Synergistic effect of PB2 283M and 526R contributes to enhanced virulence of H5N8 influenza viruses in mice

Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark

Transmission of influenza A viruses (IAVs) between pigs and humans can trigger pandemics but more often cease as isolated infections without further spread in the new host species population. In Denmark, a major pig-producing country, the first two detections of human infections with swine-like IAVs were reported in 2021. These zoonotic IAVs were reassortants of the H1N1 pandemic 2009 lineage ("H1N1pdm09," H1 lineage 1A, clade 1A.3.3.2) introduced to swine farms in Denmark through humans approximately 11 years prior. However, predicting the likelihood and outcome of such IAV spillovers is challenging without a better understanding of the viral determinants. This study traced the evolution of H1N1pdm09 from 207 sequenced genomes as the virus propagated across Danish swine farms over a decade. H1N1pdm09 diverged into several genetically distinct viral populations, largely prompted by reassortments with neuraminidase (NA) segments from other enzootic IAV lineages. The genomic segments encoding the viral envelope glycoproteins, hemagglutinin (HA) and NA, evolved at the fastest rates, while the M and NS genomic segments were among the lowest evolutionary rates. The two zoonotic IAVs emerged from separate viral populations and shared the highest number of amino acid mutations in the PB2 and HA proteins. Acquisition of additional predicted glycosylation sites on the HA proteins of the zoonotic IAVs may have facilitated infection of the human patients. Ultimately, the analysis provides a foundation from which to further explore viral genetic indicators of host adaptation and zoonotic risk.

Roles and functions of IAV proteins in host immune evasion

Influenza A viruses (IAVs) evade the immune system of the host by several regulatory mechanisms. Their genomes consist of eight single-stranded segments, including nonstructural proteins (NS), basic polymerase 1 (PB1), basic polymerase 2 (PB2), hemagglutinin (HA), acidic polymerase (PA), matrix (M), neuraminidase (NA), and nucleoprotein (NP). Some of these proteins are known to suppress host immune responses. In this review, we discuss the roles, functions and underlying strategies adopted by IAV proteins to escape the host immune system by targeting different proteins in the interferon (IFN) signaling pathway, such as tripartite motif containing 25 (TRIM25), inhibitor of nuclear factor κB kinase (IKK), mitochondrial antiviral signaling protein (MAVS), Janus kinase 1 (JAK1), type I interferon receptor (IFNAR1), interferon regulatory factor 3 (IRF3), IRF7, and nuclear factor-κB (NF-κB). To date, the IAV proteins NS1, NS2, PB1, PB1-F2, PB2, HA, and PA have been well studied in terms of their roles in evading the host immune system. However, the detailed mechanisms of NS3, PB1-N40, PA-N155, PA-N182, PA-X, M42, NA, and NP have not been well studied with respect to their roles in immune evasion. Moreover, we also highlight the future perspectives of research on IAV proteins.

The synergistic effect of residues 32T and 550L in the PA protein of H5 subtype avian influenza virus contributes to viral pathogenicity in mice

The avian influenza virus (AIV) PA protein contributes to viral replication and pathogenicity; however, its interaction with innate immunity is not well understood. Here, we report that the H5 subtype AIV PA protein strongly suppresses host antiviral defense by interacting with and degrading a key protein in interferon (IFN) signaling, Janus kinase 1 (JAK1). Specifically, the AIV PA protein catalyzes the K48-linked polyubiquitination and degradation of JAK1 at lysine residue 249. Importantly, the AIV PA protein harboring 32T/550L degrades both avian and mammalian JAK1, while the AIV PA protein with residues 32M/550I degrades avian JAK1 only. Furthermore, the residues 32T/550L in PA protein confer optimum polymerase activity and AIV growth in mammalian cells. Notably, the replication and virulence of the AIV PA T32M/L550I mutant are attenuated in infected mice. Collectively, these data reveal an interference role for H5 subtype AIV PA protein in host innate immunity, which can be targeted for the development of specific and effective anti-influenza therapeutics.

