Impact of the variations in potential glycosylation sites of the hemagglutinin of H9N2 influenza virus

Genetic insights of H9N2 avian influenza viruses circulating in Mali and phylogeographic patterns in Northern and Western Africa

Avian influenza viruses (AIVs) of the H9N2 subtype have become widespread in Western Africa since their first detection in 2017 in Burkina Faso. However, the genetic characteristics and diffusion patterns of the H9N2 virus remain poorly understood in Western Africa, mainly due to limited surveillance activities. In addition, Mali, a country considered to play an important role in the epidemiology of AIVs in the region, lacks more comprehensive data on the genetic characteristics of these viruses, especially the H9N2 subtype. To better understand the genetic characteristics and spatio-temporal dynamics of H9N2 virus within this region, we carried out a comprehensive genetic characterization of H9N2 viruses collected through active surveillance in live bird markets in Mali between 2021 and 2022. We also performed a continuous phylogeographic analysis to unravel the dispersal history of H9N2 lineages between Northern and Western Africa. The identified Malian H9N2 virus belonged to the G1 lineage, similar to viruses circulating in both Western and Northern Africa, and possessed multiple molecular markers associated with an increased potential for zoonotic transmission and virulence. Notably, some Malian strains carried the R-S-N-R motif at their cleavage site, mainly observed in H9N2 strains in Asia. Our continuous phylogeographic analysis revealed a single and significant long-distance lineage dispersal event of the H9N2 virus to Western Africa, likely to have originated from Morocco in 2015, shaping the westward diffusion of the H9N2 virus. Our study highlights the need for long-term surveillance of H9N2 viruses in poultry populations in Western Africa, which is crucial for a better understanding of virus evolution and effective management against potential zoonotic AIV strain emergence.

Loss of amino acids 67-76 in the neuraminidase protein under antibody selection pressure alters the tropism, transmissibility and innate immune response of H9N2 avian influenza virus in chickens

H9N2 virus has become the most widespread subtype of avian influenza in Chinese poultry. Although many studies have been published on this disease, the pathogenesis of the H9N2 virus remains to be fully understood. In our previous work, we identified 44 viral strains with 67-76 amino acid deletions in the neuraminidase protein (NA∆67-76) from trachea and lung tissues after 20 successive generations in vaccinated chickens. Interestingly, these 10 amino acid deletions are located in the stalk of the NA protein, and all mutations were unique to the viruses under the selection pressure of vaccine antibodies. To investigate the effect of NA∆67-76 on the H9N2 virus, the NA∆67-76 deletion mutant (rF/NAΔ67-76) was constructed in the H9N2 virus A/Chicken/Shanghai/F/98 (F/98) to assess the phenotypic changes between the parental and mutant strains. The results showed that the recombinant virus rF/NAΔ67-76 had no significantly effect on the antigenicity of the virus or on the infectivity of the host cells, but it significantly inhibited the release of virions from host cells. In addition, rF/NAΔ67-76 efficiently enhanced the neuraminidase activity and improved the receptor binding ability of the virus, indicating that the influence of receptor binding ability on the rF/NAΔ67-76 virus is much greater than that of neuraminidase activity. Furthermore, this study revealed that rF/NAΔ67-76 reduced the viral replication ability at 6 and 12 h post-infection, but improved it at 24, 48, and 72 h post-infection. Chicken experiments showed that rF/NAΔ67-76 exhibits a much higher tissue tropism for the trachea rather than lung tissue. rF/NAΔ67-76 still had the ability to infect the upper respiratory tract through aerosol, but its cloaca replication capacity was significantly reduced. Both in vivo and in vitro experiments confirmed that rF/NAΔ67-76 could produce a stronger innate immune response after infecting cells and chickens, especially significantly enhancing the transcription levels of TLR3, TLR4, TLR7, TLR21, MDA5, and NLRP3. Altogether, the results of this study propose that antibody selection pressure plays an important role in the evolution of H9N2 avian influenza virus.

