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Liang Y. Pathogenicity and virulence of influenza. Virulence 2023; 14:2223057. [PMID: 37339323 DOI: 10.1080/21505594.2023.2223057] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
Influenza viruses, including four major types (A, B, C, and D), can cause mild-to-severe and lethal diseases in humans and animals. Influenza viruses evolve rapidly through antigenic drift (mutation) and shift (reassortment of the segmented viral genome). New variants, strains, and subtypes have emerged frequently, causing epidemic, zoonotic, and pandemic infections, despite currently available vaccines and antiviral drugs. In recent years, avian influenza viruses, such as H5 and H7 subtypes, have caused hundreds to thousands of zoonotic infections in humans with high case fatality rates. The likelihood of these animal influenza viruses acquiring airborne transmission in humans through viral evolution poses great concern for the next pandemic. Severe influenza viral disease is caused by both direct viral cytopathic effects and exacerbated host immune response against high viral loads. Studies have identified various mutations in viral genes that increase viral replication and transmission, alter tissue tropism or species specificity, and evade antivirals or pre-existing immunity. Significant progress has also been made in identifying and characterizing the host components that mediate antiviral responses, pro-viral functions, or immunopathogenesis following influenza viral infections. This review summarizes the current knowledge on viral determinants of influenza virulence and pathogenicity, protective and immunopathogenic aspects of host innate and adaptive immune responses, and antiviral and pro-viral roles of host factors and cellular signalling pathways. Understanding the molecular mechanisms of viral virulence factors and virus-host interactions is critical for the development of preventive and therapeutic measures against influenza diseases.
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Affiliation(s)
- Yuying Liang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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2
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Hickerson BT, Petrovskaya SN, Dickensheets H, Donnelly RP, Ince WL, Ilyushina NA. Impact of Baloxavir Resistance-Associated Substitutions on Influenza Virus Growth and Drug Susceptibility. J Virol 2023; 97:e0015423. [PMID: 37404185 PMCID: PMC10373543 DOI: 10.1128/jvi.00154-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/10/2023] [Indexed: 07/06/2023] Open
Abstract
Baloxavir marboxil (baloxavir) is a recently FDA-approved influenza virus polymerase acidic (PA) endonuclease inhibitor. Several PA substitutions have been demonstrated to confer reduced susceptibility to baloxavir; however, their impacts on measurements of antiviral drug susceptibility and replication capacity when present as a fraction of the viral population have not been established. We generated recombinant A/California/04/09 (H1N1)-like viruses (IAV) with PA I38L, I38T, or E199D substitutions and B/Victoria/504/2000-like virus (IBV) with PA I38T. These substitutions reduced baloxavir susceptibility by 15.3-, 72.3-, 5.4-, and 54.5-fold, respectively, when tested in normal human bronchial epithelial (NHBE) cells. We then assessed the replication kinetics, polymerase activity, and baloxavir susceptibility of the wild-type:mutant (WT:MUT) virus mixtures in NHBE cells. The percentage of MUT relative to WT virus necessary to detect reduced baloxavir susceptibility in phenotypic assays ranged from 10% (IBV I38T) to 92% (IAV E199D). While I38T did not alter IAV replication kinetics or polymerase activity, IAV PA I38L and E199D MUTs and the IBV PA I38T MUT exhibited reduced replication levels and significantly altered polymerase activity. Differences in replication were detectable when the MUTs comprised ≥90%, ≥90%, or ≥75% of the population, respectively. Droplet digital PCR (ddPCR) and next-generation sequencing (NGS) analyses showed that WT viruses generally outcompeted the respective MUTs after multiple replication cycles and serial passaging in NHBE cells when initial mixtures contained ≥50% of the WT viruses; however, we also identified potential compensatory substitutions (IAV PA D394N and IBV PA E329G) that emerged and appeared to improve the replication capacity of baloxavir-resistant virus in cell culture. IMPORTANCE Baloxavir marboxil, an influenza virus polymerase acidic endonuclease inhibitor, represents a recently approved new class of influenza antivirals. Treatment-emergent resistance to baloxavir has been observed in clinical trials, and the potential spread of resistant variants could diminish baloxavir effectiveness. Here, we report the impact of the proportion of drug-resistant subpopulations on the ability to detect resistance in clinical isolates and the impact of substitutions on viral replication of mixtures containing both drug-sensitive and drug-resistant variants. We also show that ddPCR and NGS methods can be successfully used for detection of resistant subpopulations in clinical isolates and to quantify their relative abundance. Taken together, our data shed light on the potential impact of baloxavir-resistant I38T/L and E199D substitutions on baloxavir susceptibility and other biological properties of influenza virus and the ability to detect resistance in phenotypic and genotypic assays.