H5N8 Subtype avian influenza virus isolated from migratory birds emerging in Eastern China possessed a high pathogenicity in mammals

Novel H5N8 highly pathogenic avian influenza viruses (HPAIVs) bearing the clade 2.3.4.4b HA gene have been widely spread through wild migratory birds since 2020. One H5N8 HPAIV (A/Wild bird/Cixi/Cixi02/2020; here after Cixi02) was isolated from migratory birds in Zhejiang Province, Eastern China in 25 November 2020. However, its pathogenicity in avian and mammal remains unknown. Hemagglutinin gene genetic analysis indicated that Cixi02 virus belonged to the branch II of H5 clade 2.3.4.4b originated from Iraq in May 2020. Cixi02 virus showed a binding affinity to both SA α-2, 3-galactose (Gal) and SA α-2, 6 Gal receptors, good pH stability, thermostability, and replication ability in both avian and mammal cells. The poultry pathogenicity indicated that Cixi02 virus was lethal to chickens. Moreover, the mammalian pathogenicity showed that the 50% mouse lethal dose (MLD50 ) is 2.14 lgEID50 /50 μl, indicating a high pathogenicity in mice. Meanwhile, Cixi02 virus was widely detected in multiple organs, including heart, liver, spleen, lung, kidney, turbinate, and brain after nasal infection. In addition, we found high level gene expressions of TNF-α, IL-12p70, CXCL10, and IFN-α in lungs, IL-8 and IL-1β in brains, and observed severe histopathological change in lungs and brains. Collectedly, this study provided new insights on the pathogenic and zoonotic features of an H5N8 subtype AIV isolated from migratory birds.

The influenza virus PB2 protein evades antiviral innate immunity by inhibiting JAK1/STAT signalling

Influenza A virus (IAV) polymerase protein PB2 has been shown to partially inhibit the host immune response by blocking the induction of interferons (IFNs). However, the IAV PB2 protein that regulates the downstream signaling pathway of IFNs is not well characterized. Here, we report that IAV PB2 protein reduces cellular sensitivity to IFNs, suppressing the activation of STAT1/STAT2 and ISGs. Furthermore, IAV PB2 protein targets mammalian JAK1 at lysine 859 and 860 for ubiquitination and degradation. Notably, the H5 subtype of highly pathogenic avian influenza virus with I283M/K526R mutations on PB2 increases the ability to degrade mammalian JAK1 and exhibits higher replicate efficiency in mammalian (but not avian) cells and mouse lung tissues, and causes greater mortality in infected mice. Altogether, these data describe a negative regulatory mechanism involving PB2-JAK1 and provide insights into an evasion strategy from host antiviral immunity employed by IAV.

Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness

2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.

Co-circulation of multiple influenza A reassortants in swine harboring genes from seasonal human and swine influenza viruses

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018. In total, 3800 submissions were received with a steady increase in swIAV-positive submissions, reaching 56% in 2018. Full-genome sequences were obtained from 129 swIAV-positive samples. Altogether, 17 different circulating genotypes were identified including six novel reassortants harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx (clade 1A.3.3.2) viruses. The results provide essential data for the control of swIAV in pigs and emphasize the importance of contemporary surveillance for discovering novel swIAV strains posing a potential threat to the human population.

Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene

H5N8 subtype highly pathogenic avian influenza viruses (HPAIVs) pose a huge threat to poultry industry and general public health. Our previous study demonstrated that synergistic effect of 283M and 526R in PB2 gene was a critical factor for viral high pathogenicity in mammals. However, the potential pathogenic mechanism of the mutant virus is still unclear. Here, RNA-seq method was used to analyze the global host response of murine lungs after infecting with parental r-JY virus and JY-PB2-I283M-K526R mutant virus. We found that both amounts and the expression levels of host differentially expressed genes (DEGs) were higher in mutant virus-infected mice compared with the group of parental virus. Furthermore, the DEGs mainly related with innate immune response by GO and KEGG analysis. Especially, PB2-I283M-K526R mutation strongly induced a sharp expression of cytokine storm-related genes, including MX1, CXCL10, and IFN-γ, performed by qRT-PCR. We also found that PB2-I283M-K526R mutation accelerated the level of cell apoptosis by heat map analysis of apoptosis-related DEGs in lungs and apoptosis assay in vitro. Taken together, our data demonstrated that PB2-I283M-K526R of H5N8 subtype HPAIV exacerbated the innate immune response and the level of cell apoptosis, which might be a key pathogenic mechanism for the enhanced pathogenicity of mutants in mammals.

