1
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Alkie TN, Cox S, Embury-Hyatt C, Stevens B, Pople N, Pybus MJ, Xu W, Hisanaga T, Suderman M, Koziuk J, Kruczkiewicz P, Nguyen HH, Fisher M, Lung O, Erdelyan CNG, Hochman O, Ojkic D, Yason C, Bravo-Araya M, Bourque L, Bollinger TK, Soos C, Giacinti J, Provencher J, Ogilvie S, Clark A, MacPhee R, Parsons GJ, Eaglesome H, Gilbert S, Saboraki K, Davis R, Jerao A, Ginn M, Jones MEB, Berhane Y. Characterization of neurotropic HPAI H5N1 viruses with novel genome constellations and mammalian adaptive mutations in free-living mesocarnivores in Canada. Emerg Microbes Infect 2023; 12:2186608. [PMID: 36880345 PMCID: PMC10026807 DOI: 10.1080/22221751.2023.2186608] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The GsGd lineage (A/goose/Guangdong/1/1996) H5N1 virus was introduced to Canada in 2021/2022 through the Atlantic and East Asia-Australasia/Pacific flyways by migratory birds. This was followed by unprecedented outbreaks affecting domestic and wild birds, with spillover into other animals. Here, we report sporadic cases of H5N1 in 40 free-living mesocarnivore species such as red foxes, striped skunks, and mink in Canada. The clinical presentations of the disease in mesocarnivores were consistent with central nervous system infection. This was supported by the presence of microscopic lesions and the presence of abundant IAV antigen by immunohistochemistry. Some red foxes that survived clinical infection developed anti-H5N1 antibodies. Phylogenetically, the H5N1 viruses from the mesocarnivore species belonged to clade 2.3.4.4b and had four different genome constellation patterns. The first group of viruses had wholly Eurasian (EA) genome segments. The other three groups were reassortant viruses containing genome segments derived from both North American (NAm) and EA influenza A viruses. Almost 17 percent of the H5N1 viruses had mammalian adaptive mutations (E627 K, E627V and D701N) in the polymerase basic protein 2 (PB2) subunit of the RNA polymerase complex. Other mutations that may favour adaptation to mammalian hosts were also present in other internal gene segments. The detection of these critical mutations in a large number of mammals within short duration after virus introduction inevitably highlights the need for continually monitoring and assessing mammalian-origin H5N1 clade 2.3.4.4b viruses for adaptive mutations, which potentially can facilitate virus replication, horizontal transmission and posing pandemic risks for humans.
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Affiliation(s)
- Tamiru N Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Sherri Cox
- College of Biological Science, University of Guelph, Guelph, Canada
| | - Carissa Embury-Hyatt
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Brian Stevens
- Canadian Wildlife Health Cooperative, Guelph, Canada
| | - Neil Pople
- Veterinary Diagnostic Services, Manitoba Agriculture, Winnipeg, Canada
| | - Margo J Pybus
- Fish and Wildlife, Alberta Environment and Parks, Edmonton, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Wanhong Xu
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Tamiko Hisanaga
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Matthew Suderman
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Janice Koziuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Peter Kruczkiewicz
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Hoang Hai Nguyen
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Mathew Fisher
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Cassidy N G Erdelyan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Orie Hochman
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, Canada
| | - Carmencita Yason
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, Canada
| | - Trent K Bollinger
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Catherine Soos
- Environment and Climate Change Canada, Saskatoon, Canada
| | | | | | - Sarah Ogilvie
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | - Amanda Clark
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | - Robyn MacPhee
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | - Glen J Parsons
- Nova Scotia Department of Natural Resources and Renewables, Kentville, Canada
| | | | - Sayrah Gilbert
- Wildlife Haven Rehabilitation Centre, Île-des-Chênes, Canada
| | - Kelsey Saboraki
- Fish and Wildlife Branch, Manitoba Natural Resources and Northern Development, Gimli, Canada
| | - Richard Davis
- Fish and Wildlife Branch, Manitoba Natural Resources and Northern Development, Gimli, Canada
| | - Alexandra Jerao
- Office of the Chief Veterinarian, Manitoba Agriculture, Winnipeg, Canada
| | - Matthew Ginn
- Prince Edward Island Department of Environment, Energy and Climate Action, Charlottetown, Canada
| | - Megan E B Jones
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, Canada
- Nova Scotia Department of Natural Resources and Renewables, Kentville, Canada
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, Canada
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2
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Gilbertson B, Duncan M, Subbarao K. Role of the viral polymerase during adaptation of influenza A viruses to new hosts. Curr Opin Virol 2023; 62:101363. [PMID: 37672875 DOI: 10.1016/j.coviro.2023.101363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 09/08/2023]
Abstract
As a group, influenza-A viruses (IAV) infect a wide range of animal hosts, however, they are constrained to infecting selected host species by species-specific interactions between the host and virus, that are required for efficient replication of the viral RNA genome. When IAV cross the species barrier, they acquire mutations in the viral genome to enable interactions with the new host factors, or to compensate for their loss. The viral polymerase genes polymerase basic 1, polymerase basic 2, and polymerase-acidic are important sites of host adaptation. In this review, we discuss why the viral polymerase is so vital to the process of host adaptation, look at some of the known viral mutations, and host factors involved in adaptation, particularly of avian IAV to mammalian hosts.
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Affiliation(s)
- Brad Gilbertson
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Melanie Duncan
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia; WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
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3
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Effect of serial in vivo passages on the adaptation of H1N1 avian influenza virus to pigs. J Vet Res 2022; 66:9-19. [PMID: 35582490 PMCID: PMC8959685 DOI: 10.2478/jvetres-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/02/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction The lack of proofreading activity of the viral polymerase and the segmented nature of the influenza A virus (IAV) genome are responsible for the genetic diversity of IAVs and for their ability to adapt to a new host. We tried to adapt avian IAV (avIAV) to the pig by serial passages in vivo and assessed the occurrence of point mutations and their influence on viral fitness in the pig’s body. Material and Methods A total of 25 in vivo avIAV passages of the A/duck/Bavaria/77 strain were performed by inoculation of 50 piglets, and after predetermined numbers of passages 20 uninoculated piglets were exposed to the virus through contact with inoculated animals. Clinical signs of swine influenza were assessed daily. Nasal swabs and lung tissue were used to detect IAV RNA by real-time RT-PCR and isolates from selected passages were sequenced. Results Apart from a rise in rectal temperature and a sporadic cough, no typical clinical signs were observed in infected pigs. The original strain required 20 passages to improve its replication ability noticeably. A total of 29 amino-acid substitutions were identified. Eighteen of them were detected in the first sequenced isolate, of which 16 were also in all other analysed strains. Additional mutations were detected with more passages. One substitution, threonine (T) 135 to serine (S) in neuraminidase (NA), was only detected in an IAV isolate from a contact-exposed piglet. Conclusion Passaging 25 times allowed us to obtain a partially swine-adapted IAV. The improvement in isolate replication ability was most likely related to S654 to glycine (G) substitution in the basic protein (PB) 1 as well as to aspartic acid (D) 701 to asparagine (N) and arginine (R) 477 to G in PB2, glutamic acid (E) 204 to D and G239E in haemagglutinin and T135S in NA.
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4
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Cárdenas M, Michelson S, Pérez DR, Montoya M, Toledo J, Vásquez-Martínez Y, Cortez-San Martin M. Infectious Salmon Anemia Virus Infectivity Is Determined by Multiple Segments with an Important Contribution from Segment 5. Viruses 2022; 14:v14030631. [PMID: 35337038 PMCID: PMC8954079 DOI: 10.3390/v14030631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious salmon anemia virus (ISAV) is the etiological agent of infectious salmon anemia. It belongs to the genus isavirus, one of the genera of the Orthomyxoviridae family, as does Influenzavirus A. The ISAV genome comprises eight negative-sense single-stranded RNA segments that code for at least 10 proteins. Although some ISAV strains can reach 100% mortality rates, the factors that determine isavirus infectivity remain unknown. However, some studies suggest that segments 5 and 6 are responsible for the different degrees of virulence and infectivity among ISAV subtypes, unlike the influenza A virus, where most segments are involved in the virus infectivity. In this work, synthetic reassortant viruses for the eight segments of ISAV were generated by reverse genetics, combining a highly virulent virus, ISAV 752_09 (HPR7b), and an avirulent strain, SK779/06 (HPR0). We characterized the rescued viruses and their capacity to replicate and infect different cell lines, produce plaques in ASK cells, and their ability to induce and modulate the cellular immune response in vitro. Our results show that the majority of ISAV segments are involved in at least one of the analyzed characteristics, segment 5 being one of the most important, allowing HPR0 viruses, among other things, to produce plaques and replicate in CHSE-214 cells. We determined that segments 5 and 6 participate in different stages of the viral cycle, and their compatibility is critical for viral infection. Additionally, we demonstrated that segment 2 can modulate the cellular immune response. Our results indicate a high degree of genetic compatibility between the genomic segments of HPR7b and HPR0, representing a latent risk of reassortant that would give rise to a new virus with an unknown phenotype.