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Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Svetlana N. Petrovskaya
- Division of Biotechnology Review and Research III, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Harold Dickensheets
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
| | - William L. Ince
- Division of Antivirals, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, Maryland, USA
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3
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Oh DY, Milde J, Ham Y, Ramos Calderón JP, Wedde M, Dürrwald R, Duwe SC. Preparing for the Next Influenza Season: Monitoring the Emergence and Spread of Antiviral Resistance. Infect Drug Resist 2023; 16:949-959. [PMID: 36814825 PMCID: PMC9939793 DOI: 10.2147/idr.s389263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/17/2023] Open
Abstract
Purpose The relaxation of pandemic restrictions in 2022 has led to a reemergence of respiratory virus circulation worldwide and anticipation of substantial influenza waves for the 2022/2023 Northern Hemisphere winter. Therefore, the antiviral susceptibility profiles of human influenza viruses circulating in Germany were characterized. Methods Between October 2019 (week 40/2019) and March 2022 (week 12/2022), nasal swabs from untreated patients with acute respiratory symptoms were collected in the national German influenza surveillance system. A total of 598 influenza viruses were isolated and analyzed for susceptibility to oseltamivir, zanamivir and peramivir, using a neuraminidase (NA) inhibition assay. In addition, next-generation sequencing was applied to assess molecular markers of resistance to NA, cap-dependent endonuclease (PA) and M2 ion channel inhibitors (NAI, PAI, M2I) in 367 primary clinical samples. Furthermore, a genotyping assay based on RT-PCR and pyrosequencing to rapidly assess the molecular resistance marker PA-I38X in PA genes was designed and established. Results While NAI resistance in the strict sense, defined by a ≥ 10-fold (influenza A) or ≥5-fold (influenza B) increase of NAI IC50, was not detected, a subtype A(H1N1)pdm09 isolate displayed 2.3- to 7.5-fold IC50 increase for all three NAI. This isolate carried the NA-S247N substitution, which is known to enhance NAI resistance induced by NA-H275Y. All sequenced influenza A viruses carried the M2-S31N substitution, which confers resistance to M2I. Of note, one A(H3N2) virus displayed the PA-I38M substitution, which is associated with reduced susceptibility to the PAI baloxavir marboxil. Pyrosequencing analysis confirmed these findings in the original clinical specimen and in cultured virus isolate, suggesting sufficient replicative fitness of this virus mutant. Conclusion Over the last three influenza seasons, the vast majority of influenza viruses in this national-level sentinel were susceptible to NAIs and PAIs. These findings support the use of antivirals in the upcoming influenza season.
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Affiliation(s)
- Djin-Ye Oh
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Jeanette Milde
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Youngsun Ham
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Julia Patricia Ramos Calderón
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Marianne Wedde
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Ralf Dürrwald
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
| | - Susanne C Duwe
- Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza and Other Respiratory Viruses, National Influenza Center, Berlin, Germany
- Correspondence: Susanne C Duwe, Robert Koch Institute, Department 1: Infectious Diseases, Unit 17: Influenza Viruses and Other Respiratory Viruses | National Influenza Center, Seestr. 10, Berlin, 13353, Germany, Tel +49 30 18754 2283, Fax +49 30 18754 2699, Email
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Effect of Baloxavir and Oseltamivir in Combination on Infection with Influenza Viruses with PA/I38T or PA/E23K Substitutions in the Ferret Model. mBio 2022; 13:e0105622. [PMID: 35938724 PMCID: PMC9426601 DOI: 10.1128/mbio.01056-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Amino acid substitutions I38T and E23K in the influenza polymerase acidic (PA) protein lead to reduced susceptibility to the influenza antiviral drug baloxavir. The in vivo effectiveness of baloxavir and oseltamivir for treatment of these viruses is currently unknown. Using patient-derived influenza isolates, combination therapy was equally effective as monotherapy in reducing viral titers in the upper respiratory tract of ferrets infected with A(H1N1pdm09)-PA/E23K or A(H3N2)-PA/I38T. When treated with baloxavir plus oseltamivir, infection with a mixture of PA/I38T or PA/E23K and corresponding wild-type virus was characterized by a lower selection of viruses with reduced baloxavir susceptibility over the course of infection compared to baloxavir monotherapy. De novo emergence of the oseltamivir resistance mutation NA/H275Y occurred in ferrets treated with oseltamivir alone but not in ferrets treated with baloxavir plus oseltamivir. Our data suggest that combination therapy with influenza drugs with different mechanisms of action decreased the selection pressure for viruses with reduced drug susceptibility.
