Estimating the Fitness Advantage Conferred by Permissive Neuraminidase Mutations in Recent Oseltamivir-Resistant A(H1N1)pdm09 Influenza Viruses

Oseltamivir is relied upon worldwide as the drug of choice for the treatment of human influenza infection. Surveillance for oseltamivir resistance is routinely performed to ensure the ongoing efficacy of oseltamivir against circulating viruses. Since the emergence of the pandemic 2009 A(H1N1) influenza virus (A(H1N1)pdm09), the proportion of A(H1N1)pdm09 viruses that are oseltamivir resistant (OR) has generally been low. However, a cluster of OR A(H1N1)pdm09 viruses, encoding the neuraminidase (NA) H275Y oseltamivir resistance mutation, was detected in Australia in 2011 amongst community patients that had not been treated with oseltamivir. Here we combine a competitive mixtures ferret model of influenza infection with a mathematical model to assess the fitness, both within and between hosts, of recent OR A(H1N1)pdm09 viruses. In conjunction with data from in vitro analyses of NA expression and activity we demonstrate that contemporary A(H1N1)pdm09 viruses are now more capable of acquiring H275Y without compromising their fitness, than earlier A(H1N1)pdm09 viruses circulating in 2009. Furthermore, using reverse engineered viruses we demonstrate that a pair of permissive secondary NA mutations, V241I and N369K, confers robust fitness on recent H275Y A(H1N1)pdm09 viruses, which correlated with enhanced surface expression and enzymatic activity of the A(H1N1)pdm09 NA protein. These permissive mutations first emerged in 2010 and are now present in almost all circulating A(H1N1)pdm09 viruses. Our findings suggest that recent A(H1N1)pdm09 viruses are now more permissive to the acquisition of H275Y than earlier A(H1N1)pdm09 viruses, increasing the risk that OR A(H1N1)pdm09 will emerge and spread worldwide.     

Species-Specific Contribution of the Four C-Terminal Amino Acids of Influenza A Virus NS1 Protein to Virulence

