1
|
Goletic S, Softic A, Omeragic J, Koro-Spahic A, Kapo N, Sabic E, Kasagic D, Goletic T. Molecular characterization and phylogenetic analysis of highly pathogenic H5N1 clade 2.3.4.4b virus in Bosnia and Herzegovina. Front Vet Sci 2023; 10:1255213. [PMID: 37954666 PMCID: PMC10637570 DOI: 10.3389/fvets.2023.1255213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Influenza A virus continues to represent a growing problem affecting mainly birds but with an increasing number of mammal transmission events reported each year. Nevertheless, molecular characterization and phylogenetic analysis of influenza A viruses originating from all confirmed cases have not been systematically performed in all parts of the world. In this study, we investigated a sample originating from a mute swan that died in November 2021 in the northern part of Bosnia and Herzegovina with RT-qPCR and whole genome sequencing using ONT MinION. It was diagnosed as a highly pathogenic Influenza A virus, subtype H5N1 of 2.3.4.4b clade, and phylogenetic analysis revealed high sequence homology with other European HPAI H5N1 sequences at the time. The notable detected mutations in HA (N110S and T139P) and NA genes (H155Y), that facilitate the host specificity shift and enable the resistance to some antiviral drugs respectively, underscore the necessity of virus evolution surveillance. Therefore, the rapid dissemination of information, including virological and molecular data, is essential for the introduction of tailored prevention measures for infected animals, providing clearer insight and better awareness of a potential public health threat.
Collapse
Affiliation(s)
- Sejla Goletic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Adis Softic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Jasmin Omeragic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Amira Koro-Spahic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Naida Kapo
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Emina Sabic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Dragan Kasagic
- PI Veterinary Institute of the Republic of Srpska “Dr Vaso Butozan”, Banja Luka, Bosnia and Herzegovina
| | - Teufik Goletic
- Veterinary Faculty, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| |
Collapse
|
2
|
Mortazavi M, Pirbonyeh N, Javanmardi F, Emami A. Bioinformatics and Structural Analysis of Antigenic Variation in the Hemagglutinin Gene of the Influenza A(H1N1)pdm09 Virus Circulating in Shiraz (2013 to 2015). Microbiol Spectr 2023; 11:e0463022. [PMID: 37436149 PMCID: PMC10433955 DOI: 10.1128/spectrum.04630-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 06/20/2023] [Indexed: 07/13/2023] Open
Abstract
Circulating influenza A virus provided an excellent opportunity to study the adaptation of the influenza A(H1N1)pdm09 virus to the human host. Particularly, due to the availability of sequences taken from isolates, we could monitor amino acid changes and the stability of mutations that occurred in hemagglutinin (HA). HA is crucial to viral infection because it binds to ciliated cell receptors and mediates the fusion of cells and viral membranes; because antibodies that bind to HA may block virus entry to the cell, this protein is subjected to high selective pressure. In this study, the locations of mutations in the structures of mutant HA were analyzed and the three-dimensional (3D) structures of these mutations were modeled in I-TASSER. Also, the location of these mutations was visualized and studied using Swiss PDB Viewer software and the PyMOL Molecular Graphics System. The crystal structure of the HA from A/California/07/2009 (3LZG) was used for further analysis. The new noncovalent bond formations in mutant luciferases were analyzed via WHAT IF and PIC, and protein stability was evaluated in the iStable server. We identified 33 and 23 mutations in A/Shiraz/106/2015 and A/California/07/2009 isolates, respectively; some mutations are located on the antigenic sites of Sa, Sb, Ca1, Ca2, and Cb HA1 and the fusion peptide of HA2. The results show that with the mutation some interactions are lost and new interactions are formed with other amino acids. The results of the free-energy analysis suggested that these new interactions have a destabilizing effect, which needs confirmation experimentally. IMPORTANCE Due to the fact that the mutations that occurred in the influenza virus HA cause the instability of the protein produced by the virus and antigenic changes and the escape of the virus from the immune system, the mutations that occurred in A/Shiraz/1/2013 were investigated in terms of energy level and stability. The mutations located in a globular portion of the HA are S188T, Q191H, S270P, K285Q, and P299L. On the other hand, the E374K, E46K-B, S124N-B, and I321V mutations are located in the stem portion of the HA (HA2). The change V252L mutation eliminates interactions with Ala181, Phe147, Leu151, and Trp153 and forms new interactions with Gly195, Asn264, Phe161, Met244, Tyr246, Leu165, and Trp167 which can change the stability of the HA structure. The K166Q mutation, which is located within the antigenic site Sa, causes the virus to escape from the immune response.
Collapse
Affiliation(s)
- Mojtaba Mortazavi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Neda Pirbonyeh
- Microbiology Department, Burn and Wound Healing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Javanmardi
- Biostatistics Department, Shiraz Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Emami
- Microbiology Department, Burn and Wound Healing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
3
|
Morita R, Kubota-Koketsu R, Lu X, Sasaki T, Nakayama EE, Liu YC, Okuzaki D, Motooka D, Wing JB, Fujikawa Y, Ichida Y, Amo K, Goto T, Hara J, Shirano M, Yamasaki S, Shioda T. COVID-19 relapse associated with SARS-CoV-2 evasion from CD4 + T-cell recognition in an agammaglobulinemia patient. iScience 2023; 26:106685. [PMID: 37124420 PMCID: PMC10116114 DOI: 10.1016/j.isci.2023.106685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023] Open
Abstract
A 25-year-old patient with a primary immunodeficiency lacking immunoglobulin production experienced a relapse after a 239-day period of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral genetic sequencing demonstrated that SARS-CoV-2 had evolved during the infection period, with at least five mutations associated with host cellular immune recognition. Among them, the T32I mutation in ORF3a was found to evade recognition by CD4+ T cells. The virus found after relapse showed an increased proliferative capacity in vitro. SARS-CoV-2 may have evolved to evade recognition by CD4+ T cells and increased in its proliferative capacity during the persistent infection, likely leading to relapse. These mutations may further affect viral clearance in hosts with similar types of human leukocyte antigens. The early elimination of SARS-CoV-2 in immunocompromised patients is therefore important not only to improve the condition of patients but also to prevent the emergence of mutants that threaten public health.
Collapse
Affiliation(s)
- Ryo Morita
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - James Badger Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Yasunori Fujikawa
- Department of Medical Laboratory, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Yuji Ichida
- Department of Pharmacy, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Kiyoko Amo
- Department of Pediatric Emergency Medicine, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Tetsushi Goto
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Michinori Shirano
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| |
Collapse
|
4
|
Klenow L, Elfageih R, Gao J, Wan H, Withers SG, de Gier JW, Daniels R. Influenza virus and pneumococcal neuraminidases enhance catalysis by similar yet distinct sialic acid-binding strategies. J Biol Chem 2023; 299:102891. [PMID: 36634846 PMCID: PMC9929470 DOI: 10.1016/j.jbc.2023.102891] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Influenza A viruses and the bacterium Streptococcus pneumoniae (pneumococci) both express neuraminidases that catalyze release of sialic acid residues from oligosaccharides and glycoproteins. Although these respiratory pathogen neuraminidases function in a similar environment, it remains unclear if these enzymes use similar mechanisms for sialic acid cleavage. Here, we compared the enzymatic properties of neuraminidases from two influenza A subtypes (N1 and N2) and the pneumococcal strain TIGR4 (NanA, NanB, and NanC). Insect cell-produced N1 and N2 tetramers exhibited calcium-dependent activities and stabilities that varied with pH. In contrast, E. coli-produced NanA, NanB, and NanC were isolated as calcium insensitive monomers with stabilities that were more resistant to pH changes. Using a synthetic substrate (MUNANA), all neuraminidases showed similar pH optimums (pH 6-7) that were primarily defined by changes in catalytic rate rather than substrate binding affinity. Upon using a multivalent substrate (fetuin sialoglycans), much higher specific activities were observed for pneumococcal neuraminidases that contain an additional lectin domain. In virions, N1 and especially N2 also showed enhanced specific activity toward fetuin that was lost upon the addition of detergent, indicating the sialic acid-binding capacity of neighboring hemagglutinin molecules likely contributes to catalysis of natural multivalent substrates. These results demonstrate that influenza and pneumococcal neuraminidases have evolved similar yet distinct strategies to optimize their catalytic activity.
