Virulence of H5N1 avian influenza virus enhanced by a 15-nucleotide deletion in the viral nonstructural gene

Variability of NS1 proteins among H9N2 avian influenza viruses isolated in Israel during 2000-2009

The main aims of the present study were to characterize NS1 protein from H9N2 avian influenza viruses (AIVs) isolated in Israel and to investigate the possibility to use NS1-based indirect ELISA. To achieve these purposes, the non-structural gene (NS1) of 79 AIVs of the H9N2 subtype isolated in Israel in 2000-2009 was sequenced and genetically analyzed. The phylogenetic analysis demonstrated that four distinct introductions of H9N2 occurred in Israel during this period. Analysis of the inferred amino acid sequences of the NS1 proteins showed high, about 10%, differences between viruses of the 3rd and 4th introductions. Antibodies against NS1 protein in immune sera were tested by means of indirect ELISA using recombinant NS1 as antigen. Immune sera were obtained from experimentally H9N2-infected chicken after infection on 4, 7, 10, 14, and 21 days. All sera from chickens experimentally infected with 3rd- or 4th-introduction AIV contained anti-NS1 antibodies that were detected by enzyme-linked immunosorbent assay (NS1-ELISA) even though the recombinant NS1 used as antigen for NS1-ELISA differed significantly in its amino acid sequences from the NS1 protein of AIV that caused infection in experimental birds. These findings indicate that the sites of the NS1 protein by which viruses belonging to 3rd and 4th introduction are out of antigenic epitope positions were responsible for the results of NS1-based iELISA.

OpenFluDB, a database for human and animal influenza virus

Although research on influenza lasted for more than 100 years, it is still one of the most prominent diseases causing half a million human deaths every year. With the recent observation of new highly pathogenic H5N1 and H7N7 strains, and the appearance of the influenza pandemic caused by the H1N1 swine-like lineage, a collaborative effort to share observations on the evolution of this virus in both animals and humans has been established. The OpenFlu database (OpenFluDB) is a part of this collaborative effort. It contains genomic and protein sequences, as well as epidemiological data from more than 27 000 isolates. The isolate annotations include virus type, host, geographical location and experimentally tested antiviral resistance. Putative enhanced pathogenicity as well as human adaptation propensity are computed from protein sequences. Each virus isolate can be associated with the laboratories that collected, sequenced and submitted it. Several analysis tools including multiple sequence alignment, phylogenetic analysis and sequence similarity maps enable rapid and efficient mining. The contents of OpenFluDB are supplied by direct user submission, as well as by a daily automatic procedure importing data from public repositories. Additionally, a simple mechanism facilitates the export of OpenFluDB records to GenBank. This resource has been successfully used to rapidly and widely distribute the sequences collected during the recent human swine flu outbreak and also as an exchange platform during the vaccine selection procedure. Database URL: http://openflu.vital-it.ch.

Avian influenza: our current understanding

Avian influenza (AI) virus is one of the most important diseases of the poultry industry around the world. The virus has a broad host range in birds and mammals, although the natural reservoir is wild birds where it typically causes an asymptomatic to mild infection. The virus in poultry can cause a range of clinical diseases and is defined either as low pathogenic AI (LPAI) or highly pathogenic AI (HPAI) depending on the type of disease it causes in chickens. Viruses that replicate primarily on mucosal surfaces and cause mild disease with low mortality are termed LPAI. Viruses that replicate on mucosal surfaces and systemically and cause severe disease with a mortality rate of 75% or greater in experimentally infected chickens are referred to as HPAI. A virus that is highly pathogenic in chickens may infect but result in a completely different disease and replication pattern in other host species. Outbreaks of HPAI have been relatively uncommon around the world in the last 50 years and have had limited spread within a country or region with one major exception, Asian lineage H5N1 that was first identified in 1996. This lineage of virus has spread to over 60 countries and has become endemic in poultry in at least four countries. AI virus also represents a public health threat, with some infected humans having severe disease and with a high case fatality rate. AI remains a difficult disease to control because of the highly infectious nature of the virus and the interface of domestic and wild animals. A better understanding of the disease and its transmission is important for control.

