine host range restriction. Subtypes commonly detected in poultry were in wild birds most frequently detected in mallards and geese. Different temporal patterns in virus prevalence were observed between wild bird species. Virus detections in domestic ducks coincided with the prevalence peak in wild ducks, whereas virus detections in other poultry types were made throughout the year. Genetic analysis of the surface genes demonstrated that most poultry viruses were related to locally circulating wild bird viruses, but no direct spatiotemporal link was observed. Results indicate prolonged undetected virus circulation and frequent reassortment events with local and newly introduced viruses within the wild bird population. Increased knowledge on LPAI virus circulation can be used to improve surveillance strategies.

Molecular pathogenic and host range determinants of reassortant Egyptian low pathogenic avian influenza H9N2 viruses from backyard chicken

Since the introduction of H9N2 low pathogenic avian influenza virus in Egypt, it became an endemic disease causing considerable economic losses in different poultry sectors especially in the presence of other secondary bacterial and viral infections. The H9N2 viruses in Egypt are in continuous evolution that needs deep analysis for their evolution pattern based on the genetic constitutions of the pathogenic determinant genes (HA, PB2, PB1, PA, and NS). In this work, samples were collected from the backyard chickens from 3 Egyptian governorates. Five selected viruses were sequenced and analyzed for the hemagglutinin gene which showed genetic relatedness to the Asian G1 lineage group B, similar to the circulating H9N2 viruses in Egypt since 2013. The sequence for PB2, PB1, PA, HA and NS genes of the selected five viruses indicate a natural re-assortment event with recent Eurasian subtypes and similar to Egyptian H9N2 virus isolated from pigeon in Egypt during 2014. The Egyptian viruses of our study possess amino acids signatures including S42, V127, L550, L672 and V504 in the internal genes NS1, PA, and PB2, of respectively of an impact on virus transmission and replication. This work indicates that the H9N2 is in continuous evolution with alarming to the reassortment occurrence.

The PB2 and M genes of genotype S H9N2 virus contribute to the enhanced fitness of H5Nx and H7N9 avian influenza viruses in chickens

Genotype S H9N2 viruses frequently donate their internal genes to facilitate the generation of novel influenza viruses, e.g., H5N6, H7N9, and H10N8, which have caused human infection. Genotype S was originated from the replacement of F/98-like M and PB2 genes of the genotype H with those from G1-like lineage. However, whether this gene substitution will influence the viral fitness of emerging influenza viruses remains unclear. We found that H5Nx and H7N9 viruses with G1-like PB2 or M gene exhibited higher virulence and replication than those with F/98-like PB2 or M in chickens. We also determined the functional significance of G1-like PB2 in conferring increased polymerase activity and improved nucleus transportation efficiency, and facilitated RNP nuclear export by G1-like M. Our results suggest that G1-like PB2 and M genes optimize viral fitness, and thus play a crucial role in the genesis of emerging influenza viruses that cause rising prevalence in chickens.

A Global Perspective on H9N2 Avian Influenza Virus

H9N2 avian influenza viruses have become globally widespread in poultry over the last two decades and represent a genuine threat both to the global poultry industry but also humans through their high rates of zoonotic infection and pandemic potential. H9N2 viruses are generally hyperendemic in affected countries and have been found in poultry in many new regions in recent years. In this review, we examine the current global spread of H9N2 avian influenza viruses as well as their host range, tropism, transmission routes and the risk posed by these viruses to human health.

Co-subsistence of avian influenza virus subtypes of low and high pathogenicity in Bangladesh: Challenges for diagnosis, risk assessment and control

