101
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Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China. Virology 2017; 505:33-41. [PMID: 28222327 DOI: 10.1016/j.virol.2017.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/13/2017] [Accepted: 02/13/2017] [Indexed: 12/22/2022]
Abstract
Live poultry markets (LPMs) are an important source of novel avian influenza viruses (AIV). During 2015-2016 we surveyed AIV diversity in ten LPMs in Hubei, Zhejiang and Jiangxi provinces, China. A high diversity and prevalence of AIVs (totaling 12 subtypes) was observed in LPMs in these provinces. Strikingly, however, the subtypes discovered during 2015-2016 were markedly different to those reported by us in these same localities one year previously, suggesting a dynamic shift in viral genetic diversity over the course of a single year. Phylogenetic analyses revealed frequent reassortment, including between high and low pathogenic AIV subtypes and among those that circulate in domestic and wild birds. Notably, the novel H5N6 reassortant virus, which contains a set of H9N2-like internal genes, was prevalent in all three regions surveyed. Overall, these data highlight the profound changes in genetic diversity and in patterns of reassortment in those AIVs that circulate in LPMs.
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102
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Joseph U, Su YCF, Vijaykrishna D, Smith GJD. The ecology and adaptive evolution of influenza A interspecies transmission. Influenza Other Respir Viruses 2017; 11:74-84. [PMID: 27426214 PMCID: PMC5155642 DOI: 10.1111/irv.12412] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/16/2022] Open
Abstract
Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.
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MESH Headings
- Animals
- Animals, Wild
- Asia/epidemiology
- China/epidemiology
- Disease Reservoirs/virology
- Ducks/virology
- Evolution, Molecular
- Geese/virology
- Humans
- Influenza A Virus, H5N1 Subtype/genetics
- Influenza A Virus, H5N1 Subtype/pathogenicity
- Influenza A Virus, H5N1 Subtype/physiology
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/pathogenicity
- Influenza A Virus, H7N9 Subtype/physiology
- Influenza A virus/genetics
- Influenza A virus/pathogenicity
- Influenza A virus/physiology
- Influenza in Birds/virology
- Influenza, Human/transmission
- Influenza, Human/virology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/virology
- Phylogeny
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Reassortant Viruses/physiology
- Zoonoses
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Affiliation(s)
| | | | | | - Gavin J. D. Smith
- Duke‐NUS Medical SchoolSingapore
- Duke Global Health InstituteDuke UniversityDurhamNCUSA
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103
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Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
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104
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Bourret V, Lyall J, Frost SDW, Teillaud A, Smith CA, Leclaire S, Fu J, Gandon S, Guérin JL, Tiley LS. Adaptation of avian influenza virus to a swine host. Virus Evol 2017; 3:vex007. [PMID: 28458917 PMCID: PMC5399929 DOI: 10.1093/ve/vex007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence of pathogenic RNA viruses into new hosts can have dramatic consequences for both livestock and public health. Here we characterize the viral genetic changes that were observed in a previous study which experimentally adapted a field isolate of duck influenza virus to swine respiratory cells. Both pre-existing and de novo mutations were selected during this adaptation. We compare the in vitro growth dynamics of the adapted virus with those of the original strain as well as all possible reassortants using reverse genetics. This full factorial design showed that viral gene segments are involved in complex epistatic interactions on virus fitness, including negative and sign epistasis. We also identify two point mutations at positions 67 and 113 of the HA2 subunit of the hemagglutinin protein conferring a fast growth phenotype on the naïve avian virus in swine cells. These HA2 mutations enhance the pH dependent, HA-mediated membrane fusion. A global H1 maximum-likelihood phylogenetic analysis, combined with comprehensive ancestry reconstruction and tests for directional selection, confirmed the field relevance of the mutation at position 113 of HA2. Most notably, this mutation was associated with the establishment of the H1 'avian-like' swine influenza lineage, regarded as the most likely to cause the next influenza pandemic in humans. This multidisciplinary approach to study the genetics of viral adaptation provides unique insights on the underlying processes leading to influenza emergence in a new host species, and identifies specific targets for future surveillance and functional studies.
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Affiliation(s)
- Vincent Bourret
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Jon Lyall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angélique Teillaud
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Catherine A Smith
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Leclaire
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - JinQi Fu
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sylvain Gandon
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Jean-Luc Guérin
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Laurence S Tiley
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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105
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Hurtado R, de Azevedo-Júnior SM, Vanstreels RET, Fabrizio T, Walker D, Rodrigues RC, Seixas MMM, de Araújo J, Thomazelli LM, Ometto TL, Webby RJ, Webster RG, Jerez JA, Durigon EL. Surveillance of Avian Influenza Virus in Aquatic Birds on the Brazilian Amazon Coast. ECOHEALTH 2016; 13:813-818. [PMID: 27645753 DOI: 10.1007/s10393-016-1169-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/18/2016] [Accepted: 08/23/2016] [Indexed: 06/06/2023]
Abstract
The occurrence of avian influenza viruses (AIV) has been extensively studied in aquatic birds in the Northern hemisphere; however, much less information is available for the South American region. In 2009-2010, we sampled 1006 wild aquatic birds (90% Charadriiformes, 9% Anseriformes, and 1% other groups) at three locations on the Brazilian Amazon coast, a region that serves as a major stop-over and wintering site along the Atlantic Americas flyway. Real-time RT-PCR identified five samples as positive; however, no AIV isolates could be obtained and Illumina sequencing did not produce gene sequences that would allow further characterization of the virus.
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Affiliation(s)
- Renata Hurtado
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil.
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- , Av. Silvestre 103, Condomínio Arujazinho IV, Arujá, SP, CEP: 07434-530, Brazil.
| | | | - Ralph Eric Thijl Vanstreels
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Thomas Fabrizio
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David Walker
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Marina M M Seixas
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jansen de Araújo
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Luciano M Thomazelli
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tatiana Lopes Ometto
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Richard J Webby
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Robert G Webster
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - José Antonio Jerez
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Edison Luiz Durigon
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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106
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Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J. Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic. Cell 2016; 167:1088-1098.e6. [PMID: 27814506 PMCID: PMC5115602 DOI: 10.1016/j.cell.2016.10.014] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022]
Abstract
The magnitude of the 2013-2016 Ebola virus disease (EVD) epidemic enabled an unprecedented number of viral mutations to occur over successive human-to-human transmission events, increasing the probability that adaptation to the human host occurred during the outbreak. We investigated one nonsynonymous mutation, Ebola virus (EBOV) glycoprotein (GP) mutant A82V, for its effect on viral infectivity. This mutation, located at the NPC1-binding site on EBOV GP, occurred early in the 2013-2016 outbreak and rose to high frequency. We found that GP-A82V had heightened ability to infect primate cells, including human dendritic cells. The increased infectivity was restricted to cells that have primate-specific NPC1 sequences at the EBOV interface, suggesting that this mutation was indeed an adaptation to the human host. GP-A82V was associated with increased mortality, consistent with the hypothesis that the heightened intrinsic infectivity of GP-A82V contributed to disease severity during the EVD epidemic.
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Affiliation(s)
- William E Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Aaron E Lin
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Luiz Max Carvalho
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kyusik Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Pyae Phyo Kyawe
- Department of Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01605, USA
| | - Sean M McCauley
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Elisa Donnard
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Alper Kucukural
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Patrick McDonel
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Stephen F Schaffner
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, Scotland, UK
| | - Kristian G Andersen
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Scripps Translational Science Institute, 3344 North Torrey Pines Court, La Jolla, CA 92037, USA.
| | - Pardis C Sabeti
- Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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107
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Selection Pressure in the Human Adenovirus Fiber Knob Drives Cell Specificity in Epidemic Keratoconjunctivitis. J Virol 2016; 90:9598-9607. [PMID: 27512073 PMCID: PMC5068513 DOI: 10.1128/jvi.01010-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/05/2016] [Indexed: 11/20/2022] Open
Abstract
Human adenoviruses (HAdVs) contain seven species (HAdV-A to -G), each associated with specific disease conditions. Among these, HAdV-D includes those viruses associated with epidemic keratoconjunctivitis (EKC), a severe ocular surface infection. The reasons for corneal tropism for some but not all HAdV-Ds are not known. The fiber protein is a major capsid protein; its C-terminal "knob" mediates binding with host cell receptors to facilitate subsequent viral entry. In a comprehensive phylogenetic analysis of HAdV-D capsid genes, fiber knob gene sequences of HAdV-D types associated with EKC formed a unique clade. By proteotyping analysis, EKC virus-associated fiber knobs were uniquely shared. Comparative structural modeling showed no distinct variations in fiber knobs of EKC types but did show variation among HAdV-Ds in a region overlapping with the known CD46 binding site in HAdV-B. We also found signature amino acid positions that distinguish EKC from non-EKC types, and by in vitro studies we showed that corneal epithelial cell tropism can be predicted by the presence of a lysine or alanine at residue 240. This same amino acid residue in EKC viruses shows evidence for positive selection, suggesting that evolutionary pressure enhances fitness in corneal infection, and may be a molecular determinant in EKC pathogenesis. IMPORTANCE Viruses adapt various survival strategies to gain entry into target host cells. Human adenovirus (HAdV) types are associated with distinct disease conditions, yet evidence for connections between genotype and cellular tropism is generally lacking. Here, we provide a structural and evolutionary basis for the association between specific genotypes within HAdV species D and epidemic keratoconjunctivitis, a severe ocular surface infection. We find that HAdV-D fiber genes of major EKC pathogens, specifically the fiber knob gene region, share a distinct phylogenetic clade. Deeper analysis of the fiber gene revealed that evolutionary pressure at crucial amino acid sites has a significant impact on its structural conformation, which is likely important in host cell binding and entry. Specific amino acids in hot spot residues provide a link to ocular cell tropism and possibly to corneal pathogenesis.