Collapse
Affiliation(s)
- Laura Klenow
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rageia Elfageih
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jin Gao
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert Daniels
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA.
| |
Collapse
|
5
|
Chauhan RP, Gordon ML. An overview of influenza A virus genes, protein functions, and replication cycle highlighting important updates. Virus Genes 2022; 58:255-269. [PMID: 35471490 DOI: 10.1007/s11262-022-01904-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
The recent research findings on influenza A virus (IAV) genome biology prompted us to present a comprehensive overview of IAV genes, protein functions, and replication cycle. The eight gene segments of the IAV genome encode 17 proteins, each having unique functions contributing to virus fitness in the host. The polymerase genes are essential determinants of IAV pathogenicity and virulence; however, other viral components also play crucial roles in the IAV replication, transmission, and adaptation. Specific adaptive mutations within polymerase (PB2, PB1, and PA) and glycoprotein-hemagglutinin (HA) and neuraminidase (NA) genes, may facilitate interspecies transmission and adaptation of IAV. The HA-NA interplay is essential for establishing the IAV infection; the low pH triggers the inactivation of HA-receptor binding, leading to significantly lower NA activities, indicating that the enzymatic function of NA is dependent on HA binding. While the HA and NA glycoproteins are required to initiate infection, M1, M2, NS1, and NEP proteins are essential for cytoplasmic trafficking of viral ribonucleoproteins (vRNPs) and the assembly of the IAV virions. The mechanisms that enable IAV to exploit the host cell resources to advance the infection are discussed. A comprehensive understanding of IAV genome biology is essential for developing antivirals to combat the IAV disease burden.
Collapse
Affiliation(s)
- Ravendra P Chauhan
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Michelle L Gordon
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa.
| |
Collapse
|
6
|
Ellis D, Lederhofer J, Acton OJ, Tsybovsky Y, Kephart S, Yap C, Gillespie RA, Creanga A, Olshefsky A, Stephens T, Pettie D, Murphy M, Sydeman C, Ahlrichs M, Chan S, Borst AJ, Park YJ, Lee KK, Graham BS, Veesler D, King NP, Kanekiyo M. Structure-based design of stabilized recombinant influenza neuraminidase tetramers. Nat Commun 2022; 13:1825. [PMID: 35383176 PMCID: PMC8983682 DOI: 10.1038/s41467-022-29416-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity. Here we show that recombinant NAs across non-bat subtypes adopt various tetrameric conformations, including an "open" state that may help explain poorly understood variations in NA stability across viral strains and subtypes. We use homology-directed protein design to uncover the structural principles underlying these distinct tetrameric conformations and stabilize multiple recombinant NAs in the "closed" state, yielding two near-atomic resolution structures of NA by cryo-EM. In addition to enhancing thermal stability, conformational stabilization improves affinity to protective antibodies elicited by viral infection, including antibodies targeting a quaternary epitope and the broadly conserved catalytic site. Stabilized NAs can also be integrated into viruses without affecting fitness. Our findings provide a deeper understanding of NA structure, stability, and antigenicity, and establish design strategies for reinforcing the conformational integrity of recombinant NA proteins.
Collapse
Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA, 98195, USA
- Icosavax Inc., Seattle, WA, 98102, USA
| | - Julia Lederhofer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oliver J Acton
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Sally Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Christina Yap
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Audrey Olshefsky
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, 21702, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Claire Sydeman
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
7
|
Abstract
The neuraminidase (NA) of influenza A and B viruses plays a distinct role in viral replication and has a highly conserved catalytic site. Numerous sialic (neuraminic) acid analogs that competitively bind to the NA active site and potently inhibit enzyme activity have been synthesized and tested. Four NA inhibitors are now licensed in various parts of the world (zanamivir, oseltamivir, peramivir, and laninamivir) to treat influenza A and B infections. NA changes, naturally occurring or acquired under selective pressure, have been shown to reduce drug binding, thereby affecting the effectiveness of NA inhibitors. Drug resistance and other drawbacks have prompted the search for the next-generation NA-targeting therapeutics. One of the promising approaches is the identification of monoclonal antibodies (mAbs) targeting the conserved NA epitopes. Anti-NA mAbs demonstrate Fab-based antiviral activity supplemented with Fc-mediated immune effector functions. Antiviral Fc-conjugates offer another cutting-edge strategy that is based on a multimodal mechanism of action. These novel antiviral agents are composed of a small-molecule NA inhibitor and an Fc-region that simultaneously engages the immune system. The significant advancements made in recent years further support the value of NA as an attractive target for the antiviral development.
Collapse
Affiliation(s)
- Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| | - Teena Mohan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| |
Collapse
|
8
|
Bull MB, Cohen CA, Leung NH, Valkenburg SA. Universally Immune: How Infection Permissive Next Generation Influenza Vaccines May Affect Population Immunity and Viral Spread. Viruses 2021; 13:1779. [PMID: 34578360 PMCID: PMC8472936 DOI: 10.3390/v13091779] [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: 07/07/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Next generation influenza vaccines that target conserved epitopes are becoming a clinical reality but still have challenges to overcome. Universal next generation vaccines are considered a vital tool to combat future pandemic viruses and have the potential to vastly improve long-term protection against seasonal influenza viruses. Key vaccine strategies include HA-stem and T cell activating vaccines; however, they could have unintended effects for virus adaptation as they recognise the virus after cell entry and do not directly block infection. This may lead to immune pressure on residual viruses. The potential for immune escape is already evident, for both the HA stem and T cell epitopes, and mosaic approaches for pre-emptive immune priming may be needed to circumvent key variants. Live attenuated influenza vaccines have not been immunogenic enough to boost T cells in adults with established prior immunity. Therefore, viral vectors or peptide approaches are key to harnessing T cell responses. A plethora of viral vector vaccines and routes of administration may be needed for next generation vaccine strategies that require repeated long-term administration to overcome vector immunity and increase our arsenal against diverse influenza viruses.
Collapse
Affiliation(s)
- Maireid B. Bull
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - Carolyn A. Cohen
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| | - Nancy H.L. Leung
- World Health Organization Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong, China;
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China; (M.B.B.); (C.A.C.)
| |
Collapse
|
9
|
Mohr PG, Williams J, Tashiro M, Streltsov VA, McKimm-Breschkin JL. Substitutions at H134 and in the 430-loop region in influenza B neuraminidases can confer reduced susceptibility to multiple neuraminidase inhibitors. Antiviral Res 2020; 182:104895. [PMID: 32750469 DOI: 10.1016/j.antiviral.2020.104895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/26/2022]
Abstract
With the introduction of the influenza specific neuraminidase inhibitors (NAIs) in 1999, there were concerns about the emergence and spread of resistant viruses in the community setting. Surveillance and testing of community isolates for their susceptibility to the NAIs was initially carried out by the Neuraminidase Inhibitor Susceptibility Network (NISN) and has subsequently been taken on by the global WHO influenza network laboratories. During the NISN surveillance, we identified two Yamagata lineage influenza B viruses with amino acid substitutions of H134Y (B/Auckland/2/2001) or W438R (B/Yokohama/12/2005) which had slightly elevated IC50 values for zanamivir and/or oseltamivir, but not sufficiently to be characterized as mild outliers at the time. As it has now been well demonstrated that mixed populations can mask the true magnitude of resistance of a mutant, we re-examined both of these isolates by plaque purification to see if the true susceptibilities were being masked due to mixed populations. Results confirmed that the B/Auckland isolate contained both wild type and H134Y mutant populations, with mutant IC50 values > 250 nM for both oseltamivir and peramivir in the enzyme inhibition assay. The B/Yokohama isolate also contained both wild type and W438R mutant populations, the latter now demonstrating IC50 values > 400 nM for zanamivir, oseltamivir and peramivir. In addition, plaque purification of the B/Yokohama isolate identified viruses with other single neuraminidase substitutions H134Y, H134R, H431R, or T436P. H134R and H431R viruses had IC50 values > 400 nM and >250 nM respectively against all three NAIs. All changes conferred much greater resistance to peramivir than to zanamivir, and less to oseltamivir, and affected the kinetics of binding and dissociation of the NAIs. Most affected affinity (Km) for the MUNANA substrate, but some had decreased while others had increased affinity. Despite resistance in the enzyme assay, no reduced susceptibility was seen in plaque reduction assays in MDCK cells for any of the mutant viruses. None of these substitutions was in the active site. Modelling suggests that these substitutions affect the 150 and 430-loop regions described for influenza A NAs, suggesting they may also be important for substrate and inhibitor binding for influenza B NAs.
