451
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Pourmand N, Diamond L, Garten R, Erickson JP, Kumm J, Donis RO, Davis RW. Rapid and highly informative diagnostic assay for H5N1 influenza viruses. PLoS One 2006; 1:e95. [PMID: 17183727 PMCID: PMC1762361 DOI: 10.1371/journal.pone.0000095] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 11/20/2006] [Indexed: 11/19/2022] Open
Abstract
A highly discriminative and information-rich diagnostic assay for H5N1 avian influenza would meet immediate patient care needs and provide valuable information for public health interventions, e.g., tracking of new and more dangerous variants by geographic area as well as avian-to-human or human-to-human transmission. In the present study, we have designed a rapid assay based on multilocus nucleic acid sequencing that focuses on the biologically significant regions of the H5N1 hemagglutinin gene. This allows the prediction of viral strain, clade, receptor binding properties, low- or high-pathogenicity cleavage site and glycosylation status. H5 HA genes were selected from nine known high-pathogenicity avian influenza subtype H5N1 viruses, based on their diversity in biologically significant regions of hemagglutinin and/or their ability to cause infection in humans. We devised a consensus pre-programmed pyrosequencing strategy, which may be used as a faster, more accurate alternative to de novo sequencing. The available data suggest that the assay described here is a reliable, rapid, information-rich and cost-effective approach for definitive diagnosis of H5N1 avian influenza. Knowledge of the predicted functional sequences of the HA will enhance H5N1 avian influenza surveillance efforts.
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MESH Headings
- Animals
- Base Sequence
- Birds
- DNA Primers/genetics
- DNA, Viral/genetics
- Genes, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/isolation & purification
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza in Birds/virology
- Influenza, Human/diagnosis
- Influenza, Human/transmission
- Influenza, Human/virology
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction/methods
- Sequence Analysis, RNA/methods
- Virology/methods
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Affiliation(s)
- Nader Pourmand
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America.
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452
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Chen GW, Chang SC, Mok CK, Lo YL, Kung YN, Huang JH, Shih YH, Wang JY, Chiang C, Chen CJ, Shih SR. Genomic signatures of human versus avian influenza A viruses. Emerg Infect Dis 2006; 12:1353-60. [PMID: 17073083 PMCID: PMC3294750 DOI: 10.3201/eid1209.060276] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fifty-two species-associated amino acid residues were found between human and avian influenza viruses. Position-specific entropy profiles created from scanning 306 human and 95 avian influenza A viral genomes showed that 228 of 4,591 amino acid residues yielded significant differences between these 2 viruses. We subsequently used 15,785 protein sequences from the National Center for Biotechnology Information (NCBI) to assess the robustness of these signatures and obtained 52 "species-associated" positions. Specific mutations on those points may enable an avian influenza virus to become a human virus. Many of these signatures are found in NP, PA, and PB2 genes (viral ribonucleoproteins [RNPs]) and are mostly located in the functional domains related to RNP-RNP interactions that are important for viral replication. Upon inspecting 21 human-isolated avian influenza viral genomes from NCBI, we found 19 that exhibited >1 species-associated residue changes; 7 of them contained >2 substitutions. Histograms based on pairwise sequence comparison showed that NP disjointed most between human and avian influenza viruses, followed by PA and PB2.
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Affiliation(s)
- Guang-Wu Chen
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | | | - Chee-Keng Mok
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Yu-Luan Lo
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Yu-Nong Kung
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Ji-Hung Huang
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Yun-Han Shih
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Ji-Yi Wang
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Chiayn Chiang
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Chi-Jene Chen
- Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Shin-Ru Shih
- Chang Gung University, Taoyuan, Taiwan, Republic of China
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453
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Abstract
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.
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Affiliation(s)
- Rubing Chen
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, PA, USA
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454
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Abstract
In 1997, during an outbreak in chickens in Hong Kong the avian H5N1 influenza virus crossed the species barrier and infected 18 people, of which 6 cases were fatal. The virus also infected wild birds and continued to circulate and mutate in geese and ducks in southeastern China. Since this occurrence, new antigenic variants that are highly pathogenic for humans as well as wild, domestic, and exotic waterfowl continue to appear in Hong Kong. This virus is spreading across Asia, and is encroaching upon Europe and other continents. Wild birds are now considered as the main reservoir of H5N1 virus. Humans become infected with this H5N1 virus usually via close contact with infected birds or a highly contaminated environment. The very low transmissibility of this virus prevented further person-to-person dissemination in spite of the complete absence of immunity in the human population to H5N1 viruses. Viruses of the H5N1 subtype are characterized by an exceptionally high pathogenicity for humans. The cause of the viral virulence is not known so far; however, several virulence factors are considered. The unprecedented capability of H5N1 viruses to kill humans intensifies the concern about its pandemic potential with catastrophic consequences. The effectiveness of existing antivirals as well as vaccines for humans and birds are reviewed.