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Affiliation(s)
- Matías Cárdenas
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (M.C.); (S.M.); (Y.V.-M.)
- Poultry Diagnostic and Research Center, Department of Population Health, University of Georgia, Athens, GE 30602, USA;
| | - Sofía Michelson
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (M.C.); (S.M.); (Y.V.-M.)
| | - Daniel R. Pérez
- Poultry Diagnostic and Research Center, Department of Population Health, University of Georgia, Athens, GE 30602, USA;
| | - Margarita Montoya
- Cell Biochemistry Laboratory, Department of Biology, Faculty of Chemistry and Biology, University of Santiago, Santiago 9170022, Chile;
| | - Jorge Toledo
- Biotechnology and Biopharmaceutical Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4070386, Chile;
| | - Yesseny Vásquez-Martínez
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (M.C.); (S.M.); (Y.V.-M.)
- Programa Centro de Investigaciones Biomédicas Aplicadas, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago, Santiago 9170022, Chile
| | - Marcelo Cortez-San Martin
- Molecular Virology and Pathogen Control Laboratory, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile; (M.C.); (S.M.); (Y.V.-M.)
- Correspondence:
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5
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Yu M, Sun L, Zhang Z, Zhang Y, Zhang H, Na L, Wang X. KPNA6 is a Cofactor of ANP32A/B in Supporting Influenza Virus Polymerase Activity. Microbiol Spectr 2022; 10:e0207321. [PMID: 35044222 PMCID: PMC8768627 DOI: 10.1128/spectrum.02073-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Influenza A virus (IAV) RNA-dependent RNA polymerase (vPol) is a heterotrimer composed of PB2, PB1, and PA, which, together with vRNA and nucleoprotein (NP), forms viral ribonucleoprotein (vRNP) complex to direct the transcription and replication of the viral genome. Host factor ANP32 proteins have been proved to be associated with vRNP and are essential for polymerase activity and cross-species restriction of avian influenza virus. However, the molecular mechanism by which ANP32 supports polymerase activity is largely unknown. Here, we identified that KPNA6 is associated with ANP32A/B and vRNP of the influenza virus. Both knockout and overexpression of KPNA6 downregulate the replication of the influenza virus by inhibiting the polymerase activity, indicating that a certain level of KPNA6 is beneficial for efficient replication of the influenza virus. Furthermore, we demonstrate that overexpression of KPNA6 or its nuclear importing domain negative mutation inhibited the interaction between ANP32 and vRNP, thus reducing the polymerase activity. Our results revealed the role of KPNA6 in interacting with both ANP32A/B and vRNP to maintain viral polymerase activity and provided new insights for further understanding of the mechanism by which ANP32 supports influenza polymerase. IMPORTANCE Host factor ANP32 plays a fundamental role in supporting the polymerase activity of influenza viruses, but the underlying mechanism is largely unknown. Here, we propose that KPNA6 is involved in the function of ANP32A/B to support influenza virus polymerase by interacting with both vRNP and ANP32A/B. The proper amount of KPNA6 and ANP32 proteins in the KPNA6-ANP32-vRNP complex is crucial for maintaining the viral polymerase activity. The KPNA6 may contribute to maintaining stable interaction between vRNA and ANP32 proteins in the nucleus, and this function is independent of the known importing domain of KPNA6. Our research reveals a role of KNPA6 associated with ANP32 proteins that support the viral polymerase and suggests a new perspective for developing antiviral strategies.
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Affiliation(s)
- Mengmeng Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Liuke Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhenyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Haili Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lei Na
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
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6
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Yeo JY, Gan SKE. Peering into Avian Influenza A(H5N8) for a Framework towards Pandemic Preparedness. Viruses 2021; 13:2276. [PMID: 34835082 PMCID: PMC8622263 DOI: 10.3390/v13112276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
2014 marked the first emergence of avian influenza A(H5N8) in Jeonbuk Province, South Korea, which then quickly spread worldwide. In the midst of the 2020-2021 H5N8 outbreak, it spread to domestic poultry and wild waterfowl shorebirds, leading to the first human infection in Astrakhan Oblast, Russia. Despite being clinically asymptomatic and without direct human-to-human transmission, the World Health Organization stressed the need for continued risk assessment given the nature of Influenza to reassort and generate novel strains. Given its promiscuity and easy cross to humans, the urgency to understand the mechanisms of possible species jumping to avert disastrous pandemics is increasing. Addressing the epidemiology of H5N8, its mechanisms of species jumping and its implications, mutational and reassortment libraries can potentially be built, allowing them to be tested on various models complemented with deep-sequencing and automation. With knowledge on mutational patterns, cellular pathways, drug resistance mechanisms and effects of host proteins, we can be better prepared against H5N8 and other influenza A viruses.
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Affiliation(s)
- Joshua Yi Yeo
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, EDDC-BII, Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore;
- APD SKEG Pte Ltd., Singapore 439444, Singapore
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7
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Staller E, Barclay WS. Host Cell Factors That Interact with Influenza Virus Ribonucleoproteins. Cold Spring Harb Perspect Med 2021; 11:a038307. [PMID: 32988980 PMCID: PMC8559542 DOI: 10.1101/cshperspect.a038307] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Influenza viruses hijack host cell factors at each stage of the viral life cycle. After host cell entry and endosomal escape, the influenza viral ribonucleoproteins (vRNPs) are released into the cytoplasm where the classical cellular nuclear import pathway is usurped for nuclear translocation of the vRNPs. Transcription takes place inside the nucleus at active host transcription sites, and cellular mRNA export pathways are subverted for export of viral mRNAs. Newly synthesized RNP components cycle back into the nucleus using various cellular nuclear import pathways and host-encoded chaperones. Replication of the negative-sense viral RNA (vRNA) into complementary RNA (cRNA) and back into vRNA requires complex interplay between viral and host factors. Progeny vRNPs assemble at the host chromatin and subsequently exit from the nucleus-processes orchestrated by sets of host and viral proteins. Finally, several host pathways appear to play a role in vRNP trafficking from the nuclear envelope to the plasma membrane for egress.
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Affiliation(s)
- Ecco Staller
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
| | - Wendy S Barclay
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, St. Mary's Campus, London W2 1NY, United Kingdom
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8
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Massari S, Desantis J, Nizi MG, Cecchetti V, Tabarrini O. Inhibition of Influenza Virus Polymerase by Interfering with Its Protein-Protein Interactions. ACS Infect Dis 2021; 7:1332-1350. [PMID: 33044059 PMCID: PMC8204303 DOI: 10.1021/acsinfecdis.0c00552] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza (flu) virus is a serious threat to global health with the potential to generate devastating pandemics. The availability of broad spectrum antiviral drugs is an unequaled weapon during pandemic events, especially when a vaccine is still not available. One of the most promising targets for the development of new antiflu therapeutics is the viral RNA-dependent RNA polymerase (RdRP). The assembly of the flu RdRP heterotrimeric complex from the individual polymerase acidic protein (PA), polymerase basic protein 1 (PB1), and polymerase basic protein 2 (PB2) subunits is a prerequisite for RdRP functions, such as mRNA synthesis and genome replication. In this Review, we report the known protein-protein interactions (PPIs) occurring by RdRP that could be disrupted by small molecules and analyze their benefits and drawbacks as drug targets. An overview of small molecules able to interfere with flu RdRP functions exploiting the PPI inhibition approach is described. In particular, an update on the most recent inhibitors targeting the well-consolidated RdRP PA-PB1 subunit heterodimerization is mainly reported, together with pioneer inhibitors targeting other virus-virus or virus-host interactions involving RdRP subunits. As demonstrated by the PA-PB1 interaction inhibitors discussed herein, the inhibition of flu RdRP functions by PPI disrupters clearly represents a valid means to identify compounds endowed with a broad spectrum of action and a reduced propensity to develop drug resistance, which are the main issues of antiviral drugs.
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Affiliation(s)
- Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Jenny Desantis
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Maria Giulia Nizi
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
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9
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Mammalian cells use the autophagy process to restrict avian influenza virus replication. Cell Rep 2021; 35:109213. [PMID: 34107256 DOI: 10.1016/j.celrep.2021.109213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/07/2021] [Accepted: 05/12/2021] [Indexed: 01/06/2023] Open
Abstract
Host adaptive mutations in the influenza A virus (IAV) PB2 protein are critical for human infection, but their molecular action is not well understood. We observe that when IAV containing avian PB2 infects mammalian cells, viral ribonucleoprotein (vRNP) aggregates that localize to the microtubule-organizing center (MTOC) are formed. These vRNP aggregates resemble LC3B-associated autophagosome structures, with aggresome-like properties, in that they cause the re-distribution of vimentin. However, electron microscopy reveals that these aggregates represent an accumulation of autophagic vacuoles. Compared to mammalian-PB2 virus, avian-PB2 virus induces higher autophagic flux in infected cells, indicating an increased rate of autophagosomes containing avian vRNPs fusing with lysosomes. We found that p62 is essential for the formation of vRNP aggregates and that the Raptor-interacting region of p62 is required for interaction with vRNPs through the PB2 polymerase subunit. Selective autophagic sequestration during late-stage virus replication is thus an additional strategy for host restriction of avian-PB2 IAV.