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Pleiotropic Effects of Influenza H1, H3, and B Baloxavir-Resistant Substitutions on Replication, Sensitivity to Baloxavir, and Interferon Expression. Antimicrob Agents Chemother 2022; 66:e0000922. [PMID: 35262375 DOI: 10.1128/aac.00009-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Baloxavir is an anti-influenza endonuclease inhibitor that targets the polymerase acidic (PA) protein of influenza A and B viruses. Our knowledge regarding the pleiotropic effects of baloxavir resistance-associated substitutions is limited. We generated recombinant A/California/04/09 (H1N1)-, A/Hong Kong/218849/2006 (H3N2)-, and B/Victoria/504/2000-like viruses that contained PA substitutions identified in baloxavir clinical trials and surveillance that could potentially be associated with baloxavir resistance. We characterized their susceptibility to baloxavir, impact on polymerase activity, viral growth, and ability to induce interferon (IFN) and IFN-stimulated genes expression in vitro. Four PA substitutions, H1N1 I38L/T, E199D, and B G199R, significantly reduced the sensitivity of the recombinant viruses to baloxavir (14.1-fold). We confirmed our findings by using the luciferase-based ribonucleoprotein minigenome assay and by using virus yield reduction assay in Calu-3 and normal human bronchial epithelial (NHBE) cells. We observed that I38L and E199D resulted in decreased viral replication of the H1N1 wild-type virus (1.4-fold) but the H1N1 I38T and B G199R substitutions did not significantly alter replication capacity in Calu-3 cells. In addition, H1N1 variants with PA I38L/T and E199D induced significantly higher levels of IFNB1 gene expression compared to the wild-type virus (4.2-fold). In contrast, the B variant, G199R, triggered the lowest levels of IFN genes in Calu-3 cells (1.6-fold). Because baloxavir is a novel anti-influenza therapeutic agent, identifying and characterizing substitutions associated with reduced sensitivity to baloxavir, as well as the impact of these substitutions on viral fitness, is paramount to the strategic implementation of this novel countermeasure.
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Mhamdi Z, Carbonneau J, Venable MC, Baz M, Abed Y, Boivin G. Replication and transmission of an influenza A(H3N2) virus harboring the polymerase acidic I38T substitution, in guinea pigs. J Gen Virol 2021; 102. [PMID: 34661516 DOI: 10.1099/jgv.0.001659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The polymerase acidic (PA) I38T substitution is a dominant marker of resistance to baloxavir. We evaluated the impact of I38T on the fitness of a contemporary influenza A(H3N2) virus. Influenza A/Switzerland/9715293/2013 (H3N2) wild-type (WT) virus and its I38T mutant were rescued by reverse genetics. Replication kinetics were compared using ST6GalI-MDCK and A549 cells and infectivity/contact transmissibility were evaluated in guinea pigs. Nasal wash (NW) viral titres were determined by TCID50 ml-1 in ST6GalI-MDCK cells. Competition experiments were performed and the evolution of viral population was assessed by droplet digital RT-PCR. I38T did not alter in vitro replication. I38T induced comparable titres vs the WT in guinea pigs NWs and the two viruses transmitted equally by direct contact. However, a 50 %:50 % mixture inoculum evolved to mean WT/I38T ratios of 71 %:29 % and 66.4 %:33.6 % on days 4 and 6 p.i., respectively. Contemporary influenza A(H3N2)-I38T PA variants may conserve a significant level of viral fitness.
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Affiliation(s)
- Zeineb Mhamdi
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
| | - Julie Carbonneau
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
| | - Marie-Christine Venable
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
| | - Mariana Baz
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
| | - Yacine Abed
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
| | - Guy Boivin
- Research Center in Infectious Diseases of the "CHU de Québec" and Laval University, Québec City, Québec, Canada
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Baloxavir Treatment Delays Influenza B Virus Transmission in Ferrets and Results in Limited Generation of Drug-Resistant Variants. Antimicrob Agents Chemother 2021; 65:e0113721. [PMID: 34424039 DOI: 10.1128/aac.01137-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Clinical efficacy of the influenza antiviral baloxavir marboxil (baloxavir) is compromised by treatment-emergent variants harboring a polymerase acidic protein I38T (isoleucine-38-threonine) substitution. However, the fitness of I38T-containing influenza B viruses (IBVs) remains inadequately defined. After the pharmacokinetics of the compound were confirmed in ferrets, animals were injected subcutaneously with 8 mg/kg of baloxavir acid (BXA) at 24 h postinoculation with recombinant BXA-sensitive (BXA-Sen, I38) or BXA-resistant (BXA-Res, I38T) B/Brisbane/60/2008 (Victoria lineage) virus. BXA treatment of donor ferrets reduced virus replication and delayed transmission of the BXA-Sen but not the BXA-Res IBV. The I38 genotype remained dominant in the BXA-Sen-infected animals, even with BXA treatment. In competitive-mixture experiments, no transmission to aerosol contacts was seen from BXA-treated donors coinfected with the BXA-Sen and BXA-Res B/Brisbane/60/2008 viruses. However, in parallel mixed infections with the B/Phuket/3073/2013 (Yamagata lineage) virus background, BXA treatment failed to block airborne transmission of the BXA-Res virus, and the I38T genotype generally predominated. Therefore, the relative fitness of BXA-Res IBVs is complex and dependent on the virus backbone and within-host virus competition. BXA treatment of single-virus-infected ferrets hampers aerosol transmission of the BXA-Sen virus and does not readily generate BXA-Res variants, whereas mixed infections may result in propagation of BXA-Res IBVs of the Yamagata lineage. Our findings confirm the antiviral potency of baloxavir against IBVs, while supporting optimization of the dosing regimen to maximize clinical benefit.