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455
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Pirovano W, Feenstra KA, Heringa J. Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Res 2006; 34:6540-8. [PMID: 17130172 PMCID: PMC1702503 DOI: 10.1093/nar/gkl901] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple sequence alignments are often used to reveal functionally important residues within a protein family. They can be particularly useful for the identification of key residues that determine functional differences between protein subfamilies. We present a new entropy-based method, Sequence Harmony (SH) that accurately detects subfamily-specific positions from a multiple sequence alignment. The SH algorithm implements a novel formula, able to score compositional differences between subfamilies, without imposing conservation, in a simple manner on an intuitive scale. We compare our method with the most important published methods, i.e. AMAS, TreeDet and SDP-pred, using three well-studied protein families: the receptor-binding domain (MH2) of the Smad family of transcription factors, the Ras-superfamily of small GTPases and the MIP-family of integral membrane transporters. We demonstrate that SH accurately selects known functional sites with higher coverage than the other methods for these test-cases. This shows that compositional differences between protein subfamilies provide sufficient basis for identification of functional sites. In addition, SH selects a number of sites of unknown function that could be interesting candidates for further experimental investigation.
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Affiliation(s)
| | | | - Jaap Heringa
- To whom correspondence should be addressed. Tel: +31 20 59 87649; Fax: +31 20 59 87653;
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456
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Gultyaev AP, Heus HA, Olsthoorn RCL. An RNA conformational shift in recent H5N1 influenza A viruses. ACTA ACUST UNITED AC 2006; 23:272-6. [PMID: 17090581 DOI: 10.1093/bioinformatics/btl559] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED Recent outbreaks of avian influenza are being caused by unusually virulent H5N1 strains. It is unknown what makes these recent H5N1 strains more aggressive than previously circulating strains. Here, we have compared more than 3000 RNA sequences of segment 8 of type A influenza viruses and found a unique single nucleotide substitution typically associated with recent H5N1 strains. By phylogenetic analysis, biochemical and biophysical experiments, we demonstrate that this substitution dramatically affects the equilibrium between a hairpin and a pseudoknot conformation near the 3' splice-site of the NS gene. This conformational shift may have consequences for splicing regulation of segment 8 mRNA. Our data suggest that besides changes at the protein level, changes in RNA secondary structure should be seriously considered when attempting to explain influenza virus evolution. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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457
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Hiscott J, Nguyen TLA, Arguello M, Nakhaei P, Paz S. Manipulation of the nuclear factor-kappaB pathway and the innate immune response by viruses. Oncogene 2006; 25:6844-67. [PMID: 17072332 PMCID: PMC7100320 DOI: 10.1038/sj.onc.1209941] [Citation(s) in RCA: 210] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Viral and microbial constituents contain specific motifs or pathogen-associated molecular patterns (PAMPs) that are recognized by cell surface- and endosome-associated Toll-like receptors (TLRs). In addition, intracellular viral double-stranded RNA is detected by two recently characterized DExD/H box RNA helicases, RIG-I and Mda-5. Both TLR-dependent and -independent pathways engage the IkappaB kinase (IKK) complex and related kinases TBK-1 and IKKvarepsilon. Activation of the nuclear factor kappaB (NF-kappaB) and interferon regulatory factor (IRF) transcription factor pathways are essential immediate early steps of immune activation; as a result, both pathways represent prime candidates for viral interference. Many viruses have developed strategies to manipulate NF-kappaB signaling through the use of multifunctional viral proteins that target the host innate immune response pathways. This review discusses three rapidly evolving areas of research on viral pathogenesis: the recognition and signaling in response to virus infection through TLR-dependent and -independent mechanisms, the involvement of NF-kappaB in the host innate immune response and the multitude of strategies used by different viruses to short circuit the NF-kappaB pathway.
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Affiliation(s)
- J Hiscott
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada.
