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Hickerson BT, Huang BK, Petrovskaya SN, Ilyushina NA. Genomic Analysis of Influenza A and B Viruses Carrying Baloxavir Resistance-Associated Substitutions Serially Passaged in Human Epithelial Cells. Viruses 2023; 15:2446. [PMID: 38140689 PMCID: PMC10748225 DOI: 10.3390/v15122446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Baloxavir marboxil (baloxavir) is an FDA-approved inhibitor of the influenza virus polymerase acidic (PA) protein. Here, we used next-generation sequencing to compare the genomic mutational profiles of IAV H1N1 and H3N2, and IBV wild type (WT) and mutants (MUT) viruses carrying baloxavir resistance-associated substitutions (H1N1-PA I38L, I38T, and E199D; H3N2-PA I38T; and IBV-PA I38T) during passaging in normal human bronchial epithelial (NHBE) cells. We determined the ratio of nonsynonymous to synonymous nucleotide mutations (dN/dS) and identified the location and type of amino acid (AA) substitutions that occurred at a frequency of ≥30%. We observed that IAV H1N1 WT and MUT viruses remained relatively stable during passaging. While the mutational profiles for IAV H1N1 I38L, I38T, and E199D, and IBV I38T MUTs were relatively similar after each passage compared to the respective WTs, the mutational profile of the IAV H3N2 I38T MUT was significantly different for most genes compared to H3N2 WT. Our work provides insight into how baloxavir resistance-associated substitutions may impact influenza virus evolution in natural settings. Further characterization of the potentially adaptive mutations identified in this study is needed.
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Affiliation(s)
- Brady T. Hickerson
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Bruce K. Huang
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Svetlana N. Petrovskaya
- Division of Biotechnology Review and Research III, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Natalia A. Ilyushina
- Division of Biotechnology Review and Research II, Food and Drug Administration, Silver Spring, MD 20993, USA
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2
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Lobinska G, Pilpel Y, Nowak MA. Evolutionary safety of lethal mutagenesis driven by antiviral treatment. PLoS Biol 2023; 21:e3002214. [PMID: 37552682 PMCID: PMC10409280 DOI: 10.1371/journal.pbio.3002214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing lethal mutagenesis of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of mutants. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of such virus mutants as a function of the timing of treatment and the immune competence of patients, employing realistic assumptions about the vulnerability of the viral genome and its potential to generate viable mutants. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against Coronavirus Disease-2019 (COVID-19). We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment with this drug to individuals with a low immunological clearance rate and, in future, by designing treatments that lead to a greater increase in mutation rate. We report a simple mathematical rule to determine the fold increase in mutation rate required to obtain evolutionary safety that is also applicable to other pathogen-treatment combinations.
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Affiliation(s)
- Gabriela Lobinska
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin A. Nowak
- Department of Mathematics, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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3
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Smyk JM, Szydłowska N, Szulc W, Majewska A. Evolution of Influenza Viruses-Drug Resistance, Treatment Options, and Prospects. Int J Mol Sci 2022; 23:12244. [PMID: 36293099 PMCID: PMC9602850 DOI: 10.3390/ijms232012244] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Viral evolution refers to the genetic changes that a virus accumulates during its lifetime which can arise from adaptations in response to environmental changes or the immune response of the host. Influenza A virus is one of the most rapidly evolving microorganisms. Its genetic instability may lead to large changes in its biological properties, including changes in virulence, adaptation to new hosts, and even the emergence of infectious diseases with a previously unknown clinical course. Genetic variability makes it difficult to implement effective prophylactic programs, such as vaccinations, and may be responsible for resistance to antiviral drugs. The aim of the review was to describe the consequences of the variability of influenza viruses, mutations, and recombination, which allow viruses to overcome species barriers, causing epidemics and pandemics. Another consequence of influenza virus evolution is the risk of the resistance to antiviral drugs. Thus far, one class of drugs, M2 protein inhibitors, has been excluded from use because of mutations in strains isolated in many regions of the world from humans and animals. Therefore, the effectiveness of anti-influenza drugs should be continuously monitored in reference centers representing particular regions of the world as a part of epidemiological surveillance.