Large-scale sequence analyses of influenza viruses revealed that nonstructural 1 (NS1) proteins from avian influenza viruses have a conserved C-terminal ESEV amino acid motif, while NS1 proteins from typical human influenza viruses have a C-terminal RSKV motif. To test the influence of the C-terminal domains of NS1 on the virulence of an avian influenza virus, we generated a wild-type H7N1 virus with an ESEV motif and a mutant virus with an NS1 protein containing a C-terminal RSKV motif by reverse genetics. We compared the phenotypes of these viruses in vitro in human, mouse, and duck cells as well as in vivo in mice and ducks. In human cells, the human C-terminal RSKV domain increased virus replication. In contrast, the avian C-terminal ESEV motif of NS1 increased virulence in mice. We linked this increase in pathogenicity in mice to an increase in virus replication and to a more severe lung inflammation associated with a higher level of production of type I interferons. Interestingly, the human C-terminal RSKV motif of NS1 increased viral replication in ducks. H7N1 virus with a C-terminal RSKV motif replicated to higher levels in ducks and induced higher levels of Mx, a type I interferon-stimulated gene. Thus, we identify the C-terminal domain of NS1 as a species-specific virulence domain.Interspecies transmission of influenza viruses can lead to the introduction of new subtypes of influenza virus into the human population (31). The emergence of a new influenza virus that is able to spread efficiently between humans can cause a pandemic, as evidenced by the recent introduction of the swine-origin 2009 A/H1N1 virus to humans (10). The spread of avian influenza A viruses from birds to humans could also lead to the introduction of a new viral subtype with pandemic potential (22). Fortunately, the efficient replication of avian influenza A viruses in humans and interhuman transmission are generally limited and require further adaptations of the virus to humans. One determinant of host adaptation lies in the receptor binding specificity of hemagglutinin (HA) (52). In addition, several reports have underlined the role of amino acid 627 of the PB2 polymerase subunit in determining viral host range and virulence (15, 36, 44, 45). Large-scale sequence analyses of viruses isolated from different bird and mammalian species have been performed in order to identify previously unrecognized determinants of host adaptation and virulence (2, 32). Those studies have identified a 4-amino-acid motif in the C-terminal domain of NS1 that could represent a previously unnoticed host adaptation motif. Indeed, the vast majority of avian influenza viruses have an NS1 protein with a C-terminal ESEV domain, while typical human viruses have a conserved RSKV domain. The conservation of these species-specific motifs in the NS1 protein despite important sequence variability in the rest of the protein suggests that these four C-terminal amino acids are under strong selection pressure in their respective natural hosts (3, 5, 25).NS1 is a multifunctional protein implicated in the regulation of viral gene expression and in the inhibition of the host antiviral response (12). In order to test the role of these newly identified NS1 domains, Jackson et al. previously introduced various C-terminal motifs into NS1 of the mouse-adapted human influenza virus A/WSN/33 strain by use of reverse genetics (24). Mice inoculated with a virus containing an avian C-terminal ESEV NS1 domain had high viral loads in the lungs and decreased survival compared to mice inoculated with a virus containing a C-terminal RSKV domain. These results showed that the C-terminal ESEV motif found in avian NS1 proteins increases virulence in mice when introduced into a human strain of influenza virus. Whether this finding also applies to avian influenza viruses remains unknown. Moreover, whether the C-terminal ESEV domain of NS1 increases replication in human cells remains unknown. Finally, how the C-terminal domains of NS1 modulate virulence in nonmammalian hosts, such as birds, is also unknown.Here, we assessed the contribution of the C-terminal domains of NS1 to the pathogenicity of an avian influenza virus. By using reverse genetics, we generated H7N1 viruses containing an NS1 protein with a C-terminal avian ESEV domain or a C-terminal human RSKV domain. The replications of these viruses in human, mouse, and duck cell were compared. In addition, we assessed their pathogenicity in mice and ducks. Our results show that the C-terminal RSKV domain increases the replication of an avian influenza virus in human cells. To our surprise, we observed that the C-terminal RSKV domain increases replication in ducks. In contrast, the C-terminal ESEV domain increases virulence in mice. Thus, we identify the C-terminal domain of NS1 as a species-specific virulence domain.     

Transfectant Influenza A Viruses with Long Deletions in the NS1 Protein Grow Efficiently in Vero Cells

We established a reverse genetics system for the nonstructural (NS) gene segment of influenza A virus. This system is based on the use of the temperature-sensitive (ts) reassortant virus 25A-1. The 25A-1 virus contains the NS gene from influenza A/Leningrad/134/57 virus and the remaining gene segments from A/Puerto Rico (PR)/8/34 virus. This particular gene constellation was found to be responsible for the ts phenotype. For reverse genetics of the NS gene, a plasmid-derived NS gene from influenza A/PR/8/34 virus was ribonucleoprotein transfected into cells that were previously infected with the 25A-1 virus. Two subsequent passages of the transfection supernatant at 40°C selected viruses containing the transfected NS gene derived from A/PR/8/34 virus. The high efficiency of the selection process permitted the rescue of transfectant viruses with large deletions of the C-terminal part of the NS1 protein. Viable transfectant viruses containing the N-terminal 124, 80, or 38 amino acids of the NS1 protein were obtained. Whereas all deletion mutants grew to high titers in Vero cells, growth on Madin-Darby canine kidney (MDCK) cells and replication in mice decreased with increasing length of the deletions. In Vero cells expression levels of viral proteins of the deletion mutants were similar to those of the wild type. In contrast, in MDCK cells the level of the M1 protein was significantly reduced for the deletion mutants.     