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Jones JC, Pascua PNQ, Harrington WN, Webby RJ, Govorkova EA. Multiple polymerase acidic (PA) I38X substitutions in influenza A(H1N1)pdm09 virus permit polymerase activity and cause reduced baloxavir inhibition. J Antimicrob Chemother 2021; 76:957-960. [PMID: 33351916 DOI: 10.1093/jac/dkaa527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/18/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Baloxavir marboxil is an antiviral drug that targets the endonuclease activity of the influenza virus polymerase acidic (PA) protein. PA I38T/M/F substitutions reduce its antiviral efficacy. OBJECTIVES To understand the effects of the 19 possible amino acid (AA) substitutions at PA 38 on influenza A(H1N1)pdm09 polymerase activity and inhibition by baloxavir acid, the active metabolite of baloxavir marboxil. METHODS Influenza A(H1N1)pdm09 viral polymerase complexes containing all 19 I38X AA substitutions were reconstituted in HEK293T cells in a mini-replicon assay. Polymerase complex activity and baloxavir inhibitory activity were measured in the presence or absence of 50 nM baloxavir acid. RESULTS Only three substitutions (R, K, P) reduced polymerase activity to <79% of I38-WT. When compared with the prototypical baloxavir marboxil resistance marker T38, 5 substitutions conferred 10%-35% reductions in baloxavir acid inhibitory activity (M, L, F, Y, C) and 11 substitutions conferred >50% reductions (R, K, S, N, G, W, A, Q, E, D, H), while two substitutions (V, P) maintained baloxavir acid inhibitory activity. CONCLUSIONS Most PA 38 substitutions permit a functional replication complex retaining some drug resistance in the mini-replicon assay. This study provides a targeted approach for virus rescue and analysis of novel baloxavir marboxil reduced-susceptibility markers, supports the consideration of a broader range of these markers during antiviral surveillance and adds to the growing knowledge of baloxavir marboxil resistance profiles.
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Affiliation(s)
- Jeremy C Jones
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Philippe N Q Pascua
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walter N Harrington
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elena A Govorkova
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
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Whole-Genome Analysis Surveillance of Influenza A Virus Resistance to Polymerase Complex Inhibitors in Eastern Spain from 2016 to 2019. Antimicrob Agents Chemother 2021; 65:AAC.02718-20. [PMID: 33782005 DOI: 10.1128/aac.02718-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Molecular surveillance by whole-genome sequencing was used to monitor the susceptibility of circulating influenza A viruses to three polymerase complex inhibitors. A total of 12 resistance substitutions were found among 285 genomes analyzed, but none were associated with high levels of resistance. Natural resistance to these influenza A antivirals is currently uncommon.
