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Fleming-Canepa X, Aldridge JR, Canniff L, Kobewka M, Jax E, Webster RG, Magor KE. Duck innate immune responses to high and low pathogenicity H5 avian influenza viruses. Vet Microbiol 2018; 228:101-111. [PMID: 30593354 DOI: 10.1016/j.vetmic.2018.11.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/28/2022]
Abstract
Ducks are the reservoir host of influenza A viruses, and are permissive for replication of most strains, yet can elicit robust innate immune responses to highly pathogenic strains. Tissue tropism and viral amino acid differences affect virulence, but we have limited knowledge about how viral differences influence the host innate immune response. Here we compare the innate immune response in Pekin ducks to a recombinant highly-pathogenic avian influenza (HPAI) H5N1 virus and a naturally arising attenuated variant of this strain that differs at one amino acid in polymerase A (T515A), as well as ducks infected with two different H5 strains of low pathogenic avian influenza (LPAI). Using qPCR we examined the relative abundance of transcripts for RIG-I and interferon-beta (IFNβ), and downstream interferon stimulated genes (ISGs). The polymerase PA (T515A) mutation did not significantly affect replication in vivo but greatly attenuated host interferon responses. ISG induction was robust for both H5N1 strains, but was three times lower for the PA mutant strain. Low pathogenic viruses elicited detectable induction of RIG-I, IFNβ and ISGs in lung and intestine tissues that correlated with the recovery of viruses from tracheal or cloacal swabs. Several genes in the MAVS signaling pathway were also upregulated by H5N1, which contributed to further amplification of the signal. We also examined hematoxylin-eosin stained tissue sections and observe evidence of lung pathology and splenocyte depletion with both H5N1 viruses at 3 dpi, and recovery by 6 dpi. However, for both H5N1 strains we observed inflammation around neurons in brain, with increased cytokine expression in some individuals. Our findings reveal HPAI H5N1 viruses induced stronger innate immune responses to the infection, while LPAI viruses elicit a milder response.
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Affiliation(s)
- Ximena Fleming-Canepa
- Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jerry R Aldridge
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA; Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lauren Canniff
- Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Michelle Kobewka
- Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Elinor Jax
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, 78315, Germany
| | - Robert G Webster
- Division of Virology, Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katharine E Magor
- Department of Biological Sciences, CW405 Biological Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton, T6G 2E1, Canada.
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Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2. Virology 2016; 496:116-126. [PMID: 27289560 DOI: 10.1016/j.virol.2016.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
To be incorporated into progeny virions, the viral genome must be transported to the inner leaflet of the plasma membrane (PM) and accumulate there. Some viruses utilize lipid components to assemble at the PM. For example, simian virus 40 (SV40) targets the ganglioside GM1 and human immunodeficiency virus type 1 (HIV-1) utilizes phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2]. Recent studies clearly indicate that Rab11-mediated recycling endosomes are required for influenza A virus (IAV) trafficking of vRNPs to the PM but it remains unclear how IAV vRNP localized or accumulate underneath the PM for viral genome incorporation into progeny virions. In this study, we found that the second intrinsically disordered region (IDR2) of NP regulates two binding steps involved in viral genome packaging. First, IDR2 facilitates NP oligomer binding to viral RNA to form vRNP. Secondly, vRNP assemble by interacting with PI(4,5)P2 at the PM via IDR2. These findings suggest that PI(4,5)P2 functions as the determinant of vRNP accumulation at the PM.
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DesRochers BL, Chen RE, Gounder AP, Pinto AK, Bricker T, Linton CN, Rogers CD, Williams GD, Webby RJ, Boon ACM. Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice. Virology 2016; 494:89-99. [PMID: 27105450 DOI: 10.1016/j.virol.2016.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 12/22/2022]
Abstract
Replication and transmission of avian influenza virus in humans poses a pandemic threat. The molecular determinants that facilitate this process are not well understood. We used DBA/2 mice to identify viral factors that mediate the difference in pathogenesis between a virulent (H7N3) and a non-virulent (H7N9) avian influenza virus from North America. In vitro and in vivo characterization of reassortant viruses identified the PB2 and PA polymerase genes as major determinants of H7N3 pathogenesis. Analysis of individual residues in the PB2 and PA genes identified position 358 (E358V) in PB2 and positions 190 (P190S) and 400 (Q400P) in PA that reduced the virulence of H7N3 virus. The E358V and P190S substitutions also caused reduced inflammation after infection. Our results suggest that specific residues in the polymerase proteins PB2 and PA are important for replication and virulence of avian influenza viruses in a mammalian host.
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Affiliation(s)
- Brittany L DesRochers
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Rita E Chen
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Anshu P Gounder
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Amelia K Pinto
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Traci Bricker
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Camille N Linton
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Corianne D Rogers
- Department of Infectious Diseases, St. Jude Children׳s Research Hospital, Memphis, TN 38105, USA
| | - Graham D Williams
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children׳s Research Hospital, Memphis, TN 38105, USA
| | - Adrianus C M Boon
- Departments of Internal Medicine, Molecular Microbiology, and Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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Wu NC, Olson CA, Du Y, Le S, Tran K, Remenyi R, Gong D, Al-Mawsawi LQ, Qi H, Wu TT, Sun R. Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality. PLoS Genet 2015; 11:e1005310. [PMID: 26132554 PMCID: PMC4489113 DOI: 10.1371/journal.pgen.1005310] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 05/28/2015] [Indexed: 12/31/2022] Open
Abstract
Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available. The analysis of sequence conservation is a common approach to identify functional residues within a protein. However, not all functional residues are conserved as natural evolution and species diversification permit continuous innovation of protein functionality through the retention of advantageous mutations. Non-conserved functional residues, which are often species-specific, may not be identified by conventional analysis of sequence conservation despite being biologically important. Here we described a novel approach to identify functional residues within a protein by coupling a high-throughput experimental fitness profiling approach with computational protein modeling. Our methodology is independent of sequence conservation and is applicable to any protein where structural information is available. In this study, we systematically mapped the functional residues on the influenza A PA protein and revealed that non-conserved functional residues are prevalent. Our results not only have significant implication on how functionality evolves during natural evolution, but also highlight the caveats when applying conservation-based approaches to identify functional residues within a protein.
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Affiliation(s)
- Nicholas C. Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - C. Anders Olson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Shuai Le
- Department of Microbiology, Third Military Medical University, Chongqing, 400038, China
| | - Kevin Tran
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Roland Remenyi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Laith Q. Al-Mawsawi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Hangfei Qi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America,
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America,
- AIDS Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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