Mutant Influenza Viruses with a Defective NS1 Protein Cannot Block the Activation of PKR in Infected Cells

A short model genome RNA and also the genome RNA of influenza A virus bearing both 5′- and 3′-terminal common sequences activated the interferon-induced double-stranded-RNA-dependent protein kinase, PKR, by stimulating autophosphorylation in vitro. The activated PKR catalyzed phosphorylation of the alpha subunit of eucaryotic translation initiation factor 2 (eIF2α). The NS1 protein efficiently eliminated the PKR-activating activity of these RNAs by binding to them. Two mutant NS1 proteins, each harboring a single amino acid substitution at different regions, exhibited temperature sensitivity in their RNA binding activity in the mutant virus-infected cell lysates as well as when they were prepared as fusion proteins expressed in bacteria. The virus strains carrying these mutant NS1 proteins exhibited temperature sensitivity in virus protein synthesis at the translational level, as reported previously, and could not repress the autophosphorylation of PKR developing during the virus growth, which is normally suppressed by a viral function(s). As a result, the level of eIF2α phosphorylation was elevated 2.5- to 3-fold. The defect in virus protein synthesis was well correlated with the level of phosphorylation of PKR and eIF2α.     

Roles of the Phosphorylation of Specific Serines and Threonines in the NS1 Protein of Human Influenza A Viruses

We demonstrate that phosphorylation of the NS1 protein of a human influenza A virus occurs not only at the threonine (T) at position 215 but also at serines (Ss), specifically at positions 42 and 48. By generating recombinant influenza A/Udorn/72 (Ud) viruses that encode mutant NS1 proteins, we determined the roles of these phosphorylations in virus replication. At position 215 only a T-to-A substitution attenuated replication, whereas other substitutions (T to E to mimic constitutive phosphorylation, T to N, and T to P, the amino acid in avian influenza A virus NS1 proteins) had no effect. We conclude that attenuation resulting from the T-to-A substitution at position 215 is attributable to a deleterious structural change in the NS1 protein that is not caused by other amino acid substitutions and that phosphorylation of T215 does not affect virus replication. At position 48 neither an S-to-A substitution nor an S-to-D substitution that mimics constitutive phosphorylation affected virus replication. In contrast, at position 42, an S-to-D, but not an S-to-A, substitution caused attenuation. The S-to-D substitution eliminates detectable double-stranded RNA binding by the NS1 protein, accounting for attenuation of virus replication. We show that protein kinase C α (PKCα) catalyzes S42 phosphorylation. Consequently, the only phosphorylation of the NS1 protein of this human influenza A virus that regulates its replication is S42 phosphorylation catalyzed by PKCα. In contrast, phosphorylation of Ts or Ss in the NS1 protein of the 2009 H1N1 pandemic virus was not detected, indicating that NS1 phosphorylation probably does not play any role in the replication of this virus.     

Detection of Extensive Cross-Neutralization between Pandemic and Seasonal A/H1N1 Influenza Viruses Using a Pseudotype Neutralization Assay

Background

Cross-immunity between seasonal and pandemic A/H1N1 influenza viruses remains uncertain. In particular, the extent that previous infection or vaccination by seasonal A/H1N1 viruses can elicit protective immunity against pandemic A/H1N1 is unclear.

Methodology/Principal Findings

Neutralizing titers against seasonal A/H1N1 (A/Brisbane/59/2007) and against pandemic A/H1N1 (A/California/04/2009) were measured using an HIV-1-based pseudovirus neutralization assay. Using this highly sensitive assay, we found that a large fraction of subjects who had never been exposed to pandemic A/H1N1 express high levels of pandemic A/H1N1 neutralizing titers. A significant correlation was seen between neutralization of pandemic A/H1N1 and neutralization of a standard seasonal A/H1N1 strain. Significantly higher pandemic A/H1N1 neutralizing titers were measured in subjects who had received vaccination against seasonal influenza in 2008–2009. Higher pandemic neutralizing titers were also measured in subjects over 60 years of age.

Conclusions/Significance

Our findings reveal that the extent of protective cross-immunity between seasonal and pandemic A/H1N1 influenza viruses may be more important than previously estimated. This cross-immunity could provide a possible explanation of the relatively mild profile of the recent influenza pandemic.     