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Affiliation(s)
| | | | | | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland
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4
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Sousa TDC, Martins JSCC, Miranda MD, Garcia CC, Resende PC, Santos CA, Debur MDC, Rodrigues RR, Cavalcanti AC, Gregianini TS, Iani FCDM, Pereira FM, Fernandes SB, Ferreira JDA, Santos KCDO, Motta F, Brown D, de Almeida WAF, Siqueira MM, Matos ADR. Low prevalence of influenza A strains with resistance markers in Brazil during 2017-2019 seasons. Front Public Health 2022; 10:944277. [PMID: 36187691 PMCID: PMC9516282 DOI: 10.3389/fpubh.2022.944277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 08/15/2022] [Indexed: 01/21/2023] Open
Abstract
The influenza A virus (IAV) is of a major public health concern as it causes annual epidemics and has the potential to cause pandemics. At present, the neuraminidase inhibitors (NAIs) are the most widely used anti-influenza drugs, but, more recently, the drug baloxavir marboxil (BXM), a polymerase inhibitor, has also been licensed in some countries. Mutations in the viral genes that encode the antiviral targets can lead to treatment resistance. Worldwide, a low prevalence of antiviral resistant strains has been reported. Despite that, this situation can change rapidly, and resistant strain surveillance is a priority. Thus, the aim of this was to evaluate Brazilian IAVs antiviral resistance from 2017 to 2019 through the identification of viral mutations associated with reduced inhibition of the drugs and by testing the susceptibility of IAV isolates to oseltamivir (OST), the most widely used NAI drug in the country. Initially, we analyzed 282 influenza A(H1N1)pdm09 and 455 A(H3N2) genetic sequences available on GISAID. The amino acid substitution (AAS) NA:S247N was detected in one A(H1N1)pdm09 strain. We also identified NA:I222V (n = 6) and NA:N329K (n = 1) in A(H3N2) strains. In addition, we performed a molecular screening for NA:H275Y in 437 A(H1N1)pdm09 samples, by pyrosequencing, which revealed a single virus harboring this mutation. Furthermore, the determination of OST IC50 values for 222 A(H1N1)pdm09 and 83 A(H3N2) isolates revealed that all isolates presented a normal susceptibility profile to the drug. Interestingly, we detected one A(H3N2) virus presenting with PA:E119D AAS. Moreover, the majority of the IAV sequences had the M2:S31N adamantanes resistant marker. In conclusion, we show a low prevalence of Brazilian IAV strains with NAI resistance markers, in accordance with what is reported worldwide, indicating that NAIs still remain an option for the treatment of influenza infections in Brazil. However, surveillance of influenza resistance should be strengthened in the country for improving the representativeness of investigated viruses and the robustness of the analysis.
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Affiliation(s)
- Thiago das Chagas Sousa
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | | | - Milene Dias Miranda
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - Cristiana Couto Garcia
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - Cliomar A. Santos
- Laboratório Central de Saúde Publica de Sergipe (LACEN-SE), Aracaju, Sergipe, Brazil
| | | | - Rodrigo Ribeiro Rodrigues
- Laboratório de Saúde Pública do Estado do Espírito Santo, Secretaria de Saúde do Estado do Espírito Santo (LACEN-ES), Vitória, Espirito Santo, Brazil,Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Espirito Santo, Brazil
| | - Andrea Cony Cavalcanti
- Laboratório Central de Saúde Pública do Rio de Janeiro (LACEN-RJ), Rio de Janeiro, Brazil
| | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública da Secretaria de Saúde do estado do Rio Grande do Sul, (LACEN-RS)/CEVS/SES-RS, Porto Alegre, Rio Grande do Sul, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Fernando Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - David Brown
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - Walquiria Aparecida Ferreira de Almeida
- Departamento de Imunização e Doenças Transmissíveis (DEIDT)/Secretaria de Vigilância em Saúde (SVS)/Ministério da Saúde (MS), Brasília, Distrito Federal, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil
| | - Aline da Rocha Matos
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ Fundation, Rio de Janeiro, Brazil,*Correspondence: Aline da Rocha Matos
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5