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10
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Xie Q, Wang W, Li L, Kan Q, Fu H, Geng T, Li T, Wan Z, Gao W, Shao H, Qin A, Ye J. Domain in Fiber-2 interacted with KPNA3/4 significantly affects the replication and pathogenicity of the highly pathogenic FAdV-4. Virulence 2021; 12:754-765. [PMID: 33616472 PMCID: PMC7901544 DOI: 10.1080/21505594.2021.1888458] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The outbreaks of hepatitis-hydropericardium syndrome (HPS) caused by the highly pathogenic serotype 4 fowl adenovirus (FAdV-4) have caused a huge economic loss to the poultry industry globally since 2013. Although the Fiber-2 has been identified as a key virulent related factor for FAdV-4, little is known about its molecular basis. In this study, we identified the efficient interaction of the Fiber-2 with the karyopherin alpha 3/4 (KPNA3/4) protein via its N-terminus of 1–40aa. The analysis of the overexpression and knockout of KPNA3/4 showed that KPNA3/4 could efficiently assist the replication of FAdV-4. Moreover, a fiber-2-edited virus FAV-4_Del with a deletion of 7–40aa in Fiber-2 was rescued through the CRISPR-Cas9 technique. In comparison with the wild type FAdV-4, FAV-4_Del was highly attenuated in vitro and in vivo. Notably, the inoculation of FAV-4_Del in chickens could provide full protection against the lethal challenge with the wild type FAdV-4. All these findings not only give novel insights into the molecular basis for the pathogenesis of Fiber-2 but also provide efficient targets for developing antiviral strategies and live-attenuated vaccine candidates against the highly pathogenic FAdV-4.
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Affiliation(s)
- Quan Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Weikang Wang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Luyuan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Qiuqi Kan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Hui Fu
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University , Yangzhou, China
| | - Tuofan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Zhimin Wan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Wei Gao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University , Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, China.,Institutes of Agricultural Science and Technology Development, Yangzhou University , Yangzhou, China
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11
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Liu WJ, Li J, Zou R, Pan J, Jin T, Li L, Liu P, Zhao Y, Yu X, Wang H, Liu G, Jiang H, Bi Y, Liu L, Yuen KY, Liu Y, Gao GF. Dynamic PB2-E627K substitution of influenza H7N9 virus indicates the in vivo genetic tuning and rapid host adaptation. Proc Natl Acad Sci U S A 2020; 117:23807-23814. [PMID: 32873642 PMCID: PMC7519270 DOI: 10.1073/pnas.2013267117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Avian-origin influenza viruses overcome the bottleneck of the interspecies barrier and infect humans through the evolution of variants toward more efficient replication in mammals. The dynamic adaptation of the genetic substitutions and the correlation with the virulence of avian-origin influenza virus in patients remain largely elusive. Here, based on the one-health approach, we retrieved the original virus-positive samples from patients with H7N9 and their surrounding poultry/environment. The specimens were directly deep sequenced, and the subsequent big data were integrated with the clinical manifestations. Unlike poultry/environment-derived samples with the consistent dominance of avian signature 627E of H7N9 polymerase basic protein 2 (PB2), patient specimens had diverse ratios of mammalian signature 627K, indicating the rapid dynamics of H7N9 adaptation in patients during the infection process. In contrast, both human- and poultry/environment-related viruses had constant dominance of avian signature PB2-701D. The intrahost dynamic adaptation was confirmed by the gradual replacement of 627E by 627K in H7N9 in the longitudinally collected specimens from one patient. These results suggest that host adaptation for better virus replication to new hosts, termed "genetic tuning," actually occurred in H7N9-infected patients in vivo. Notably, our findings also demonstrate the correlation between rapid host adaptation of H7N9 PB2-E627K and the fatal outcome and disease severity in humans. The feature of H7N9 genetic tuning in vivo and its correlation with the disease severity emphasize the importance of testing for the evolution of this avian-origin virus during the course of infection.
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Affiliation(s)
- William J Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Jun Li
- Hangzhou Center for Disease Control and Prevention, 310021 Hangzhou, China
| | - Rongrong Zou
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China
| | - Jingcao Pan
- Hangzhou Center for Disease Control and Prevention, 310021 Hangzhou, China
| | - Tao Jin
- BGI-Shenzhen, 518083 Shenzhen, China
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Peipei Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
| | - Xinfen Yu
- Hangzhou Center for Disease Control and Prevention, 310021 Hangzhou, China
| | - Haoqiu Wang
- Hangzhou Center for Disease Control and Prevention, 310021 Hangzhou, China
| | - Guang Liu
- BGI-Shenzhen, 518083 Shenzhen, China
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Hui Jiang
- BGI-Shenzhen, 518083 Shenzhen, China
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Yuhai Bi
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, 100101 Beijing, China
| | - Lei Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases and the HKU-Shenzhen Hospital, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China;
| | - George F Gao
- Shenzhen Key Laboratory of Pathogen and Immunity, State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, 518112 Shenzhen, China;
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
- Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, 100101 Beijing, China
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12
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Differential Behaviours and Preferential Bindings of Influenza Nucleoproteins on Importins-α. Viruses 2020; 12:v12080834. [PMID: 32751671 PMCID: PMC7472415 DOI: 10.3390/v12080834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Influenza viruses are negative single-stranded RNA viruses with nuclear transcription and replication. They enter the nucleus by using the cellular importin-α/-β nuclear import machinery. Influenza nucleoproteins from influenza A, B, C and D viruses possess a nuclear localization signal (NLS) localized on an intrinsically disordered extremity (NPTAIL). In this paper, using size exclusion chromatography (SEC), SEC-multi-angle laser light scattering (SEC-MALLS) analysis, surface plasmon resonance (SPR) and fluorescence anisotropy, we provide the first comparative study designed to dissect the interaction between the four NPTAILs and four importins-α identified as partners. All interactions between NPTAILs and importins-α have high association and dissociation rates and present a distinct and specific behaviour. D/NPTAIL interacts strongly with all importins-α while B/NPTAIL shows weak affinity for importins-α. A/NPTAIL and C/NPTAIL present preferential importin-α partners. Mutations in B/NPTAIL and D/NPTAIL show a loss of importin-α binding, confirming key NLS residues. Taken together, our results provide essential highlights of this complex translocation mechanism.
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13
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A Single Amino Acid at Position 431 of the PB2 Protein Determines the Virulence of H1N1 Swine Influenza Viruses in Mice. J Virol 2020; 94:JVI.01930-19. [PMID: 31996432 PMCID: PMC7108842 DOI: 10.1128/jvi.01930-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/20/2020] [Indexed: 11/20/2022] Open
Abstract
The frequent reassortment among different influenza viruses in pigs adds complexity to the epidemiology of swine influenza. The diverse viral virulence phenotypes underline the need to investigate the possible genetic determinants for evaluating the pandemic potential to human public health. Here, we found that multiple genotypes of influenza viruses cocirculate in the swine population in Liaoning Province, China. Furthermore, we pinpointed a single amino acid at position 431 in the PB2 protein which plays a critical role in the virulence of H1N1 viruses in mice and found that the alteration of viral polymerase activities is the cause of the different virulence. Our study further indicated that the virulence of influenza virus is a polygenic trait, and the newly identified virulence-related residue in the PB2 provides important information for broadening knowledge on the genetic basis of viral virulence of influenza viruses. Genetic reassortments occurred continuously among multiple subtypes or genotypes of influenza viruses prevalent in pigs. Of note, some reassortant viruses bearing the internal genes of the 2009 pandemic H1N1 (2009/H1N1) virus sporadically caused human infection, which highlights their potential threats to human public health. In this study, we performed phylogenetic analysis on swine influenza viruses (SIVs) circulating in Liaoning Province, China. A total of 22 viruses, including 18 H1N1 and 4 H1N2 viruses, were isolated from 5,750 nasal swabs collected from pigs in slaughterhouses from 2014 to 2016. H1N1 viruses formed four genotypes, which included Eurasian avian-like H1N1 (EA H1N1) and double/triple reassortant H1N1 derived from EA H1N1, 2009/H1N1, and triple reassortant H1N2 (TR H1N2) viruses. H1N1 SIVs with different genotypes and even those within the same genotypes represented different pathogenicities in mice. We further characterized two naturally isolated H1N1 SIVs that had similar viral genomes but differed substantially in their virulence in mice and found that a single amino acid at position 431 in the basic polymerase 2 (PB2) protein significantly affected the viral replication capacity and virulence of these two viruses. Taken together, our findings revealed the diverse genomic origins and virulence of the SIVs prevalent in Liaoning Province during 2014 to 2016, which highlights that continuous surveillance is essential to monitor the evolution of SIVs. We identified a naturally occurring amino acid mutation in the PB2 protein of H1N1 SIVs that impacts the viral replication and virulence in mice by altering the viral polymerase activity. IMPORTANCE The frequent reassortment among different influenza viruses in pigs adds complexity to the epidemiology of swine influenza. The diverse viral virulence phenotypes underline the need to investigate the possible genetic determinants for evaluating the pandemic potential to human public health. Here, we found that multiple genotypes of influenza viruses cocirculate in the swine population in Liaoning Province, China. Furthermore, we pinpointed a single amino acid at position 431 in the PB2 protein which plays a critical role in the virulence of H1N1 viruses in mice and found that the alteration of viral polymerase activities is the cause of the different virulence. Our study further indicated that the virulence of influenza virus is a polygenic trait, and the newly identified virulence-related residue in the PB2 provides important information for broadening knowledge on the genetic basis of viral virulence of influenza viruses.