Productive Infection of Human Skeletal Muscle Cells by Pandemic and Seasonal Influenza A(H1N1) Viruses

Besides the classical respiratory and systemic symptoms, unusual complications of influenza A infection in humans involve the skeletal muscles. Numerous cases of acute myopathy and/or rhabdomyolysis have been reported, particularly following the outbreak of pandemic influenza A(H1N1) in 2009. The pathogenesis of these influenza-associated myopathies (IAM) remains unkown, although the direct infection of muscle cells is suspected. Here, we studied the susceptibility of cultured human primary muscle cells to a 2009 pandemic and a 2008 seasonal influenza A(H1N1) isolate. Using cells from different donors, we found that differentiated muscle cells (i. e. myotubes) were highly susceptible to infection by both influenza A(H1N1) isolates, whereas undifferentiated cells (i. e. myoblasts) were partially resistant. The receptors for influenza viruses, α2-6 and α2-3 linked sialic acids, were detected on the surface of myotubes and myoblasts. Time line of viral nucleoprotein (NP) expression and nuclear export showed that the first steps of the viral replication cycle could take place in muscle cells. Infected myotubes and myoblasts exhibited budding virions and nuclear inclusions as observed by transmission electron microscopy and correlative light and electron microscopy. Myotubes, but not myoblasts, yielded infectious virus progeny that could further infect naive muscle cells after proteolytic treatment. Infection led to a cytopathic effect with the lysis of muscle cells, as characterized by the release of lactate dehydrogenase. The secretion of proinflammatory cytokines by muscle cells was not affected following infection. Our results are compatible with the hypothesis of a direct muscle infection causing rhabdomyolysis in IAM patients.     

MORC3 Is a Target of the Influenza A Viral Protein NS1

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华南流感病毒NS1基因特性研究

为了解H9N2和H5N1亚型流行性感冒病毒株的NS1基因特性,采用RT-PCR方法测定了12株2000～2003年间在华南地区分离的禽流感病毒株的NS1基因核苷酸序列. 测序显示6株H9N2亚型流感病毒NS1基因开放阅读框(ORF)长654 bp,编码217个氨基酸. 6株H5N1亚型毒株NS1基因ORF长678 bp,编码225个氨基酸. 核苷酸和氨基酸同源性分析表明,同一亚型分离株之间有很高的同源性,而不同亚型的H9N2和H5N1毒株之间存在较大差异. BLAST分析表明,H5N1和H9N2亚型流感病毒分离株的NS1基因分别与近两年从香港特区和华南地区的鸭中分离的毒株A/Duck/Hong Kong/646.3/01 (H5N1)、A/Duck/Shantou/2143/01 (H9N2)有很高的亲缘关系. 该研究结果为进一步进行NS1功能研究奠定了基础.     

Evidence of Cross-Reactive Immunity to 2009 Pandemic Influenza A Virus in Workers Seropositive to Swine H1N1 Influenza Viruses Circulating in Italy

Background

Pigs play a key epidemiologic role in the ecology of influenza A viruses (IAVs) emerging from animal hosts and transmitted to humans. Between 2008 and 2010, we investigated the health risk of occupational exposure to swine influenza viruses (SIVs) in Italy, during the emergence and spread of the 2009 H1N1 pandemic (H1N1pdm) virus.

Methodology/Principal Findings

Serum samples from 123 swine workers (SWs) and 379 control subjects (Cs), not exposed to pig herds, were tested by haemagglutination inhibition (HI) assay against selected SIVs belonging to H1N1 (swH1N1), H1N2 (swH1N2) and H3N2 (swH3N2) subtypes circulating in the study area. Potential cross-reactivity between swine and human IAVs was evaluated by testing sera against recent, pandemic and seasonal, human influenza viruses (H1N1 and H3N2 antigenic subtypes). Samples tested against swH1N1 and H1N1pdm viruses were categorized into sera collected before (n. 84 SWs; n. 234 Cs) and after (n. 39 SWs; n. 145 Cs) the pandemic peak. HI-antibody titers ≥10 were considered positive. In both pre-pandemic and post-pandemic peak subperiods, SWs showed significantly higher swH1N1 seroprevalences when compared with Cs (52.4% vs. 4.7% and 59% vs. 9.7%, respectively). Comparable HI results were obtained against H1N1pdm antigen (58.3% vs. 7.7% and 59% vs. 31.7%, respectively). No differences were found between HI seroreactivity detected in SWs and Cs against swH1N2 (33.3% vs. 40.4%) and swH3N2 (51.2 vs. 55.4%) viruses. These findings indicate the occurrence of swH1N1 transmission from pigs to Italian SWs.

