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We report here a targeting method that exploits the expression pattern of cell surface proteases to induce gene delivery to specific tissues. We describe retroviral vectors harboring modified surface glycoproteins derived from an avian influenza virus hemagglutinin (HA) for which the cell entry properties, dependent on HA cleavage by producer cells, were conditionally blocked at a postbinding step by insertion of matrix metalloproteinase (MMP) substrates. We demonstrate that such vectors induce gene transfer, both in vitro and in mice harboring human tumor xenografts, only through contact with target cells expressing MMPs that cleave the substrate introduced into the recombinant HA. This selective gene transfer in MMP-rich cells was specifically inhibited by 1,10-phenanthroline, a broad-range MMP inhibitor. Importantly, such MMP-activatable vectors selectively transduced MMP-rich cells in heterogeneous populations containing MMP-rich and MMP-poor cells. These vectors will allow useful gene transfer applications into target cells exhibiting specific protease activities.
Mol Ther 2006 Nov
PMID:Targeted retroviral vectors displaying a cleavage site-engineered hemagglutinin (HA) through HA-protease interactions. 1678 93

Attempts to develop peptide vaccines, based on a limited number of peptides face two problems: HLA polymorphism and the high mutation rate of viral epitopes. We have developed a new genomic method that ensures maximal coverage and thus maximal applicability of the peptide vaccine. The same method also promises a large number of epitopes per HLA to prevent escape via mutations. Our design can be applied swiftly in order to face rapidly emerging viral diseases. We use a genomic scan of all candidate peptides and join them optimally. For a given virus, we use algorithms computing: peptide cleavage probability, transfer through TAP and MHC binding for a large number of HLA alleles. The resulting peptide libraries are pruned for peptides that are not conserved or are too similar to self peptides. We then use a genetic algorithm to produce an optimal protein composed of peptides from this list properly ordered for cleavage. The selected peptides represent an optimal combination to cover all HLA alleles and all viral proteins. We have applied this method to HCV and found that some HCV proteins (mainly envelope proteins) represent much less peptide than expected. A more detailed analysis of the peptide variability shows a balance between the attempts of the immune system to detect less mutating peptides, and the attempts of viruses to mutate peptides and avoid detection by the immune system. In order to show the applicability of our method, we have further used it on HIV-I, Influenza H3N2 and the Avian Flu Viruses.
Mol Immunol 2007 Feb
PMID:Virus-epitope vaccine design: informatic matching the HLA-I polymorphism to the virus genome. 1693 Jul 10

Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for rate variation among lineages. The rates observed were extremely high, at >10(-3) substitutions per site, per year, with little difference among wild and domestic host species or viral subtypes and were similar to those seen in mammalian influenza A viruses. Influenza A virus therefore exhibits rapid evolutionary dynamics across its host range, consistent with a high background mutation rate and rapid replication. Using the same approach, we also estimated that the common ancestors of the hemagglutinin and neuraminidase sequences of AIV arose within the last 3,000 years, with most intrasubtype diversity emerging within the last 100 years and suggestive of a continual selective turnover.
Mol Biol Evol 2006 Dec
PMID:Avian influenza virus exhibits rapid evolutionary dynamics. 1694 80

Recent outbreaks of highly pathogenic avian influenza A virus (H5N1 subtype) infections in poultry and humans (through direct contact with infected birds) have raised concerns that a new influenza pandemic might occur in the near future. Effective vaccines against H5N1 virus are, therefore, urgently needed. Reverse-genetics-based inactivated vaccines have been prepared according to World Health Organization (WHO) recommendations and are now undergoing clinical evaluation in several countries. Here, we review the current strategies for the development of H5N1 influenza vaccines, and future directions for vaccine development.
Trends Mol Med 2006 Nov
PMID:Strategies for developing vaccines against H5N1 influenza A viruses. 1701 Dec 35

The recent wide spreading of the H5N1 avian influenza virus (AIV) in Asia, Europe and Africa and its ability to cause fatal infections in human has raised serious concerns about a pending global flu pandemic. Neuraminidase (NA) inhibitors are currently the only option for treatment or prophylaxis in humans infected with this strain. However, drugs currently on the market often meet with rapidly emerging resistant mutants and only have limited application as inadequate supply of synthetic material. To dig out helpful information for designing potent inhibitors with novel structures against the NA, we used automated docking, CoMFA, CoMSIA, and HQSAR methods to investigate the quantitative structure-activity relationship for 126 NA inhibitors (NIs) with great structural diversities and wide range of bioactivities against influenza A virus. Based on the binding conformations discovered via molecular docking into the crystal structure of NA, CoMFA and CoMSIA models were successfully built with the cross-validated q (2) of 0.813 and 0.771, respectively. HQSAR was also carried out as a complementary study in that HQSAR technique does not require 3D information of these compounds and could provide a detailed molecular fragment contribution to the inhibitory activity. These models also show clearly how steric, electrostatic, hydrophobicity, and individual fragments affect the potency of NA inhibitors. In addition, CoMFA and CoMSIA field distributions are found to be in well agreement with the structural characteristics of the corresponding binding sites. Therefore, the final 3D-QSAR models and the information of the inhibitor-enzyme interaction should be useful in developing novel potent NA inhibitors.
J Comput Aided Mol Des 2006 Sep
PMID:QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. 1710 17