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108
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Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity. J Virol 2016; 90:9263-84. [PMID: 27489273 PMCID: PMC5044859 DOI: 10.1128/jvi.01205-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Two alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types. Exemplar reassortant viruses also replicated to similar titers in mice, although mice infected with viruses with the avian virus-derived segment 8s had reduced weight loss compared to that achieved in mice infected with the A/Puerto Rico/8/1934 (H1N1) parent. In vitro, the viruses coped similarly with type I interferons. Temporal proteomics analysis of cellular responses to infection showed that the avian virus-derived NS segments provoked lower levels of expression of interferon-stimulated genes in cells than wild type-derived NS segments. Thus, neither the A nor the B allele of avian virus-derived NS segments necessarily attenuates virus replication in a mammalian host, although the alleles can attenuate disease. Phylogenetic analyses identified 32 independent incursions of an avian virus-derived A allele into mammals, whereas 6 introductions of a B allele were identified. However, A-allele isolates from birds outnumbered B-allele isolates, and the relative rates of Aves-to-Mammalia transmission were not significantly different. We conclude that while the introduction of an avian virus segment 8 into mammals is a relatively rare event, the dogma of the B allele being especially restricted is misleading, with implications in the assessment of the pandemic potential of avian influenza viruses. IMPORTANCE Influenza A virus (IAV) can adapt to poultry and mammalian species, inflicting a great socioeconomic burden on farming and health care sectors. Host adaptation likely involves multiple viral factors. Here, we investigated the role of IAV segment 8. Segment 8 has evolved into two distinct clades: the A and B alleles. The B-allele genes have previously been suggested to be restricted to avian virus species. We introduced a selection of avian virus A- and B-allele segment 8s into human H1N1 and H3N2 virus backgrounds and found that these reassortant viruses were fully competent in mammalian host systems. We also analyzed the currently available public data on the segment 8 gene distribution and found surprisingly little evidence for specific avian host restriction of the B-clade segment. We conclude that B-allele segment 8 genes are, in fact, capable of supporting infection in mammals and that they should be considered during the assessment of the pandemic risk of zoonotic influenza A viruses.
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109
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Barba M, Daly JM. The Influenza NS1 Protein: What Do We Know in Equine Influenza Virus Pathogenesis? Pathogens 2016; 5:pathogens5030057. [PMID: 27589809 PMCID: PMC5039437 DOI: 10.3390/pathogens5030057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/24/2016] [Accepted: 08/27/2016] [Indexed: 12/22/2022] Open
Abstract
Equine influenza virus remains a serious health and potential economic problem throughout most parts of the world, despite intensive vaccination programs in some horse populations. The influenza non-structural protein 1 (NS1) has multiple functions involved in the regulation of several cellular and viral processes during influenza infection. We review the strategies that NS1 uses to facilitate virus replication and inhibit antiviral responses in the host, including sequestering of double-stranded RNA, direct modulation of protein kinase R activity and inhibition of transcription and translation of host antiviral response genes such as type I interferon. Details are provided regarding what it is known about NS1 in equine influenza, especially concerning C-terminal truncation. Further research is needed to determine the role of NS1 in equine influenza infection, which will help to understand the pathophysiology of complicated cases related to cytokine imbalance and secondary bacterial infection, and to investigate new therapeutic and vaccination strategies.
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Affiliation(s)
- Marta Barba
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
| | - Janet M Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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110
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Genetic characterization of H5N2 influenza viruses isolated from wild birds in Japan suggests multiple reassortment. Arch Virol 2016; 161:3309-3322. [DOI: 10.1007/s00705-016-3023-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/20/2016] [Indexed: 10/21/2022]
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111
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Fang S, Bai T, Yang L, Wang X, Peng B, Liu H, Geng Y, Zhang R, Ma H, Zhu W, Wang D, Cheng J, Shu Y. Sustained live poultry market surveillance contributes to early warnings for human infection with avian influenza viruses. Emerg Microbes Infect 2016; 5:e79. [PMID: 27485495 PMCID: PMC5034097 DOI: 10.1038/emi.2016.75] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/22/2016] [Accepted: 05/12/2016] [Indexed: 12/27/2022]
Abstract
Sporadic human infections with the highly pathogenic avian influenza (HPAI) A (H5N6) virus have been reported in different provinces in China since April 2014. From June 2015 to January 2016, routine live poultry market (LPM) surveillance was conducted in Shenzhen, Guangdong Province. H5N6 viruses were not detected until November 2015. The H5N6 virus-positive rate increased markedly beginning in December 2015, and viruses were detected in LPMs in all districts of the city. Coincidently, two human cases with histories of poultry exposure developed symptoms and were diagnosed as H5N6-positive in Shenzhen during late December 2015 and early January 2016. Similar viruses were identified in environmental samples collected in the LPMs and the patients. In contrast to previously reported H5N6 viruses, viruses with six internal genes derived from the H9N2 or H7N9 viruses were detected in the present study. The increased H5N6 virus-positive rate in the LPMs and the subsequent human infections demonstrated that sustained LPM surveillance for avian influenza viruses provides an early warning for human infections. Interventions, such as LPM closures, should be immediately implemented to reduce the risk of human infection with the H5N6 virus when the virus is widely detected during LPM surveillance.
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Affiliation(s)
- Shisong Fang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Tian Bai
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xin Wang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Bo Peng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Hui Liu
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Yijie Geng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Renli Zhang
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Hanwu Ma
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jinquan Cheng
- Major Infectious Disease Control Key Laboratory, Key Reference Laboratory of Pathogen and Biosafety, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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112
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Cui H, Shi Y, Ruan T, Li X, Teng Q, Chen H, Yang J, Liu Q, Li Z. Phylogenetic analysis and pathogenicity of H3 subtype avian influenza viruses isolated from live poultry markets in China. Sci Rep 2016; 6:27360. [PMID: 27270298 PMCID: PMC4895239 DOI: 10.1038/srep27360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/12/2016] [Indexed: 12/17/2022] Open
Abstract
H3 subtype influenza A virus is one of the main subtypes that threats both public and animal health. However, the evolution and pathogenicity of H3 avian influenza virus (AIV) circulating in domestic birds in China remain largely unclear. In this study, seven H3 AIVs (four H3N2 and three H3N8) were isolated from poultry in live poultry market (LPM) in China. Phylogenetic analyses of full genomes showed that all viruses were clustered into Eurasian lineage, except N8 genes of two H3N8 isolates fell into North American lineage. Intriguingly, the N8 gene of one H3N8 and PB2, PB1, NP and NS of two H3N2 isolates have close relationship with those of the highly pathogenic H5N8 viruses circulating in Korea and United States, suggesting that the H3-like AIV may contribute internal genes to the highly pathogenic H5N8 viruses. Phylogenetic tree of HA gene and antigenic cross-reactivity results indicated that two antigenically different H3 viruses are circulating in LPM in China. Most of the H3 viruses replicated in mice lung and nasal turbinate without prior adaptation, and the representative H3 viruses infected chickens without causing clinical signs. The reassortment of H3 subtype influenza viruses warrants continuous surveillance in LPM in China.
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MESH Headings
- Animals
- Antibodies, Viral/immunology
- China
- Cluster Analysis
- Cross Reactions
- Disease Models, Animal
- Genetic Variation
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza A Virus, H3N8 Subtype/classification
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/isolation & purification
- Influenza A Virus, H3N8 Subtype/pathogenicity
- Influenza in Birds/virology
- Mice
- Orthomyxoviridae Infections/pathology
- Orthomyxoviridae Infections/virology
- Phylogeny
- Poultry
- RNA, Viral/genetics
- Sequence Analysis, DNA
- Whole Genome Sequencing
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Affiliation(s)
- Hongrui Cui
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Ying Shi
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Tao Ruan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Xuesong Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Jianmei Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Qinfang Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, People’s Republic of China
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113
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Thulasi Raman SN, Zhou Y. Networks of Host Factors that Interact with NS1 Protein of Influenza A Virus. Front Microbiol 2016; 7:654. [PMID: 27199973 PMCID: PMC4855030 DOI: 10.3389/fmicb.2016.00654] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/19/2016] [Indexed: 11/13/2022] Open
Abstract
Pigs are an important host of influenza A viruses due to their ability to generate reassortant viruses with pandemic potential. NS1 protein of influenza A viruses is a key virulence factor and a major antagonist of innate immune responses. It is also involved in enhancing viral mRNA translation and regulation of virus replication. Being a protein with pleiotropic functions, NS1 has a variety of cellular interaction partners. Hence, studies on swine influenza viruses (SIV) and identification of swine influenza NS1-interacting host proteins is of great interest. Here, we constructed a recombinant SIV carrying a Strep-tag in the NS1 protein and infected primary swine respiratory epithelial cells (SRECs) with this virus. The Strep-tag sequence in the NS1 protein enabled us to purify intact, the NS1 protein and its interacting protein complex specifically. We identified cellular proteins present in the purified complex by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and generated a dataset of these proteins. 445 proteins were identified by LC-MS/MS and among them 192 proteins were selected by setting up a threshold based on MS parameters. The selected proteins were analyzed by bioinformatics and were categorized as belonging to different functional groups including translation, RNA processing, cytoskeleton, innate immunity, and apoptosis. Protein interaction networks were derived using these data and the NS1 interactions with some of the specific host factors were verified by immunoprecipitation. The novel proteins and the networks revealed in our study will be the potential candidates for targeted study of the molecular interaction of NS1 with host proteins, which will provide insights into the identification of new therapeutic targets to control influenza infection and disease pathogenesis.