Conclusion/Significance

A significant increase of H1N1pdm seroprevalences occurred in the post-pandemic peak subperiod in the Cs (p<0.001) whereas SWs showed no differences between the two subperiods, suggesting a possible occurrence of cross-protective immunity related to previous swH1N1 infections. These data underline the importance of risk assessment and occupational health surveillance activities aimed at early detection and control of SIVs with pandemic potential in humans.     

Novel Genotypes of H9N2 Influenza A Viruses Isolated from Poultry in Pakistan Containing NS Genes Similar to Highly Pathogenic H7N3 and H5N1 Viruses

The impact of avian influenza caused by H9N2 viruses in Pakistan is now significantly more severe than in previous years. Since all gene segments contribute towards the virulence of avian influenza virus, it was imperative to investigate the molecular features and genetic relationships of H9N2 viruses prevalent in this region. Analysis of the gene sequences of all eight RNA segments from 12 viruses isolated between 2005 and 2008 was undertaken. The hemagglutinin (HA) sequences of all isolates were closely related to H9N2 viruses isolated from Iran between 2004 and 2007 and contained leucine instead of glutamine at position 226 in the receptor binding pocket, a recognised marker for the recognition of sialic acids linked α2–6 to galactose. The neuraminidase (NA) of two isolates contained a unique five residue deletion in the stalk (from residues 80 to 84), a possible indication of greater adaptation of these viruses to the chicken host. The HA, NA, nucleoprotein (NP), and matrix (M) genes showed close identity with H9N2 viruses isolated during 1999 in Pakistan and clustered in the A/Quail/Hong Kong/G1/97 virus lineage. In contrast, the polymerase genes clustered with H9N2 viruses from India, Iran and Dubai. The NS gene segment showed greater genetic diversity and shared a high level of similarity with NS genes from either H5 or H7 subtypes rather than with established H9N2 Eurasian lineages. These results indicate that during recent years the H9N2 viruses have undergone extensive genetic reassortment which has led to the generation of H9N2 viruses of novel genotypes in the Indian sub-continent. The novel genotypes of H9N2 viruses may play a role in the increased problems observed by H9N2 to poultry and reinforce the continued need to monitor H9N2 infections for their zoonotic potential.     

Contribution of NS1 Effector Domain Dimerization to Influenza A Virus Replication and Virulence

Conserved tryptophan-187 facilitates homodimerization of the influenza A virus NS1 protein effector domain. We generated a mutant influenza virus strain expressing NS1-W187R to destabilize this self-interaction. NS1-W187R protein exhibited lower double-stranded RNA (dsRNA)-binding activity, showed a temporal redistribution during infection, and was minimally compromised for interferon antagonism. The mutant virus replicated similarly to the wild type in vitro, but it was slightly attenuated for replication in mice, causing notably reduced morbidity and mortality. These data suggest biological relevance for the W187-mediated homotypic interaction of NS1.     