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458
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Macken CA, Webby RJ, Bruno WJ. Genotype turnover by reassortment of replication complex genes from avian influenza A virus. J Gen Virol 2006; 87:2803-2815. [PMID: 16963738 DOI: 10.1099/vir.0.81454-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reassortment among the RNA segments of Influenza A virus caused the two most recent human influenza pandemics; recently, reassortment has generated viral genotypes associated with outbreaks of avian H5N1 influenza in Asia and Europe. A statistical analysis has been developed for the systematic identification and characterization of reassortant viruses. The analysis was applied to the genes of the replication complex of 152 avian influenza A viruses isolated between 1966 and 2004 from predominantly terrestrial and domestic aquatic avian species. The results indicated that reassortment among these genes was pervasive throughout this period and throughout both the Eurasian and North American lineages of the virus. Evidence is presented that the circulating genotypes of the replication complex are being replaced continually by novel genotypes created by reassortment. No constraints for coordinated reassortment among genes of the replication complex were evident; rather, reassortment almost always proceeded one segment at a time. A maximum-likelihood estimate of the rate of reassortment was derived. For significantly diverged Asian avian influenza A viruses from the period 1991-2004, it was estimated that the median duration between creation of a new genotype and its next segment reassortment was 3 years. Reassortments that introduced previously unobserved influenza genetic material were detected. These findings point to substantial potential for rapid generation of novel avian influenza A viruses, emphasizing the importance of intensive surveillance of these host species in preparation for a possible pandemic.
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Affiliation(s)
- Catherine A Macken
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, T-10 MS-K710, Los Alamos, NM 87545, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105-2794, USA
| | - William J Bruno
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, T-10 MS-K710, Los Alamos, NM 87545, USA
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459
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Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res 2006; 35:D376-80. [PMID: 17065465 PMCID: PMC1781131 DOI: 10.1093/nar/gkl779] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have established the Influenza Virus Database (IVDB) to integrate information and create an analysis platform for genetic, genomic, and phylogenetic studies of the virus. IVDB hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. Our Q-Filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity. IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships. A search system has been developed for users to retrieve a combination of different data types by setting search options. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to pre-computed alignments and polymorphisms of IV genes and proteins, and presents the results as SNP distribution plots and minor allele distributions. IVDB is publicly available at
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Affiliation(s)
- Suhua Chang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
- Institute of Computing Technology, Chinese Academy of SciencesBeijing 100080, China
| | - Jiajie Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Xiaoyun Liao
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Xinxing Zhu
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
- James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou 310007China
| | - Dahai Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Jiang Zhu
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Tao Feng
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Baoli Zhu
- Joint Center for Microbial Genomics, Chinese Academy of SciencesBeijing 101300, China
- Center for Molecular Virology, Institute of Microbiology, Chinese Academy of SciencesBeijing 100080, China
| | - George F. Gao
- Joint Center for Microbial Genomics, Chinese Academy of SciencesBeijing 101300, China
- Center for Molecular Virology, Institute of Microbiology, Chinese Academy of SciencesBeijing 100080, China
| | - Jian Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
| | - Huanming Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
- Joint Center for Microbial Genomics, Chinese Academy of SciencesBeijing 101300, China
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
- To whom correspondence should be addressed. Tel: +86 10 80485492; Fax: +86 10 80498676;
| | - Jing Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, B-6 Airport Industrial ZoneBeijing 101300, China
- Joint Center for Microbial Genomics, Chinese Academy of SciencesBeijing 101300, China
- To whom correspondence should be addressed. Tel: +86 10 80485492; Fax: +86 10 80498676;
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460
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Bruns K, Studtrucker N, Sharma A, Fossen T, Mitzner D, Eissmann A, Tessmer U, Röder R, Henklein P, Wray V, Schubert U. Structural characterization and oligomerization of PB1-F2, a proapoptotic influenza A virus protein. J Biol Chem 2006; 282:353-63. [PMID: 17052982 DOI: 10.1074/jbc.m606494200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, a novel 87-amino acid influenza A virus protein with proapoptotic properties, PB1-F2, has been reported that originates from an alternative reading frame in the PB1 polymerase gene and is encoded in most known human influenza A virus isolates. Here we characterize the molecular structure of a biologically active synthetic version of the protein (sPB1-F2). Western blot analysis, chemical cross-linking, and NMR spectroscopy afforded direct evidence of the inherent tendency of sPB1-F2 to undergo oligomerization mediated by two distinct domains located in the N and C termini, respectively. CD and (1)H NMR spectroscopic analyses indicate that the stability of structured regions in the molecule clearly depends upon the hydrophobicity of the solvent. In aqueous solutions, the behavior of sPB1-F2 is typical of a largely random coil peptide that, however, adopts alpha-helical structure upon the addition of membrane mimetics. (1)H NMR analysis of three overlapping peptides afforded, for the first time, direct experimental evidence of the presence of a C-terminal region with strong alpha-helical propensity comprising amino acid residues Ile(55)-Lys(85) connected via an essentially random coil structure to a much weaker helix-like region, located in the N terminus between residues Trp(9) and Lys(20). The C-terminal helix is not a true amphipathic helix and is more compact than previously predicted. It corresponds to a positively charged region previously shown to include the mitochondrial targeting sequence of PB1-F2. The consequences of the strong oligomerization and helical propensities of the molecule are discussed and used to formulate a hypothetical model of its interaction with the mitochondrial membrane.