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Lee LY, Zhou J, Koszalka P, Frise R, Farrukee R, Baba K, Miah S, Shishido T, Galiano M, Hashimoto T, Omoto S, Uehara T, Mifsud EJ, Collinson N, Kuhlbusch K, Clinch B, Wildum S, Barclay WS, Hurt AC. Evaluating the fitness of PA/I38T-substituted influenza A viruses with reduced baloxavir susceptibility in a competitive mixtures ferret model. PLoS Pathog 2021; 17:e1009527. [PMID: 33956888 PMCID: PMC8130947 DOI: 10.1371/journal.ppat.1009527] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/18/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
Baloxavir is approved in several countries for the treatment of uncomplicated influenza in otherwise-healthy and high-risk patients. Treatment-emergent viruses with reduced susceptibility to baloxavir have been detected in clinical trials, but the likelihood of widespread occurrence depends on replication capacity and onward transmission. We evaluated the fitness of A/H3N2 and A/H1N1pdm09 viruses with the polymerase acidic (PA) I38T-variant conferring reduced susceptibility to baloxavir relative to wild-type (WT) viruses, using a competitive mixture ferret model, recombinant viruses and patient-derived virus isolates. The A/H3N2 PA/I38T virus showed a reduction in within-host fitness but comparable between-host fitness to the WT virus, while the A/H1N1pdm09 PA/I38T virus had broadly similar within-host fitness but substantially lower between-host fitness. Although PA/I38T viruses replicate and transmit between ferrets, our data suggest that viruses with this amino acid substitution have lower fitness relative to WT and this relative fitness cost was greater in A/H1N1pdm09 viruses than in A/H3N2 viruses. Influenza viruses are associated with considerable disease burden and circulate annually causing seasonal epidemics. Antiviral drugs can be used to treat influenza infections and help reduce the disease burden. Occasionally, treatment can lead to the emergence of viruses with reduced antiviral susceptibility. Normally such viruses have reduced ‘fitness’, meaning they do not tend to spread or transmit widely, however on rare occasions, oseltamivir-resistant variants have become widespread in the community, thereby reducing the utility of the drug for treatment. Baloxavir is an antiviral recently licensed in many parts of the world for the treatment of influenza. Viruses with reduced susceptibility to baloxavir have been observed in clinical trials, but the frequency of such variants in the community has remained low (<0.1% globally since 2017–2018). We evaluated the fitness of viruses in ferrets and found that although A/H1N1 and A/H3N2 viruses with reduced baloxavir susceptibility were able to replicate and transmit among ferrets, they had a moderate reduction in fitness compared to normal ‘wild-type’ viruses, suggesting a reduced likelihood of spread. Surveillance to monitor for the frequency of viruses with reduced baloxavir susceptibility remains important.
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Affiliation(s)
- Leo Y Lee
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paulina Koszalka
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Biomedicine Discovery Institute & Department of Microbiology, Monash University, Victoria, Australia
| | - Rebecca Frise
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Rubaiyea Farrukee
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | | | | | | | | | | | | | | | - Edin J Mifsud
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | | | | | - Barry Clinch
- Roche Products Ltd, Welwyn Garden City, United Kingdom
| | | | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia.,F. Hoffmann-La Roche Ltd, Basel, Switzerland
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Abstract
Baloxavir marboxil (Xofluza®; hereafter referred to as baloxavir), the prodrug of baloxavir acid, is a first-in-class, small molecule inhibitor of the polymerase acidic (PA) protein subunit of the influenza virus polymerase complex. Baloxavir (after conversion to baloxavir acid) acts to block influenza virus replication by inhibiting the cap-dependent endonuclease activity of the PA protein. Taken orally as a single dose, baloxavir is approved in the USA for the treatment of acute uncomplicated influenza in patients ≥ 12 years of age who have been symptomatic for ≤ 48 h. Data from randomized, double-blind, placebo- and oseltamivir-controlled phase III trials have shown that baloxavir is efficacious in improving influenza symptoms both in otherwise healthy adolescents and adults and in those at high risk of influenza complications, displaying similar efficacy to that of oseltamivir. Furthermore, there is evidence that baloxavir can reduce influenza viral load more rapidly than oseltamivir. Baloxavir has activity against influenza A and B viruses (including strains resistant to neuraminidase inhibitors) and is well tolerated. Evidence of the emergence and likely human-to-human transmission of variant viruses with reduced susceptibility to baloxavir highlights the importance of monitoring and surveillance for changes in influenza virus drug susceptibility patterns. However, currently available evidence suggests that baloxavir, with the benefits of a single oral dose regimen, provides a useful alternative to neuraminidase inhibitors for the treatment of acute uncomplicated influenza in adolescents and adults.
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Affiliation(s)
- Matt Shirley
- Springer Nature, Private Bag 65901, Mairangi Bay, Auckland, 0754, New Zealand.