Collapse
Affiliation(s)
- Peter G Mohr
- CSIRO Australian Centre for Disease Preparedness, 5 Portarlington Rd., East Geelong, 3219, Australia.
| | - Janelle Williams
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia.
| | - Masato Tashiro
- Influenza Virus Research Center, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan.
| | | | | |
Collapse
|
10
|
Qiu H, Andersen H, Tarbet EB, Muhammad FS, Carnelley T, Pronyk R, Barker D, Kodihalli S. Efficacy of anti-influenza immunoglobulin (FLU-IGIV) in ferrets and mice infected with 2009 pandemic influenza virus. Antiviral Res 2020; 180:104753. [PMID: 32114033 DOI: 10.1016/j.antiviral.2020.104753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 11/19/2022]
Abstract
Seasonal influenza causes significant morbidity and mortality around the world each year, even with the use of vaccines and antivirals. There is a need for more effective treatments for severe and hospitalized cases of influenza. In this study, we have tested the efficacy of a human plasma-derived IgG product (FLU-IGIV) against seasonal influenza in mouse and ferret models of influenza infection. FLU-IGIV successfully protected mice (100% survival) against lethal influenza infection. Also, the survival rate observed with FLU-IGIV treatment was better than the survival rate observed with oseltamivir (60% survival). FLU-IGIV significantly reduced the viral load in the lungs compared to placebo (PBS) in ferrets infected with influenza A/California/07/2009 (H1N1pdm09) virus. Overall, these studies demonstrate the efficacy of human plasma-derived FLU-IGIV in relevant animal models of influenza virus infection.
Collapse
Affiliation(s)
- Hongyu Qiu
- Research and Development, Emergent BioSolutions Canada Inc, Winnipeg, Canada
| | | | | | | | - Trevor Carnelley
- Research and Development, Emergent BioSolutions Canada Inc, Winnipeg, Canada
| | - Russell Pronyk
- Research and Development, Emergent BioSolutions Canada Inc, Winnipeg, Canada
| | - Douglas Barker
- Research and Development, Emergent BioSolutions Canada Inc, Winnipeg, Canada
| | - Shantha Kodihalli
- Research and Development, Emergent BioSolutions Canada Inc, Winnipeg, Canada.
| |
Collapse
|
11
|
Lipničanová S, Chmelová D, Ondrejovič M, Frecer V, Miertuš S. Diversity of sialidases found in the human body - A review. Int J Biol Macromol 2020; 148:857-868. [PMID: 31945439 DOI: 10.1016/j.ijbiomac.2020.01.123] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/31/2022]
Abstract
Sialidases are enzymes essential for numerous organisms including humans. Hydrolytic sialidases (EC 3.2.1.18), trans-sialidases and anhydrosialidases (intramolecular trans-sialidases, EC 4.2.2.15) are glycoside hydrolase enzymes that cleave the glycosidic linkage and release sialic acid residues from sialyl substrates. The paper summarizes diverse sialidases present in the human body and their potential impact on development of antiviral compounds - inhibitors of viral neuraminidases. It includes a brief overview of catalytic mechanisms of action of sialidases and describes the origin of sialidases in the human body. This is followed by description of the structure and function of sialidase families with a special focus on the GH33 and GH34 families. Various effects of sialidases on human body are also briefly described. Modulation of sialidase activity may be considered a useful tool for effective treatment of various diseases. In some cases, it is desired to completely suppress the activity of sialidases by suitable inhibitors. Specific sialidase inhibitors are useful for the treatment of influenza, epilepsy, Alzheimer's disease, diabetes, different types of cancer, or heart defects. Challenges and future directions are shortly depicted in the final part of the paper.
Collapse
Affiliation(s)
- Sabina Lipničanová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia.
| | - Vladimír Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-83232 Bratislava, Slovakia; ICARST n.o., Jamnického 19, SK-84101, Bratislava, Slovakia.
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Nám. J. Herdu 2, SK-91701 Trnava, Slovakia; ICARST n.o., Jamnického 19, SK-84101, Bratislava, Slovakia.
| |
Collapse
|
12
|
Ilyushina NA, Komatsu TE, Ince WL, Donaldson EF, Lee N, O'Rear JJ, Donnelly RP. Influenza A virus hemagglutinin mutations associated with use of neuraminidase inhibitors correlate with decreased inhibition by anti-influenza antibodies. Virol J 2019; 16:149. [PMID: 31783761 PMCID: PMC6884823 DOI: 10.1186/s12985-019-1258-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
Background Vaccination and the use of neuraminidase inhibitors (NAIs) are currently the front lines of defense against seasonal influenza. The activity of influenza vaccines and antivirals drugs such as the NAIs can be affected by mutations in the influenza hemagglutinin (HA) protein. Numerous HA substitutions have been identified in nonclinical NAI resistance-selection experiments as well as in clinical specimens from NAI treatment or surveillance studies. These mutations are listed in the prescribing information (package inserts) for FDA-approved NAIs, including oseltamivir, zanamivir, and peramivir. Methods NAI treatment-emergent H1 HA mutations were mapped onto the H1N1 HA1 trimeric crystal structure and most of them localized to the HA antigenic sites predicted to be important for anti-influenza immunity. Recombinant A/California/04/09 (H1N1)-like viruses carrying HA V152I, G155E, S162 N, S183P, and D222G mutations were generated. We then evaluated the impact of these mutations on the immune reactivity and replication potential of the recombinant viruses in a human respiratory epithelial cell line, Calu− 3. Results We found that the G155E and D222G mutations significantly increased viral titers ~ 13-fold compared to the wild-type virus. The hemagglutination and microneutralization activity of goat and ferret antisera, monoclonal antibodies, and human serum samples raised against pandemic A(H1N1)pdm09 viruses was ~ 100-fold lower against mutants carrying G155E or D222G compared to the wild-type virus. Conclusions Although the mechanism by which HA mutations emerge during NAI treatment is uncertain, some NAI treatment-emergent HA mutations correlate with decreased immunity to influenza virus.
Collapse
Affiliation(s)
- Natalia A Ilyushina
- Division of Biotechnology Review and Research II, Food and Drug Administration CDER, WO Bldg. 52/72, Room 2105, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| | - Takashi E Komatsu
- Division of Antiviral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - William L Ince
- Division of Antiviral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Eric F Donaldson
- Division of Antiviral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Nicolette Lee
- Division of Biotechnology Review and Research II, Food and Drug Administration CDER, WO Bldg. 52/72, Room 2105, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Julian J O'Rear
- Division of Antiviral Products, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Raymond P Donnelly
- Division of Biotechnology Review and Research II, Food and Drug Administration CDER, WO Bldg. 52/72, Room 2105, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| |
Collapse
|
13
|
McKimm-Breschkin JL, Barrett S, McKenzie-Kludas C, McAuley J, Streltsov VA, Withers SG. Passaging of an influenza A(H1N1)pdm09 virus in a difluoro sialic acid inhibitor selects for a novel, but unfit I106M neuraminidase mutant. Antiviral Res 2019; 169:104542. [PMID: 31233807 DOI: 10.1016/j.antiviral.2019.104542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/17/2023]
Abstract
An influenza A(H1N1)pdm09 and an influenza B virus were passaged in 3-fluoro(eq)-4-guanidino difluoro sialic acid (3Feq4Gu DFSA), an inhibitor of the influenza neuraminidase (NA) to determine whether resistant variants could be selected. 3Feq4Gu DFSA is a mechanism-based inhibitor, forming a covalent link to Y406 in the NA active site. Given its similarity to the natural substrate, sialic acid, we predicted resistant variants would be difficult to select. Yields of both viruses decreased with passaging, so that after 12 passages both viruses were only growing to low titers. Drug concentrations were decreased for another three passages. There was no difference in NA sensitivity in the MUNANA fluorescence-based assay, nor in plaque assays for the passaged virus stocks. All influenza B plaques were still wild type in all assays. There were isolated small diffuse plaques in the P15 pdm09 stock, which after purification had barely detectable NA or hemagglutinin (HA) activity. These had a novel non-active site I106M substitution in the NA gene, but unexpectedly no HA changes. The I106M may impact NA function through steric effects on the movement of the 150 and 430-loops. The I106M viruses had similar replication kinetics in MDCK cells as wild type viruses, but their ability to bind to and infect CHO-K1 cells expressing high levels of cell-bound mucin was compromised. The I106M substitution was unstable, with progeny rapidly reverting to wild type by three different mechanisms. Some had reverted to I106, some had V106, both with wild type NA and HA properties. A third group retained the I106M, but had a compensating R363K substitution, which regained almost wild type NA properties. These viruses now agglutinated chicken red blood cells (CRBCs) but unlike the I/V106, they rebound after elution at 37 °C. There were no mutations in the HA, but each phenotype correlated with the NA sequence. We propose that the activity in the I106M mutant is insufficient to remove carbohydrates from the virion HA and NA, sterically limiting HA access to CRBC receptors, thus resulting in poor HA binding.