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Affiliation(s)
- Karsten Bruns
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg, Erlangen D-91054, Germany
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461
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Chen JM, Ma HC, Chen JW, Sun YX, Li JM, Wang ZL. A preliminary panorama of the diversity of N1 subtype influenza viruses. Virus Genes 2006; 35:33-40. [PMID: 17019634 DOI: 10.1007/s11262-006-0025-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 06/28/2006] [Indexed: 10/24/2022]
Abstract
N1 subtype influenza viruses have caused many epidemics and even a few pandemics in humans, pigs and fowls including 1918 human H1N1 pandemic, which killed 20-50 million people and the current avian H5N1 pandemic in the Eastern Hemisphere, which has caused great economic losses and posed a severe threat to human public health. To elucidate the whole diversity of N1 influenza viruses from a dynamic view, 202 neuraminidase (NA) sequences of N1 subtype influenza isolates were selected and analyzed in this study. Our results showed that N1 influenza isolates could be divided into three distinct lineages (Human, Classic Swine and Avian), which largely circulated in the humans, pigs and fowls respectively, though viruses in the Avian lineage could infect mammals and even there was a sublineage in the Avian lineage wholly isolated from pigs. The Avian lineage and the Human lineage, which have existed at least for decades, possibly began divergence around in 1890 through regression analysis. Both of the Human and Avian lineages could be further divided into some sublineages, and the correlation between these lineages (or sublineages) and their isolation places, isolation time, hemagglutinin (HA) subtypes, host species, virulence, or epidemics were discussed. The panorama of the diversity of N1 influenza viruses presented in this study provided a framework for the studies on the evolution and epidemiology of N1 influenza viruses.
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Affiliation(s)
- Ji-Ming Chen
- Chinese Center for Animal Health and Epidemiology, Nanjing Road 369, Qingdao, 266032, China.
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462
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de Jong MD, Simmons CP, Thanh TT, Hien VM, Smith GJD, Chau TNB, Hoang DM, Chau NVV, Khanh TH, Dong VC, Qui PT, Cam BV, Ha DQ, Guan Y, Peiris JSM, Chinh NT, Hien TT, Farrar J. Fatal outcome of human influenza A (H5N1) is associated with high viral load and hypercytokinemia. Nat Med 2006; 12:1203-7. [PMID: 16964257 PMCID: PMC4333202 DOI: 10.1038/nm1477] [Citation(s) in RCA: 1477] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/09/2006] [Indexed: 12/14/2022]
Abstract
Avian influenza A (H5N1) viruses cause severe disease in humans, but the basis for their virulence remains unclear. In vitro and animal studies indicate that high and disseminated viral replication is important for disease pathogenesis. Laboratory experiments suggest that virus-induced cytokine dysregulation may contribute to disease severity. To assess the relevance of these findings for human disease, we performed virological and immunological studies in 18 individuals with H5N1 and 8 individuals infected with human influenza virus subtypes. Influenza H5N1 infection in humans is characterized by high pharyngeal virus loads and frequent detection of viral RNA in rectum and blood. Viral RNA in blood was present only in fatal H5N1 cases and was associated with higher pharyngeal viral loads. We observed low peripheral blood T-lymphocyte counts and high chemokine and cytokine levels in H5N1-infected individuals, particularly in those who died, and these correlated with pharyngeal viral loads. Genetic characterization of H5N1 viruses revealed mutations in the viral polymerase complex associated with mammalian adaptation and virulence. Our observations indicate that high viral load, and the resulting intense inflammatory responses, are central to influenza H5N1 pathogenesis. The focus of clinical management should be on preventing this intense cytokine response, by early diagnosis and effective antiviral treatment.
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Affiliation(s)
- Menno D de Jong
- Oxford University Clinical Research Unit, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam.