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14
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Long JS, Mistry B, Haslam SM, Barclay WS. Host and viral determinants of influenza A virus species specificity. Nat Rev Microbiol 2020; 17:67-81. [PMID: 30487536 DOI: 10.1038/s41579-018-0115-z] [Citation(s) in RCA: 318] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza A viruses cause pandemics when they cross between species and an antigenically novel virus acquires the ability to infect and transmit between these new hosts. The timing of pandemics is currently unpredictable but depends on ecological and virological factors. The host range of an influenza A virus is determined by species-specific interactions between virus and host cell factors. These include the ability to bind and enter cells, to replicate the viral RNA genome within the host cell nucleus, to evade host restriction factors and innate immune responses and to transmit between individuals. In this Review, we examine the host barriers that influenza A viruses of animals, especially birds, must overcome to initiate a pandemic in humans and describe how, on crossing the species barrier, the virus mutates to establish new interactions with the human host. This knowledge is used to inform risk assessments for future pandemics and to identify virus-host interactions that could be targeted by novel intervention strategies.
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Affiliation(s)
- Jason S Long
- Department of Medicine, Imperial College London, London, UK
| | - Bhakti Mistry
- Department of Medicine, Imperial College London, London, UK
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Wendy S Barclay
- Department of Medicine, Imperial College London, London, UK.
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15
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Ivan FX, Kwoh CK. Rule-based meta-analysis reveals the major role of PB2 in influencing influenza A virus virulence in mice. BMC Genomics 2019; 20:973. [PMID: 31874643 PMCID: PMC6929465 DOI: 10.1186/s12864-019-6295-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Background Influenza A virus (IAV) poses threats to human health and life. Many individual studies have been carried out in mice to uncover the viral factors responsible for the virulence of IAV infections. Nonetheless, a single study may not provide enough confident about virulence factors, hence combining several studies for a meta-analysis is desired to provide better views. For this, we documented more than 500 records of IAV infections in mice, whose viral proteins could be retrieved and the mouse lethal dose 50 or alternatively, weight loss and/or survival data, was/were available for virulence classification. Results IAV virulence models were learned from various datasets containing aligned IAV proteins and the corresponding two virulence classes (avirulent and virulent) or three virulence classes (low, intermediate and high virulence). Three proven rule-based learning approaches, i.e., OneR, JRip and PART, and additionally random forest were used for modelling. PART models achieved the best performance, with moderate average model accuracies ranged from 65.0 to 84.4% and from 54.0 to 66.6% for the two-class and three-class problems, respectively. PART models were comparable to or even better than random forest models and should be preferred based on the Occam’s razor principle. Interestingly, the average accuracy of the models was improved when host information was taken into account. For model interpretation, we observed that although many sites in HA were highly correlated with virulence, PART models based on sites in PB2 could compete against and were often better than PART models based on sites in HA. Moreover, PART had a high preference to include sites in PB2 when models were learned from datasets containing the concatenated alignments of all IAV proteins. Several sites with a known contribution to virulence were found as the top protein sites, and site pairs that may synergistically influence virulence were also uncovered. Conclusion Modelling IAV virulence is a challenging problem. Rule-based models generated using viral proteins are useful for its advantage in interpretation, but only achieve moderate performance. Development of more advanced approaches that learn models from features extracted from both viral and host proteins shall be considered for future works.
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Affiliation(s)
- Fransiskus Xaverius Ivan
- Biomedical Informatics Lab, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Chee Keong Kwoh
- Biomedical Informatics Lab, School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
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16
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Wasik BR, de Wit E, Munster V, Lloyd-Smith JO, Martinez-Sobrido L, Parrish CR. Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover? Philos Trans R Soc Lond B Biol Sci 2019; 374:20190017. [PMID: 31401954 PMCID: PMC6711314 DOI: 10.1098/rstb.2019.0017] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The critical step in the emergence of a new epidemic or pandemic viral pathogen occurs after it infects the initial spillover host and then is successfully transmitted onwards, causing an outbreak chain of transmission within that new host population. Crossing these choke points sets a pathogen on the pathway to epidemic emergence. While many viruses spill over to infect new or alternative hosts, only a few accomplish this transition—and the reasons for the success of those pathogens are still unclear. Here, we consider this issue related to the emergence of animal viruses, where factors involved likely include the ability to efficiently infect the new animal host, the demographic features of the initial population that favour onward transmission, the level of shedding and degree of susceptibility of individuals of that population, along with pathogen evolution favouring increased replication and more efficient transmission among the new host individuals. A related form of emergence involves mutations that increased spread or virulence of an already-known virus within its usual host. In all of these cases, emergence may be due to altered viral properties, changes in the size or structure of the host populations, ease of transport, climate change or, in the case of arboviruses, to the expansion of the arthropod vectors. Here, we focus on three examples of viruses that have gained efficient onward transmission after spillover: influenza A viruses that are respiratory transmitted, HIV, a retrovirus, that is mostly blood or mucosal transmitted, and canine parvovirus that is faecal:oral transmitted. We describe our current understanding of the changes in the viruses that allowed them to overcome the barriers that prevented efficient replication and spread in their new hosts. We also briefly outline how we could gain a better understanding of the mechanisms and variability in order to better anticipate these events in the future. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
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Affiliation(s)
- Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 9095-7239, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luis Martinez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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17
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Liu X, Yang C, Sun X, Lin X, Zhao L, Chen H, Jin M. Evidence for a novel mechanism of influenza A virus host adaptation modulated by PB2-627. FEBS J 2019; 286:3389-3400. [PMID: 31034753 DOI: 10.1111/febs.14867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/29/2019] [Accepted: 04/26/2019] [Indexed: 12/21/2022]
Abstract
Influenza virus cross-species transmission is restricted by the host, but viruses overcome this restriction by accumulating mutations which allow them to adapt to a new host. Among the many factors which facilitate virus host adaptation, polymerase basic protein 2 (PB2) 627 plays an important role, although the underlying molecular mechanism has not been fully understood. In a previous study, we found that histone H1.2 (encoded by HIST1H1C) regulates human or avian influenza virus replication in different ways, indicating that it might be involved in virus host adaptation. Herein, we found that HIST1H1C expression, phosphorylation and methylation levels are decreased when infected with H1N1 influenza virus and increased when infected with H5N1 influenza virus. Overexpressing the eight gene segments of the influenza virus, we found that only PB2 significantly affects HIST1H1C expression and modifications. Since the 627 site is different between the H5N1 and H1N1 influenza viruses we constructed PB2-627E (avian variant) and PB2-627K (human variant) mutant viruses, and observed that the effects of the wild-type and the mutant viruses on HIST1H1C expression and modifications are the opposite of one another. Further analysis showed that influenza virus PB2-627 regulates HIST1H1C expression via Sp1, and specifically that PB2-627K down-regulates Sp1 and HIST1H1C while PB2-627E up-regulates Sp1 and HIST1H1C. In addition, HIST1H1C can feedback regulate DNA-dependent protein kinase and euchromatic histone-lysine N-methyltransferase 1/2, leading to altered HIST1H1C phosphorylation and methylation levels, and affecting influenza virus replication accordingly. In summary, this study illustrates the mechanism of PB2-627E/K-mediated regulation of influenza virus host adaptation.
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Affiliation(s)
- Xiaokun Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Cha Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiaomei Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xian Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Lianzhong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agro-Microbiology Resources Development - Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Animal Disease Diagnosis and Immunization - Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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18
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The structure of the nucleoprotein of Influenza D shows that all Orthomyxoviridae nucleoproteins have a similar NP CORE, with or without a NP TAIL for nuclear transport. Sci Rep 2019; 9:600. [PMID: 30679709 PMCID: PMC6346101 DOI: 10.1038/s41598-018-37306-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023] Open
Abstract
This paper focuses on the nucleoprotein (NP) of the newly identified member of the Orthomyxoviridae family, Influenza D virus. To date several X-ray structures of NP of Influenza A (A/NP) and B (B/NP) viruses and of infectious salmon anemia (ISA/NP) virus have been solved. Here we purified, characterized and solved the X-ray structure of the tetrameric D/NP at 2.4 Å resolution. The crystal structure of its core is similar to NP of other Influenza viruses. However, unlike A/NP and B/NP which possess a flexible amino-terminal tail containing nuclear localization signals (NLS) for their nuclear import, D/NP possesses a carboxy-terminal tail (D/NPTAIL). We show that D/NPTAIL harbors a bipartite NLS and designed C-terminal truncated mutants to demonstrate the role of D/NPTAIL for nuclear transport.