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Predicting Permissive Mutations That Improve the Fitness of A(H1N1)pdm09 Viruses Bearing the H275Y Neuraminidase Substitution. J Virol 2022; 96:e0091822. [PMID: 35867563 PMCID: PMC9364793 DOI: 10.1128/jvi.00918-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Oseltamivir-resistant influenza viruses arise due to amino acid mutations in key residues of the viral neuraminidase (NA). These changes often come at a fitness cost; however, it is known that permissive mutations in the viral NA can overcome this cost. This result was observed in former seasonal A(H1N1) viruses in 2007 which expressed the H275Y substitution (N1 numbering) with no apparent fitness cost and lead to widespread oseltamivir resistance. Therefore, this study aims to predict permissive mutations that may similarly enable fit H275Y variants to arise in currently circulating A(H1N1)pdm09 viruses. The first approach in this study utilized in silico analyses to predict potentially permissive mutations. The second approach involved the generation of a virus library which encompassed all possible NA mutations while keeping H275Y fixed. Fit variants were then selected by serially passaging the virus library either through ferrets by transmission or passaging once in vitro. The fitness impact of selected substitutions was further evaluated experimentally. The computational approach predicted three candidate permissive NA mutations which, in combination with each other, restored the replicative fitness of an H275Y variant. The second approach identified a stringent bottleneck during transmission between ferrets; however, three further substitutions were identified which may improve transmissibility. A comparison of fit H275Y variants in vitro and in experimentally infected animals showed a statistically significant correlation in the variants that were positively selected. Overall, this study provides valuable tools and insights into potential permissive mutations that may facilitate the emergence of a fit H275Y A(H1N1)pdm09 variant. IMPORTANCE Oseltamivir (Tamiflu) is the most widely used antiviral for the treatment of influenza infections. Therefore, resistance to oseltamivir is a public health concern. This study is important as it explores the different evolutionary pathways available to current circulating influenza viruses that may lead to widespread oseltamivir resistance. Specifically, this study develops valuable experimental and computational tools to evaluate the fitness landscape of circulating A(H1N1)pmd09 influenza viruses bearing the H275Y mutation. The H275Y substitution is most commonly reported to confer oseltamivir resistance but also leads to loss of virus replication and transmission fitness, which limits its spread. However, it is known from previous influenza seasons that influenza viruses can evolve to overcome this loss of fitness. Therefore, this study aims to prospectively predict how contemporary A(H1N1)pmd09 influenza viruses may evolve to overcome the fitness cost of bearing the H275Y NA substitution, which could result in widespread oseltamivir resistance.
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6
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Uehara T, Hayden FG, Kawaguchi K, Omoto S, Hurt AC, De Jong MD, Hirotsu N, Sugaya N, Lee N, Baba K, Shishido T, Tsuchiya K, Portsmouth S, Kida H. Treatment-Emergent Influenza Variant Viruses With Reduced Baloxavir Susceptibility: Impact on Clinical and Virologic Outcomes in Uncomplicated Influenza. J Infect Dis 2019; 221:346-355. [DOI: 10.1093/infdis/jiz244] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023] Open
Abstract
Abstract
Background
Single-dose baloxavir rapidly reduces influenza virus titers and symptoms in patients with uncomplicated influenza, but viruses with reduced in vitro susceptibility due to amino acid substitutions at position 38 of polymerase acidic protein (PA/I38X) sometimes emerge.
Methods
We evaluated the kinetics, risk factors, and effects on clinical and virologic outcomes of emergence of PA/I38X-substituted viruses.
Results
Viruses containing PA/I38X substitutions were identified 3–9 days after baloxavir treatment in 9.7% (36/370) of patients, of whom 85.3% had transient virus titer rises. Median time to sustained cessation of infectious virus detection was 192, 48, and 96 hours in the baloxavir recipients with PA/I38X-substituted viruses, without PA/I38X-substituted viruses, and placebo recipients, respectively. The corresponding median times to alleviation of symptoms were 63.1, 51.0, and 80.2 hours, respectively. After day 5, symptom increases occurred in 11.5%, 8.0%, and 13.0%, respectively, and in 8.9% of oseltamivir recipients. Variant virus emergence was associated with lower baseline neutralizing antibody titers.