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Affiliation(s)
- Sathya N Thulasi Raman
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
| | - Yan Zhou
- Vaccine and Infectious Disease Organization - International Vaccine Centre, University of Saskatchewan, SaskatoonSK, Canada; Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, SaskatoonSK, Canada
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114
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Shanmuganatham KK, Jones JC, Marathe BM, Feeroz MM, Jones-Engel L, Walker D, Turner J, Rabiul Alam SM, Kamrul Hasan M, Akhtar S, Seiler P, McKenzie P, Krauss S, Webby RJ, Webster RG. The replication of Bangladeshi H9N2 avian influenza viruses carrying genes from H7N3 in mammals. Emerg Microbes Infect 2016; 5:e35. [PMID: 27094903 PMCID: PMC4855072 DOI: 10.1038/emi.2016.29] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/29/2015] [Accepted: 01/06/2016] [Indexed: 01/28/2023]
Abstract
H9N2 avian influenza viruses are continuously monitored by the World Health Organization because they are endemic; they continually reassort with H5N1, H7N9 and H10N8 viruses; and they periodically cause human infections. We characterized H9N2 influenza viruses carrying internal genes from highly pathogenic H7N3 viruses, which were isolated from chickens or quail from live-bird markets in Bangladesh between 2010 and 2013. All of the H9N2 viruses used in this study carried mammalian host-specific mutations. We studied their replication kinetics in normal human bronchoepithelial cells and swine tracheal and lung explants, which exhibit many features of the mammalian airway epithelium and serve as a mammalian host model. All H9N2 viruses replicated to moderate-to-high titers in the normal human bronchoepithelial cells and swine lung explants, but replication was limited in the swine tracheal explants. In Balb/c mice, the H9N2 viruses were nonlethal, replicated to moderately high titers and the infection was confined to the lungs. In the ferret model of human influenza infection and transmission, H9N2 viruses possessing the Q226L substitution in hemagglutinin replicated well without clinical signs and spread via direct contact but not by aerosol. None of the H9N2 viruses tested were resistant to the neuraminidase inhibitors. Our study shows that the Bangladeshi H9N2 viruses have the potential to infect humans and highlights the importance of monitoring and characterizing this influenza subtype to better understand the potential risk these viruses pose to humans.
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Affiliation(s)
| | - Jeremy C Jones
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bindumadhav M Marathe
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mohammed M Feeroz
- Department of Zoology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Lisa Jones-Engel
- National Primate Research Center University of Washington, Seattle, WA 98195-5502, USA
| | - David Walker
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jasmine Turner
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - S M Rabiul Alam
- Department of Zoology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - M Kamrul Hasan
- Department of Zoology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Sharmin Akhtar
- Department of Zoology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Patrick Seiler
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pamela McKenzie
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott Krauss
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert G Webster
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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115
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Arai Y, Kawashita N, Daidoji T, Ibrahim MS, El-Gendy EM, Takagi T, Takahashi K, Suzuki Y, Ikuta K, Nakaya T, Shioda T, Watanabe Y. Novel Polymerase Gene Mutations for Human Adaptation in Clinical Isolates of Avian H5N1 Influenza Viruses. PLoS Pathog 2016; 12:e1005583. [PMID: 27097026 PMCID: PMC4838241 DOI: 10.1371/journal.ppat.1005583] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
A major determinant in the change of the avian influenza virus host range to humans is the E627K substitution in the PB2 polymerase protein. However, the polymerase activity of avian influenza viruses with a single PB2-E627K mutation is still lower than that of seasonal human influenza viruses, implying that avian viruses require polymerase mutations in addition to PB2-627K for human adaptation. Here, we used a database search of H5N1 clade 2.2.1 virus sequences with the PB2-627K mutation to identify other polymerase adaptation mutations that have been selected in infected patients. Several of the mutations identified acted cooperatively with PB2-627K to increase viral growth in human airway epithelial cells and mouse lungs. These mutations were in multiple domains of the polymerase complex other than the PB2-627 domain, highlighting a complicated avian-to-human adaptation pathway of avian influenza viruses. Thus, H5N1 viruses could rapidly acquire multiple polymerase mutations that function cooperatively with PB2-627K in infected patients for optimal human adaptation. Avian influenza (AI) virus H5N1 subtype strains have been sporadically transmitted to humans with high mortality (>60%), presenting a serious global health threat. In particular, 63% of recent human H5N1 infection cases worldwide have been reported in Egypt, which is now regarded as a hot spot for H5N1 virus evolution. H5N1 clade 2.2.1 viruses are unique to Egypt and probably have the greatest evolutionary potential for adaptation from avian to human hosts. Here, using a comprehensive database approach, we identified various novel polymerase mutations in clade 2.2.1 virus strains, isolated from patients, that enabled enhanced viral replication in both human airway epithelial cells and mouse lungs. Interestingly, the mutations identified acted cooperatively with the PB2-E627K mutation, the most well-known human adaptation mutation, to produce a further increase in viral replication in human hosts. These results provide the first broad-spectrum data on the polymerase characteristics of AI viruses that have been selected in infected patients, and also give new insight into the human adaptation mechanisms of AI viruses.
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Affiliation(s)
- Yasuha Arai
- Department of Viral infection, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Norihito Kawashita
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Madiha S. Ibrahim
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Microbiology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Emad M. El-Gendy
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Microbiology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kazuo Takahashi
- Department of Laboratory Examination, International University of Health and Welfare Hospital, Tochigi, Japan
| | - Yasuo Suzuki
- Health Science Hills, College of Life and Health Sciences, Chubu University, Aichi, Japan
| | - Kazuyoshi Ikuta
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuo Shioda
- Department of Viral infection, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yohei Watanabe
- Department of Viral infection, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
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116
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Affiliation(s)
- Daniel Marc
- a ISP, INRA, Université Tours , Nouzilly , France
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117
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Ramey AM, Walther P, Link P, Poulson RL, Wilcox BR, Newsome G, Spackman E, Brown JD, Stallknecht DE. Optimizing Surveillance for South American Origin Influenza A Viruses Along the United States Gulf Coast Through Genomic Characterization of Isolates from Blue-winged Teal (Anas discors). Transbound Emerg Dis 2016; 63:194-202. [PMID: 25056712 PMCID: PMC4305350 DOI: 10.1111/tbed.12244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 11/27/2022]
Abstract
Relative to research focused on inter-continental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue-winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes was detected in IAVs isolated from blue-winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue-winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g., the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue-winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.
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Affiliation(s)
- Andrew M. Ramey
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Patrick Walther
- US Fish and Wildlife Service, Texas Chenier Plain Refuge Complex, P.O. Box 278 4017 FM 563, Anahuac, Texas 77514, USA
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, 2000 Quail Drive, Room 436, Baton Rouge, Louisiana 70808, USA
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Benjamin R. Wilcox
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - George Newsome
- City of Beaumont Wastewater Treatment Plant, 4900 Lafin Road, Beaumont, Texas 77705, USA
| | - Erica Spackman
- US Department of Agriculture, Agriculture Research Service, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
| | - Justin D. Brown
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
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118
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Nguyen TH, Than VT, Thanh HD, Hung VK, Nguyen DT, Kim W. Intersubtype Reassortments of H5N1 Highly Pathogenic Avian Influenza Viruses Isolated from Quail. PLoS One 2016; 11:e0149608. [PMID: 26900963 PMCID: PMC4765837 DOI: 10.1371/journal.pone.0149608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/03/2016] [Indexed: 11/18/2022] Open
Abstract
H5N1 highly pathogenic avian influenza (HPAI) viruses are considered a threat to national animal industries, causing production losses and high mortality in domestic poultry. In recent years, quail has become a popular terrestrial poultry species raised for production of meat and eggs in Asia. In this study, to better understand the roles of quail in H5N1 viral evolution, two H5N1-positive samples, designated A/quail/Vietnam/CVVI-49/2010 (CVVI-49/2010) and A/quail/Vietnam/CVVI-50/2014 (CVVI-50/2014), were isolated from quail during H5N1 outbreaks in Vietnam, and their whole genome were analyzed. The phylogenetic analysis reveals new evolutionary variation in the worldwide H5N1 viruses. The quail HA genes were clustered into clades 1.1.1 (CVVI-49/2010) and clade 2.3.2.1c (CVVI-50/2014), which may have evolved from viruses circulating from chickens and/or ducks in Cambodia, mainland of China, Taiwan, Indonesia, and South Korea in recent years. Interestingly, the M2 gene of the CVVI-49/2010 strain contained amino acid substitutions at position 26L-I and 31S-N that are related to amantadine-resistance. In particular, the CVVI-50/2014 strain revealed evidence of multiple intersubtype reassortment events between virus clades 2.3.2.1c, 2.3.2.1b, and 2.3.2.1a. Data from this study supports the possible role of quail as an important intermediate host in avian influenza virus evolution. Therefore, additional surveillance is needed to monitor these HPAI viruses both serologically and virologically in quail.