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19
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Structural analysis of the complex between influenza B nucleoprotein and human importin-α. Sci Rep 2017; 7:17164. [PMID: 29215074 PMCID: PMC5719345 DOI: 10.1038/s41598-017-17458-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/27/2017] [Indexed: 12/29/2022] Open
Abstract
Influenza viruses are negative strand RNA viruses that replicate in the nucleus of the cell. The viral nucleoprotein (NP) is the major component of the viral ribonucleoprotein. In this paper we show that the NP of influenza B has a long N-terminal tail of 70 residues with intrinsic flexibility. This tail contains the Nuclear Location Signal (NLS). The nuclear trafficking of the viral components mobilizes cellular import factors at different stages, making these host-pathogen interactions promising targets for new therapeutics. NP is imported into the nucleus by the importin-α/β pathway, through a direct interaction with importin-α isoforms. Here we provide a combined nuclear magnetic resonance and small-angle X-ray scattering (NMR/SAXS) analysis to describe the dynamics of the interaction between influenza B NP and the human importin-α. The NP of influenza B does not have a single NLS nor a bipartite NLS but our results suggest that the tail harbors several adjacent NLS sequences, located between residues 30 and 71.
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20
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Kirby TW, Gassman NR, Smith CE, Zhao ML, Horton JK, Wilson SH, London RE. DNA polymerase β contains a functional nuclear localization signal at its N-terminus. Nucleic Acids Res 2017; 45:1958-1970. [PMID: 27956495 PMCID: PMC5389473 DOI: 10.1093/nar/gkw1257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/02/2016] [Indexed: 12/23/2022] Open
Abstract
DNA polymerase β (pol β) requires nuclear localization to fulfil its DNA repair function. Although its small size has been interpreted to imply the absence of a need for active nuclear import, sequence and structural analysis suggests that a monopartite nuclear localization signal (NLS) may reside in the N-terminal lyase domain. Binding of this domain to Importin α1 (Impα1) was confirmed by gel filtration and NMR studies. Affinity was quantified by fluorescence polarization analysis of a fluorescein-tagged peptide corresponding to pol β residues 2–13. These studies indicate high affinity binding, characterized by a low micromolar Kd, that is selective for the murine Importin α1 (mImpα1) minor site, with the Kd strengthening to ∼140 nM for the full lyase domain (residues 2–87). A further reduction in Kd obtains in binding studies with human Importin α5 (hImpα5), which in some cases has been demonstrated to bind small domains connected to the NLS. The role of this NLS was confirmed by fluorescent imaging of wild-type and NLS-mutated pol β(R4S,K5S) in mouse embryonic fibroblasts lacking endogenous pol β. Together these data demonstrate that pol β contains a specific NLS sequence in the N-terminal lyase domain that promotes transport of the protein independent of its interaction partners. Active nuclear uptake allows development of a nuclear/cytosolic concentration gradient against a background of passive diffusion.
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Affiliation(s)
- Thomas W Kirby
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Natalie R Gassman
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cassandra E Smith
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ming-Lang Zhao
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert E London
- National Institute of Environmental Health Sciences, Genome Integrity and Structural Biology Laboratory, National Institutes of Health, Research Triangle Park, NC 27709, USA
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21
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Zhao M, Wang L, Li S. Influenza A Virus-Host Protein Interactions Control Viral Pathogenesis. Int J Mol Sci 2017; 18:ijms18081673. [PMID: 28763020 PMCID: PMC5578063 DOI: 10.3390/ijms18081673] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/20/2022] Open
Abstract
The influenza A virus (IAV), a member of the Orthomyxoviridae family, is a highly transmissible respiratory pathogen and represents a continued threat to global health with considerable economic and social impact. IAV is a zoonotic virus that comprises a plethora of strains with different pathogenic profiles. The different outcomes of viral pathogenesis are dependent on the engagement between the virus and the host cellular protein interaction network. The interactions may facilitate virus hijacking of host molecular machinery to fulfill the viral life cycle or trigger host immune defense to eliminate the virus. In recent years, much effort has been made to discover the virus–host protein interactions and understand the underlying mechanisms. In this paper, we review the recent advances in our understanding of IAV–host interactions and how these interactions contribute to host defense and viral pathogenesis.
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Affiliation(s)
- Mengmeng Zhao
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Lingyan Wang
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Shitao Li
- 156 McElroy Hall, Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
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22
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Li J, Zheng W, Hou L, Chen C, Fan W, Qu H, Jiang J, Liu J, Gao GF, Zhou J, Sun L, Liu W. Differential nucleocytoplasmic shuttling of the nucleoprotein of influenza a viruses and association with host tropism. Cell Microbiol 2016; 19. [DOI: 10.1111/cmi.12692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 10/13/2016] [Accepted: 11/02/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
| | - Weinan Zheng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
| | - Lidan Hou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- China Institute of Veterinary Drug Control; Beijing China
| | - Can Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
| | - Hongren Qu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
| | - Jingwen Jiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- School of Life Sciences; University of Science and Technology of China; Hefei China
| | - Jinhua Liu
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine; China Agricultural University; Beijing China
| | - George F. Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing China
- Office of Director-General; Chinese Center for Disease Control and Prevention; Beijing China
| | - Jiyong Zhou
- College of Veterinary Medicine; Nanjing Agricultural University; Nanjing China
| | - Lei Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology; Institute of Microbiology, Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
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Delaforge E, Milles S, Huang JR, Bouvier D, Jensen MR, Sattler M, Hart DJ, Blackledge M. Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions. Front Mol Biosci 2016; 3:54. [PMID: 27679800 PMCID: PMC5020063 DOI: 10.3389/fmolb.2016.00054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered linkers provide multi-domain proteins with degrees of conformational freedom that are often essential for function. These highly dynamic assemblies represent a significant fraction of all proteomes, and deciphering the physical basis of their interactions represents a considerable challenge. Here we describe the difficulties associated with mapping the large-scale domain dynamics and describe two recent examples where solution state methods, in particular NMR spectroscopy, are used to investigate conformational exchange on very different timescales.
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Affiliation(s)
- Elise Delaforge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Sigrid Milles
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Jie-Rong Huang
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Denis Bouvier
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum MünchenNeuherberg, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR, Technische Universität MünchenGarching, Germany
| | - Darren J Hart
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale, CEA, Centre National de la Recherche Scientifique, University Grenoble Alpes Grenoble, France
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Chen GW, Kuo SM, Yang SL, Gong YN, Hsiao MR, Liu YC, Shih SR, Tsao KC. Genomic Signatures for Avian H7N9 Viruses Adapting to Humans. PLoS One 2016; 11:e0148432. [PMID: 26845764 PMCID: PMC4742285 DOI: 10.1371/journal.pone.0148432] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/18/2016] [Indexed: 11/19/2022] Open
Abstract
An avian influenza A H7N9 virus emerged in March 2013 and caused a remarkable number of human fatalities. Genome variability in these viruses may provide insights into host adaptability. We scanned over 140 genomes of the H7N9 viruses isolated from humans and identified 104 positions that exhibited seven or more amino acid substitutions. Approximately half of these substitutions were identified in the influenza ribonucleoprotein (RNP) complex. Although PB2 627K of the avian virus promotes replication in humans, 45 of the 147 investigated PB2 sequences retained the E signature at this position, which is an avian characteristic. We discovered 10 PB2 substitutions that covaried with K627E. An RNP activity assay showed that Q591K, D701N, and M535L restored the polymerase activity in human cells when 627K transformed to an avian-like E. Genomic analysis of the human-isolated avian influenza virus is crucial in assessing genome variability, because relationships between position-specific variations can be observed and explored. In this study, we observed alternative positions that can potentially compensate for PB2 627K, a well-known marker for cross-species infection. An RNP assay suggested Q591K, D701N, and M535L as potential markers for an H7N9 virus capable of infecting humans.
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Affiliation(s)
- Guang-Wu Chen
- Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- * E-mail: (GWC); (KCT)
| | - Shu-Ming Kuo
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shu-Li Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Nong Gong
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Mei-Ren Hsiao
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Chun Liu
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- * E-mail: (GWC); (KCT)
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Shin WJ, Nam KY, Kim ND, Kim SH, No KT, Seong BL. Identification of a Small Benzamide Inhibitor of Influenza Virus Using a Cell-Based Screening. Chemotherapy 2016; 61:159-66. [PMID: 26821172 DOI: 10.1159/000441941] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND The zoonotic transmission of highly pathogenic avian influenza viruses and the global pandemic of H1N1 influenza in 2009 signified the need for a wider coverage of therapeutic options for the control of influenza. METHODS An in-house compound library was screened using a cytopathic effect inhibition assay. Selected hits were then tested in vivo and used as a core skeleton for derivative synthesis. RESULTS The hit compound (BMD-2601505) was effective [50% effective concentration (EC50) of 60-70 μM] in reducing the death rate of cells infected with human influenza A and B viruses as well as avian influenza A virus. Furthermore, BMD-2601505 reduced the weight loss and increased the survival after lethal infection. The compound was further modified to enhance its antiviral potency. Results show that one derivative with bromobenzene moiety was most effective (EC50 of 22-37 μM) against the influenza viruses tested. CONCLUSION We identified a small benzamide compound exhibiting antiviral activity against influenza viruses. The results warrant further evaluation of antiviral activities against drug-resistant influenza isolates.