Conclusions
The emergence of viruses with PA/I38X substitutions following baloxavir treatment was associated with transient rises in infectious virus titers, prolongation of virus detectability, initial delay in symptom alleviation, and uncommonly with symptom rebound. The potential transmissibility of PA/I38X-substituted viruses requires careful study.
Clinical Trial Registration
NCT02954354.
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Affiliation(s)
| | | | | | | | - Aeron C Hurt
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
| | - Menno D De Jong
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, the Netherlands
| | | | - Norio Sugaya
- Department of Pediatrics, Keiyu Hospital, Yokohama, Japan
| | - Nelson Lee
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
| | | | | | | | | | - Hiroshi Kida
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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7
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Akand EH, Downard KM. Mechanisms of antiviral resistance in influenza neuraminidase revealed by a mass spectrometry based phylonumerics approach. Mol Phylogenet Evol 2019; 135:286-296. [DOI: 10.1016/j.ympev.2019.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/11/2019] [Accepted: 03/17/2019] [Indexed: 12/01/2022]
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8
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Matos AR, Resende PC, Miranda MD, Garcia CC, Caetano BC, Lopes JC, Debur MC, Cury AL, Vianna LA, Lima MC, Schirmer M, Gubareva L, Hurt AC, Brown DW, Siqueira MM. Susceptibility of Brazilian influenza A(H1N1)pdm09 viruses to neuraminidase inhibitors in the 2014–2016 seasons: Identification of strains bearing mutations associated with reduced inhibition profile. Antiviral Res 2018; 154:35-43. [DOI: 10.1016/j.antiviral.2018.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/20/2018] [Accepted: 03/26/2018] [Indexed: 10/17/2022]
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9
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Shin JS, Ku KB, Jang Y, Yoon YS, Shin D, Kwon OS, Go YY, Kim SS, Bae MA, Kim M. Comparison of anti-influenza virus activity and pharmacokinetics of oseltamivir free base and oseltamivir phosphate. J Microbiol 2017; 55:979-983. [PMID: 29214495 DOI: 10.1007/s12275-017-7371-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
Influenza viruses are major human respiratory pathogens that cause high morbidity and mortality worldwide. Currently, prophylactic vaccines and therapeutic antiviral agents are used to prevent and control influenza virus infection. Oseltamivir free base (OSV-FB), a modified generic antiviral drug of Tamiflu (oseltamivir phosphate, OSV-P), was launched in the Republic of Korea last year. Here, we examine the bioequivalence of these two compounds by assessing their antiviral efficacy in infected cells and in a mouse model. It was observed that both antivirals showed comparable efficacy against 11 different influenza A and B viruses in vitro. Moreover, in mice infected with influenza A virus (mouse-adapted A/Puerto Rico/8/34), they showed a dose-dependent therapeutic activity and alleviated infection-mediated reductions in body weight, leading to significantly better survival. There was histopathological disappearance of virus-induced inflammatory cell infiltration of the lung after oral treatment with either antiviral agent (at 10 mg/kg). Pharmacokinetic analysis also exhibited similar plasma concentrations of the active drug, oseltamivir carboxylate, metabolised from both OSV-B and OSV-P. This is the first report showing bioequivalence of OSV-FB to its phosphate salt form in the mouse system. The free base drug has some beneficial points including simple drug formulation process and reduced risk of undesirable cation-phosphate precipitation within solution. The long term stability of OSV-FB requires further monitoring when it is provided as a national stock in readiness for an influenza pandemic.