Assessing Antigenic Drift of Seasonal Influenza A(H3N2) and A(H1N1)pdm09 Viruses

Under selective pressure from the host immune system, antigenic epitopes of influenza virus hemagglutinin (HA) have continually evolved to escape antibody recognition, termed antigenic drift. We analyzed the genomes of influenza A(H3N2) and A(H1N1)pdm09 virus strains circulating in Thailand between 2010 and 2014 and assessed how well the yearly vaccine strains recommended for the southern hemisphere matched them. We amplified and sequenced the HA gene of 120 A(H3N2) and 81 A(H1N1)pdm09 influenza virus samples obtained from respiratory specimens and calculated the perfect-match vaccine efficacy using the p_epitope model, which quantitated the antigenic drift in the dominant epitope of HA. Phylogenetic analysis of the A(H3N2) HA1 genes classified most strains into genetic clades 1, 3A, 3B, and 3C. The A(H3N2) strains from the 2013 and 2014 seasons showed very low to moderate vaccine efficacy and demonstrated antigenic drift from epitopes C and A to epitope B. Meanwhile, most A(H1N1)pdm09 strains from the 2012–2014 seasons belonged to genetic clades 6A, 6B, and 6C and displayed the dominant epitope mutations at epitopes B and E. Finally, the vaccine efficacy for A(H1N1)pdm09 (79.6–93.4%) was generally higher than that of A(H3N2). These findings further confirmed the accelerating antigenic drift of the circulating influenza A(H3N2) in recent years.     

我国部分鸡源H9N2亚型流感病毒NS1基因序列分析

对1996年至2001年间自我国部分养鸡场发病鸡或死亡鸡分离鉴定的8株H9N2亚型禽流感病毒的非结构蛋白基因(NS1)进行了扩增和序列测定,并分析和比较了其核苷酸和氨基酸的同源性。结果表明, NS1基因核苷酸和氨基酸同源性分别为96.5%～99.5% 和94.5～98.6%, 说明NS1基因在遗传进化上高度保守,稳定遗传。与中国香港、韩国、巴基斯坦及人源H9N2分离株相比较,发现中国大陆的鸡源H9N2分离株的NS1基因在其羧基端缺少13个氨基酸。系统进化树分析表明,该8株病毒的NS1基因属于相同的进化分支,而且中国的早年分离株A/chicken/Beijing/1/94位于该进化分支的根部,暗示这些分离株的NS1基因是由A/chicken/Beijing/1/94演化而来;尚未发现NS1基因属于A/quail/Hong Kong/G1/97like分支的分离株。同时,系统进化树也说明了我国的H9N2分离株与韩国、巴基斯坦等地的H9N2分离株隶属于不同的进化分支,H9N2亚型禽流感的发生和流行与地域有一定的相关性。     

Virulence Determinants of Avian H5N1 Influenza A Virus in Mammalian and Avian Hosts: Role of the C-Terminal ESEV Motif in the Viral NS1 Protein