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26
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Abstract
In this issue of Structure, Pumroy and colleagues have solved the crystal structure of the influenza virus polymerase PB2 C-terminal domain complexed with different Importin αs. Combining molecular dynamics with structural and biochemical data, the so-far elusive basis for selectivity of binding to distinct different importin αs is beginning to become accessible.
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Affiliation(s)
- Gualtiero Alvisi
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - David A Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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27
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Delaforge E, Milles S, Bouvignies G, Bouvier D, Boivin S, Salvi N, Maurin D, Martel A, Round A, Lemke EA, Ringkjøbing Jensen M, Hart DJ, Blackledge M. Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α. J Am Chem Soc 2015; 137:15122-34. [DOI: 10.1021/jacs.5b07765] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Elise Delaforge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Sigrid Milles
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Guillaume Bouvignies
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Denis Bouvier
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
| | - Stephane Boivin
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Damien Maurin
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Anne Martel
- Institut Laue-Langevin, F-38044 Grenoble, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Malene Ringkjøbing Jensen
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
| | - Darren J. Hart
- Univ. Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Martin Blackledge
- Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France
- CEA, DSV, IBS, F-38044 Grenoble, France
- CNRS, IBS, F-38044 Grenoble, France
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28
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Zhu W, Li L, Yan Z, Gan T, Li L, Chen R, Chen R, Zheng Z, Hong W, Wang J, Smith DK, Guan Y, Zhu H, Shu Y. Dual E627K and D701N mutations in the PB2 protein of A(H7N9) influenza virus increased its virulence in mammalian models. Sci Rep 2015; 5:14170. [PMID: 26391278 PMCID: PMC4585756 DOI: 10.1038/srep14170] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/18/2015] [Indexed: 02/05/2023] Open
Abstract
The ongoing avian H7N9 influenza outbreaks in China have caused significant human fatal cases and the virus is becoming established in poultry. Mutations with potential to increase mammalian adaptation have occurred in the polymerase basic protein 2 (PB2) and other viral genes. Here we found that dual 627K and 701N mutations could readily occur during transmission of the virus among ferrets via direct physical contact, and these mutations conferred higher polymerase activity and improved viral replication in mammalian cells, and enhanced virulence in mice. Special attention needs to be paid to patients with such mutations, as these may serve as an indicator of higher virus replication and increased pathogenicity.
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Affiliation(s)
- Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Long Li
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
| | - Zhigang Yan
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
| | - Tanhuan Gan
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Lifeng Li
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Rirong Chen
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Ruidong Chen
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
| | - Zuoyi Zheng
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Wenshan Hong
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
| | - Jia Wang
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - David K. Smith
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Yi Guan
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Huachen Zhu
- Joint Influenza Research Centre, Shantou University Medical College, Shantou, Guangdong
- State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong SAR
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing
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29
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Nuclear Localization of the DNA Repair Scaffold XRCC1: Uncovering the Functional Role of a Bipartite NLS. Sci Rep 2015; 5:13405. [PMID: 26304019 PMCID: PMC4548243 DOI: 10.1038/srep13405] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/17/2015] [Indexed: 12/23/2022] Open
Abstract
We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs of the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior provides a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.
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30
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Caly L, Ghildyal R, Jans DA. Respiratory virus modulation of host nucleocytoplasmic transport; target for therapeutic intervention? Front Microbiol 2015; 6:848. [PMID: 26322040 PMCID: PMC4536372 DOI: 10.3389/fmicb.2015.00848] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/03/2015] [Indexed: 01/02/2023] Open
Abstract
The respiratory diseases caused by rhinovirus, respiratory syncytial virus, and influenza virus represent a large social and financial burden on healthcare worldwide. Although all three viruses have distinctly unique properties in terms of infection and replication, they share the ability to exploit/manipulate the host-cell nucleocytoplasmic transport system in order to replicate effectively and efficiently. This review outlines the various ways in which infection by these viruses impacts on the host nucleocytoplasmic transport system, and examples where inhibition thereof in turn decreases viral replication. The highly conserved nature of the nucleocytoplasmic transport system and the viral proteins that interact with it make this virus–host interface a prime candidate for the development of specific antiviral therapeutics in the future.
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Affiliation(s)
- Leon Caly
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
| | - Reena Ghildyal
- Faculty of ESTeM, University of Canberra, Bruce, ACT Australia
| | - David A Jans
- Nuclear Signaling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
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31
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Nucleocytoplasmic shuttling of influenza A virus proteins. Viruses 2015; 7:2668-82. [PMID: 26008706 PMCID: PMC4452925 DOI: 10.3390/v7052668] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/20/2015] [Indexed: 12/31/2022] Open
Abstract
Influenza viruses transcribe and replicate their genomes in the nuclei of infected host cells. The viral ribonucleoprotein (vRNP) complex of influenza virus is the essential genetic unit of the virus. The viral proteins play important roles in multiple processes, including virus structural maintenance, mediating nucleocytoplasmic shuttling of the vRNP complex, virus particle assembly, and budding. Nucleocytoplasmic shuttling of viral proteins occurs throughout the entire virus life cycle. This review mainly focuses on matrix protein (M1), nucleoprotein (NP), nonstructural protein (NS1), and nuclear export protein (NEP), summarizing the mechanisms of their nucleocytoplasmic shuttling and the regulation of virus replication through their phosphorylation to further understand the regulation of nucleocytoplasmic shuttling in host adaptation of the viruses.
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32
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Chen GW, Gong YN, Shih SR. Influenza A virus plasticity—A temporal analysis of species-associated genomic signatures. J Formos Med Assoc 2015; 114:456-63. [DOI: 10.1016/j.jfma.2015.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 10/23/2022] Open
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33
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Abstract
The human genome encodes seven isoforms of importin α which are grouped into three subfamilies known as α1, α2 and α3. All isoforms share a fundamentally conserved architecture that consists of an N-terminal, autoinhibitory, importin-β-binding (IBB) domain and a C-terminal Arm (Armadillo)-core that associates with nuclear localization signal (NLS) cargoes. Despite striking similarity in amino acid sequence and 3D structure, importin-α isoforms display remarkable substrate specificity in vivo. In the present review, we look at key differences among importin-α isoforms and provide a comprehensive inventory of known viral and cellular cargoes that have been shown to associate preferentially with specific isoforms. We illustrate how the diversification of the adaptor importin α into seven isoforms expands the dynamic range and regulatory control of nucleocytoplasmic transport, offering unexpected opportunities for pharmacological intervention. The emerging view of importin α is that of a key signalling molecule, with isoforms that confer preferential nuclear entry and spatiotemporal specificity on viral and cellular cargoes directly linked to human diseases.
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34
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Molecular determinants for nuclear import of influenza A PB2 by importin α isoforms 3 and 7. Structure 2015; 23:374-84. [PMID: 25599645 DOI: 10.1016/j.str.2014.11.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 11/23/2022]
Abstract
Influenza A virus polymerase subunit PB2 is a major virulence determinant implicated in pathogenicity and host adaptation. During cross-species virus transfer from avian to mammalian cells, PB2 switches specificity from importin α3 to α7. This specificity is not recapitulated in vitro, where PB2 binds all importin α isoforms with comparably high affinity. In this study, we investigated the structure, conformational dynamics, and autoinhibition of importin α isoforms 1, 3, and 7 in complex with PB2. Our data suggest that association of PB2 with α3 and α7 is favored by reduced autoinhibition of these isoforms and by the unique structure of the nuclear localization signal (NLS) domain of PB2. We propose that by recruiting importin α3 or α7 in the absence of importin β, PB2 reduces the complexity of adaptor-mediated import to a pseudo-bimolecular reaction, thereby acquiring a kinetic advantage over classical NLS cargos, which form an import complex only when importin α and β are simultaneously available.
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35
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Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules. Nat Commun 2015; 6:6011. [PMID: 25586196 PMCID: PMC4309443 DOI: 10.1038/ncomms7011] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/02/2014] [Indexed: 01/27/2023] Open
Abstract
General transcription factor TFIID is a cornerstone of RNA polymerase II transcription initiation in eukaryotic cells. How human TFIID-a megadalton-sized multiprotein complex composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs)-assembles into a functional transcription factor is poorly understood. Here we describe a heterotrimeric TFIID subcomplex consisting of the TAF2, TAF8 and TAF10 proteins, which assembles in the cytoplasm. Using native mass spectrometry, we define the interactions between the TAFs and uncover a central role for TAF8 in nucleating the complex. X-ray crystallography reveals a non-canonical arrangement of the TAF8-TAF10 histone fold domains. TAF2 binds to multiple motifs within the TAF8 C-terminal region, and these interactions dictate TAF2 incorporation into a core-TFIID complex that exists in the nucleus. Our results provide evidence for a stepwise assembly pathway of nuclear holo-TFIID, regulated by nuclear import of preformed cytoplasmic submodules.