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Affiliation(s)
- Tinh Huu Nguyen
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Hien Dang Thanh
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Vu-Khac Hung
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Duc Tan Nguyen
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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119
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James CD, Roberts S. Viral Interactions with PDZ Domain-Containing Proteins-An Oncogenic Trait? Pathogens 2016; 5:pathogens5010008. [PMID: 26797638 PMCID: PMC4810129 DOI: 10.3390/pathogens5010008] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 02/06/2023] Open
Abstract
Many of the human viruses with oncogenic capabilities, either in their natural host or in experimental systems (hepatitis B and C, human T cell leukaemia virus type 1, Kaposi sarcoma herpesvirus, human immunodeficiency virus, high-risk human papillomaviruses and adenovirus type 9), encode in their limited genome the ability to target cellular proteins containing PSD95/ DLG/ZO-1 (PDZ) interaction modules. In many cases (but not always), the viruses have evolved to bind the PDZ domains using the same short linear peptide motifs found in host protein-PDZ interactions, and in some cases regulate the interactions in a similar fashion by phosphorylation. What is striking is that the diverse viruses target a common subset of PDZ proteins that are intimately involved in controlling cell polarity and the structure and function of intercellular junctions, including tight junctions. Cell polarity is fundamental to the control of cell proliferation and cell survival and disruption of polarity and the signal transduction pathways involved is a key event in tumourigenesis. This review focuses on the oncogenic viruses and the role of targeting PDZ proteins in the virus life cycle and the contribution of virus-PDZ protein interactions to virus-mediated oncogenesis. We highlight how many of the viral associations with PDZ proteins lead to deregulation of PI3K/AKT signalling, benefitting virus replication but as a consequence also contributing to oncogenesis.
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Affiliation(s)
- Claire D James
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
- Present address; Virginia Commonwealth University, School of Dentistry, W. Baxter Perkinson Jr. Building, 521 North 11th Street, P.O. Box 980566, Richmond, VA 23298-0566, USA.
| | - Sally Roberts
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
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120
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Lu PX, Jing Y, Xiao-Hua L, Zhou BP, Yu-Xin S, Zhi-Yong Z, Yu-Shen Z, Ying-Ying D, Xian-Gui R, Yang G, Jian H, Jia-Fu L, Qing-Si Z, Jing-Jing L, De-Min Y, Xiang-Rong H. Human Avian Influenza A H5N1, H7N9, H10N8 and H5N6 Virus Infection. DIAGNOSTIC IMAGING OF EMERGING INFECTIOUS DISEASES 2016. [PMCID: PMC7193729 DOI: 10.1007/978-94-017-7363-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Avian influenza is an infectious disease induced by avian influenza viruses in poultry, commonly called genuine fowl plague or European fowl plague.
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121
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Arnal A, Vittecoq M, Pearce-Duvet J, Gauthier-Clerc M, Boulinier T, Jourdain E. Laridae: A neglected reservoir that could play a major role in avian influenza virus epidemiological dynamics. Crit Rev Microbiol 2015; 41:508-19. [DOI: 10.3109/1040841x.2013.870967] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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122
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Hurtado R, Fabrizio T, Vanstreels RET, Krauss S, Webby RJ, Webster RG, Durigon EL. Molecular Characterization of Subtype H11N9 Avian Influenza Virus Isolated from Shorebirds in Brazil. PLoS One 2015; 10:e0145627. [PMID: 26689791 PMCID: PMC4687026 DOI: 10.1371/journal.pone.0145627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/07/2015] [Indexed: 11/18/2022] Open
Abstract
Migratory aquatic birds play an important role in the maintenance and spread of avian influenza viruses (AIV). Many species of aquatic migratory birds tend to use similar migration routes, also known as flyways, which serve as important circuits for the dissemination of AIV. In recent years there has been extensive surveillance of the virus in aquatic birds in the Northern Hemisphere; however in contrast only a few studies have been attempted to detect AIV in wild birds in South America. There are major flyways connecting South America to Central and North America, whereas avian migration routes between South America and the remaining continents are uncommon. As a result, it has been hypothesized that South American AIV strains would be most closely related to the strains from North America than to those from other regions in the world. We characterized the full genome of three AIV subtype H11N9 isolates obtained from ruddy turnstones (Arenaria interpres) on the Amazon coast of Brazil. For all gene segments, all three strains consistently clustered together within evolutionary lineages of AIV that had been previously described from aquatic birds in North America. In particular, the H11N9 isolates were remarkably closely related to AIV strains from shorebirds sampled at the Delaware Bay region, on the Northeastern coast of the USA, more than 5000 km away from where the isolates were retrieved. Additionally, there was also evidence of genetic similarity to AIV strains from ducks and teals from interior USA and Canada. These findings corroborate that migratory flyways of aquatic birds play an important role in determining the genetic structure of AIV in the Western hemisphere, with a strong epidemiological connectivity between North and South America.
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Affiliation(s)
- Renata Hurtado
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
| | - Thomas Fabrizio
- Division of Virology, Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Ralph Eric Thijl Vanstreels
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Scott Krauss
- Division of Virology, Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Division of Virology, Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Division of Virology, Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Edison Luiz Durigon
- Laboratory Biosafety Level 3+, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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123
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Muzyka D, Pantin-Jackwood M, Starick E, Fereidouni S. Evidence for genetic variation of Eurasian avian influenza viruses of subtype H15: the first report of an H15N7 virus. Arch Virol 2015; 161:605-12. [PMID: 26650037 DOI: 10.1007/s00705-015-2629-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 09/25/2015] [Indexed: 11/29/2022]
Abstract
Since the first detection of H15 avian influenza viruses (AIVs) in Australia in 1979, only seven H15 strains have been reported. A new H15 AIV was detected in Ukraine in 2010, carrying the unique HA-NA subtype combination H15N7. This virus replicated efficiently in chicken eggs, and antisera against it reacted strongly with the homologous antigen, but with lower titers when using the reference Australian antigen. The amino acid motifs of the HA cleavage site and receptor-binding site were different from those in the Australian viruses. The new virus, together with an H15 virus from Siberia from 2008, constitutes a new clade of H15 AIV isolates.
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Affiliation(s)
- Denys Muzyka
- National Scientific Center, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Mary Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Elke Starick
- Friedrich Loeffler Institute, Greifswald, Insel Riems, Germany
| | - Sasan Fereidouni
- Friedrich Loeffler Institute, Greifswald, Insel Riems, Germany. .,WESCA Wildlife Network, Greifswald, Germany. .,University of Veterinary Medicine Vienna, Research Institute of Wildlife Ecology, Vienna, Austria.
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124
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Chaudhry M, Angot A, Rashid HB, Cattoli G, Hussain M, Trovò G, Drago A, Valastro V, Thrusfield M, Welburn S, Eisler MC, Capua I. Reassortant Avian Influenza A(H9N2) viruses in chickens in retail poultry shops, Pakistan, 2009-2010. Emerg Infect Dis 2015; 21:673-6. [PMID: 25811830 PMCID: PMC4378488 DOI: 10.3201/eid2104.141570] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Phylogenetic analysis of influenza viruses collected during December 2009–February 2010 from chickens in live poultry retail shops in Lahore, Pakistan, showed influenza A(H9N2) lineage polymerase and nonstructural genes generate through inter- and intrasubtypic reassortments. Many amino acid signatures observed were characteristic of human isolates; hence, their circulation could enhance inter- or intrasubtypic reassortment.
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125
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Dahiru Rogo L, Rezaei F, Shafiei-Jandaghi NZ, Ghavami N, Fatemi-Nasab G, Mokhtari-Azad T. Analysis of amino acid changes in NS protein of influenza A/(H3N2) virus in Iranian isolates. Future Virol 2015. [DOI: 10.2217/fvl.15.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Roles of NS gene of influenza A virus in virulence and replication are well established but extent of its variation in seasonal influenza A (H3N2) viruses in Iran is not well known. Materials & methods: NS gene of 37 (A/H3N2) virus isolates were sequenced and analyzed for information on genetic changes. Results: Data analysis of NS1 protein revealed two amino acid substitutions E26K and Q193R in almost all strains. Substitutions in T58P in 27.0%, A86S in 13.5% and each of V11G, M81I and P85T in 2.7% Iranian strains were also observed. Mutations in NS2/NEP protein were observed in K36E, Q101L and F107S. Conclusion: Many mutations were observed for the first time in Iranian strains. Their function remains to be determined.