Collapse
Affiliation(s)
- Jennifer L McKimm-Breschkin
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Susan Barrett
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia.
| | - Charley McKenzie-Kludas
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, 3000, Australia.
| | - Victor A Streltsov
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, 30 Royal Parade, Parkville, 3052, Australia.
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada.
| |
Collapse
|
14
|
McAuley JL, Gilbertson BP, Trifkovic S, Brown LE, McKimm-Breschkin JL. Influenza Virus Neuraminidase Structure and Functions. Front Microbiol 2019; 10:39. [PMID: 30761095 PMCID: PMC6362415 DOI: 10.3389/fmicb.2019.00039] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/10/2019] [Indexed: 12/31/2022] Open
Abstract
With the constant threat of emergence of a novel influenza virus pandemic, there must be continued evaluation of the molecular mechanisms that contribute to virulence. Although the influenza A virus surface glycoprotein neuraminidase (NA) has been studied mainly in the context of its role in viral release from cells, accumulating evidence suggests it plays an important, multifunctional role in virus infection and fitness. This review investigates the various structural features of NA, linking these with functional outcomes in viral replication. The contribution of evolving NA activity to viral attachment, entry and release of virions from infected cells, and maintenance of functional balance with the viral hemagglutinin are also discussed. Greater insight into the role of this important antiviral drug target is warranted.
Collapse
Affiliation(s)
- Julie L McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Brad P Gilbertson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sanja Trifkovic
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Lorena E Brown
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer L McKimm-Breschkin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| |
Collapse
|
15
|
Koul P, Potdar V, Mir H, Chadha M. The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. PLOS CURRENTS 2018; 10. [PMID: 30245911 PMCID: PMC6122875 DOI: 10.1371/currents.outbreaks.519e170f2740fabd4ccd1642ff533364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction: Following the initial outbreak of A/H1N1pdm09, periodic resurgences of the virus, with variable morbidity and mortality, have been reported from various parts of India including the temperate Kashmir region of northern India. An outbreak of A/H1N1 was reported in early 2015 across India with a high morbidity and mortality. We studied patients during the outbreak in Kashmir. Methods: Patients (n=1780, age 1 month to 90 years, median 35 years) presenting with acute respiratory illness to a tertiary care hospital in Srinagar, Kashmir from October 2014 to April 2015 were recruited. After clinical data recording, combined throat and nasal swabs were collected in viral transport medium and tested by real-time RT-PCR for influenza viruses. All influenza A positive samples were further subtyped using primers and probes for A/H1N1pdm09 and A/H3 whereas influenza B samples were further subtyped into B/Yamagata and B/Victoria lineages. Virus isolation, hemagglutination inhibition testing, sequencing and phylogenetic analysis was carried out using standard procedures. Testing for H275Y mutation was done to determine sensitivity to oseltamivir. All patients received symptomatic therapy and influenza positive patients were administered oseltamivir. Results: Of the 1780 patients, 540 (30%) required hospitalization and 533 tested positive for influenza [influenza A=517(A/H1N1pdm09=437, A/H3N2=78 with co-infection of both in 2 cases); influenza B=16 (B/Yamgata=15)]. About 14% (n=254) had been vaccinated against influenza, having received the NH 2014-15 vaccine, 27 (11.3%) of these testing positive for influenza. Sixteen patients, including 4 pregnant females, died due to multi-organ failure. HA sequencing depicted that 2015 isolates belonged to Clade 6B.1. No H275Y mutation was reported from A/H1N1 positives. Conclusion: Resurgent outbreak of A/H1N1pdm09, with emergence of clade 6B.1, in 2014-15 resulted in high rate of hospitalizations, morbidity and mortality. Periodic resurgences and appearance of mutants emphasize continued surveillance so as to identify newer mutations with potential for outbreaks and severe outcomes.
Collapse
Affiliation(s)
- Parvaiz Koul
- Internal & Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K, India
| | | | - Hyder Mir
- Internal & Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K, India
| | | |
Collapse
|
16
|
Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses. Antimicrob Agents Chemother 2018; 62:AAC.00766-18. [PMID: 29891600 DOI: 10.1128/aac.00766-18] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 05/31/2018] [Indexed: 01/29/2023] Open
Abstract
Morbidity and mortality resulting from influenza-like disease are a threat, especially for older adults. To improve case management, next-generation broad-spectrum antiviral therapeutics that are efficacious against major drivers of influenza-like disease, including influenza viruses and respiratory syncytial virus (RSV), are urgently needed. Using a dual-pathogen high-throughput screening protocol for influenza A virus (IAV) and RSV inhibitors, we have identified N4-hydroxycytidine (NHC) as a potent inhibitor of RSV, influenza B viruses, and IAVs of human, avian, and swine origins. Biochemical in vitro polymerase assays and viral RNA sequencing revealed that the ribonucleotide analog is incorporated into nascent viral RNAs in place of cytidine, increasing the frequency of viral mutagenesis. Viral passaging in cell culture in the presence of an inhibitor did not induce robust resistance. Pharmacokinetic profiling demonstrated dose-dependent oral bioavailability of 36 to 56%, sustained levels of the active 5'-triphosphate anabolite in primary human airway cells and mouse lung tissue, and good tolerability after extended dosing at 800 mg/kg of body weight/day. The compound was orally efficacious against RSV and both seasonal and highly pathogenic avian IAVs in mouse models, reducing lung virus loads and alleviating disease biomarkers. Oral dosing reduced IAV burdens in a guinea pig transmission model and suppressed virus spread to uninfected contact animals through direct transmission. Based on its broad-spectrum efficacy and pharmacokinetic properties, NHC is a promising candidate for future clinical development as a treatment option for influenza-like diseases.
Collapse
|
17
|
McKimm-Breschkin JL, Barrett S, Wong FYK, Pudjiatmoko, Azhar M, Selleck P, Davies KR, Hartaningsih N, McGrane J. Identification of Indonesian clade 2.1 highly pathogenic influenza A(H5N1) viruses with N294S and S246N neuraminidase substitutions which further reduce oseltamivir susceptibility. Antiviral Res 2018; 153:95-100. [PMID: 29574145 DOI: 10.1016/j.antiviral.2018.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 01/04/2023]
Abstract
We have tested the in vitro susceptibility to the neuraminidase (NA) inhibitors of 96 highly pathogenic clade 2.1 A(H5N1) viruses from Indonesia, isolated between 2008 and 2011. HPAI virus samples obtained through the Influenza Virus Monitoring (IVM) surveillance program in Indonesia were tested for susceptibility to oseltamivir and zanamivir. The NAs of four viruses were identified as extreme outliers to oseltamivir, based on statistical analysis by box plots, with IC50 values ranging from 46 to 62 nM. The NAs of two of these viruses from Sumatra and Aceh, had an N294S substitution, while one virus from Sulawesi had an S246N NA substitution. The NAs of all four viruses showed a specific loss of slow binding to oseltamivir in an IC50 kinetics assay. As observed in our previous surveillance, there was only a minimal effect on the sensitivity to zanamivir or peramivir for these mutants or any of the other isolates tested. The continued circulation of subtype H5N1 viruses in avian species poses an on-going zoonotic threat. The fact that we continue to identify avian isolates with naturally occurring mutations conferring reduced oseltamivir susceptibility remains a concern, given oseltamivir will be a key antiviral in the event of a new pandemic emerging.