We assessed the prediction that access of the viral NS1 protein to cellular PDZ domain protein networks enhances the virulence of highly pathogenic avian influenza A viruses. The NS1 proteins of most avian influenza viruses bear the C-terminal ligand sequence Glu-Ser-Glu-Val (ESEV) for PDZ domains present in multiple host proteins, whereas no such motif is found in the NS1 homologues of seasonal human virus strains. Previous analysis showed that a C-terminal ESEV motif increases viral virulence when introduced into the NS1 protein of mouse-adapted H1N1 influenza virus. To examine the role of the PDZ domain ligand motif in avian influenza virus virulence, we generated three recombinants, derived from the prototypic H5N1 influenza A/Vietnam/1203/04 virus, expressing NS1 proteins that either have the C-terminal ESEV motif or the human influenza virus RSKV consensus or bear a natural truncation of this motif, respectively. Cell biological analyses showed strong control of NS1 nuclear migration in infected mammalian and avian cells, with only minor differences between the three variants. The ESEV sequence attenuated viral replication on cultured human, murine, and duck cells but not on chicken fibroblasts. However, all three viruses caused highly lethal infections in mice and chickens, with little difference in viral titers in organs, mean lethal dose, or intravenous pathogenicity index. These findings demonstrate that a PDZ domain ligand sequence in NS1 contributes little to the virulence of H5N1 viruses in these hosts, and they indicate that this motif modulates viral replication in a strain- and host-dependent manner.The transmission of highly pathogenic avian influenza A viruses (HPAIV) of the H5N1 subtype to humans since the year 1997 has caused a high mortality rate of almost 60% (62). Patients infected with H5N1 influenza virus developed mainly severe respiratory disease, characterized by fever, cough, shortness of breath, and pneumonia, that frequently progressed to acute respiratory distress syndrome (ARDS) and multiorgan failure (28, 68, 69). In fatal cases, the median time from onset to death was 9 to 10 days (1). Systemic spread (18) and hypercytokinemia (11) have been described as possible disease-aggravating factors of HPAIV-H5N1 viruses, but the reasons for their high virulence in humans are incompletely understood.Due to the potential pandemic threat presented by H5N1 viruses, there is great interest in the identification of viral virulence determinants and their mode of action. This is critical not only for a better understanding of the pathogenic mechanisms induced by these viruses but also for the development of new drugs to treat the infections. The high virulence of HPAIV-H5N1 isolates in the avian host correlates with the presence of a polybasic cleavage site in the hemagglutinin (HA), facilitating its intracellular cleavage by furin-like proteases (27, 50). Further, amino acid substitutions in the PA protein (T515A) (30) and in the NS1 protein (V149A) (40) have been reported to regulate the virulence of corresponding HPAIV-H5N1 isolates in ducks and chickens. The known molecular determinants of virulence in mammalian hosts also include the polybasic cleavage site in the HA (23) and several polymorphisms in the PB2 polymerase subunit and the proapoptotic PB1-F2 protein. Thus, a serine residue at position 66 in the PB1-F2 protein increased viral replication and decreased survival in the mouse model (9). Also, specific amino acid polymorphisms within PB2 (E627K or D701N) can increase virulence in mice (23, 39) and viral replication in mammalian cells (7, 57, 58). Furthermore, the nonstructural NS1 protein, which has a major function in the inhibition of type I interferon (IFN) (17, 19) and in the limitation of the antiviral effects of IFN-induced proteins, including PKR (4, 22), OAS/RNase L (45), and RIG-I (16, 48, 63, 64), contributes to virulence in mammals (34, 55).The domain structure of the NS1 protein is well characterized; it includes an N-terminal RNA binding and dimerization domain and a nuclear localization signal (NLS) at positions 34 to 38 (summarized in reference 19). The NS1 proteins of most human strains circulating between 1950 and 1986 also contain a second NLS at positions 219 to 227 (NLS-2), which includes four conserved basic amino acids (K219, R220, R224, R227) (44). A large-scale sequence analysis showed that the NS1 proteins of avian and human influenza viruses differ in their C-terminal sequences, indicating possible differences in the associated activity (46). Among most high- and low-pathogenicity avian influenza viruses, the last four NS1 amino acids consist of the conserved sequence ESEV (3,007 of 3,692 isolates described in the NCBI database [3]), while for the majority of seasonal human influenza viruses, the motif RSKV is typical (1,911 of 2,713 isolates). Significantly, only the NS1 protein carrying the “avian” ESEV motif interacted in vitro with 24 cellular factors carrying a PDZ (postsynaptic density protein 95, Drosophila disc large tumor suppressor, and zonula occludens 1 protein) domain. The human genome encodes at least 214 proteins containing one or more of these protein interaction modules that recognize short peptide motifs, which are most often present at the C termini of their targets (36, 38). Many PDZ domain proteins have been shown to mediate the formation and localization of higher-order complexes and to participate in various cellular signaling events regulating, for instance, cell polarity and neuronal function (31). Therefore, it was hypothesized that the abundant expression of “avian” NS1 protein capable of interacting with human PDZ domains could possibly disturb their function and aggravate disease severity in H5N1 infections (46). However, there is only limited experimental support for the universal validity of this hypothesis. The grafting of the “avian” ESEV sequence into the C terminus of NS1 protein expressed by mouse-adapted influenza A/WSN/33 virus (H1N1) decreased the mean lethal dose by about 1 order of magnitude (32). Still, it is not clear to what extent this motif contributes to the virulence of HPAIV-H5N1 and other natural influenza A viruses in avian and mammalian hosts.The goal of the present study was to elucidate the role of the C-terminal NS1 motif in viral replication and disease caused by the prototypic influenza A/Vietnam/1203/04 (VN/1203) virus, isolated in a fatal human case (60). This virus expresses an NS1 protein that is very similar or identical at positions 1 to 215 to homologues expressed by other HPAIV-H5N1 strains but naturally lacks the 10 C-terminal amino acids (aa), including the terminal ESEV motif, due to a premature stop codon (Fig. ​(Fig.1).1). We used reverse genetics to produce a recombinant VN/1203 wild-type (WT) virus and two variants with reconstituted NS1 C termini ending either with the “avian” ESEV or with the “human” RSKV sequence. Experimental infections of mice and chickens revealed that all three viruses caused highly lethal infections in both species, with only moderate differences in viral titers in the organs of the mice. Thus, we show that the C-terminal ESEV motif of the NS1 protein contributes little to the virulence of H5N1 viruses in mice and chickens, and we suggest that this motif modulates viral virulence in a strain- and host-dependent manner.Open in a separate windowFIG. 1.Growth kinetics of recombinant VN/1203 viruses expressing WT or elongated NS1 proteins in human, murine, and avian cells. (A) Scheme of the viral VN/1203-NS1 protein with the RNA binding domain and the nuclear localization signals (NLS) at positions 34 to 38 and 214 to 225 indicated. Amino acids involved in NLS2 function are underlined. The C-terminal sequences of the WT and elongated mutant NS1 proteins are given, and the PL motif is shown in boldface. (B to E) Human A549 alveolar cells, murine NIH 3T3 fibroblasts, chicken embryo fibroblasts (CEFs), or EFB-R1 duck embryo fibroblasts (DEFs) were infected with recombinant VN/1203-WT, -ESEV, or -RSKV viruses at an MOI of 0.001. Aliquots of supernatants were harvested at the indicated time points, and samples were titrated by plaque assays in MDCK cells. (F) Human A549 cells were infected at an MOI of 2, and virus titers in supernatants taken at the indicated time points were determined by plaque assays. Results are averages for at least two independent experiments with biological duplicates. Error bars indicate standard deviations.     