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36
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Chin AWH, Li OTW, Mok CKP, Ng MKW, Peiris M, Poon LLM. Influenza A viruses with different amino acid residues at PB2-627 display distinct replication properties in vitro and in vivo: revealing the sequence plasticity of PB2-627 position. Virology 2014; 468-470:545-555. [PMID: 25262472 DOI: 10.1016/j.virol.2014.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/23/2014] [Accepted: 09/08/2014] [Indexed: 11/26/2022]
Abstract
Sequence analyses of influenza PB2 sequences indicate that the 627 position almost exclusively contains either lysine (K) or glutamic acid (E), suggesting a high sequence constraint at this genetic marker. Here, we used a site-directed random mutagenesis method to demonstrate that PB2-627 position has a high sequence plasticity. Recombinant viruses carrying various amino acid residues at this position are viable in cell cultures. These PB2-627 mutants showed various polymerase activities and replication kinetics in mammalian and avian cells as well as pathogenicity in mice. Serially passaging these mutants in MDCK cells generated some compensatory PB2 mutations that can restore polymerase activities of the PB2-627 mutants. Of these, PB2-D309N was identified as a novel one. Besides showing that influenza virus can tolerate a wide range of amino acid residues at the PB2-627 position, this study also demonstrates a potential strategy to identify novel mutations that can enhance viral polymerase.
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Affiliation(s)
- Alex W H Chin
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Olive T W Li
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Chris K P Mok
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Miko K W Ng
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Malik Peiris
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong; The HKU-Pasteur Research Pole & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Leo L M Poon
- Centre of Influenza Research & School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong.
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Abstract
The influenza A virus causes a highly contagious respiratory disease that significantly impacts our economy and health. Its replication and transcription is catalyzed by the viral RNA polymerase. This enzyme is also crucial for the virus, because it is involved in the adaptation of zoonotic strains. It is thus of major interest for the development of antiviral therapies and is being intensively studied. In this article, we will discuss recent advances that have improved our knowledge of the structure of the RNA polymerase and how mutations in the polymerase help the virus to spread effectively among new hosts.
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Affiliation(s)
- Thomas M Stubbs
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK ; Babraham Institute, Brabraham Research Campus, Cambridge, CB22 3AT, UK
| | - Aartjan Jw Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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PB2 mutations D701N and S714R promote adaptation of an influenza H5N1 virus to a mammalian host. J Virol 2014; 88:8735-42. [PMID: 24899203 DOI: 10.1128/jvi.00422-14] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Mutation D701N in the PB2 protein is known to play a prominent role in the adaptation of avian influenza A viruses to mammalian hosts. In contrast, little is known about the nearby mutations S714I and S714R, which have been observed in some avian influenza viruses highly pathogenic for mammals. We have generated recombinant H5N1 viruses with PB2 displaying the avian signature 701D or the mammalian signature 701N and serine, isoleucine, and arginine at position 714 and compared them for polymerase activity and virus growth in avian and mammalian cells, as well as for pathogenicity in mice. Mutation D701N led to an increase in polymerase activity and replication efficiency in mammalian cells and in mouse pathogenicity, and this increase was significantly enhanced when mutation D701N was combined with mutation S714R. Stimulation by mutation S714I was less distinct. These observations indicate that PB2 mutation S714R, in combination with the mammalian signature at position 701, has the potential to promote the adaptation of an H5N1 virus to a mammalian host. IMPORTANCE Influenza A/H5N1 viruses are avian pathogens that have pandemic potential, since they are spread over large parts of Asia, Africa, and Europe and are occasionally transmitted to humans. It is therefore of high scientific interest to understand the mechanisms that determine the host specificity and pathogenicity of these viruses. It is well known that the PB2 subunit of the viral polymerase is an important host range determinant and that PB2 mutation D701N plays an important role in virus adaptation to mammalian cells. In the present study, we show that mutation S714R is also involved in adaptation and that it cooperates with D701N in exposing a nuclear localization signal that mediates importin-α binding and entry of PB2 into the nucleus, where virus replication and transcription take place.
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Conserved features of the PB2 627 domain impact influenza virus polymerase function and replication. J Virol 2014; 88:5977-86. [PMID: 24623411 DOI: 10.1128/jvi.00508-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
UNLABELLED Successful replication of influenza virus requires the coordinated expression of viral genes and replication of the genome by the viral polymerase, composed of the subunits PA, PB1, and PB2. Polymerase activity is regulated by both viral and host factors, yet the mechanisms of regulation and how they contribute to viral pathogenicity and tropism are poorly understood. To characterize these processes, we created a series of mutants in the 627 domain of the PB2 subunit. This domain contains a conserved "P[F/P]AAAPP" sequence motif and the well-described amino acid 627, whose identity regulates host range. A lysine present at position 627 in most mammalian viral isolates creates a basic face on the domain surface and confers high-level activity in humans compared to the glutamic acid found at this position in avian isolates. Mutation of the basic face or the P[F/P]AAAPP motif impaired polymerase activity, assembly of replication complexes, and viral replication. Most of these residues are required for general polymerase activity, whereas PB2 K586 and R589 were preferentially required for function in human versus avian cells. Thus, these data identify residues in the 627 domain and other viral proteins that regulate polymerase activity, highlighting the importance of the surface charge and structure of this domain for virus replication and host adaptation. IMPORTANCE Influenza virus faces barriers to transmission across species as it emerges from its natural reservoir in birds to infect mammals. The viral polymerase is an important regulator of this process and undergoes discrete changes to adapt to replication in mammals. Many of these changes occur in the polymerase subunit PB2. Here we describe the systematic analysis of a key region in PB2 that controls species-specific polymerase activity. We report the importance of conserved residues that contribute to the overall charge of the protein as well as those that likely affect protein structure. These findings provide further insight into the molecular events dictating species-specific polymerase function and viral replication.
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Daikoku T, Yoshida Y, Okuda T, Shiraki K. Characterization of Susceptibility Variants of Influenza Virus Grown in the Presence of T-705. J Pharmacol Sci 2014; 126:281-4. [DOI: 10.1254/jphs.14156sc] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Abstract
The influenza A viruses cause yearly epidemics and occasional pandemics of respiratory disease, which constitute a serious health and economic burden. Their genome consists of eight single-stranded, negative-polarity RNAs that associate to the RNA polymerase and many nucleoprotein monomers to form ribonucleoprotein complexes (RNPs). Here, we focus on the organization of these RNPs, as well as on the structure and interactions of its constitutive elements and we discuss the mechanisms by which the RNPs transcribe and replicate the viral genome.
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Aguas R, Ferguson NM. Feature selection methods for identifying genetic determinants of host species in RNA viruses. PLoS Comput Biol 2013; 9:e1003254. [PMID: 24130470 PMCID: PMC3794897 DOI: 10.1371/journal.pcbi.1003254] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 08/20/2013] [Indexed: 12/31/2022] Open
Abstract
Despite environmental, social and ecological dependencies, emergence of zoonotic viruses in human populations is clearly also affected by genetic factors which determine cross-species transmission potential. RNA viruses pose an interesting case study given their mutation rates are orders of magnitude higher than any other pathogen – as reflected by the recent emergence of SARS and Influenza for example. Here, we show how feature selection techniques can be used to reliably classify viral sequences by host species, and to identify the crucial minority of host-specific sites in pathogen genomic data. The variability in alleles at those sites can be translated into prediction probabilities that a particular pathogen isolate is adapted to a given host. We illustrate the power of these methods by: 1) identifying the sites explaining SARS coronavirus differences between human, bat and palm civet samples; 2) showing how cross species jumps of rabies virus among bat populations can be readily identified; and 3) de novo identification of likely functional influenza host discriminant markers. Moving away from genome scan methods used for human GWAS (ultimately inappropriate for the short highly polymorphic genomes of RNA viruses), our work shows the power and potential of multi-class machine learning algorithms in inferring the functional genetic changes associated with phenotypic change (e.g. crossing a species barrier). We show that even distantly related viruses within a viral family share highly conserved genetic signatures of host specificity; reinforce how fitness landscapes of host adaptation are shaped by host phylogeny; and highlight the evolutionary trajectories of RNA viruses in rapid expansion and under great evolutionary pressure. We do so by (for each dataset) unveiling a set of phenotype characteristic mutations which are shown to be functionally relevant, thus providing new insights into phenotypic relationships between RNA viruses. These methods also provide a solid statistical framework with which the degree of host adaptation can be inferred, thus serving as a valuable tool for studying host transition events with particular relevance for emerging infectious diseases. These methods can then serve as rigorous tools of emergence potential assessment, specifically in scenarios where rapid host classification of newly emerging viruses can be more important than identifying putative functional sites.