Collapse
Affiliation(s)
| | - Susan Barrett
- CSIRO Manufacturing, 343 Royal Parade, Parkville, 3052 Australia.
| | - Frank Y K Wong
- CSIRO Australian Animal Health Laboratory, Geelong, Australia.
| | - Pudjiatmoko
- Directorate of Animal Health, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Jakarta, Indonesia.
| | - Muhammad Azhar
- Directorate of Animal Health, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture, Jakarta, Indonesia.
| | - Paul Selleck
- CSIRO Australian Animal Health Laboratory, Geelong, Australia
| | - Kelly R Davies
- CSIRO Australian Animal Health Laboratory, Geelong, Australia.
| | - Nining Hartaningsih
- Food and Agriculture Organization of the United Nations Emergency Centre for Transboundary Animal Diseases (ECTAD), Jakarta, Indonesia.
| | - James McGrane
- Food and Agriculture Organization of the United Nations Emergency Centre for Transboundary Animal Diseases (ECTAD), Jakarta, Indonesia.
| |
Collapse
|
18
|
McKimm-Breschkin JL, Barrett S, Pilling PA, Hader S, Watts AG, Streltsov VA. Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives. J Med Chem 2018; 61:1921-1933. [PMID: 29397718 DOI: 10.1021/acs.jmedchem.7b01467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Competitive inhibitors of the influenza neuraminidase (NA) were discovered almost 20 years ago, with zanamivir and oseltamivir licensed globally. These compounds are based on a transition state analogue of the sialic acid substrate. We recently showed that 5- N-(acetylamino)-2,3,5-trideoxy-2,3-difluoro-d-erythro-β-l-manno-2-nonulopyranosonic acid (DFSA) and its derivatives are also potent inhibitors of the influenza NA. They are mechanism based inhibitors, forming a covalent bond between the C2 of the sugar ring and Y406 in the NA active site, thus inactivating the enzyme. We have now synthesized a series of deoxygenated DFSA derivatives in order to understand the contribution of each hydroxyl in DFSA to binding and inhibition of the influenza NA. We have investigated their relative efficacy in enzyme assays in vitro, in cell culture, and by X-ray crystallography. We found loss of the 8- and 9-OH had the biggest impact on the affinity of binding and antiviral potency.
Collapse
Affiliation(s)
| | - Susan Barrett
- CSIRO Manufacturing , 343 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Patricia A Pilling
- CSIRO Manufacturing , 343 Royal Parade , Parkville , Victoria 3052 , Australia
| | - Stefan Hader
- Department of Pharmacy and Pharmacology , University of Bath , Claverton Down, Bath BA2 7AY , United Kingdom
| | - Andrew G Watts
- Department of Pharmacy and Pharmacology , University of Bath , Claverton Down, Bath BA2 7AY , United Kingdom
| | - Victor A Streltsov
- The Florey Institute of Neuroscience and Mental Health , 30 Royal Parade , Parkville , Victoria 3052 , Australia
| |
Collapse
|
19
|
Neri-Bazán RM, García-Machorro J, Méndez-Luna D, Tolentino-López LE, Martínez-Ramos F, Padilla-Martínez II, Aguilar-Faisal L, Soriano-Ursúa MA, Trujillo-Ferrara JG, Fragoso-Vázquez MJ, Barrón BL, Correa-Basurto J. Design, in silico studies, synthesis and in vitro evaluation of oseltamivir derivatives as inhibitors of neuraminidase from influenza A virus H1N1. Eur J Med Chem 2017; 128:154-167. [PMID: 28182988 DOI: 10.1016/j.ejmech.2017.01.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 02/07/2023]
Abstract
Since the neuraminidase (NA) enzyme of the influenza A virus plays a key role in the process of release of new viral particles from a host cell, it is often a target for new drug design. The emergence of NA mutations, such as H275Y, has led to great resistance against neuraminidase inhibitors, including oseltamivir and zanamivir. Hence, we herein designed a set of derivatives by modifying the amine and/or carboxylic groups of oseltamivir. After being screened for their physicochemical (Lipinski's rule) and toxicological properties, the remaining compounds were submitted to molecular and theoretical studies. The docking simulations provided insights into NA recognition patterns, demonstrating that oseltamivir modified at the carboxylic moiety and coupled with anilines had higher affinity and a better binding pose for NA than the derivatives modified at the amine group. Based on these theoretical studies, the new oseltamivir derivatives may have higher affinity to mutant variants and possibly to other viral subtypes. Accordingly, two compounds were selected for synthesis, which together with their respective intermediates were evaluated for their cytotoxicity and antiviral activities. Their biological activity was then tested in cells infected with the A/Puerto Rico/916/34 (H1N1) influenza virus, and virus yield reduction assays were performed. Additionally, by measuring neuraminidase activity with the neuraminidase assay kit it was found that the compounds produced inhibitory activity on this enzyme. Finally, the infected cells were analysed with atomic force microscopy (AFM), observing morphological changes strongly suggesting that these compounds interfered with cellular release of viral particles.
Collapse
Affiliation(s)
- Rocío M Neri-Bazán
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Jazmín García-Machorro
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico.
| | - David Méndez-Luna
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Luis E Tolentino-López
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Federico Martínez-Ramos
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - Itzia I Padilla-Martínez
- Departamento de Ciencia Básica, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n., Barrio La Laguna Ticomán, 07340, Mexico
| | - Leopoldo Aguilar-Faisal
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Marvin A Soriano-Ursúa
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - José G Trujillo-Ferrara
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - M Jonathan Fragoso-Vázquez
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - Blanca L Barrón
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - José Correa-Basurto
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico.
| |
Collapse
|
20
|
Hoffmann A, Richter M, von Grafenstein S, Walther E, Xu Z, Schumann L, Grienke U, Mair CE, Kramer C, Rollinger JM, Liedl KR, Schmidtke M, Kirchmair J. Discovery and Characterization of Diazenylaryl Sulfonic Acids as Inhibitors of Viral and Bacterial Neuraminidases. Front Microbiol 2017; 8:205. [PMID: 28261167 PMCID: PMC5309245 DOI: 10.3389/fmicb.2017.00205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/30/2017] [Indexed: 11/13/2022] Open
Abstract
Viral neuraminidases are an established drug target to combat influenza. Severe complications observed in influenza patients are primarily caused by secondary infections with e.g., Streptococcus pneumoniae. These bacteria engage in a lethal synergism with influenza A viruses (IAVs) and also express neuraminidases. Therefore, inhibitors with dual activity on viral and bacterial neuraminidases are expected to be advantageous for the treatment of influenza infections. Here we report on the discovery and characterization of diazenylaryl sulfonic acids as dual inhibitors of viral and Streptococcus pneumoniae neuraminidase. The initial hit came from a virtual screening campaign for inhibitors of viral neuraminidases. For the most active compound, 7-[2-[4-[2-[4-[2-(2-hydroxy-3,6-disulfo-1-naphthalenyl)diazenyl]-2-methylphenyl]diazenyl]-2-methylphenyl]diazenyl]-1,3-naphthalenedisulfonic acid (NSC65847; 1), the Ki-values measured in a fluorescence-based assay were lower than 1.5 μM for both viral and pneumococcal neuraminidases. The compound also inhibited N1 virus variants containing neuraminidase inhibitor resistance-conferring substitutions. Via enzyme kinetics and nonlinear regression modeling, 1 was suggested to impair the viral neuraminidases and pneumococcal neuraminidase with a mixed-type inhibition mode. Given its antiviral and antipneumococcal activity, 1 was identified as a starting point for the development of novel, dual-acting anti-infectives.