Endemic co-circulation of potentially zoonotic avian influenza viruses (AIV) of subtypes H5N1 and H9N2 (G1 lineage) in poultry in Bangladesh accelerated diversifying evolution. Two clinical samples from poultry obtained in 2016 yielded five different subtypes (highly pathogenic [HP] H5N1, HP H5N2, HP H7N1, HP H7N2, H9N2) and eight genotypes of AIV by plaque purification. H5 sequences grouped with clade 2.3.2.1a viruses while N1 was related to an older, preceding clade, 2.2.2. The internal genome segments of the plaque-purified viruses originated from clade 2.2.2 of H5N1 or from G1/H9N2 viruses. H9 and N2 segments clustered with contemporary H9N2 strains. In addition, HP H7 sequences were detected for the first time in samples and linked to Pakistani HP H7N3 viruses of 2003. The unexpected findings of mixtures of reassorted HP H5N1 and G1-like H9N2 viruses, which carry genome segments of older clades in association with the detection of HP H7 HA segments calls for confirmation of these results by targeted surveillance in the area of origin of the investigated samples. Hidden niches and obscured transmission pathways may exist that retain or re-introduce genome segments of older viruses or reassortants thereof which causes additional challenges for diagnosis, risk assessment and disease control.

Avian influenza A (H9N2) virus infections among poultry workers, swine workers, and the general population in Beijing, China, 2013-2016: A serological cohort study

Background

Few studies have reported on the seroprevalence of antibodies against avian influenza A (H9N2) virus and the incidence of these infections in the northern China and among swine workers.

Methods

We conducted a serological cohort study among people working with poultry or swine or the general population in Beijing, China. It comprised four cross‐sectional serological surveys in November 2013, April 2014, April 2015, and April 2016. Blood samples collected from the participants were tested for anti‐H9N2 antibodies using a hemagglutination‐inhibition (HI) assay. Multivariable Poisson regression model was then used to compare the person‐month incidence rates for H9N2 viral infections among the three groups, assessed by incidence rate ratio (IRR).

Results

In the four cross‐sectional surveys, the highest seroprevalence of anti‐H9N2 antibodies (HI titer ≥ 80) was recorded in the poultry workers (2.77%, 19/685) in April 2016, while the lowest was recorded in the general population (0.09%, 1/1135) in April 2015. The highest incidence density rate for H9N2 infections across the whole study period was recorded among the poultry workers (3.75/1000 person‐months), followed by the swine workers (1.94/1000 person‐months) and the general population (1.78/1000 person‐months). Multivariable analysis showed that the poultry workers were at higher risk (IRR: 2.42, 95% CI: 1.07‐5.48; P = 0.034) of contracting H9N2 virus than the general population.

Conclusions

Although the seroprevalence of H9N2 antibodies was low in Beijing, the poultry workers were at higher risk of contracting H9N2 viral infections than the general population. Closer monitoring and strengthened protection measures for poultry workers are warranted.

The evolution and molecular characteristics of H9N2 avian influenza viruses in Jiangxi of China

To understand the evolution and molecular characteristics of Jiangxi H9N2 viruses, we isolated 17 viruses in 2011 and analyzed their characteristics. Phylogenetic analyses revealed that their hemagglutinin genes originate from JS/1/00-like sublineage, neuraminidase genes originate from BJ/94-like sublineage, PB1, PA, NP, and NS genes all come from SH/F/98-like sublineage, PB2 genes originate from ST/163/04-like sublineage, while M genes come from G1-like sublineage. Genotype analysis showed that our isolates were classified as genotype 57. Molecular analyses indicated that our strains contained specific sites characteristic of low-pathogenic viruses. The current study once again highlights the necessity for continued surveillance of novel H9N2 viruses.

Phylogenetic classification of hemagglutinin gene of H9N2 avian influenza viruses isolated in China during 2012-2016 and evaluation of selected candidate vaccine strains

H9N2 subtype avian influenza virus (AIV) was the highly contagious pathogen which has caused severe losses in the poultry industry throughout China in recent years. Using current epidemic viruses as vaccine was an effective way to prevent infection of H9N2 subtype AIV. In this study, a total of 23 H9N2 subtype AIV strains were isolated in 200 samples from 13 provinces of China during 2012-2016. The sequencing and phylogenetic analysis of the hemagglutinin gene sequence of the isolation strains showed that 22 isolation strains were clustered to h9.4.2.5 lineage, while only 1 belonged to h9.4.2.6. The data of cross-HI, neutralization and cross-immune protection shown that the A/chicken/Hunan/HN/2015 (HN) and A/chicken/Shandong/SD/2014 (SD) strains as vaccine could effectively protect present viruses infection compared with other strains. These results indicated that current epidemic viruses were mainly belong to h9.4.2.5 lineage and HN and SD strains as candidate vaccine strains were potentiality for the protection of present H9N2 subtype AIV infection.