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Affiliation(s)
- Ricardo Aguas
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Faculty of Medicine, London, United Kingdom
- * E-mail:
| | - Neil M. Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, Faculty of Medicine, London, United Kingdom
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Rusnati M, Chiodelli P, Bugatti A, Urbinati C. Bridging the past and the future of virology: surface plasmon resonance as a powerful tool to investigate virus/host interactions. Crit Rev Microbiol 2013; 41:238-60. [PMID: 24059853 DOI: 10.3109/1040841x.2013.826177] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite decades of antiviral drug research and development, viruses still remain a top global healthcare problem. Compared to eukaryotic cells, viruses are composed by a limited numbers of proteins that, nevertheless, set up multiple interactions with cellular components, allowing the virus to take control of the infected cell. Each virus/host interaction can be considered as a therapeutical target for new antiviral drugs but, unfortunately, the systematic study of a so huge number of interactions is time-consuming and expensive, calling for models overcoming these drawbacks. Surface plasmon resonance (SPR) is a label-free optical technique to study biomolecular interactions in real time by detecting reflected light from a prism-gold film interface. Launched 20 years ago, SPR has become a nearly irreplaceable technology for the study of biomolecular interactions. Accordingly, SPR is increasingly used in the field of virology, spanning from the study of biological interactions to the identification of putative antiviral drugs. From the literature available, SPR emerges as an ideal link between conventional biological experimentation and system biology studies functional to the identification of highly connected viral or host proteins that act as nodal points in virus life cycle and thus considerable as therapeutical targets for the development of innovative antiviral strategies.
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Affiliation(s)
- Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia , Brescia , Italy
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Zhang H, Hale BG, Xu K, Sun B. Viral and host factors required for avian H5N1 influenza A virus replication in mammalian cells. Viruses 2013; 5:1431-46. [PMID: 23752648 PMCID: PMC3717715 DOI: 10.3390/v5061431] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/07/2013] [Accepted: 05/23/2013] [Indexed: 12/18/2022] Open
Abstract
Following the initial and sporadic emergence into humans of highly pathogenic avian H5N1 influenza A viruses in Hong Kong in 1997, we have come to realize the potential for avian influenza A viruses to be transmitted directly from birds to humans. Understanding the basic viral and cellular mechanisms that contribute to infection of mammalian species with avian influenza viruses is essential for developing prevention and control measures against possible future human pandemics. Multiple physical and functional cellular barriers can restrict influenza A virus infection in a new host species, including the cell membrane, the nuclear envelope, the nuclear environment, and innate antiviral responses. In this review, we summarize current knowledge on viral and host factors required for avian H5N1 influenza A viruses to successfully establish infections in mammalian cells. We focus on the molecular mechanisms underpinning mammalian host restrictions, as well as the adaptive mutations that are necessary for an avian influenza virus to overcome them. It is likely that many more viral and host determinants remain to be discovered, and future research in this area should provide novel and translational insights into the biology of influenza virus-host interactions.
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Affiliation(s)
- Hong Zhang
- Molecular Virus Unit, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai 200025, China; E-Mail:
| | - Benjamin G. Hale
- Medical Research Council (MRC), University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow, G11 5JR, Scotland, UK; E-Mail:
| | - Ke Xu
- Molecular Virus Unit, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai 200025, China; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (K.X.); (B.S.); Tel.: +86-21-6385-1929 (K.X.); +86-21-6385-1927 (B.S.); Fax: +86-21-6384-3571 (K.X. and B.S.)
| | - Bing Sun
- Molecular Virus Unit, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Shanghai institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai 200025, China; E-Mail:
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Authors to whom correspondence should be addressed; E-Mails: (K.X.); (B.S.); Tel.: +86-21-6385-1929 (K.X.); +86-21-6385-1927 (B.S.); Fax: +86-21-6384-3571 (K.X. and B.S.)
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Gabriel G, Czudai-Matwich V, Klenk HD. Adaptive mutations in the H5N1 polymerase complex. Virus Res 2013; 178:53-62. [PMID: 23732876 DOI: 10.1016/j.virusres.2013.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 04/04/2013] [Accepted: 05/20/2013] [Indexed: 12/28/2022]
Abstract
Adaptation of the viral polymerase to host factors plays an important role in interspecies transmission of H5N1 viruses. Several adaptive mutations have been identified that, in general, determine not only host range, but also pathogenicity and transmissibility of the virus. The available evidence indicates that most of these mutations are found in the PB2 subunit of the polymerase. Particularly prominent mutations are located in the C-terminal domain of PB2 involving the amino acid exchanges E627K and D701N. Both mutations, that are also responsible for the adaptation of other avian viruses to mammalian hosts, have been described in human H5N1 isolates. In animal models, it could be demonstrated that they enhance pathogenicity in mice and induce contact transmission in guinea pigs. Mutation E627K has also been identified as a determinant of air-borne H5N1 transmission in ferrets. We are only beginning to understand the underlying mechanisms at the molecular level. Thus, mutation D701N promotes importin-α mediated nuclear transport in mammalian cells. Mutation E627K also enhances the replication rate in an importin-α dependent fashion in mammalian cells, yet without affecting nuclear entry of PB2. Numerous other adaptive mutations, some of which compensate for the lack of PB2 E627K, have been observed in PB2 as well as in the polymerase subunit PB1, the nucleoprotein NP, and the nuclear export protein NEP (NS2).
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Affiliation(s)
- Gülsah Gabriel
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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46
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Resa-Infante P, Gabriel G. The nuclear import machinery is a determinant of influenza virus host adaptation. Bioessays 2012; 35:23-7. [DOI: 10.1002/bies.201200138] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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47
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Cellular protein HAX1 interacts with the influenza A virus PA polymerase subunit and impedes its nuclear translocation. J Virol 2012; 87:110-23. [PMID: 23055567 DOI: 10.1128/jvi.00939-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Transcription and replication of the influenza A virus RNA genome occur in the nucleus through the viral RNA-dependent RNA polymerase consisting of PB1, PB2, and PA. Cellular factors that associate with the viral polymerase complex play important roles in these processes. To look for cellular factors that could associate with influenza A virus PA protein, we have carried out a yeast two-hybrid screen using a HeLa cell cDNA library. We identified six cellular proteins that may interact with PA. We focused our study on one of the new PA-interacting proteins, HAX1, a protein with antiapoptotic function. By using glutathione S-transferase pulldown and coimmunoprecipitation assays, we demonstrate that HAX1 specifically interacts with PA in vitro and in vivo and that HAX1 interacts with the nuclear localization signal domain of PA. Nuclear accumulation of PA was increased in HAX1-knockdown cells, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can impede nuclear transport of PA. As a consequence, knockdown of HAX1 resulted in a significant increase in virus yield and polymerase activity in a minigenome assay, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can inhibit influenza A virus propagation. Together, these results not only provide insight into the mechanism underlying nuclear transport of PA but also identify an intrinsic host factor that restricts influenza A virus infection.
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48
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Interferon-inducible protein Mx1 inhibits influenza virus by interfering with functional viral ribonucleoprotein complex assembly. J Virol 2012; 86:13445-55. [PMID: 23015724 DOI: 10.1128/jvi.01682-12] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mx1 is a GTPase that is part of the antiviral response induced by type I and type III interferons in the infected host. It inhibits influenza virus infection by blocking viral transcription and replication, but the molecular mechanism is not known. Polymerase basic protein 2 (PB2) and nucleoprotein (NP) were suggested to be the possible target of Mx1, but a direct interaction between Mx1 and any of the viral proteins has not been reported. We investigated the interplay between Mx1, NP, and PB2 to identify the mechanism of Mx1's antiviral activity. We found that Mx1 inhibits the PB2-NP interaction, and the strength of this inhibition correlated with a decrease in viral polymerase activity. Inhibition of the PB2-NP interaction is an active process requiring enzymatically active Mx1. We also demonstrate that Mx1 interacts with the viral proteins NP and PB2, which indicates that Mx1 protein has a direct effect on the viral ribonucleoprotein complex. In a minireplicon system, avian-like NP from swine virus isolates was more sensitive to inhibition by murine Mx1 than NP from human influenza A virus isolates. Likewise, murine Mx1 displaced avian NP from the viral ribonucleoprotein complex more easily than human NP. The stronger resistance of the A/H1N1 pandemic 2009 virus against Mx1 also correlated with reduced inhibition of the PB2-NP interaction. Our findings support a model in which Mx1 interacts with the influenza ribonucleoprotein complex and interferes with its assembly by disturbing the PB2-NP interaction.
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Caly L, Wagstaff KM, Jans DA. Nuclear trafficking of proteins from RNA viruses: potential target for antivirals? Antiviral Res 2012; 95:202-6. [PMID: 22750233 DOI: 10.1016/j.antiviral.2012.06.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 06/08/2012] [Accepted: 06/21/2012] [Indexed: 10/28/2022]
Abstract
A key aspect of the infectious cycle of many viruses is the transport of specific viral proteins into the host cell nucleus to perturb the antiviral response. Examples include a number of RNA viruses that are significant human pathogens, such as human immunodeficiency virus (HIV)-1, influenza A, dengue, respiratory syncytial virus and rabies, as well agents that predominantly infect livestock, such as Rift valley fever virus and Venezuelan equine encephalitis virus. Inhibiting the nuclear trafficking of viral proteins as a therapeutic strategy offers an attractive possibility, with important recent progress having been made with respect to HIV-1 and dengue. The results validate nuclear protein import as an antiviral target, and suggest the identification and development of nuclear transport inhibitors as a viable therapeutic approach for a range of human and zoonotic pathogenic viruses.
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Affiliation(s)
- Leon Caly
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, VIC, Australia
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50
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Affiliation(s)
- Kalyan Das
- Department of Chemistry and Chemical Biology, Center for Advanced Biotechnology and Medicine, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA.
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