Collapse
Affiliation(s)
- Anja Hoffmann
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Martina Richter
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Susanne von Grafenstein
- Centre for Chemistry and Biomedicine, Institute of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruck, Austria
| | - Elisabeth Walther
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Zhongli Xu
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Lilia Schumann
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Ulrike Grienke
- Department of Pharmacognosy, Faculty of Life Sciences, University of ViennaVienna, Austria
| | - Christina E. Mair
- Department of Pharmacognosy, Faculty of Life Sciences, University of ViennaVienna, Austria
| | - Christian Kramer
- Centre for Chemistry and Biomedicine, Institute of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruck, Austria
| | - Judith M. Rollinger
- Department of Pharmacognosy, Faculty of Life Sciences, University of ViennaVienna, Austria
| | - Klaus R. Liedl
- Centre for Chemistry and Biomedicine, Institute of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruck, Austria
| | - Michaela Schmidtke
- Department of Virology and Antiviral Therapy, Jena University HospitalJena, Germany
| | - Johannes Kirchmair
- Centre for Chemistry and Biomedicine, Institute of General, Inorganic and Theoretical Chemistry, University of InnsbruckInnsbruck, Austria
- Center for Bioinformatics, University of HamburgHamburg, Germany
| |
Collapse
|
21
|
Montgomery AP, Xiao K, Wang X, Skropeta D, Yu H. Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design. STRUCTURAL AND MECHANISTIC ENZYMOLOGY 2017; 109:25-76. [DOI: 10.1016/bs.apcsb.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
22
|
Antiviral Resistance in Influenza Viruses: Clinical and Epidemiological Aspects. ANTIMICROBIAL DRUG RESISTANCE 2017. [PMCID: PMC7122614 DOI: 10.1007/978-3-319-47266-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
There are three classes of antiviral drugs approved for the treatment of influenza: the M2 ion channel inhibitors (amantadine, rimantadine), neuraminidase (NA) inhibitors (laninamivir, oseltamivir, peramivir, zanamivir), and the protease inhibitor (favipiravir); some of the agents are only available in selected countries [1, 2]. These agents are effective at treating the signs and symptoms of influenza in patients infected with susceptible viruses. Clinical failure has been demonstrated in patients infected with viruses with primary resistance, i.e., antivirals can be present in the virus initially infecting the patient, or resistance may emerge during the course of therapy [3–5]. NA inhibitors are active against all nine NA subtypes recognized in nature [6], including highly pathogenic avian influenza A/H5N1 and recent low-pathogenic avian influenza A/H7N9 viruses [7]. Since seasonal influenza is usually an acute, self-limited illness in which viral clearance usually occurs rapidly due to innate and adaptive host immune responses, the emergence of drug-resistant variants would be anticipated to have limited effect on clinical recovery in otherwise healthy patients, as has been demonstrated clinically [3, 8, 9]. Unfortunately, immunocompromised or immunologically naïve hosts, such as young children and infants or those exposed to novel strains, are more likely to have mutations that confer resistance emergence during therapy; such resistant variants may also result in clinically significant adverse outcomes [10–13].
Collapse
|
23
|
Kossyvakis A, Mentis AFA, Tryfinopoulou K, Pogka V, Kalliaropoulos A, Antalis E, Lytras T, Meijer A, Tsiodras S, Karakitsos P, Mentis AF. Antiviral susceptibility profile of influenza A viruses; keep an eye on immunocompromised patients under prolonged treatment. Eur J Clin Microbiol Infect Dis 2016; 36:361-371. [PMID: 27848039 DOI: 10.1007/s10096-016-2809-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022]
Abstract
There was an increase in severe and fatal influenza cases in Greece during the 2011-2015 post-pandemic period. To investigate causality, we determined neuraminidase (NA) inhibitor susceptibility and resistance-conferring NA and hemagglutinin (HA) mutations in circulating influenza type A viruses during the pandemic (2009-2010) and post-pandemic periods in Greece. One hundred thirty-four influenza A(H1N1)pdm09 and 95 influenza A(H3N2) viruses submitted to the National Influenza Reference Laboratory of Southern Greece were tested for susceptibility to oseltamivir and zanamivir. Antiviral resistance was assessed by neuraminidase sequence analysis, as well as the fluorescence-based 50 % inhibitory concentration (IC50) method. Five influenza A(H1N1)pdm09 viruses (2.2 %) showed significantly reduced inhibition by oseltamivir (average IC50 300.60nM vs. 1.19nM) by Gaussian kernel density plot analysis. These viruses were isolated from immunocompromised patients and harbored the H275Y oseltamivir resistance-conferring NA substitution. All A(H1N1)pdm09 viruses were zanamivir-susceptible, and all A(H3N2) viruses were susceptible to both drugs. Oseltamivir-resistant viruses did not form a distinct cluster by phylogenetic analysis. Permissive mutations were detected in immunogenic and non immunogenic NA regions of both oseltamivir- resistant and susceptible viruses in the post-pandemic seasons. Several amino acid substitutions in the HA1 domain of the HA gene of post-pandemic viruses were identified. This study indicated low resistance to NAIs among tested influenza viruses. Antiviral resistance emerged only in immunocompromised patients under long-term oseltamivir treatment. Sequential sample testing in this vulnerable group of patients is recommended to characterise resistance or reinfection and viral evolution.
Collapse
Affiliation(s)
- A Kossyvakis
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, 127, Vas. Sofias Ave., 11521, Athens, Greece
| | - A-F A Mentis
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, 127, Vas. Sofias Ave., 11521, Athens, Greece.,Johns Hopkins University, AAP, Baltimore, MD, USA
| | - K Tryfinopoulou
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden.,Antimicrobial Resistance and Healthcare-associated Infections Laboratory, National School of Public Health, Athens, Greece.,Hellenic Central Public Health Laboratory, Hellenic Centre for Disease Control and Prevention, Athens, Greece
| | - V Pogka
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, 127, Vas. Sofias Ave., 11521, Athens, Greece
| | - A Kalliaropoulos
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, 127, Vas. Sofias Ave., 11521, Athens, Greece
| | - E Antalis
- 4th Academic Department of Internal Medicine and Infectious Diseases, Attikon University Hospital, University of Athens Medical School, Athens, Greece
| | - T Lytras
- Department of Epidemiological Surveillance and Intervention, Hellenic Centre for Disease Control and Prevention, Athens, Greece.,Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - A Meijer
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - S Tsiodras
- 4th Academic Department of Internal Medicine and Infectious Diseases, Attikon University Hospital, University of Athens Medical School, Athens, Greece
| | - P Karakitsos
- Department of Cytopathology, Attikon University Hospital, University of Athens Medical School, Athens, Greece
| | - A F Mentis
- National Influenza Reference Laboratory of Southern Greece, Hellenic Pasteur Institute, 127, Vas. Sofias Ave., 11521, Athens, Greece.
| |
Collapse
|
24
|
Hoffmann A, Schade D, Kirchmair J, Clement B, Sauerbrei A, Schmidtke M. Platform for determining the inhibition profile of neuraminidase inhibitors in an influenza virus N1 background. J Virol Methods 2016; 237:192-199. [PMID: 27659246 DOI: 10.1016/j.jviromet.2016.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/04/2016] [Accepted: 09/19/2016] [Indexed: 01/21/2023]
Abstract
Efforts to develop novel neuraminidase inhibitors (NAIs) for the treatment of influenza are ongoing. Novel NAIs should in particular be also effective against seasonal and/or pandemic N1 that carry a H274Y or N294S substitution (N2 numbering), which are most commonly linked to oseltamivir resistance. Here we report a platform for profiling the efficacy of novel NAIs in the N1 genetic background of influenza A virus. Employing reverse genetics, a set of influenza virus variants containing an amino acid substitution associated with oseltamivir resistance in N1 isolates (H274Y, N294S, Y155H or Q136L) was generated. In parallel, so far unreported mutations of I427 (I427Q and I427M) were investigated. These possibly interfere with the side chain orientation of R371 and alter the binding affinity of most relevant NAIs. The profiling platform was validated with both oseltamivir and zanamivir and exemplarily applied to three analogs with differing decorations at positions 4 and 5. Besides confirming the inhibition profile of zanamivir and oseltamivir, the distinct effect of I427Q/M on the activity of both NAIs was shown. For 5-amidino and 5-guanidino analogs of oseltamivir a significantly stronger inhibition of virus variants carrying a NA-H274Y was confirmed, and additionally shown for NA-N294S and NA-Y155H substitutions as compared to the parent compound. Hence, the herein presented profiling platform is a valid tool for defining the inhibition profile of novel NAIs in the N1 background.
Collapse
Affiliation(s)
- Anja Hoffmann
- Jena University Hospital, Department of Virology and Antiviral Therapy, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Dennis Schade
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Bernd Clement
- Department of Pharmaceutical Chemistry, Pharmaceutical Institute, Christian-Albrechts University of Kiel, Gutenbergstrasse 76, 24118 Kiel, Germany
| | - Andreas Sauerbrei
- Jena University Hospital, Department of Virology and Antiviral Therapy, Hans-Knoell-Strasse 2, 07745 Jena, Germany
| | - Michaela Schmidtke
- Jena University Hospital, Department of Virology and Antiviral Therapy, Hans-Knoell-Strasse 2, 07745 Jena, Germany.
| |
Collapse
|
25
|
Tharakaraman K, Sasisekharan R. Influenza surveillance: 2014-2015 H1N1 "swine"-derived influenza viruses from India. Cell Host Microbe 2015; 17:279-282. [PMID: 25766285 DOI: 10.1016/j.chom.2015.02.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The 2014-15 H1N1 outbreak in India has reportedly led to 800 fatalities. The reported influenza hemagglutinin sequences from India indicate that these viruses contain amino acid changes linked to enhanced virulence and are potentially antigenically distinct from the current vaccine containing 2009 (Cal0709) H1N1 viral hemagglutinin.