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Affiliation(s)
- Lawal Dahiru Rogo
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Health Sciences, Bayero University Kano, PMB 3011, Nigeria
| | - Farhad Rezaei
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- National Influenza Center, Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nazanin Z Shafiei-Jandaghi
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- National Influenza Center, Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nastaran Ghavami
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- National Influenza Center, Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazal Fatemi-Nasab
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- National Influenza Center, Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, International Campus, Tehran, Iran
- National Influenza Center, Department of Medical Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Meunier I, Morisseau O, Garneau É, Marois I, Cloutier A, Richter MV. Infection with a Mouse-Adapted Strain of the 2009 Pandemic Virus Causes a Highly Severe Disease Associated with an Impaired T Cell Response. PLoS One 2015; 10:e0138055. [PMID: 26381265 PMCID: PMC4575127 DOI: 10.1371/journal.pone.0138055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/24/2015] [Indexed: 12/31/2022] Open
Abstract
Despite a relatively low fatality rate, the 2009 H1N1 pandemic virus differed from other seasonal viruses in that it caused mortality and severe pneumonia in the young and middle-aged population (18–59 years old). The mechanisms underlying this increased disease severity are still poorly understood. In this study, a human isolate of the 2009 H1N1 pandemic virus was adapted to the mouse (MAp2009). The pathogenicity of the MAp2009 virus and the host immune responses were evaluated in the mouse model and compared to the laboratory H1N1 strain A/Puerto Rico/8/1934 (PR8). The MAp2009 virus reached consistently higher titers in the lungs over 14 days compared to the PR8 virus, and caused severe disease associated with high morbidity and 85% mortality rate, contrasting with the 0% death rate in the PR8 group. During the early phase of infection, both viruses induced similar pathology in the lungs. However, MAp2009-induced lung inflammation was sustained until the end of the study (day 14), while there was no sign of inflammation in the PR8-infected group by day 10. Furthermore, at day 3 post-infection, MAp2009 induced up to 10- to 40-fold more cytokine and chemokine gene expression, respectively. More importantly, the numbers of CD4+ T cells and virus-specific CD8+ T cells were significantly lower in the lungs of MAp2009-infected mice compared to PR8-infected mice. Interestingly, there was no difference in the number of dendritic cells in the lung and in the draining lymph node. Moreover, mice infected with PR8 or MAp2009 had similar numbers of CCR5 and CXCR3-expressing T cells, suggesting that the impaired T cell response was not due to a lack of chemokine responsiveness or priming of T cells. This study demonstrates that a mouse-adapted virus from an isolate of the 2009 pandemic virus interferes with the adaptive immune response leading to a more severe disease.
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Affiliation(s)
- Isabelle Meunier
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
| | - Olivier Morisseau
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
| | - Émilie Garneau
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
| | - Isabelle Marois
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
| | - Alexandre Cloutier
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
| | - Martin V. Richter
- Pulmonary Division, Department of Medicine, Faculty of Medicine and Health Sciences, Université de Sherbrooke and Centre de Recherche du CHUS, Sherbrooke, Québec, Canada
- * E-mail:
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127
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Yang D, Liu J, Ju H, Ge F, Wang J, Li X, Zhou J, Liu P. Genetic analysis of H3N2 avian influenza viruses isolated from live poultry markets and poultry slaughterhouses in Shanghai, China in 2013. Virus Genes 2015; 51:25-32. [PMID: 25899857 DOI: 10.1007/s11262-015-1198-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 04/09/2015] [Indexed: 11/29/2022]
Abstract
Five H3N2 avian influenza viruses (AIVs) were isolated from live poultry markets (LPMs) and poultry slaughterhouses in Shanghai, China in 2013. All viruses were characterized by whole-genome sequencing with subsequent genetic comparison and phylogenetic analysis. The hemagglutinin cleavage site of all viruses indicated that the five strains were low-pathogenic AIVs. Phylogenetic analysis of all eight viral genes showed that the five H3N2 viruses clustered in the Eurasian lineage of influenza viruses. The eight genes showed evidence of reassortment events between these H3 subtype viruses and other subtype viruses, especially H5 and H7 subtypes, probably in pigeons, domestic ducks, and wild birds. These findings emphasized the importance of AIV surveillance in LPMs and poultry slaughterhouses for understanding the genesis and emergence of novel reassortants with pandemic potential.
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Affiliation(s)
- Dequan Yang
- Shanghai Animal Disease Control Center, 855 Hongjing Road, Shanghai, 201103, People's Republic of China
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128
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Neumann G. H5N1 influenza virulence, pathogenicity and transmissibility: what do we know? Future Virol 2015; 10:971-980. [PMID: 26617665 DOI: 10.2217/fvl.15.62] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Highly pathogenic influenza viruses of the H5N1 subtype have infected more than 600 people since 1997, resulting in the deaths of approximately 60% of those infected. Multiple studies have established the viral hemagglutinin (HA) surface glycoprotein as the major determinant of H5N1 virulence. HA mediates host-specific virus binding to cells, and mutations that allow efficient binding to viral receptors on mammalian cells are critical (although not sufficient) for H5N1 transmissibility among mammals. The viral polymerase PB2 protein is also a critical virulence determinant, and adaptive mutations in this protein are crucial for efficient H5N1 virus replication in mammals. Additionally, viral proteins (such as NS1 and PB1-F2) with roles in innate immune responses also affect the virulence of highly pathogenic H5N1 viruses.
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Affiliation(s)
- Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA; Tel.: +1 608 890 2907; ;
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129
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Marazzi I, Garcia-Sastre A. Interference of viral effector proteins with chromatin, transcription, and the epigenome. Curr Opin Microbiol 2015; 26:123-9. [PMID: 26232586 DOI: 10.1016/j.mib.2015.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
Pathogens exploit cellular functions to create an environment conducive to their persistence and propagation. Viruses and bacteria express effector-proteins or virulence factors, known to interfere at the molecular level with regulatory 'checkpoints' of numerous physiological events in the cell. A newly prominent area of research is the identification of pathogenic effector proteins that function on the host chromatin, their subversion/interference with chromatin regulatory processes, the short/long/heritable effects on the infected cell and the ultimate consequence of their expression at the organismal level.
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Affiliation(s)
- Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, NY, USA.
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130
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Koçer ZA, Carter R, Wu G, Zhang J, Webster RG. The Genomic Contributions of Avian H1N1 Influenza A Viruses to the Evolution of Mammalian Strains. PLoS One 2015. [PMID: 26208281 PMCID: PMC4514870 DOI: 10.1371/journal.pone.0133795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Among the influenza A viruses (IAVs) in wild aquatic birds, only H1, H2, and H3 subtypes have caused epidemics in humans. H1N1 viruses of avian origin have also caused 3 of 5 pandemics. To understand the reappearance of H1N1 in the context of pandemic emergence, we investigated whether avian H1N1 IAVs have contributed to the evolution of human, swine, and 2009 pandemic H1N1 IAVs. On the basis of phylogenetic analysis, we concluded that the polymerase gene segments (especially PB2 and PA) circulating in North American avian H1N1 IAVs have been reintroduced to swine multiple times, resulting in different lineages that led to the emergence of the 2009 pandemic H1N1 IAVs. Moreover, the similar topologies of hemagglutinin and nucleoprotein and neuraminidase and matrix gene segments suggest that each surface glycoprotein coevolved with an internal gene segment within the H1N1 subtype. The genotype of avian H1N1 IAVs of Charadriiformes origin isolated in 2009 differs from that of avian H1N1 IAVs of Anseriformes origin. When the antigenic sites in the hemagglutinin of all 31 North American avian H1N1 IAVs were considered, 60%-80% of the amino acids at the antigenic sites were identical to those in 1918 and/or 2009 pandemic H1N1 viruses. Thus, although the pathogenicity of avian H1N1 IAVs could not be inferred from the phylogeny due to the small dataset, the evolutionary process within the H1N1 IAV subtype suggests that the circulation of H1N1 IAVs in wild birds poses a continuous threat for future influenza pandemics in humans.