Hemagglutinin (HA) is the major immunogen on the envelope of avian influenza virus (AIV). Therefore we constructed two recombinant baculoviruses: Bac-HA, expressing histidine-tagged HA with the cytoplasmic domain (CTD) derived from HA, and Bac-HA64, expressing histidine-tagged HA with the CTD derived from baculovirus envelope protein gp64. After infection, HA with either CTD was expressed and anchored on the plasma membrane of Sf-9 cells, as revealed by confocal microscopy. Immunogold electron microscopy demonstrated that both Bac-HA and Bac-HA64 displayed HA on the viral surface. However, analyses of purified viruses revealed that significantly more HA was incorporated into Bac-HA64 than into Bac-HA. In comparison with Bac-HA, Bac-HA64 significantly improved the gene delivery and transgene expression in mammalian cells, as determined by quantitative real-time polymerase chain reaction and flow cytometry. Bac-HA64 elicited significantly higher hemagglutination inhibition titers in mouse models than Bac-HA and the negative controls. These data collectively confirmed that the gp64 CTD, in comparison with HA CTD, resulted in more efficient HA incorporation into baculovirus, more efficient transgene delivery and expression, and elevated immunogenicity. This is the first report demonstrating the potential of HA-pseudotyped baculovirus as an avian influenza vaccine and that the choice of CTD tremendously affects baculovirus properties and vaccine efficacy.
Mol Ther 2007 May
PMID:Avian influenza virus hemagglutinin display on baculovirus envelope: cytoplasmic domain affects virus properties and vaccine potential. 1737 72

The outbreak of H5N1 avian influenza strains infectious to human has dire neurological and pathological consequences. This led to the massive vaccination of host poultry, resulting in a Fujian-like variant (vFJ) resistant to immunization with two mutations at the furin-processing site of hemagglutinin: loss of the P2 Lys and P9 substitution of Gln to Leu within the cleavage site. We synthesized 14mer peptides mimicking the processing site of Fujian-like strains. We found that the peptide with the vFJ sequence is less cleaved as compared to the parent FJ-derived peptide by furin at either neutral or acidic pH values. We hypothesize that the double hemagglutinin mutations in vFJ may result in viruses with less processed hemagglutinin, thereby providing a mechanism for evading immune neutralization.
J Mol Neurosci 2008 Jul
PMID:The H5N1 influenza variant Fujian-like hemagglutinin selected following vaccination exhibits a compromised furin cleavage : neurological Consequences of highly pathogenic Fujian H5N1 strains. 1830 58

Isolation and characterization of the influenza virus A/H5N1 strains, isolated from chicken in the Yandovka village (Tula Region) and from wild swan near the orifice of the Volga River that died during an outbreak of avian flu in autumn 2005, were carried out. Genetic and phylogenetic analyses were performed. The goals of the analysis were to determine possible geographical origin of the strain, genetic similarity of isolated strains to earlier sequenced isolates, epidemic potential, existence of pathogenicity markers, and resistance to antiviral drugs. It was shown that the isolated influenza virus belonged to highly pathogenic variants of China origin by a reassortment of viruses genotypes Z and V circulated in poultry and wild birds. A number of molecular markers of pathogenicity to gallinaceous birds and mammals were found out. Mutations in the hemagglutinin gene promoting potentially high rate of replication in humans as well as mutations causing the resistance to amantadine/rimantadine were not found. The strain isolated from wild swan had the mutation causing resistance to tamiflu/ozeltamivir.
Mol Gen Mikrobiol Virusol 2008
PMID:[Isolation and molecular characterization of the influenza virus A/H5N1 strains isolated during outbreak of avian influenza among birds in the European part of Russia in 2005: strain with ozeltamivir-resistance mutation was found]. 1836 79

The avian influenza (AI) virus is type A influenza isolated from and adapted to an avian host. Type A influenza belongs to the orthomyxovirdae virus family, is enveloped, and is pleiomorphic with a size ranging from 80-120 nm (reviewed in [1]). Type A influenza strains are classified by the serological subtypes of the primary viral surface proteins, the hemagglutinin (HA) and neuraminidase (NA). The HA has 16 subtypes (H1-H16) and contains neutralizing epitopes. Antibodies against the NA are not neutralizing, and there are nine neuraminidase or "N" subtypes. The "H" and N subtypes seem to be able to assort into any combination, and many of the 144 possible combinations have been found in natural reservoir species, although some combinations are more common than others. All 16 subtypes have been found in ducks, gulls, or shorebirds, the natural reservoir host species of the virus. However, in these species certain subtypes are more common than others; for example, H3, H4, and H6 are most common in ducks in North America [2, 3] and although there is no clear association between host range or host restriction based on HA subtype, some subtypes are more common in some species than others, i.e., H1 and H3 in swine, H3 in horses, and H5 and H7 in chickens.
Methods Mol Biol 2008
PMID:A brief introduction to the avian influenza virus. 1837 34

Successful detection of the avian influenza (AI) virus, viral antigen, nucleic acid, or antibody is dependent upon the collection of the appropriate sample type, the quality of the sample, and the proper storage and handling of the sample. The diagnostic tests to be performed should be considered prior to sample collection. Sera are acceptable samples for ELISA or agar gel precipitin tests, but not for real-time RT-PCR. Likewise, swabs and/or tissues are acceptable for real-time RT-PCR and virus isolation. The sample type will also depend on the type of birds that are being tested; oropharyngeal swabs should be collected from poultry, and cloacal swabs should be collected from waterfowl. This chapter will outline the collection of different specimen types and procedures for proper specimen handling.
Methods Mol Biol 2008
PMID:Avian influenza virus sample types, collection, and handling. 1837 35


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