Collapse
Affiliation(s)
- Kannan Tharakaraman
- Department of Biological Engineering, Skolkovo-MIT Center for Biomedical Engineering, Singapore-MIT Alliance for Research and Technology, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ram Sasisekharan
- Department of Biological Engineering, Skolkovo-MIT Center for Biomedical Engineering, Singapore-MIT Alliance for Research and Technology, Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| |
Collapse
|
26
|
Catalytic mechanism and novel receptor binding sites of human parainfluenza virus type 3 hemagglutinin-neuraminidase (hPIV3 HN). Antiviral Res 2015; 123:216-23. [DOI: 10.1016/j.antiviral.2015.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 12/25/2022]
|
27
|
Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA. Coordinated Evolution of Influenza A Surface Proteins. PLoS Genet 2015; 11:e1005404. [PMID: 26247472 PMCID: PMC4527594 DOI: 10.1371/journal.pgen.1005404] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 06/30/2015] [Indexed: 11/18/2022] Open
Abstract
The surface proteins hemagglutinin (HA) and neuraminidase (NA) of human influenza A virus evolve under selection pressures to escape adaptive immune responses and antiviral drug treatments. In addition to these external selection pressures, some mutations in HA are known to affect the adaptive landscape of NA, and vice versa, because these two proteins are physiologically interlinked. However, the extent to which evolution of one protein affects the evolution of the other one is unknown. Here we develop a novel phylogenetic method for detecting the signatures of such genetic interactions between mutations in different genes – that is, inter-gene epistasis. Using this method, we show that influenza surface proteins evolve in a coordinated way, with mutations in HA affecting subsequent spread of mutations in NA and vice versa, at many sites. Of particular interest is our finding that the oseltamivir-resistance mutations in NA in subtype H1N1 were likely facilitated by prior mutations in HA. Our results illustrate that the adaptive landscape of a viral protein is remarkably sensitive to its genomic context and, more generally, that the evolution of any single protein must be understood within the context of the entire evolving genome. The fitness of an organism depends on the coordinated function of many genes. Thus, how a mutation in one gene affects fitness often depends on what mutations are present in other genes. This dependence is called “genetic interaction” or “epistasis”. The prevalence and type of such interactions are not well understood. Epistasis can be inferred from time-series sequencing data when a mutation in one gene is observed to facilitate the spread of a mutation in another gene. However, the situation is much more complicated when new combinations of genes are formed by processes such as recombination or reassortment. In such cases, deducing the time and order of genetic changes is difficult. Here, we devise a method to infer pairs of mutations in different genes which closely follow one another in the presence of reassortment. We apply it to evolution of two surface proteins of influenza A virus, hemagglutinin and neuraminidase, which are important targets for the human immune system and drugs. We show that mutations in one of these proteins are often facilitated by prior mutations, or compensated by subsequent mutations, in the other protein. In particular, drug-resistance mutations in neuraminidase were likely made possible by prior mutation in hemagglutinin. Knowledge of such interactions is necessary to fully understand and predict evolution.
Collapse
Affiliation(s)
| | - Sergey Kryazhimskiy
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Joshua B. Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Georgii A. Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- * E-mail:
| |
Collapse
|
28
|
Richter M, Schumann L, Walther E, Hoffmann A, Braun H, Grienke U, Rollinger JM, von Grafenstein S, Liedl KR, Kirchmair J, Wutzler P, Sauerbrei A, Schmidtke M. Complementary assays helping to overcome challenges for identifying neuraminidase inhibitors. Future Virol 2015. [DOI: 10.2217/fvl.14.97] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ABSTRACT Aims: In this study, we analyze the challenges involved in detecting novel neuraminidase inhibitors (NAIs) and offer strategies to overcome them with complementary bioassays. Materials & Methods: We investigated the inhibitory activities of NAIs (oseltamivir, zanamivir, DANA, katsumadain A and remazol) as well as non-NAIs (amantadine, nucleozin and rifampicin) on influenzaviral and bacterial (Streptococcus pneumoniae, Clostridium perfringens and Vibrio cholerae) neuraminidases (NAs) with chemiluminescence (CL)- and fluorescence (FL)-based assays. Furthermore, hemagglutination-based NA inhibition assays were established. Results: Our study shows three types of signal interference affecting the readout of biochemical assays: self-FL (katsumadain A and remazol), FL quenching (rifampicin) and CL quenching (rifampicin, remazol, nucleozin and katsumadain A). These challenges were overcome by hemagglutination-based assays. Conclusion: The latter allow a robust performance in discriminating NAIs and non-NAIs.
Collapse
Affiliation(s)
- Martina Richter
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Lilia Schumann
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Elisabeth Walther
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Anja Hoffmann
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Heike Braun
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Ulrike Grienke
- Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, Innsbruck, Austria
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, Vienna, Austria
| | - Judith M Rollinger
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, Vienna, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic & Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic & Theoretical Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, Innsbruck, Austria
| | - Johannes Kirchmair
- Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, Hamburg, Germany
| | - Peter Wutzler
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Andreas Sauerbrei
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| | - Michaela Schmidtke
- Department of Virology & Antiviral Therapy, Jena University Hospital, Hans-Knoell-Strasse 2, Jena, Germany
| |
Collapse
|
29
|
Hata A, Akashi-Ueda R, Takamatsu K, Matsumura T. Safety and efficacy of peramivir for influenza treatment. DRUG DESIGN DEVELOPMENT AND THERAPY 2014; 8:2017-38. [PMID: 25368514 PMCID: PMC4216046 DOI: 10.2147/dddt.s46654] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Objective This report presents a review of the efficacy and safety of peramivir, a neuraminidase inhibitor that was granted Emergency Use Authorization by the US Food and Drug Administration (FDA) from October 23, 2009 to June 23, 2010 during the 2009 H1N1 pandemic. Methods Literature was accessed via PubMed (January 2000–April 2014) using several search terms: peramivir; BCX-1812; RWJ 270201; H1N1, influenza; antivirals; and neuraminidase inhibitors. The peramivir manufacturers, Shionogi and Co Ltd and BioCryst Pharmaceuticals, were contacted to obtain unpublished data and information presented at recent scientific meetings. Information was obtained from the Centers for Disease Control and Prevention (CDC) and from US FDA websites. English-language and Japanese-language reports in the literature were reviewed and selected based on relevance, along with information from the CDC, US FDA, and the drug manufacturers. Results We obtained eleven clinical trial reports of intravenous peramivir, two of which described comparisons with oseltamivir. Seven of nine other recently reported published studies was a dose–response study. Clinical reports of critically ill patients and pediatric patients infected with pandemic H1N1 described that early treatment significantly decreased mortality. Peramivir administered at 300 mg once daily in adult patients with influenza significantly reduces the time to alleviation of symptoms or fever compared to placebo. It is likely to be as effective as other neuraminidase inhibitors. Conclusion Although peramivir shows efficacy for the treatment of seasonal and pH1N1 influenza, it has not received US FDA approval. Peramivir is used safely and efficiently in hospitalized adult and pediatric patients with suspected or laboratory-confirmed influenza. Peramivir might be a beneficial alternative antiviral treatment for many patients, including those unable to receive inhaled or oral neuraminidase inhibitors, or those requiring nonintravenous drug delivery.