A 20-Amino-Acid Deletion in the Neuraminidase Stalk and a Five-Amino-Acid Deletion in the NS1 Protein Both Contribute to the Pathogenicity of H5N1 Avian Influenza Viruses in Mallard Ducks

Since 2003, H5N1-subtype avian influenza viruses (AIVs) with both a deletion of 20 amino acids in the stalk of the neuraminidase (NA) glycoprotein (A−) and a deletion of five amino acids at positions 80 to 84 in the non-structural protein NS1 (S−) have become predominant. To understand the influence of these double deletions in the NA and NS1 proteins on the pathogenicity of H5N1-subtype AIVs, we selected A/mallard/Huadong/S/2005 as a parental strain to generate rescued wild-type A−S− and three variants (A−S+ with a five-amino-acid insertion in the NS1 protein, A+S− with a 20-amino-acid insertion in the NA stalk, and A+S+ with insertions in both NA and NS1 proteins) and evaluated their biological characteristics and virulence. The titers of the AIVs with A− and/or S− replicated in DEF cells were higher than that of A+S+, and the A−S− virus exhibited a replication predominance when co-infected with the other variants in DEF cells. In addition, A−S− induced a more significant increase in the expression of immune-related genes in peripheral blood mononuclear cells of mallard ducks in vitro compared with the other variants. Furthermore, an insertion in the NA and/or NS1 proteins of AIVs resulted in a notable decrease in virulence in ducks, as determined by intravenous pathogenicity index, and the two insertions exerted a synergistic effect on the attenuation of pathogenicity in ducks. In addition, compared with A+S+ and A+S−, the A−S+ and A−S− viruses that were introduced via the intranasal inoculation route exhibited a faster replication ability in the lungs of ducks. These data indicate that both the deletions in the NA stalk and the NS1 protein contribute to the high pathogenicity of H5N1 AIVs in ducks.