Genetic incompatibilities and reduced transmission in chickens may limit the evolution of reassortants between H9N2 and panzootic H5N8 clade 2.3.4.4 avian influenza virus showing high virulence for mammals

The unprecedented spread of H5N8- and H9N2-subtype avian influenza virus (AIV) in birds across Asia, Europe, Africa, and North America poses a serious public health threat with a permanent risk of reassortment and the possible emergence of novel virus variants with high virulence in mammals. To gain information on this risk, we studied the potential for reassortment between two contemporary H9N2 and H5N8 viruses. While the replacement of the PB2, PA, and NS genes of highly pathogenic H5N8 by homologous segments from H9N2 produced infectious H5N8 progeny, PB1 and NP of H9N2 were not able to replace the respective segments from H5N8 due to residues outside the packaging region. Furthermore, exchange of the PB2, PA, and NS segments of H5N8 by those of H9N2 increased replication, polymerase activity and interferon antagonism of the H5N8 reassortants in human cells. Notably, H5N8 reassortants carrying the H9N2-subtype PB2 segment and to lesser extent the PA or NS segments showed remarkably increased virulence in mice as indicated by rapid onset of mortality, reduced mean time to death and increased body weight loss. Simultaneously, we observed that in chickens the H5N8 reassortants, particularly with the H9N2 NS segment, demonstrated significantly reduced transmission to co-housed chickens. Together, while the limited capacity for reassortment between co-circulating H9N2 and H5N8 viruses and the reduced bird-to-bird transmission of possible H5N8 reassortants in chickens may limit the evolution of such reassortant viruses, they show a higher replication potential in human cells and increased virulence in mammals.

Outbreak Severity of Highly Pathogenic Avian Influenza A(H5N8) Viruses Is Inversely Correlated to Polymerase Complex Activity and Interferon Induction

Highly pathogenic avian influenza A(H5N8) viruses first emerged in China in 2010 and in 2014 spread throughout Asia and to Europe and the United States via migrating birds. Influenza A(H5N8) viruses were first detected in the Netherlands in 2014 and caused five outbreaks in poultry farms but were infrequently detected in wild birds. In 2016, influenza A(H5N8) viruses were reintroduced into the Netherlands, resulting in eight poultry farm outbreaks. This outbreak resulted in numerous dead wild birds with severe pathology. Phylogenetic analysis showed that the polymerase genes of these viruses had undergone extensive reassortment between outbreaks. Here, we investigated the differences in virulence between the 2014-15 and the 2016-17 outbreaks by characterizing the polymerase complex of influenza A(H5N8) viruses from both outbreaks. We found that viruses from the 2014-15 outbreak had significantly higher polymerase complex activity in both human and avian cell lines than did those from the 2016-17 outbreak. No apparent differences in the balance between transcription and replication of the viral genome were observed. Interestingly, the 2014-15 polymerase complexes induced significantly higher levels of interferon beta (IFN-β) than the polymerase complexes of the 2016-17 outbreak viruses, mediated via retinoic acid-inducible gene I (RIG-I). Inoculation of primary duck cells with recombinant influenza A(H5N8) viruses, including viruses with reassorted polymerase complexes, showed that the polymerase complexes from the 2014-15 outbreak induced higher levels of IFN-β despite relatively minor differences in replication capacity. Together, these data suggest that despite the lower levels of polymerase activity, the higher 2016-17 influenza A(H5N8) virus virulence may be attributed to the lower level of activation of the innate immune system.IMPORTANCE Compared to the 2014-15 outbreak, the 2016-17 outbreak of influenza A(H5N8) viruses in the Netherlands and Europe was more virulent; the number of dead or diseased wild birds found and the severity of pathological changes were higher during the 2016-17 outbreak. The polymerase complex plays an important role in influenza virus virulence, and the gene segments of influenza A(H5N8) viruses reassorted extensively between the outbreaks. In this study, the 2014-15 polymerase complexes were found to be more active, which is counterintuitive with the observed higher virulence of the 2016-17 outbreak viruses. Interestingly, the 2014-15 polymerase complexes also induced higher levels of IFN-β. These findings suggest that the higher virulence of influenza A(H5N8) viruses from the 2016-17 outbreak may be related to the lower induction of IFN-β. An attenuated interferon response could lead to increased dissemination, pathology, and mortality, as observed in (wild) birds infected during the 2016-2017 outbreak.