Synergism of co-mutation of two amino acid residues in NS1 protein increases the pathogenicity of influenza virus in mice

The NS1 influenza virus gene is thought to play an important role in replication and pathogenicity during infection. Previous studies have shown that mutations in the highly pathogenic avian NS1 influenza virus gene can influence virulence. However, little is known regarding the pathogenic mechanism of the NS1 gene in low pathogenic avian influenza virus. We found that NS1 genes originating from two H3 avian influenza viruses, A/duck/Beijing/40/04 (Dk/BJ/40/04) and A/duck/Beijing/61/05 (Dk/BJ/61/05), possessing three amino acid residue differences at positions 127, 205 and 209 contributed to an altered virulence in rescued NS1 recombinant viruses on a A/WSN/33 (WSN) virus background (WSN:40NS1 and WSN:61NS1) in mice. To further determine the effect on pathogenicity, we generated a series of recombinant viruses with mutations at positions 127, 205 and 209 in the NS1 gene of WSN:61NS1. Experiments in mice indicated that when compared with WSN:61NS1, viruses with only single mutations enhanced incidence of infection in mice but were not lethal. Viruses bearing substitution of two amino acid residues in the NS1 protein replicated well in lung tissue and caused 20-100% mortality in mice. Our findings demonstrate that co-mutation of amino acid residues at multiple positions in the NS1 protein can increase the pathogenicity of influenza virus in mice.

Inefficient control of host gene expression by the 2009 pandemic H1N1 influenza A virus NS1 protein

In 2009, a novel swine-origin H1N1 influenza A virus emerged. Here, we characterize the multifunctional NS1 protein of this human pandemic virus in order to understand factors that may contribute to replication efficiency or pathogenicity. Although the 2009 H1N1 virus NS1 protein (2009/NS1) is an effective interferon antagonist, we found that this NS1 (unlike those of previous human-adapted influenza A viruses) is unable to block general host gene expression in human or swine cells. This property could be restored in 2009/NS1 by replacing R108, E125, and G189 with residues corresponding to human virus consensus. Mechanistically, these previously undescribed mutations acted by increasing binding of 2009/NS1 to the cellular pre-mRNA processing protein CPSF30. A recombinant 2009 H1N1 influenza A virus (A/California/04/09) expressing NS1 with these gain-of-function substitutions was more efficient than the wild type at antagonizing host innate immune responses in primary human epithelial cells. However, such mutations had no significant effect on virus replication in either human or swine tissue culture substrates. Surprisingly, in a mouse model of pathogenicity, the mutant virus appeared to cause less morbidity, and was cleared faster, than the wild type. The mutant virus also demonstrated reduced titers in the upper respiratory tracts of ferrets; however, contact and aerosol transmissibility of the virus was unaffected. Our data highlight a potential human adaptation of NS1 that seems absent in "classically derived" swine-origin influenza A viruses, including the 2009 H1N1 virus. We discuss the impact that a natural future gain of this NS1 function may have on the new pandemic virus in humans.

Effects of NS1 variants of H5N1 influenza virus on interferon induction, TNFalpha response and p53 activity

Non-structural protein 1 (NS1) is an important virulence factor of the highly pathogenic H5N1 avian influenza virus. A five-amino-acid (5 aa) deletion at position 80-84 and an aspartic acid to glutamic acid substitution at position 92 (D92E) are two major NS1 mutations that are highly correlated with enhanced virulence. To investigate the effect of these mutations in H5N1 virulence, three H5N1-NS1 variants were constructed: NS51 (lacking 5 aa at position 80-84), NS51(I) (carrying a 5-aa insertion at position 80-84) and NS51(IM) (carrying both the 5-aa insertion and the D92E mutation). We examined the effects of these mutations on interferon (IFN) induction, tumor-necrosis factor (TNF)alpha response, p53 activity and apoptosis. We found that the D92E mutation eliminated NS1's repressive effect on IFN induction, while the 5-aa deletion resulted in enhanced resistance to TNFalpha responses. We also observed that all three variants exhibited a similar suppressive effect on p53 transcriptional activity, although none of them significantly influenced apoptosis of host cells. Our findings shed new light on the role of NS1 in the pathogenicity of H5N1 virus.

A Closer Look at the NS1 of Influenza Virus

The Non-Structural 1 (NS1) protein is a multifactorial protein of type A influenza viruses that plays an important role in the virulence of the virus. A large amount of what we know about this protein has been obtained from studies using human influenza isolates and, consequently, the human NS1 protein. The current global interest in avian influenza, however, has highlighted a number of sequence and functional differences between the human and avian NS1. This review discusses these differences in addition to describing potential uses of NS1 in the management and control of avian influenza outbreaks.