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Affiliation(s)
- Zeynep A. Koçer
- Department of Infectious Diseases, Division of Virology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert Carter
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Gang Wu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Diseases, Division of Virology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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131
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Newly Emergent Highly Pathogenic H5N9 Subtype Avian Influenza A Virus. J Virol 2015; 89:8806-15. [PMID: 26085150 DOI: 10.1128/jvi.00653-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The novel H7N9 avian influenza virus (AIV) was demonstrated to cause severe human respiratory infections in China. Here, we examined poultry specimens from live bird markets linked to human H7N9 infection in Hangzhou, China. Metagenomic sequencing revealed mixed subtypes (H5, H7, H9, N1, N2, and N9). Subsequently, AIV subtypes H5N9, H7N9, and H9N2 were isolated. Evolutionary analysis showed that the hemagglutinin gene of the novel H5N9 virus originated from A/Muscovy duck/Vietnam/LBM227/2012 (H5N1), which belongs to clade 2.3.2.1. The neuraminidase gene of the novel H5N9 virus originated from human-infective A/Hangzhou/1/2013 (H7N9). The six internal genes were similar to those of other H5N1, H7N9, and H9N2 virus strains. The virus harbored the PQRERRRKR/GL motif characteristic of highly pathogenic AIVs at the HA cleavage site. Receptor-binding experiments demonstrated that the virus binds α-2,3 sialic acid but not α-2,6 sialic acid. Identically, pathogenicity experiments also showed that the virus caused low mortality rates in mice. This newly isolated H5N9 virus is a highly pathogenic reassortant virus originating from H5N1, H7N9, and H9N2 subtypes. Live bird markets represent a potential transmission risk to public health and the poultry industry. IMPORTANCE This investigation confirms that the novel H5N9 subtype avian influenza A virus is a reassortant strain originating from H5N1, H7N9, and H9N2 subtypes and is totally different from the H5N9 viruses reported before. The novel H5N9 virus acquired a highly pathogenic H5 gene and an N9 gene from human-infecting subtype H7N9 but caused low mortality rates in mice. Whether this novel H5N9 virus will cause human infections from its avian host and become a pandemic subtype is not known yet. It is therefore imperative to assess the risk of emergence of this novel reassortant virus with potential transmissibility to public health.
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132
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Fries AC, Nolting JM, Bowman AS, Lin X, Halpin RA, Wester E, Fedorova N, Stockwell TB, Das SR, Dugan VG, Wentworth DE, Gibbs HL, Slemons RD. Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway. J Virol 2015; 89:5371-81. [PMID: 25741003 PMCID: PMC4442537 DOI: 10.1128/jvi.03249-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED While geographic distance often restricts the spread of pathogens via hosts, this barrier may be compromised when host species are mobile. Migratory waterfowl in the order Anseriformes are important reservoir hosts for diverse populations of avian-origin influenza A viruses (AIVs) and are assumed to spread AIVs during their annual continental-scale migrations. However, support for this hypothesis is limited, and it is rarely tested using data from comprehensive surveillance efforts incorporating both the temporal and spatial aspects of host migratory patterns. We conducted intensive AIV surveillance of waterfowl using the North American Mississippi Migratory Flyway (MMF) over three autumn migratory seasons. Viral isolates (n = 297) from multiple host species were sequenced and analyzed for patterns of gene dispersal between northern staging and southern wintering locations. Using a phylogenetic and nucleotide identity framework, we observed a larger amount of gene dispersal within this flyway rather than between the other three longitudinally identified North American flyways. Across seasons, we observed patterns of regional persistence of diversity for each genomic segment, along with limited survival of dispersed AIV gene lineages. Reassortment increased with both time and distance, resulting in transient AIV constellations. This study shows that within the MMF, AIV gene flow favors spread along the migratory corridor within a season, and also that intensive surveillance during bird migration is important for identifying virus dispersal on time scales relevant to pandemic responsiveness. In addition, this study indicates that comprehensive monitoring programs to capture AIV diversity are critical for providing insight into AIV evolution and ecology in a major natural reservoir. IMPORTANCE Migratory birds are a reservoir for antigenic and genetic diversity of influenza A viruses (AIVs) and are implicated in the spread of virus diversity that has contributed to previous pandemic events. Evidence for dispersal of avian-origin AIVs by migratory birds is rarely examined on temporal scales relevant to pandemic or panzootic threats. Therefore, characterizing AIV movement by hosts within a migratory season is important for implementing effective surveillance strategies. We conducted surveillance following birds along a major North American migratory route and observed that within a migratory season, AIVs rapidly reassorted and gene lineages were dispersed primarily within the migratory corridor. Patterns of regional persistence were observed across seasons for each gene segment. We show that dispersal of AIV gene lineages by migratory birds occurs quickly along migratory routes and that surveillance for AIVs threatening human and animal health should focus attention on these routes.
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Affiliation(s)
- Anthony C Fries
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Xudong Lin
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Eric Wester
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Nadia Fedorova
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Suman R Das
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Vivien G Dugan
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - Richard D Slemons
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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133
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Lewis NS, Verhagen JH, Javakhishvili Z, Russell CA, Lexmond P, Westgeest KB, Bestebroer TM, Halpin RA, Lin X, Ransier A, Fedorova NB, Stockwell TB, Latorre-Margalef N, Olsen B, Smith G, Bahl J, Wentworth DE, Waldenström J, Fouchier RAM, de Graaf M. Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data. J Gen Virol 2015; 96:2050-2060. [PMID: 25904147 PMCID: PMC4681060 DOI: 10.1099/vir.0.000155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian IAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.
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Affiliation(s)
- Nicola S Lewis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Josanne H Verhagen
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Zurab Javakhishvili
- Institute of Ecology, Ilia State University, 3/5 Cholokashvili, Tbilisi, Georgia
| | - Colin A Russell
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Pascal Lexmond
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Kim B Westgeest
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Theo M Bestebroer
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | | | - Xudong Lin
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Amy Ransier
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.,Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA, 30602, USA
| | - Björn Olsen
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Gavin Smith
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Justin Bahl
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.,Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX, 77030, USA
| | | | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Miranda de Graaf
- Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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134
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Published sequences do not support transfer of oseltamivir resistance mutations from avian to human influenza A virus strains. BMC Infect Dis 2015; 15:162. [PMID: 25887656 PMCID: PMC4387679 DOI: 10.1186/s12879-015-0860-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 02/26/2015] [Indexed: 01/06/2023] Open
Abstract
Background Tamiflu (oseltamivir phosphate ester, OE) is a widely used antiviral active against influenza A virus. Its active metabolite, oseltamivir carboxylate (OC), is chemically stable and secreted into wastewater treatment plants. OC contamination of natural habitats of waterfowl might induce OC resistance in influenza viruses persistently infecting waterfowl, and lead to transfer of OC-resistance from avian to human influenza. The aim of this study was to evaluate whether such has occurred. Methods A genomics approach including phylogenetic analysis and probability calculations for homologous recombination was applied on altogether 19,755 neuraminidase (N1 and N2) genes from virus sampled in humans and birds, with and without resistance mutations. Results No evidence for transfer of OE resistance mutations from avian to human N genes was obtained, and events suggesting recombination between human and avian influenza virus variants could not be traced in the sequence material studied. Conclusions The results indicate that resistance in influenza viruses infecting humans is due to the selection pressure posed by the global OE administration in humans rather than transfer from avian influenza A virus strains carrying mutations induced by environmental exposure to OC. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-0860-9) contains supplementary material, which is available to authorized users.
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135
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Kamal RP, Katz JM, York IA. Molecular determinants of influenza virus pathogenesis in mice. Curr Top Microbiol Immunol 2015; 385:243-74. [PMID: 25038937 DOI: 10.1007/82_2014_388] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mice are widely used for studying influenza virus pathogenesis and immunology because of their low cost, the wide availability of mouse-specific reagents, and the large number of mouse strains available, including knockout and transgenic strains. However, mice do not fully recapitulate the signs of influenza infection of humans: transmission of influenza between mice is much less efficient than in humans, and influenza viruses often require adaptation before they are able to efficiently replicate in mice. In the process of mouse adaptation, influenza viruses acquire mutations that enhance their ability to attach to mouse cells, replicate within the cells, and suppress immunity, among other functions. Many such mouse-adaptive mutations have been identified, covering all 8 genomic segments of the virus. Identification and analysis of these mutations have provided insight into the molecular determinants of influenza virulence and pathogenesis, not only in mice but also in humans and other species. In particular, several mouse-adaptive mutations of avian influenza viruses have proved to be general mammalian-adaptive changes that are potential markers of pre-pandemic viruses. As well as evaluating influenza pathogenesis, mice have also been used as models for evaluation of novel vaccines and anti-viral therapies. Mice can be a useful animal model for studying influenza biology as long as differences between human and mice infections are taken into account.
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Affiliation(s)
- Ram P Kamal
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA,
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136
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Arriero E, Müller I, Juvaste R, Martínez FJ, Bertolero A. Variation in immune parameters and disease prevalence among Lesser Black-backed Gulls (Larus fuscus sp.) with different migratory strategies. PLoS One 2015; 10:e0118279. [PMID: 25679797 PMCID: PMC4334556 DOI: 10.1371/journal.pone.0118279] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/12/2015] [Indexed: 01/08/2023] Open
Abstract
The ability to control infections is a key trait for migrants that must be balanced against other costly features of the migratory life. In this study we explored the links between migration and disease ecology by examining natural variation in parasite exposure and immunity in several populations of Lesser Black-backed Gulls (Larus fuscus) with different migratory strategies. We found higher activity of natural antibodies in long distance migrants from the nominate subspecies L.f.fuscus. Circulating levels of IgY showed large variation at the population level, while immune parameters associated with antimicrobial activity showed extensive variation at the individual level irrespective of population or migratory strategy. Pathogen prevalence showed large geographical variation. However, the seroprevalence of one of the gull-specific subtypes of avian influenza (H16) was associated to the migratory strategy, with lower prevalence among the long-distance migrants, suggesting that migration may play a role in disease dynamics of certain pathogens at the population level.