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12
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Hashimoto T, Baba K, Inoue K, Okane M, Hata S, Shishido T, Naito A, Wildum S, Omoto S. Comprehensive assessment of amino acid substitutions in the trimeric RNA polymerase complex of influenza A virus detected in clinical trials of baloxavir marboxil. Influenza Other Respir Viruses 2020; 15:389-395. [PMID: 33099886 PMCID: PMC8051730 DOI: 10.1111/irv.12821] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 01/18/2023] Open
Abstract
Background Baloxavir marboxil (BXM) is an approved drug that selectively targets cap‐dependent endonuclease on PA subunit in the RNA polymerase complex of influenza A and B viruses. Amino acid substitutions at position 38 in the PA subunit were identified as a major pathway for reduced susceptibility to baloxavir acid (BXA), the active form of BXM. Additionally, substitutions found at positions E23, A37, and E199 in the PA subunit impact BXA susceptibility by less than 10‐fold. Methods We comprehensively evaluated the impact of novel amino acid substitutions identified in PA, PB1, and PB2 subunits in BXM clinical trials and influenza sequence databases by means of drug susceptibility and replicative capacity. Results PA/I38N in A(H1N1)pdm09 and PA/I38R in A(H3N2) were newly identified as treatment‐emergent substitutions in the CAPSTONE‐2 study. The I38N substitution conferred reduced susceptibility by 24‐fold, whereas replicative capacity of the I38N‐substituted virus was impaired compared with the wild‐type. The I38R‐substituted virus was not viable in cell culture. All other mutations assessed in this extensive study did not significantly affect BXA susceptibility (< 2.4‐fold change). Conclusion These results provide additional information on the impact of amino acid substitutions in the trimeric viral polymerase complex to BXA susceptibility and will further support influenza surveillance.
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Affiliation(s)
- Takashi Hashimoto
- Shionogi & Co., Ltd., Osaka, Japan.,Shionogi Techno Advance Research, Co., Ltd., Osaka, Japan
| | | | - Kae Inoue
- Shionogi Techno Advance Research, Co., Ltd., Osaka, Japan
| | - Miyako Okane
- Shionogi Techno Advance Research, Co., Ltd., Osaka, Japan
| | - Satoshi Hata
- Shionogi Techno Advance Research, Co., Ltd., Osaka, Japan
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Porter DP, Guo Y, Perry J, Gossage DL, Watkins TR, Chien JW, Jordan R. Assessment of Drug Resistance during Phase 2b Clinical Trials of Presatovir in Adults Naturally Infected with Respiratory Syncytial Virus. Antimicrob Agents Chemother 2020; 64:e02312-19. [PMID: 32071058 PMCID: PMC7449164 DOI: 10.1128/aac.02312-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 02/04/2023] Open
Abstract
This study summarizes drug resistance analyses in 4 recent phase 2b trials of the respiratory syncytial virus (RSV) fusion inhibitor presatovir in naturally infected adults. Adult hematopoietic cell transplant (HCT) recipients, lung transplant recipients, or hospitalized patients with naturally acquired, laboratory-confirmed RSV infection were enrolled in 4 randomized, double-blind, placebo-controlled studies with study-specific presatovir dosing. Full-length RSV F sequences amplified from nasal swabs obtained at baseline and postbaseline were analyzed by population sequencing. Substitutions at RSV fusion inhibitor resistance-associated positions are reported. Genotypic analyses were performed on 233 presatovir-treated and 149 placebo-treated subjects. RSV F variant V127A was present in 8 subjects at baseline. Population sequencing detected treatment-emergent substitutions in 10/89 (11.2%) HCT recipients with upper and 6/29 (20.7%) with lower respiratory tract infection, 1/35 (2.9%) lung transplant recipients, and 1/80 (1.3%) hospitalized patients treated with presatovir; placebo-treated subjects had no emergent resistance-associated substitutions. Subjects with substitutions at resistance-associated positions had smaller decreases in viral load during treatment relative to those without, but they had similar clinical outcomes. Subject population type and dosing regimen may have influenced RSV resistance development during presatovir treatment. Subjects with genotypic resistance development had decreased virologic responses compared to those without genotypic resistance but had comparable clinical outcomes.
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Affiliation(s)
| | - Ying Guo
- Gilead Sciences, Inc., Foster City, California, USA
| | - Jason Perry
- Gilead Sciences, Inc., Foster City, California, USA
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14
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Patel MC, Mishin VP, De La Cruz JA, Chesnokov A, Nguyen HT, Wilson MM, Barnes J, Kondor RJG, Wentworth DE, Gubareva LV. Detection of baloxavir resistant influenza A viruses using next generation sequencing and pyrosequencing methods. Antiviral Res 2020; 182:104906. [PMID: 32798601 PMCID: PMC7426223 DOI: 10.1016/j.antiviral.2020.104906] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 11/11/2022]
Abstract
Baloxavir, a new antiviral drug targeting cap-dependent endonuclease activity of polymerase acidic (PA) protein of influenza viruses, is now approved in multiple countries. Several substitutions at isoleucine 38 in PA protein (e.g., PA-I38T) have been associated with decreased baloxavir susceptibility in vitro and in vivo. In recent years, next generation sequencing (NGS) analysis and pyrosequencing have been used by CDC and U.S. Public Health Laboratories to monitor drug susceptibility of influenza viruses. Here we described an improved pyrosequencing assay for detecting influenza A viruses carrying substitutions at PA-38. Cyclic and customized orders of nucleotide dispensation were evaluated, and pyrosequencing results were compared to those generated using NGS. Our data showed that the customized nucleotide dispensation has improved the pyrosequencing assay performance in identification of double mixtures (e.g., PA-38I/T); however, identification of PA-38 variants in triple mixtures remains a challenge. While NGS analysis indicated the presence of PA-I38K in one clinical specimen and isolate, our attempts to detect this mutation by pyrosequencing or recover the virus carrying PA-I38K in cell culture were unsuccessful, raising a possibility of a rarely occurring sequencing error. Overall, pyrosequencing provides a convenient means to detect baloxavir resistant influenza viruses when NGS is unavailable or a faster turnaround time is required. Pyrosequencing assay was optimized to improve detection of baloxavir resistant influenza A viruses in mixtures. Detection of PA-38 variants in virus mixtures of both subtypes was improved by using customized nucleotide dispensation. Pyrosequencing and NGS data were comparable, except for lysine at PA-38 that was detected by NGS but not by pyrosequencing. Attempts to recover virus carrying lysine at PA-38 were unsuccessful, raising the rare possibility of an NGS artifact. Pyrosequencing provides an important addition to genotypic methods that can be used for baloxavir susceptibility testing.