H5N1 influenza viruses: outbreaks and biological properties

All known subtypes of influenza A viruses are maintained in wild waterfowl, the natural reservoir of these viruses. Influenza A viruses are isolated from a variety of animal species with varying morbidity and mortality rates. More importantly, influenza A viruses cause respiratory disease in humans with potentially fatal outcome. Local or global outbreaks in humans are typically characterized by excess hospitalizations and deaths. In 1997, highly pathogenic avian influenza viruses of the H5N1 subtype emerged in Hong Kong that transmitted to humans, resulting in the first documented cases of human death by avian influenza virus infection. A new outbreak started in July 2003 in poultry in Vietnam, Indonesia, and Thailand, and highly pathogenic avian H5N1 influenza viruses have since spread throughout Asia and into Europe and Africa. These viruses continue to infect humans with a high mortality rate and cause worldwide concern of a looming pandemic. Moreover, H5N1 virus outbreaks have had devastating effects on the poultry industries throughout Asia. Since H5N1 virus outbreaks appear to originate from Southern China, we here examine H5N1 influenza viruses in China, with an emphasis on their biological properties.

Use of animal models to understand the pandemic potential of highly pathogenic avian influenza viruses

It has been 40 years since the last influenza pandemic and it is generally considered that another could occur at any time. Recent introductions of influenza A viruses from avian sources into the human population have raised concerns that these viruses may be a source of a future pandemic strain. Therefore, there is a need to better understand the pathogenicity of avian influenza viruses for mammalian species so that we may be better able to predict the pandemic potential of such viruses and develop improved methods for their prevention and control. In this review, we describe the virulence of H5 and H7 avian influenza viruses in the mouse and ferret models. The use of these models is providing exciting new insights into the contribution of virus and host responses toward avian influenza viruses, virus tropism, and virus transmissibility. Identifying the role of individual viral gene products and mapping the molecular determinants that influence the severity of disease observed following avian influenza virus infection is dependent on the use of reliable animal models. As avian influenza viruses continue to cause human disease and death, animal pathogenesis studies identify avenues of investigation for novel preventative and therapeutic agents that could be effective in the event of a future pandemic.

Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data

Highly pathogenic avian influenza (HPAI) virus H5N1 infects water and land fowl and can infect and cause mortality in mammals, including humans. However, HPAI H5N1 strains are not equally virulent in mammals, and some strains have been shown to cause only mild symptoms in experimental infections. Since most experimental studies of the basis of virulence in mammals have been small in scale, we undertook a meta-analysis of available experimental studies and used Bayesian graphical models (BGM) to increase the power of inference. We applied text-mining techniques to identify 27 individual studies that experimentally determined pathogenicity in HPAI H5N1 strains comprising 69 complete genome sequences. Amino acid sequence data in all 11 genes were coded as binary data for the presence or absence of mutations related to virulence in mammals or nonconsensus residues. Sites previously implicated as virulence determinants were examined for association with virulence in mammals in this data set, and the sites with the most significant association were selected for further BGM analysis. The analyses show that virulence in mammals is a complex genetic trait directly influenced by mutations in polymerase basic 1 (PB1) and PB2, nonstructural 1 (NS1), and hemagglutinin (HA) genes. Several intra- and intersegment correlations were also found, and we postulate that there may be two separate virulence mechanisms involving particular combinations of polymerase and NS1 mutations or of NS1 and HA mutations.

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.

Differential transcription-activating capability of NS1 proteins from different influenza virus subtypes expressed in yeast

Influenza A virus NS1 protein is an important regulatory factor with multiple functions and contributes greatly to viral pathogenesis. In the present study, transcription-activating potential of NS1 from different influenza A virus subtypes was examined in yeast two-hybrid system. The bait vectors containing different NS1 genes, along with an empty prey vector, were transformed into yeast AH109(for growth assay on QDO plate and alpha-galactosidase assay), and Y187(for beta-galactosidase assay). AH109 transformants with NS1 gene from H1N1, H5N1, and H9N2 viruses grew vigorously on the QDO plate and secreted high level of alpha-galactosidase. Also, Y187 bearing the above NS1 genes exhibited enhanced beta-galactosidase activity. Nevertheless, H3N2-NS1-transformed AH109 and Y187 yeasts did not grow on QDO plate and secrete beta-galactosidase, respectively. These findings denote the remarkable variation in NS1 proteins from different influenza A virus subtypes on the transcription-stimulating capability in yeast.