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Affiliation(s)
- Elena Arriero
- Department of Migration and Immunoecology, Max Planck Institute for Ornithology, Radolfzell,Germany
- Department of Zoology and Anthropology, University Complutense of Madrid, Madrid, Spain
- * E-mail:
| | - Inge Müller
- Department of Migration and Immunoecology, Max Planck Institute for Ornithology, Radolfzell,Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Risto Juvaste
- Department of Biology, University of Turku, Turun yliopisto, Finland
| | | | - Albert Bertolero
- Institute of Aquatic Ecosystems (IRTA), Sant Carles de la Ràpita, Spain
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Kong W, Liu L, Wang Y, He Q, Wu S, Qin Z, Wang J, Sun H, Sun Y, Zhang R, Pu J, Liu J. C-terminal elongation of NS1 of H9N2 influenza virus induces a high level of inflammatory cytokines and increases transmission. J Gen Virol 2015; 96:259-268. [DOI: 10.1099/vir.0.071001-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Weili Kong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Lirong Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Yu Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Qiming He
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Sizhe Wu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Zhihua Qin
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Jinliang Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
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Abstract
The non-structural protein 1 of influenza virus (NS1) is a relatively small polypeptide with an outstanding number of ascribed functions. NS1 is the main viral antagonist of the innate immune response during influenza virus infection, chiefly by inhibiting the type I interferon system at multiple steps. As such, its role is critical to overcome the first barrier the host presents to halt the viral infection. However, the pro-viral activities of this well-studied protein go far beyond and include regulation of viral RNA and protein synthesis, and disruption of the host cell homeostasis by dramatically affecting general gene expression while tweaking the PI3K signaling network. Because of all of this, NS1 is a key virulence factor that impacts influenza pathogenesis, and adaptation to new hosts, making it an attractive target for control strategies. Here, we will overview the many roles that have been ascribed to the NS1 protein, and give insights into the sequence features and structural properties that make them possible, highlighting the need to understand how NS1 can actually perform all of these functions during viral infection.
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Affiliation(s)
- Juan Ayllon
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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139
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Koçer ZA, Fan Y, Huether R, Obenauer J, Webby RJ, Zhang J, Webster RG, Wu G. Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses. Sci Rep 2014; 4:7455. [PMID: 25503687 PMCID: PMC4264002 DOI: 10.1038/srep07455] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/24/2014] [Indexed: 11/09/2022] Open
Abstract
Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.
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Affiliation(s)
- Zeynep A Koçer
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert Huether
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - John Obenauer
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Richard J Webby
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Robert G Webster
- Department of Infectious Diseases, Division of Virology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105, United States
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140
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Wei K, Lin Y, Li Y, Chen Y. Tracking the Evolution in Phylogeny, Structure and Function of H5N1 Influenza Virus PA Gene. Transbound Emerg Dis 2014; 63:548-63. [PMID: 25476417 DOI: 10.1111/tbed.12301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 01/24/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses have severely affected the poultry industry of Vietnam and Indonesia. The outbreaks of HPAI H5N1 viruses continue to pose a serious threat to public health, which have profound impacts on public health. In this study, we presented phylogenetic evidences for five reassortants among HPAI H5N1 viruses sampled from Vietnam and Indonesia during 2003-2013 and found that reassortment events occurred more frequently in the three gene segments (PB1, PA and HA) than in the remaining five gene segments (PB2, NA, NP, NS and MP). The sequence-based analyses have revealed that the PA protein displays high levels of DNA sequence polymorphism and variability than other internal proteins. Seven positive selection sites were detected in PA proteins, which ranked second only to the surface glycoproteins. Structure-based comparative analysis of PA proteins showed a remarkable sequence conservation between the high-pathogenic, low-pathogenic and reassortant viruses, indicating that PA appears to be a potential antiviral target. Furthermore, by analysing the published data, we compared the differential expression of genes involved in RIG-I- and MAVS-mediated intracellular type I interferon (IFN)-inducing pathway between the VN3028IIcl2-infected, IDN3006-infected and IDN3006/PA-infected groups. Our analyses indicated that the inhibitory effect of the PA protein on MAVS was not strong. In addition, transcriptional levels of 33 mitochondrial proteins involved in the induction of apoptosis have significantly increased, suggesting that PA may play an important role in apoptosis signalling pathway.
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Affiliation(s)
- K Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Chen
- School of Medicine, Tsinghua University, Beijing, China
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141
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Husain M. Avian influenza A (H7N9) virus infection in humans: Epidemiology, evolution, and pathogenesis. INFECTION GENETICS AND EVOLUTION 2014; 28:304-12. [DOI: 10.1016/j.meegid.2014.10.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/09/2022]
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142
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Zhang XL, Pang W, Hu XT, Li JL, Yao YG, Zheng YT. Experimental primates and non-human primate (NHP) models of human diseases in China: current status and progress. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2014; 35:447-64. [PMID: 25465081 PMCID: PMC4790274 DOI: 10.13918/j.issn.2095-8137.2014.6.447] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/15/2014] [Indexed: 12/16/2022]
Abstract
Non-human primates (NHPs) are phylogenetically close to humans, with many similarities in terms of physiology, anatomy, immunology, as well as neurology, all of which make them excellent experimental models for biomedical research. Compared with developed countries in America and Europe, China has relatively rich primate resources and has continually aimed to develop NHPs resources. Currently, China is a leading producer and a major supplier of NHPs on the international market. However, there are some deficiencies in feeding and management that have hampered China's growth in NHP research and materials. Nonetheless, China has recently established a number of primate animal models for human diseases and achieved marked scientific progress on infectious diseases, cardiovascular diseases, endocrine diseases, reproductive diseases, neurological diseases, and ophthalmic diseases, etc. Advances in these fields via NHP models will undoubtedly further promote the development of China's life sciences and pharmaceutical industry, and enhance China's position as a leader in NHP research. This review covers the current status of NHPs in China and other areas, highlighting the latest developments in disease models using NHPs, as well as outlining basic problems and proposing effective countermeasures to better utilize NHP resources and further foster NHP research in China.
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Affiliation(s)
- Xiao-Liang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming Yunnan 650500, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Xin-Tian Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jia-Li Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China;Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming Yunnan 650500, China.
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143
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Effects of different NS genes of avian influenza viruses and amino acid changes on pathogenicity of recombinant A/Puerto Rico/8/34 viruses. Vet Microbiol 2014; 175:17-25. [PMID: 25480165 DOI: 10.1016/j.vetmic.2014.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/04/2014] [Accepted: 11/07/2014] [Indexed: 11/21/2022]
Abstract
To examine the effects of the NS1 and NEP genes of avian influenza viruses (AIVs) on pathogenicity in mice, we generated recombinant PR8 viruses containing 3 different NS genes of AIVs. In contrast to the reverse genetics-generated PR8 (rPR8) strain and other recombinant viruses, the recombinant virus rPR8-NS(0028), which contained the NS gene of A/chicken/KBNP-0028/2000 (H9N2) (0028), was non-pathogenic to mice. The novel single mutations of 0028 NS1 to corresponding amino acid of PR8 NS1, G139D and S151T increased the pathogenicity of rPR8-NS(0028). The replacement of the PL motifs (EPEV or RSEV) of pathogenic recombinant viruses with that of 0028 (GSEV) did not reduce the pathogenicity of the viruses. However, a recombinant virus with an EPEV-grafted 0028 NS gene was more pathogenic than rPR8-NS(0028) but less than rPR8. The lower pathogenicity of rPR8-NS(0028) might be associated with the lower virus titer and IFN-β level in the lungs of infected mice, and be attributed to G139, S151 and GSEV-PL motif of NS1 gene of 0028. In conclusion we defined new amino acid residues of NS1 related to mice pathogenicity and the presence of pathogenic NS genes among low pathogenic AIVs may encourage continuous monitoring of their mammalian pathogenicity.
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144
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He S, Shi J, Qi X, Huang G, Chen H, Lu C. Lethal infection by a novel reassortant H5N1 avian influenza A virus in a zoo-housed tiger. Microbes Infect 2014; 17:54-61. [PMID: 25461468 DOI: 10.1016/j.micinf.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/22/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
In early 2013, a Bengal tiger (Panthera tigris) in a zoo died of respiratory distress. All specimens from the tiger were positive for HPAI H5N1, which were detected by real-time PCR, including nose swab, throat swab, tracheal swab, heart, liver, spleen, lung, kidney, aquae pericardii and cerebrospinal fluid. One stain of virus, A/Tiger/JS/1/2013, was isolated from the lung sample. Pathogenicity experiments showed that the isolate was able to replicate and cause death in mice. Phylogenetic analysis indicated that HA and NA of A/Tiger/JS/1/2013 clustered with A/duck/Vietnam/OIE-2202/2012 (H5N1), which belongs to clade 2.3.2.1. Interestingly, the gene segment PB2 shared 98% homology with A/wild duck/Korea/CSM-28/20/2010 (H4N6), which suggested that A/Tiger/JS/1/2013 is a novel reassortant H5N1 subtype virus. Immunohistochemical analysis also confirmed that the tiger was infected by this new reassortant HPAI H5N1 virus. Overall, our results showed that this Bengal tiger was infected by a novel reassortant H5N1, suggesting that the H5N1 virus can successfully cross species barriers from avian to mammal through reassortment.