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Affiliation(s)
- Mira C Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - Vasiliy P Mishin
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - Juan A De La Cruz
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA; Battelle Memorial Institute, Atlanta, GA, USA
| | - Anton Chesnokov
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - Ha T Nguyen
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA; Battelle Memorial Institute, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - John Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca J G Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA
| | - Larisa V Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers of Disease Control and Prevention, Atlanta, GA, USA.
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15
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Toots M, Plemper RK. Next-generation direct-acting influenza therapeutics. Transl Res 2020; 220:33-42. [PMID: 32088166 PMCID: PMC7102518 DOI: 10.1016/j.trsl.2020.01.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
Influenza viruses are a major threat to human health globally. In addition to further improving vaccine prophylaxis, disease management through antiviral therapeutics constitutes an important component of the current intervention strategy to prevent advance to complicated disease and reduce case-fatality rates. Standard-of-care is treatment with neuraminidase inhibitors that prevent viral dissemination. In 2018, the first mechanistically new influenza drug class for the treatment of uncomplicated seasonal influenza in 2 decades was approved for human use. Targeting the PA endonuclease subunit of the viral polymerase complex, this class suppresses viral replication. However, the genetic barrier against viral resistance to both drug classes is low, pre-existing resistance is observed in circulating strains, and resistant viruses are pathogenic and transmit efficiently. Addressing the resistance problem has emerged as an important objective for the development of next-generation influenza virus therapeutics. This review will discuss the status of influenza therapeutics including the endonuclease inhibitor baloxavir marboxil after its first year of clinical use and evaluate a subset of direct-acting antiviral candidates in different stages of preclinical and clinical development.
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Affiliation(s)
- Mart Toots
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia.
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16
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Toots M, Yoon JJ, Hart M, Natchus MG, Painter GR, Plemper RK. Quantitative efficacy paradigms of the influenza clinical drug candidate EIDD-2801 in the ferret model. Transl Res 2020; 218:16-28. [PMID: 31945316 PMCID: PMC7568909 DOI: 10.1016/j.trsl.2019.12.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
Abstract
Seasonal influenza viruses cause major morbidity and mortality worldwide, threatening in particular older adults and the immunocompromised. Two classes of influenza therapeutics dominate current disease management, but both are compromised by pre-existing or rapidly emerging viral resistance. We have recently reported a novel ribonucleoside analog clinical candidate, EIDD-2801, that combines potent antiviral efficacy in ferrets and human airway epithelium cultures with a high barrier against viral escape. In this study, we established fundamental EIDD-2801 efficacy paradigms against pandemic and seasonal influenza A virus (IAV) strains in ferrets that can be used to inform exposure targets and treatment regimens. Based on reduction of shed virus titers, alleviation of clinical signs, and lowered virus burden in upper and lower respiratory tract tissues, lowest efficacious oral dose concentrations of EIDD-2801, given twice daily, were 2.3 and 7 mg/kg of body weight against seasonal and pandemic IAVs, respectively. The latest opportunity for initiation of efficacious treatment was 36 hours after infection of ferrets. Administered in 12-hour intervals, three 7 mg/kg doses of EIDD-2801 were sufficient for maximal therapeutic benefit against a pandemic IAV and significantly shortened the time to resolution of clinical signs. Ferrets infected with pandemic IAV and treated following the minimally efficacious EIDD-2801 regimen demonstrated significantly less shed virus and inflammatory cellular infiltrates in nasal lavages, but mounted a robust humoral antiviral response after recovery that was indistinguishable from that of vehicle-treated animals. These results provide an experimental basis in a human disease-relevant influenza animal model for clinical testing of EIDD-2801.