Substitutions in the PB2 methionine 283 residue affect H5 subtype avian influenza virus virulence

The influenza A virus (IAV) PB2 subunit modulates viral polymerase activity, replication kinetics and pathogenicity. Here we identified novel PB2 substitutions at position 283 of H5 subtype IAV and evaluated their biological characteristics and virulence. The substitution PB2-M283L enhanced the growth capacity and polymerase activity in human and mammalian cells in comparison to the rWT virus. The substitution PB2-M283L displayed high virulence, resulting in a greater virus load in different tissues, more severe histopathological lesions and proinflammatory cytokines burst in mice. The substitution PB2-M283I had an opposite phenotype. Our data extend the important role of PB2 substitutions in the adaptation of H5 subtype IAVs to mammalian hosts.

Rule-based meta-analysis reveals the major role of PB2 in influencing influenza A virus virulence in mice

Background

Influenza A virus (IAV) poses threats to human health and life. Many individual studies have been carried out in mice to uncover the viral factors responsible for the virulence of IAV infections. Nonetheless, a single study may not provide enough confident about virulence factors, hence combining several studies for a meta-analysis is desired to provide better views. For this, we documented more than 500 records of IAV infections in mice, whose viral proteins could be retrieved and the mouse lethal dose 50 or alternatively, weight loss and/or survival data, was/were available for virulence classification.

Results

IAV virulence models were learned from various datasets containing aligned IAV proteins and the corresponding two virulence classes (avirulent and virulent) or three virulence classes (low, intermediate and high virulence). Three proven rule-based learning approaches, i.e., OneR, JRip and PART, and additionally random forest were used for modelling. PART models achieved the best performance, with moderate average model accuracies ranged from 65.0 to 84.4% and from 54.0 to 66.6% for the two-class and three-class problems, respectively. PART models were comparable to or even better than random forest models and should be preferred based on the Occam’s razor principle. Interestingly, the average accuracy of the models was improved when host information was taken into account. For model interpretation, we observed that although many sites in HA were highly correlated with virulence, PART models based on sites in PB2 could compete against and were often better than PART models based on sites in HA. Moreover, PART had a high preference to include sites in PB2 when models were learned from datasets containing the concatenated alignments of all IAV proteins. Several sites with a known contribution to virulence were found as the top protein sites, and site pairs that may synergistically influence virulence were also uncovered.

Conclusion

Modelling IAV virulence is a challenging problem. Rule-based models generated using viral proteins are useful for its advantage in interpretation, but only achieve moderate performance. Development of more advanced approaches that learn models from features extracted from both viral and host proteins shall be considered for future works.

Avian influenza overview November 2017 - February 2018

Between 16 November 2017 and 15 February 2018, one highly pathogenic avian influenza (HPAI) A(H5N6) and five HPAI A(H5N8) outbreaks in poultry holdings, two HPAI A(H5N6) outbreaks in captive birds and 22 HPAI A(H5N6) wild bird events were reported within Europe. There is a lower incursion of HPAI A(H5N6) in poultry compared to HPAI A(H5N8). There is no evidence to date that HPAI A(H5N6) viruses circulating in Europe are associated with clades infecting humans. Clinical signs in ducks infected with HPAI A(H5N8) seemed to be decreasing, based on reports from Bulgaria. However, HPAI A(H5N8) is still present in Europe and is widespread in neighbouring areas. The majority of mortality events of wild birds from HPAIV A(H5) in this three-month period involved single birds. This indicates that the investigation of events involving single dead birds of target species is important for comprehensive passive surveillance for HPAI A(H5). Moreover, 20 low pathogenic avian influenza (LPAI) outbreaks were reported in three Member States. The risk of zoonotic transmission to the general public in Europe is considered to be very low. The first human case due to avian influenza A(H7N4) was notified in China underlining the threat that newly emerging avian influenza viruses pose for transmission to humans. Close monitoring is required of the situation in Africa and the Middle East with regards to HPAI A(H5N1) and A(H5N8). Uncontrolled spread of virus and subsequent further genetic evolution in regions geographically connected to Europe may increase uncertainty and risk for further dissemination of virus. The risk of HPAI introduction from Third countries via migratory wild birds to Europe is still considered much lower for wild birds crossing the southern borders compared to birds crossing the north-eastern borders, whereas the introduction via trade is still very to extremely unlikely.