Collapse
Affiliation(s)
- Atsuko Hata
- Department of Pediatrics, Division of Respiratory Medicine, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan ; Department of Infectious Diseases, Division of Respiratory Medicine, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Ryoko Akashi-Ueda
- Department of Pediatrics, Division of Respiratory Medicine, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Kazufumi Takamatsu
- Respiratory Disease Center, Division of Respiratory Medicine, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan
| | - Takuro Matsumura
- Department of Infectious Diseases, Division of Respiratory Medicine, Kitano Hospital, The Tazuke Kofukai Medical Research Institute, Osaka, Japan
| |
Collapse
|
30
|
Seidel N, Sauerbrei A, Wutzler P, Schmidtke M. Hemagglutinin 222D/G polymorphism facilitates fast intra-host evolution of pandemic (H1N1) 2009 influenza A viruses. PLoS One 2014; 9:e104233. [PMID: 25162520 PMCID: PMC4146462 DOI: 10.1371/journal.pone.0104233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/09/2014] [Indexed: 01/17/2023] Open
Abstract
The amino acid substitution of aspartic acid to glycine in hemagglutinin (HA) in position 222 (HA-D222G) as well as HA-222D/G polymorphism of pandemic (H1N1) 2009 influenza viruses (A(H1N1)pdm09) were frequently reported in severe influenza in humans and mice. Their impact on viral pathogenicity and the course of influenza has been discussed controversially and the underlying mechanism remained unclarified. In the present study, BALB/c mice, infected with the once mouse lung- and cell-passaged A(H1N1)pdm09 isolate A/Jena/5258/09 (mpJena/5258), developed severe pneumonia. From day 2 to 3 or 4 post infection (p.i.) symptoms (body weight loss and clinical score) continuously worsened. After a short disease stagnation or even recovery phase in most mice, severity of disease further increased on days 6 and 7 p.i. Thereafter, surviving mice recovered. A 45 times higher virus titer maximum in the lung than in the trachea on day 2 p.i. and significantly higher tracheal virus titers compared to lung on day 6 p.i. indicated changes in the organ tropism during infection. Sequence analysis revealed an HA-222D/G polymorphism. HA-D222 and HA-G222 variants co-circulated in lung and trachea. Whereas, HA-D222 variant predominated in the lung, HA-G222 became the major variant in the trachea after day 4 p.i. This was accompanied by lower neutralizing antibody titers and broader receptor recognition including terminal sialic acid α-2,3-linked galactose, which is abundant on mouse trachea epithelial cells. Plaque-purified HA-G222-mpJena/5258 virus induced severe influenza with maximum symptom on day 6 p.i. These results demonstrated for the first time that HA-222D/G quasispecies of A(H1N1)pdm09 caused severe biphasic influenza because of fast viral intra-host evolution, which enabled partial antibody escape and minor changes in receptor binding.
Collapse
MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Viral/blood
- Base Sequence
- Evolution, Molecular
- Gene Expression
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Host Specificity
- Humans
- Immune Evasion
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Lung/immunology
- Lung/pathology
- Lung/virology
- Mice
- Mice, Inbred BALB C
- Molecular Sequence Data
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/pathology
- Orthomyxoviridae Infections/virology
- Polymorphism, Genetic
- Receptors, Virus/chemistry
- Receptors, Virus/immunology
- Sialic Acids/chemistry
- Sialic Acids/immunology
- Trachea/immunology
- Trachea/pathology
- Trachea/virology
- Viral Tropism
Collapse
Affiliation(s)
- Nora Seidel
- Jena University Hospital, Friedrich Schiller University Jena, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Andreas Sauerbrei
- Jena University Hospital, Friedrich Schiller University Jena, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Peter Wutzler
- Jena University Hospital, Friedrich Schiller University Jena, Department of Virology and Antiviral Therapy, Jena, Germany
| | - Michaela Schmidtke
- Jena University Hospital, Friedrich Schiller University Jena, Department of Virology and Antiviral Therapy, Jena, Germany
- * E-mail:
| |
Collapse
|
31
|
Barrett S, McKimm-Breschkin JL. Solid phase assay for comparing reactivation rates of neuraminidases of influenza wild type and resistant mutants after inhibitor removal. Antiviral Res 2014; 108:30-5. [PMID: 24854981 DOI: 10.1016/j.antiviral.2014.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 01/22/2023]
Abstract
The influenza virus neuraminidase inhibitors are normally slow binding inhibitors, but many mutations leading to resistance, also result in the loss of the slow binding phenotype. Mutations can also affect the rate of dissociation of the inhibitors from the neuraminidase, but the assays to measure this require large amounts of virus and are time consuming. To more fully understand the impacts of mutations on the binding and dissociation of the neuraminidase inhibitors we have developed a solid phase reactivation assay, which can use small amounts of crude virus sample bound to an ELISA plate. Multiple viruses can be assayed simultaneously against multiple inhibitors. Using this assay we have demonstrated differences in the relative rates of dissociation of the inhibitors and reactivation of enzyme activity among different influenza A and B viruses for zanamivir, oseltamivir and peramivir. In general oseltamivir dissociated the fastest, and dissociation of peramivir was much slower than both the other inhibitors. Viruses with H274Y, E119V and E119G mutations demonstrated faster dissociation of the inhibitor to which they were resistant. Dissociation of zanamivir and oseltamivir were faster from the D197E mutant, but not of peramivir.
Collapse
Affiliation(s)
- Susan Barrett
- CSIRO Materials Science and Engineering, 343 Royal Parade, Parkville 3052, Australia.
| | | |
Collapse
|
32
|
Effects of a hemagglutinin D222G substitution on the pathogenicity of 2009 influenza A (H1N1) virus in mice. Arch Virol 2014; 159:2559-65. [PMID: 24824345 DOI: 10.1007/s00705-014-2104-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 04/29/2014] [Indexed: 01/22/2023]
Abstract
The surface glycoprotein hemagglutinin (HA) of influenza virus initiates the infection process by binding to sialic acid receptors on upper respiratory cells in the host. In contrast to avian influenza viruses, which bind to sialic acids connected by an α2-3 linkage to the penultimate galactose, human influenza viruses prefer sialic acids with an α2-6 linkage. Recently, there have been multiple cases of severe human infections associated with an HA D222G mutant influenza virus. In this study, we have investigated the pathogenic effects of the HA D222G substitution in a 2009 pandemic H1N1 virus in mice. Compared with the A/Korea/01/2009 (K/09) virus, the HA D222G mutant showed reduced growth in cells and reduced binding avidity to human and turkey red blood cells. In a BALB/c mouse infection model, infection with the HA D222G mutant virus resulted in less body weight loss when compared to the parental K/09 virus. Altogether, our data suggest that the HA D222G substitution in the K/09 virus might be deleterious to viral fitness.
Collapse
|
33
|
Fitness costs for Influenza B viruses carrying neuraminidase inhibitor-resistant substitutions: underscoring the importance of E119A and H274Y. Antimicrob Agents Chemother 2014; 58:2718-30. [PMID: 24566185 DOI: 10.1128/aac.02628-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Influenza B viruses cause annual outbreaks of respiratory illness in humans and are increasingly recognized as a major cause of influenza-associated pediatric mortality. Neuraminidase (NA) inhibitors (NAIs) are the only available therapy for patients infected with influenza B viruses, and the potential emergence of NAI-resistant viruses is a public health concern. The NA substitutions located within the enzyme active site could not only reduce NAI susceptibility of influenza B virus but also affect virus fitness. In this study, we investigated the effect of single NA substitutions on the fitness of influenza B/Yamanashi/166/1998 viruses (Yamagata lineage). We generated recombinant viruses containing either wild-type (WT) NA or NA with a substitution in the catalytic (R371K) or framework (E119A, D198E, D198Y, I222T, H274Y, and N294S) residues. We assessed NAI susceptibility, NA biochemical properties, NA protein expression, and virus replication in vitro and in differentiated normal human bronchial epithelial (NHBE) cells. Our results showed that four NA substitutions (D198E, I222T, H274Y, and N294S) conferred reduced inhibition by oseltamivir and three (E119A, D198Y, and R371K) conferred highly reduced inhibition by oseltamivir, zanamivir, and peramivir. All NA substitutions, except for D198Y and R371K, were genetically stable after seven passages in MDCK cells. Cell surface NA protein expression was significantly increased by H274Y and N294S substitutions. Viruses with the E119A, I222T, H274Y, or N294S substitution were not attenuated in replication efficiency in vitro or in NHBE cells. Overall, viruses with the E119A or H274Y NA substitution possess fitness comparable to NAI-susceptible virus, and the acquisition of these substitutions by influenza B viruses should be closely monitored.
Collapse
|
34
|
Yu H, Griffiths TM. pKa cycling of the general acid/base in glycoside hydrolase families 33 and 34. Phys Chem Chem Phys 2014; 16:5785-92. [DOI: 10.1039/c4cp00351a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|