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Affiliation(s)
- Mart Toots
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Jeong-Joong Yoon
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Michael Hart
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia
| | - Michael G Natchus
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia
| | - George R Painter
- Emory Institute for Drug Development, Emory University, Atlanta, Georgia; Department of Pharmacology, Emory University, Atlanta, Georgia
| | - Richard K Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia.
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17
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Influenza A and B viruses with reduced baloxavir susceptibility display attenuated in vitro fitness but retain ferret transmissibility. Proc Natl Acad Sci U S A 2020; 117:8593-8601. [PMID: 32217734 DOI: 10.1073/pnas.1916825117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Baloxavir marboxil (BXM) was approved in 2018 for treating influenza A and B virus infections. It is a first-in-class inhibitor targeting the endonuclease activity of the virus polymerase acidic (PA) protein. Clinical trial data revealed that PA amino acid substitutions at residue 38 (I38T/F/M) reduced BXM potency and caused virus rebound in treated patients, although the fitness characteristics of the mutant viruses were not fully defined. To determine the fitness impact of the I38T/F/M substitutions, we generated recombinant A/California/04/2009 (H1N1)pdm09, A/Texas/71/2017 (H3N2), and B/Brisbane/60/2008 viruses with I38T/F/M and examined drug susceptibility in vitro, enzymatic properties, replication efficiency, and transmissibility in ferrets. Influenza viruses with I38T/F/M substitutions exhibited reduced baloxavir susceptibility, with 38T causing the greatest reduction. The I38T/F/M substitutions impaired PA endonuclease activity as compared to that of wild-type (I38-WT) PA. However, only 38T/F A(H3N2) substitutions had a negative effect on polymerase complex activity. The 38T/F substitutions decreased replication in cells among all viruses, whereas 38M had minimal impact. Despite variable fitness consequences in vitro, all 38T/M viruses disseminated to naive ferrets by contact and airborne transmission, while 38F-containing A(H3N2) and B viruses failed to transmit via the airborne route. Reversion of 38T/F/M to I38-WT was rare among influenza A viruses in this study, suggesting stable retention of 38T/F/M genotypes during these transmission events. BXM reduced susceptibility-associated mutations had variable effects on in vitro fitness of influenza A and B viruses, but the ability of these viruses to transmit in vivo indicates a risk of their spreading from BXM-treated individuals.
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18
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Makau JN, Watanabe K, Otaki H, Mizuta S, Ishikawa T, Kamatari YO, Nishida N. A Quinolinone Compound Inhibiting the Oligomerization of Nucleoprotein of Influenza A Virus Prevents the Selection of Escape Mutants. Viruses 2020; 12:v12030337. [PMID: 32204549 PMCID: PMC7150793 DOI: 10.3390/v12030337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of resistance to currently available anti-influenza drugs has heightened the need for antivirals with novel mechanisms of action. The influenza A virus (IAV) nucleoprotein (NP) is highly conserved and essential for the formation of viral ribonucleoprotein (vRNP), which serves as the template for replication and transcription. Recently, using in silico screening, we identified an antiviral compound designated NUD-1 (a 4-hydroxyquinolinone derivative) as a potential inhibitor of NP. In this study, we further analyzed the interaction between NUD-1 and NP and found that the compound interferes with the oligomerization of NP, which is required for vRNP formation, leading to the suppression of viral transcription, protein synthesis, and nuclear export of NP. We further assessed the selection of resistant variants by serially passaging a clinical isolate of the 2009 H1N1 pandemic influenza virus in the presence of NUD-1 or oseltamivir. NUD-1 did not select for resistant variants after nine passages, whereas oseltamivir selected for resistant variants after five passages. Our data demonstrate that NUD-1 interferes with the oligomerization of NP and less likely induces drug-resistant variants than oseltamivir; hence, it is a potential lead compound for the development of novel anti-influenza drugs.
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Affiliation(s)
- Juliann Nzembi Makau
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
| | - Ken Watanabe
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
- Department of Lifestyle Design, Faculty of Human Ecology, Yasuda Women’s University, 6-13-1 Yasuhigashi, Asaminami ward, Hiroshima 731-0153, Japan
- Correspondence: ; Tel.: +81-82-878-9139
| | - Hiroki Otaki
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (H.O.); (S.M.)
| | - Satoshi Mizuta
- Center for Bioinformatics and Molecular Medicine, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (H.O.); (S.M.)
| | - Takeshi Ishikawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan;
| | - Yuji O. Kamatari
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
| | - Noriyuki Nishida
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan; (J.N.M.); (N.N.)
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