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Affiliation(s)
- Shang He
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing 210095, China
| | - Jianzhong Shi
- Division of Animal Influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China
| | - Xian Qi
- Institute of the Prevention of Acute Disease, Jiangsu Province Center for Disease Control and Prevention, Nanjing 210009, China
| | - Guoqing Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Hualan Chen
- Division of Animal Influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150009, China
| | - Chengping Lu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China; OIE Reference Laboratory for Swine Streptococcosis, Nanjing 210095, China.
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145
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Complete Genome Sequences of H3N2 Canine Influenza Virus with the Matrix Gene from the Pandemic A/H1N1 Virus. GENOME ANNOUNCEMENTS 2014; 2:2/5/e01010-14. [PMID: 25278543 PMCID: PMC4183887 DOI: 10.1128/genomea.01010-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We analyzed the complete genome sequence containing the 3' and 5' noncoding regions (NCRs) of H3N2 canine influenza virus (CIV) with the matrix gene from the pandemic A/H1N1 virus, which will provide a better understanding of the pathogenesis, transmission, and evolution of variant CIV.
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146
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Marc D. Influenza virus non-structural protein NS1: interferon antagonism and beyond. J Gen Virol 2014; 95:2594-2611. [PMID: 25182164 DOI: 10.1099/vir.0.069542-0] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1.
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Affiliation(s)
- Daniel Marc
- Université François Rabelais, UMR1282 Infectiologie et Santé Publique, 37000 Tours, France.,Pathologie et Immunologie Aviaire, INRA, UMR1282 Infectiologie et Santé Publique, 37380 Nouzilly, France
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147
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Strayer DR, Carter WA, Stouch BC, Stittelaar KJ, Thoolen RJMM, Osterhaus ADME, Mitchell WM. Protection from pulmonary tissue damage associated with infection of cynomolgus macaques by highly pathogenic avian influenza virus (H5N1) by low dose natural human IFN-α administered to the buccal mucosa. Antiviral Res 2014; 110:175-80. [PMID: 25111905 PMCID: PMC7113766 DOI: 10.1016/j.antiviral.2014.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 07/02/2014] [Accepted: 07/17/2014] [Indexed: 11/20/2022]
Abstract
Highly pathogenic avian influenza viruses cause extensive pulmonary damage. A low dose oral formulation of natural human interferon-α (Alferon LDO) inhibits H5N1 induced pulmonary damage. All fatal human cases of H5N1 exhibit Acute Respiratory Disease Syndrome (ARDS). Emerging highly pathogenic avian influenza viruses (H5N1, H7N9, and others) are a major pandemic threat. Similar results have been observed with type-1 IFN amelioration of pulmonary damage with SARS-CoV.
Using an established nonhuman primate model for H5N1 highly pathogenic influenza virus infection in humans, we have been able to demonstrate the prophylactic mitigation of the pulmonary damage characteristic of human fatal cases from primary influenza virus pneumonia with a low dose oral formulation of a commercially available parenteral natural human interferon alpha (Alferon N Injection®). At the highest oral dose (62.5 IU/kg body weight) used there was a marked reduction in the alveolar inflammatory response with minor evidence of alveolar and interstitial edema in contrast to the hemorrhage and inflammatory response observed in the alveoli of control animals. The mitigation of severe damage to the lower pulmonary airway was observed without a parallel reduction in viral titers. Clinical trial data will be necessary to establish its prophylactic human efficacy for highly pathogenic influenza viruses.
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Affiliation(s)
- David R Strayer
- Hemispherx Biopharma, Inc., Philadelphia, PA 19103, United States
| | - William A Carter
- Hemispherx Biopharma, Inc., Philadelphia, PA 19103, United States
| | - Bruce C Stouch
- B.C.S. Consulting, Newtown Square, PA 19073, United States
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148
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Shoham D. The Eurasian genes of the 2009 pandemic influenza virus: an integrative perspective on their conveyance to and assimilation in America. Crit Rev Microbiol 2014; 42:222-32. [PMID: 25058514 DOI: 10.3109/1040841x.2014.920291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The formation of pandemic influenza genotypes varied phylogeographically and ecophylogenetically throughout their fully recognized recent 100-years natural history, involving consistently avian plus human genes, and at times swine genes. The last four traceable pandemic strains (PSs) included two American H1N1 viruses with genomes predominantly containing swine genes, of which at least one genome originated from both America and Eurasia; and two non-H1N1 Asian viruses with genomes entirely originating from Asia, and having no swine genes. This study explores whether there is a particular interhemispheric system underlying such divergence, and its properties. Unlike the assumption that transport of live pigs from Eurasia to America facilitated the formation of the 2009 H1N1 PS in America, it is suggested that conveyance of Eurasian swine genes to America, and their assimilation therein, took place through a distinct, perfectly natural ecophylogenetic machinery. The latter conjunctively involves, foremost, a native Asian duck-swine-man interface, a Holarctic chain of certain migratory Anas ducks, a native American turkey-swine-man interface, and two specific clades of American influenza A viruses. Likewise, the described machinery could have readily given rise to the 1918 H1N1, and, presumably, earlier American PSs, altogether constituting private cases of a much broader, self-sustained, permanent phylogeographic system.
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Affiliation(s)
- Dany Shoham
- a Begin-Sadat Center for Strategic Studies, Bar-Ilan University , Ramat-Gan , Israel
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149
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Wei K, Chen Y, Lin Y, Pan Y. Genetic dynamic analysis of the influenza A H5N1 NS1 gene in China. PLoS One 2014; 9:e101384. [PMID: 25003973 PMCID: PMC4086889 DOI: 10.1371/journal.pone.0101384] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/06/2014] [Indexed: 12/03/2022] Open
Abstract
The direct precursors of the A/Goose/Guangdong/1/1996 (GS/GD) virus lineage and its reassortants have been established geographically and ecologically. To investigate the variation and evolutionary dynamics of H5N1 viruses, whole-genome viral sequences (n = 164) were retrieved from the NCBI Influenza Virus Resource. Here, we present phylogenetic evidence for intrasubtype reassortments among H5N1 viruses isolated from China during 1996–2012. On the basis of phylogenetic analysis, we identified four major groups and further classified the reassortant viruses into three subgroups. Putative mosaic structures were mostly found in the viral ribonucleoprotein (vRNP) complexes and 91.0% (10/11) mosaics were obtained from terrestrial birds. Sequence variability and selection pressure analyses revealed that both surface glycoproteins (HA and NA) and nonstructural protein 1 (NS1) have higher dN/dS ratio and variability than other internal proteins. Furthermore, we detected 47 positively selected sites in genomic segments with the exception of PB2 and M1 genes. Hemagglutinin (HA) and neuraminidase (NA) are considered highly variable due to host immune pressure, however, it is not known what drives NS1 variability. Therefore, we performed a thorough analysis of the genetic variation and selective pressure of NS1 protein (462 available NS1 sequences). We found that most of positively selected sites and variable amino acids were located in the C-terminal effector domain (ED) of NS1. In addition, we focused on the NS1–RNA and NS1–protein interactions that were involved in viral replication mechanisms and host immune response. Transcriptomic analysis of H5N1-infected monkey lungs showed that certain PI3K-related genes were up-regulated.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
| | - Yanhui Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yina Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Yutian Pan
- The Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, China
- * E-mail: (KW); (YP)
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150
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Kandeil A, El-Shesheny R, Maatouq AM, Moatasim Y, Shehata MM, Bagato O, Rubrum A, Shanmuganatham K, Webby RJ, Ali MA, Kayali G. Genetic and antigenic evolution of H9N2 avian influenza viruses circulating in Egypt between 2011 and 2013. Arch Virol 2014; 159:2861-76. [PMID: 24990416 DOI: 10.1007/s00705-014-2118-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/11/2014] [Indexed: 10/25/2022]
Abstract
Avian influenza virus subtype H9N2 has been circulating in the Middle East since the 1990s. For uncertain reasons, H9N2 was not detected in Egyptian farms until the end of 2010. Circulation of H9N2 viruses in Egyptian poultry in the presence of the enzootic highly pathogenic H5N1 subtype adds a huge risk factor to the Egyptian poultry industry. In this study, 22 H9N2 viruses collected from 2011 to 2013 in Egypt were isolated and sequenced. The genomic signatures and protein sequences of these isolates were analyzed. Multiple mammalian-host-associated mutations were detected that favor transmission from avian to mammalian hosts. Other mutations related to virulence were also identified. Phylogenetic data showed that Egyptian H9N2 viruses were closely related to viruses isolated from neighboring Middle Eastern countries, and their HA gene resembled those of viruses of the G1-like lineage. No reassortment was detected with H5N1 subtypes. Serological analysis of H9N2 virus revealed antigenic conservation among Egyptian isolates. Accordingly, continuous surveillance that results in genetic and antigenic characterization of H9N2 in Egypt is warranted.
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Affiliation(s)
- Ahmed Kandeil
- Environmental Research Division, National Research Centre, El-Buhouth Street, Dokki, Giza, 12311, Egypt
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