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463
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Holmes EC, Lipman DJ, Zamarin D, Yewdell JW. Comment on "Large-scale sequence analysis of avian influenza isolates". Science 2006; 313:1573; author reply 1573. [PMID: 16973862 DOI: 10.1126/science.1131729] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Obenauer et al. (Research Articles, 17 March 2006, p. 1576) reported that the influenza A virus PB1-F2 gene is evolving under strong positive selection, as documented by an extremely high ratio of the number of nonsynonymous nucleotide substitutions to the number of synonymous substitutions (dN/dS). However, we show that this observation is likely to be an artifact related to the location of PB1-F2 in the +1 reading frame of the PB1 gene.
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Affiliation(s)
- Edward C Holmes
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
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464
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Obenauer JC, Fan Y, Naeve CW. Response to Comment on "Large-Scale Sequence Analysis of Avian Influenza Isolates". Science 2006. [DOI: 10.1126/science.1131840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- John C. Obenauer
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Yiping Fan
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Clayton W. Naeve
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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465
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Zamarin D, Ortigoza MB, Palese P. Influenza A virus PB1-F2 protein contributes to viral pathogenesis in mice. J Virol 2006; 80:7976-83. [PMID: 16873254 PMCID: PMC1563817 DOI: 10.1128/jvi.00415-06] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The influenza virus PB1-F2 protein is a novel protein previously shown to be involved in induction of cell death. Here we characterize the expression and the function of the protein within the context of influenza viral infection in tissue culture and a mouse model. We show that the C-terminal region of the protein can be expressed from a downstream initiation codon and is capable of interaction with the full-length protein. Using this knowledge, we generated influenza viruses knocked out for the expression of PB1-F2 protein and its downstream truncation products. Knocking out the PB1-F2 protein had no effect on viral replication in tissue culture but diminished virus pathogenicity and mortality in mice. The viruses replicated to similar levels in mouse lungs by day 3 postinfection, suggesting that the knockout did not impair viral replication. However, while the PB1-F2 knockout viruses were cleared after day 5, the wild-type viruses were detectable in mouse lungs until day 7, implying that expression of PB1-F2 resulted in delayed clearance of the viruses by the host immune system. Based on our findings and on the fact that the PB1 genomic segment was always newly introduced into some pandemic influenza viruses of the last century, we speculate that the PB1-F2 protein plays an important role in pathogenesis of influenza virus infection and may be an important contributor to pathogenicity of pandemic influenza viruses.
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Affiliation(s)
- Dmitriy Zamarin
- Department of Microbiology, Box 1124, Mount Sinai School of Medicine, 1 Gustave Levy Place, New York, NY 10029, USA
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466
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Richt JA, Lekcharoensuk P, Lager KM, Vincent AL, Loiacono CM, Janke BH, Wu WH, Yoon KJ, Webby RJ, Solórzano A, García-Sastre A. Vaccination of pigs against swine influenza viruses by using an NS1-truncated modified live-virus vaccine. J Virol 2006; 80:11009-18. [PMID: 16943300 PMCID: PMC1642165 DOI: 10.1128/jvi.00787-06] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Swine influenza viruses (SIV) naturally infect pigs and can be transmitted to humans. In the pig, genetic reassortment to create novel influenza subtypes by mixing avian, human, and swine influenza viruses is possible. An SIV vaccine inducing cross-protective immunity between different subtypes and strains circulating in pigs is highly desirable. Previously, we have shown that an H3N2 SIV (A/swine/Texas/4199-2/98 [TX98]) containing a deleted NS1 gene expressing a truncated NS1 protein of 126 amino acids, NS1black triangle126, was attenuated in swine. In this study, 4-week-old pigs were vaccinated with the TX98 NS1black triangle126 modified live virus (MLV). Ten days after boosting, pigs were challenged with wild-type homologous H3N2 or heterosubtypic H1N1 SIV and sacrificed 5 days later. The MLV was highly attenuated and completely protected against challenge with the homologous virus. Vaccinated pigs challenged with the heterosubtypic H1N1 virus demonstrated macroscopic lung lesions similar to those of the unvaccinated H1N1 control pigs. Remarkably, vaccinated pigs challenged with the H1N1 SIV had significantly lower microscopic lung lesions and less virus shedding from the respiratory tract than did unvaccinated, H1N1-challenged pigs. All vaccinated pigs developed significant levels of hemagglutination inhibition and enzyme-linked immunosorbent assay titers in serum and mucosal immunoglobulin A antibodies against H3N2 SIV antigens. Vaccinated pigs were seronegative for NS1, indicating the potential use of the TX98 NS1black triangle126 MLV as a vaccine to differentiate infected from vaccinated animals.