That H9N2 avian influenza viruses circulating in different regions gather in the same live-poultry market poses a potential threat to public health

H9N2 avian influenza viruses are endemic and persistent in China, but those that are prevalent in different provinces are also causes of wide epidemics, related to the spread of wild birds and the cross-regional trade in live poultry. For the past 4 years, beginning in 2018, we have sampled a live-poultry market in Foshan, Guangdong, in this ongoing study. In addition to the prevalence of H9N2 avian influenza viruses in China during this period, we identified isolates from the same market belonging to clade A and clade B, which diverged in 2012-2013, and clade C, which diverged in 2014-2016, respectively. An analysis of population dynamics revealed that, after a critical divergence period from 2014 to 2016, the genetic diversity of H9N2 viruses peaked in 2017. Our spatiotemporal dynamics analysis found that clade A, B, and C, which maintain high rates of evolution, have different prevalence ranges and transmission paths. Clades A and B were mainly prevalent in East China in the early stage, and then spread to Southern China, becoming epidemic with clade C. Strains from different regions converge at the same live-poultry market to communicate, which may be one reasons the H9N2 viruses are difficult to eradicate and increasingly dominant throughout China. Selection pressure and molecular analysis have demonstrated that single amino acid polymorphisms at key receptor binding sites 156, 160, and 190 under positive selection pressure, suggesting that H9N2 viruses are undergoing mutations to adapt to new hosts. Live-poultry markets are important because people who visit them have frequent contact with poultry, H9N2 viruses from different regions converge at these markets and spread through contact between live birds and humans, generating increased risks of human exposure to these viruses and threatening public health safety. Thus, it is important to reducing the cross-regional trade of live poultry and strengthening the monitoring of avian influenza viruses in live-poultry markets to reduce the spread of avian influenza viruses.

HA gene amino acid mutations contribute to antigenic variation and immune escape of H9N2 influenza virus

Based on differences in the amino acid sequence of the protein haemagglutinin (HA), the H9N2 avian influenza virus (H9N2 virus) has been clustered into multiple lineages, and its rapidly ongoing evolution increases the difficulties faced by prevention and control programs. The HA protein, a major antigenic protein, and the amino acid mutations that alter viral antigenicity in particular have always been of interest. Likewise, it has been well documented that some amino acid mutations in HA alter viral antigenicity in the H9N2 virus, but little has been reported regarding how these antibody escape mutations affect antigenic variation. In this study, we were able to identify 15 HA mutations that were potentially relevant to viral antigenic drift, and we also found that a key amino acid mutation, A180V, at position 180 in HA (the numbering for mature H9 HA), the only site of the receptor binding sites that is not conserved, was directly responsible for viral antigenic variation. Moreover, the recombinant virus with alanine to valine substitution at position 180 in HA in the SH/F/98 backbone (rF/HA_A180V virus) showed poor cross-reactivity to immune sera from animals immunized with the SH/F/98 (F/98, A180), SD/SS/94 (A180), JS/Y618/12 (T180), and rF/HA_A180V (V180) viruses by microneutralization (MN) assay. The A180V substitution in the parent virus caused a significant decrease in cross-MN titres by enhancing the receptor binding activity, but it did not physically prevent antibody (Ab) binding. The strong receptor binding avidity prevented viral release from cells. Moreover, the A180V substitution promoted H9N2 virus escape from an in vitro pAb-neutralizing reaction, which also slightly affected the cross-protection in vivo. Our results suggest that the A180V mutation with a strong receptor binding avidity contributed to the low reactors in MN/HI assays and slightly affected vaccine efficacy but was not directly responsible for immune escape, which suggested that the A180V mutation might play a key role in the process of the adaptive evolution of H9N2 virus.

Molecular characterization and antigenic analysis of reassortant H9N2 subtype avian influenza viruses in Eastern China in 2016

H9N2 avian influenza viruses (AIVs) can cause respiratory symptoms and decrease the egg production. Additionally, H9N2 AIVs can provide internal genes for reassortment with other subtypes. During the monitoring of live poultry markets in 2016, a total of 32 (32/179, 17.88%) H9N2 AIVs were isolated from poultry in Eastern China, and seven representative strains were selected based on the isolation time, isolation location and sequence homology for further characterization. Phylogenetic analysis of hemagglutinin and neuraminidase showed that these H9N2 AIVs clustered into the Y280 sublineage. And the phylogenetic trees of six internal genes showed that the source of these gene fragments was more abundant, suggesting that extensive reassortment has occurred in these H9N2 viruses. Molecular analysis showed that multiple specific amino acid mutations occurred that increased H9N2 AIVs' infectivity, transmissibility, and affinity to mammals, including Q226L and Q227M in hemagglutinin, E627K in polymerase basic protein 2 (PB2), L13P in polymerase basic protein 1 (PB1), and A70V and S409N in polymerase acidic protein (PA). Pathogenicity tests in mice showed these H9N2 AIVs could replicate in lungs and exhibited slight to moderate virulence. The continuous circulation of these H9N2 viruses suggests the necessity for persistent surveillance of the H9N2 AIVs in poultry.