Molecular characterization of highly pathogenic H5N1 avian influenza A viruses isolated from raccoon dogs in China

Background

The highly pathogenic avian influenza H5N1 virus can infect a variety of animals and continually poses a threat to animal and human health. While many genotypes of H5N1 virus can be found in chicken, few are associated with the infection of mammals. Characterization of the genotypes of viral strains in animal populations is important to understand the distribution of different viral strains in various hosts. This also facilitates the surveillance and detection of possible emergence of highly pathogenic strains of specific genotypes from unknown hosts or hosts that have not been previously reported to carry these genotypes.

Methodology/Principal Findings

Two H5N1 isolates were obtained from lung samples of two raccoon dogs that had died from respiratory disease in China. Pathogenicity experiments showed that the isolates were highly pathogenic to chicken. To characterize the genotypes of these viruses, their genomic sequences were determined and analyzed. The genetic contents of these isolates are virtually identical and they may come from the same progenitor virus. Phylogenetic analysis indicated that the isolates were genetically closely related to genotype V H5N1 virus, which was first isolated in China in 2003, and were distinct from the dominant virus genotypes (e.g. genotype Z) of recent years. The isolates also contain a multibasic amino acid motif at their HA cleavage sites and have an E residue at position 627 of the PB2 protein similar to the previously-identified avian viruses.

Conclusions/Significance

This is the first report that genotype V H5N1 virus is found to be associated with a mammalian host. Our results strongly suggest that genotype V H5N1 virus has the ability to cross species barriers to infect mammalian animals. These findings further highlight the risk that avian influenza H5N1 virus poses to mammals and humans, which may be infected by specific genotypes that are not known to infect these hosts.

Attenuated influenza virus vaccines with modified NS1 proteins

The development of reverse genetics techniques allowing the rescue of influenza virus from plasmid DNA has opened up the possibility of inserting mutations into the genome of this virus for the generation of novel live attenuated influenza virus vaccines. Modifications introduced into the viral NS1 gene via reverse genetics have resulted in attenuated influenza viruses with promising vaccine potential. One of the main functions of the NS1 protein of influenza virus is the inhibition of the innate host type I interferon-mediated antiviral response. Upon viral infection, influenza viruses with modified NS1 genes induce a robust local type I interferon response that limits their replication, resulting in disease attenuation in different animal models. Nevertheless, these viruses can be grown to high titers in cell- and egg-based substrates with deficiencies in the type I IFN system. Intranasal inoculation of mice, pigs, horses, and macaques with NS1-modified influenza virus strains induced robust humoral and cellular immune responses, and generated immune protection against challenge with wild-type virus. This protective response was not limited to homologous strains of influenza viruses, as reduced replication of heterologous strains was also demonstrated in animals vaccinated with NS1-modified viruses, indicating the induction of a broad cross-neutralizing response by these vaccine candidates. The immunogenicity of NS1-modified viruses correlated with enhanced activation of antigen-presenting cells. While further studies on their safety and efficacy are still needed, the results obtained so far indicate that NS1-modified viruses could represent a new generation of improved influenza virus vaccines, and they suggest that modifying viral interferon antagonists in other virus families is a promising strategy for the generation of live attenuated virus vaccines.

The multifunctional NS1 protein of influenza A viruses

The non-structural (NS1) protein of influenza A viruses is a non-essential virulence factor that has multiple accessory functions during viral infection. In recent years, the major role ascribed to NS1 has been its inhibition of host immune responses, especially the limitation of both interferon (IFN) production and the antiviral effects of IFN-induced proteins, such as dsRNA-dependent protein kinase R (PKR) and 2'5'-oligoadenylate synthetase (OAS)/RNase L. However, it is clear that NS1 also acts directly to modulate other important aspects of the virus replication cycle, including viral RNA replication, viral protein synthesis, and general host-cell physiology. Here, we review the current literature on this remarkably multifunctional viral protein. In the first part of this article, we summarize the basic biochemistry of NS1, in particular its synthesis, structure, and intracellular localization. We then discuss the various roles NS1 has in regulating viral replication mechanisms, host innate/adaptive immune responses, and cellular signalling pathways. We focus on the NS1-RNA and NS1-protein interactions that are fundamental to these processes, and highlight apparent strain-specific ways in which different NS1 proteins may act. In this regard, the contributions of certain NS1 functions to the pathogenicity of human and animal influenza A viruses are also discussed. Finally, we outline practical applications that future studies on NS1 may lead to, including the rational design and manufacture of influenza vaccines, the development of novel antiviral drugs, and the use of oncolytic influenza A viruses as potential anti-cancer agents.