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Affiliation(s)
- Jürgen A Richt
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, 2300 Dayton Ave. B-15, Ames, IA 50010, USA.
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467
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Abstract
Influenza viruses are the etiological agents of influenza. Although vaccines and drugs are available for the prophylaxis and treatment of influenza virus infections, the generation of escape mutants has been reported. To develop vaccines and drugs that are less susceptible to the generation of escape mutants, it is important to understand the evolutionary mechanisms of the viruses. Here natural selection operating on all the proteins encoded by the H3N2 human influenza A virus genome was inferred by comparing the numbers of synonymous (d(S) [D(S)]) and nonsynonymous (d(N) [D(N)]) substitutions per site. Natural selection was also inferred for the groups of functional amino acid sites involved in B-cell epitopes (BCEs), T-cell epitopes (TCEs), drug resistance, and growth in eggs. The entire region of PB1-F2 was positively selected, and positive selection also appeared to operate on BCEs, TCEs, and growth in eggs. The frequency of escape mutant generation appeared to be positively correlated with the d(N)/d(S) (D(N)/D(S)) values for the targets of vaccines and drugs, suggesting that the amino acid sites under strong functional constraint are suitable targets. In particular, TCEs may represent candidate targets because the d(N)/d(S) (D(N)/D(S)) values were small and negative selection was inferred for many of them.
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Affiliation(s)
- Yoshiyuki Suzuki
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima-shi, Shizuoka-ken, Japan.
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468
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Olsen B, Munster VJ, Wallensten A, Waldenström J, Osterhaus ADME, Fouchier RAM. Global patterns of influenza a virus in wild birds. Science 2006; 312:384-8. [PMID: 16627734 DOI: 10.1126/science.1122438] [Citation(s) in RCA: 1289] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The outbreak of highly pathogenic avian influenza of the H5N1 subtype in Asia, which has subsequently spread to Russia, the Middle East, Europe, and Africa, has put increased focus on the role of wild birds in the persistence of influenza viruses. The ecology, epidemiology, genetics, and evolution of pathogens cannot be fully understood without taking into account the ecology of their hosts. Here, we review our current knowledge on global patterns of influenza virus infections in wild birds, discuss these patterns in the context of host ecology and in particular birds' behavior, and identify some important gaps in our current knowledge.
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Affiliation(s)
- Björn Olsen
- Department of Infectious Diseases, Umeå University, SE-90187 Umeå, Sweden
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469
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Affiliation(s)
- Jonathan A McCullers
- Department of Infectious Diseases, St Jude Children’s Research Hospital, 332 N. Lauderdale Street, Memphis, TN 38105-2794, USA
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470
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- Birds/virology
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Humans
- Influenza A Virus, H5N1 Subtype/chemistry
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A virus/genetics
- Influenza in Birds/virology
- Influenza, Human/virology
- Interferon-beta/biosynthesis
- Interferon-beta/genetics
- Protein Structure, Tertiary
- RNA, Double-Stranded/metabolism
- RNA, Messenger/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Dependent RNA Polymerase/metabolism
- Sequence Analysis, DNA
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/metabolism
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virulence
- Virulence Factors/chemistry
- Virulence Factors/metabolism
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Affiliation(s)
- Robert M Krug
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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471
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Oxford JS, Lambkin R. Influenza is now a preventable disease. Int J Antimicrob Agents 2006; 27:271-3. [PMID: 16564681 PMCID: PMC7134850 DOI: 10.1016/j.ijantimicag.2006.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 02/15/2006] [Indexed: 11/12/2022]
Abstract
The world is waiting with apprehension for the predicted pandemic of H5N1 (avian) influenza as an increasing number of countries in Asia, Europe and Africa report cases of influenza in migrating birds. All is not ‘despondency’, however. Targeted and controlled administration of antiviral drugs, alone or in combination, to contacts and cases, together with well tried public health measures, should slow down the spread of the infection and allow time for vaccines to be developed, thus preventing a worldwide pandemic of the type that occurred in 1918.
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Affiliation(s)
- J S Oxford
- Retroscreen Virology Ltd., Centre for Infectious Diseases, Bart's and The London, Queen Mary's School of Medicine and Dentistry, 327 Mile End Road, London E1 4NS, UK.
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472
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Ren EC. Know the enemy. Nat Biotechnol 2006; 24:330-1. [PMID: 16525409 DOI: 10.1038/nbt0306-330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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