Identification of key residues involved in the neuraminidase antigenic variation of H9N2 influenza virus

Influenza A H9N2 virus causes economic loss to the poultry industry and has likely contributed to the genesis of H5N1 and H7N9 viruses. The neuraminidase (NA) of H9N2 virus, like haemagglutinin, is under antibody selective pressure and may undergo antigenic change; however, its antigenic structure remains to be elucidated. In this study, we used monoclonal antibodies (mAbs) to probe the H9N2 viral NA residues that are key for antibody binding/inhibition. These mAbs fell into three groups based on their binding/inhibition of the NA of H9N2 viruses isolated during 1999–2019: group I only bounded the NA of the early 2000 H9N2 viruses but possessed no neutralizing ability, group II bounded and inhibited the NA of H9N2 viruses isolated before 2012, and group III reacted with most or all tested H9N2 viruses. We showed that NA residue 356 is key for the recognition by group I mAbs, residues 344, 368, 369, and 400 are key for the binding/inhibition of NA by group II antibodies, whereas residues 248, 253, and the 125/296 combination are key for neutralizing antibodies in group III. Our findings highlighted NA antigenic change of the circulating H9N2 viruses, and provided data for a more complete picture of the antigenic structure of H9N2 viral NA.

Experimental direct-contact transmission of influenza A/H9N2 virus in the guinea pig model in Iran

Aim: The present study aims to evaluate risk factors for the transmission of A/H9N2 viruses in guinea pig model. Materials & methods: Lung tissue samples were collected from the chicken clinically infected with influenza A/H9N2 virus in 2018. Next, virus isolation and titration, as well as reverse transcription PCR were performed. Then, hemagglutnation and neuraminidase genes was sequenced to identify different positions (hotspots) involved in transmission and host adaptation. Results: Influenza A/H9N2 virus could replicate in low titers in the nasal turbinate and transmit from infected to noninfected guinea pigs. Conclusion: Hotspots on the surface glycoproteins had the potential to alter transmission properties in the new host.

A D200N hemagglutinin substitution contributes to antigenic changes and increased replication of avian H9N2 influenza virus

Influenza virus hemagglutinin (HA) plays an important role in viral antigenicity, replication and host range. However, few amino acid positions in HA were reported to play multiple functions in both viral antigenicity and replication. In the present study, through analyzing the amino acid sequences of H9N2 avian influenza viruses (AIVs) isolated from China, we identified a multi-functional substitution of D200N in HA1 protein. Firstly, the substitution of D200N changed the antigenicity of H9N2 AIVs. Secondly, the D200N increased the HA cleavage efficiency and reduced acid and thermal stability of HA protein, which triggered viral-endosomal membrane fusion whereby promoted the release of viral genome into the host cytoplasm. Finally, residue 200-N increased the replication of H9N2 viruses in both chicken embryo fibroblast (CEF) cells and chicken embryonated eggs. In summary, the D200N substitution is a newly identified antigenicity and replication determinant of H9N2 AIVs, which should be paid more attention during surveillance.

Sporadic occurrence of H9N2 avian influenza infections in human in Anhui province, eastern China: A notable problem

H9N2 viruses can cause great economic losses to the domestic poultry industry when co-infected with other influenza viruses or pathogens. . To better understand the molecular characteristics of H9N2 avian influenza viruses (AIVs) and analyze the genetic evolutionary relationship, we isolated three H9N2 subtypes AIVs from nasopharyngeal swab specimens from the three cases reported in Anhui province since 2015, and systematically reviewed the genome-wide data of 21 poultry--isolated H9N2 viruses during 1998-2017. The six internal genes of three human-isolated viruses and recent poultry-isolated viruses (since 2014) in Anhui province presented high gene homologies with HPAI H7N9, even including H10N8 and H5N6. The three human-isolated H9N2 AIVs and poultry-isolated viruses (since 2008) in Anhui province were highly similar, and classified into genotype S. Seven N-linked potential glycosylation sites in the HA protein were detected in the three human-isolated viruses, which also appeared in poultry-isolated H9N2 AIVs. None of the human-isolated H9N2 AIVs had the I368V mutation in PB1 protein, but all the poultry-isolated H9N2 viruses in 2017 carried this mutation. Multidisciplinary, cross-regional and cross-sectoral approaches are warranted to address complex public health challenges and achieve the goal of 'one health'.