Characterization of avian influenza H9N2 viruses isolated from ostriches (Struthio camelus)

H9N2 subtype avian influenza viruses (AIVs) have been isolated from various species of wild birds and domestic poultry in the world, and occasionally transmitted to humans. Although H9N2 AIVs are seldom isolated from ostriches, seven such strains were isolated from sick ostriches in China between 2013 and 2014. Sequence analysis showed several amino acid changes relating to viral adaptation in mammals were identified. The phylogenetic analyses indicated that these isolates were quadruple reassortant viruses, which are different from the early ostrich isolates from South Africa or Israel. Most of the ostrich virus carried a human-type receptor-binding property. The chicken experiments showed the ostrich strains displayed low pathogenicity, while they could cause mild to severe symptoms in chicken. Theses strains could efficiently transmit among chickens, and one strain showed higher transmissibility. The virus could not kill mice, and merely replicated in the lung of mice. The ostrich strains could not efficiently transmit between guinea pigs in the direct contact model. These results suggested we should pay attention to the interface between ostrich and other domestic fowl, and keep an eye on this population when monitoring of influenza virus.

Genetic evolution of influenza H9N2 viruses isolated from various hosts in China from 1994 to 2013

Influenza H9N2 subtype viruses and their reassortants (such as H7N9) are posing increasing threats to birds and humans in China. During 2009–2013, multiple novel subtype viruses with H9N2 original genes emerged in China. Yet, the genetic evolution of H9N2 viruses in various host organisms in China has not been systematically investigated since 2009. In the present study, we performed large-scale sequence analysis of H9N2 viral genomes from public databases, representing the spectrum of viruses isolated from birds, mammals and humans in China from 1994 to 2013, and updated the clade classification for each segment. We identified 117 distinct genotypes in 730 H9N2 viruses. We analyzed the sequences of all eight segments in each virus and found three important time points: the years 2000, 2006 and 2010. In the periods divided by these years, genotypic diversity, geographic distribution and host range changed considerably. Genotypic diversity fluctuated greatly in 2000 and 2006. Since 2010, a single genotype became predominant in poultry throughout China, and the eastern coastal region became the newly identified epidemic center. Throughout their 20-year prevalence in China, H9N2 influenza viruses have emerged and adapted from aquatic birds to chickens. The minor avian species and wild birds exacerbated H9N2 genotypes by providing diversified genes, and chickens were the most prevalent vector in which the viruses evolved and expanded their prevalence. It is the necessity for surveillance and disease control on live-bird markets, poultry farms and wild-bird habitats in China.

Respiratory phagocytes are implicated in enhanced colibacillosis in chickens co-infected with influenza virus H9N2 and Escherichia coli

1. The aim of this study was to determine the most likely time interval after infection with influenza virus H9N2 for co-infection with Escherichia coli to cause colibacillosis, the importance of lung load of E. coli and the involvement of respiratory phagocytes. 2. Specific pathogen free chickens were inoculated intranasally with 10⁶EID₅₀ of influenza virus or uninfected. After specified time intervals, 10⁷ CFU E. coli or phosphate-buffered saline was inoculated. The presence of lesions, the number of respiratory phagocytes in the respiratory lavage fluid and the E. coli load in the lung were determined after different time intervals. 3. Compared with the number of lesions in chickens receiving only E. coli inoculation, the number lesions in co-infected chickens were increased at 0- and 3-d time intervals, but reduced in the groups at 6- and 9-d intervals between co-infection. 4. At 1-3 d after E. coli inoculation, the number of lesions chickens was correlated with the number of respiratory phagocytes harvested and related to the E. coli load in the lungs at 5 d. 5. These results suggest that the lesions caused by E. coli in chickens were increased within a 0-3 d interval following H9N2 virus inoculation and that this effect is related to the number of respiratory phagocytes.