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Affiliation(s)
- Jin Soo Shin
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Keun Bon Ku
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Yejin Jang
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Yi-Seul Yoon
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Daeho Shin
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Oh Seung Kwon
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Yun Young Go
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea.,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Seong Soon Kim
- Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.,Drug Discovery Platform Technology Research Group, Korea Research Institute of Chemical Technology, Daejeon, 34113, Republic of Korea
| | - Myoung Ae Bae
- Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.,Drug Discovery Platform Technology Research Group, Korea Research Institute of Chemical Technology, Daejeon, 34113, Republic of Korea
| | - Meehyein Kim
- Center for Virus Research and Testing, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Department of Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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10
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Retamal M, Abed Y, Rhéaume C, Baz M, Boivin G. In vitro and in vivo evidence of a potential A(H1N1)pdm09 antigenic drift mediated by escape mutations in the haemagglutinin Sa antigenic site. J Gen Virol 2017. [PMID: 28631598 DOI: 10.1099/jgv.0.000800] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza A(H1N1)pdm09 virus continues to circulate worldwide without evidence of significant antigenic drift between 2009 and 2016. By using escape mutants, we previously identified six haemagglutinin (HA) changes (T80R, G143E, G158E, N159D, K166E and A198E) that were located within antigenic sites. Combinations of these mutations were introduced into the A(H1N1)pdm09 HA plasmid by mutagenesis. Reassortant 6 : 2 viruses containing both the HA and NA genes of the A(H1N1)pdm09 and the six internal gene segments of A/PR/8/34 were rescued by reverse genetics. In vitro, HA inhibition and microneutralization assays showed that the HA hexa-mutant reassortant virus (RG1) escaped A(H1N1)pdm09 hyper-immune ferret antiserum recognition. C57Black/6 mice that received the vaccine formulated with A/California/07/09 were challenged with 2×104 p.f.u. of either the 6 : 2 wild-type (WT) or RG1 viruses. Reductions in body weight loss, mortality rate and lung viral titre were observed in immunized animals challenged with the 6 : 2 WT virus compared to non-immunized mice. However, immunization did not protect mice challenged with RG1 virus. To further characterize the mutations causing this antigenic change, 11 additional RG viruses whose HA gene contained single or combinations of mutations were evaluated in vitro. Although the RG1 virus was still the least reactive against hyper-immune serum by HAI testing, mutations G158E and N159D within the Sa antigenic site appeared to play the major role in the altered antigenicity of the A(H1N1)pdm09 virus. These results show that the Sa antigenic site contains the most prominent epitopes susceptible to cause an antigenic drift, escaping actual vaccine protection.
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Affiliation(s)
- Miguel Retamal
- Research Center in Infectious Diseases of the CHU of Québec and Laval University, Québec City, Quebec, Canada
| | - Yacine Abed
- Research Center in Infectious Diseases of the CHU of Québec and Laval University, Québec City, Quebec, Canada
| | - Chantal Rhéaume
- Research Center in Infectious Diseases of the CHU of Québec and Laval University, Québec City, Quebec, Canada
| | - Mariana Baz
- Research Center in Infectious Diseases of the CHU of Québec and Laval University, Québec City, Quebec, Canada
| | - Guy Boivin
- Research Center in Infectious Diseases of the CHU of Québec and Laval University, Québec City, Quebec, Canada
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11
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Tu V, Abed Y, Barbeau X, Carbonneau J, Fage C, Lagüe P, Boivin G. The I427T neuraminidase (NA) substitution, located outside the NA active site of an influenza A(H1N1)pdm09 variant with reduced susceptibility to NA inhibitors, alters NA properties and impairs viral fitness. Antiviral Res 2016; 137:6-13. [PMID: 27838351 DOI: 10.1016/j.antiviral.2016.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/28/2016] [Accepted: 11/09/2016] [Indexed: 01/16/2023]
Abstract
Emergence of pan neuraminidase inhibitor (NAI)-resistant variants constitutes a serious clinical concern. An influenza A(H1N1)pdm09 variant containing the I427T/Q313R neuraminidase (NA) substitutions was previously identified in a surveillance study. Although these changes are not part of the NA active site, the variant showed reduced susceptibility to many NAIs. In this study, we investigated the mechanism of resistance for the I427T/Q313R substitution and its impact on the NA enzyme and viral fitness. Recombinant wild-type (WT), I427T/Q313R and I427T A(H1N1)pdm09 viruses were generated by reverse genetics and tested for their drug susceptibilities, enzymatic properties and replication kinetics in vitro as well as their virulence in mice. Molecular dynamics (MD) simulations were performed for NA structural analysis. The I427T substitution, which was responsible for the resistance phenotype observed in the double (I427T/Q313R) mutant, induced 17-, 56-, 7-, and 14-fold increases in IC50 values against oseltamivir, zanamivir, peramivir and laninamivir, respectively. The I427T substitution alone or combined to Q313R significantly reduced NA affinity. The I427T/Q313R and to a lesser extent I427T recombinant viruses displayed reduced viral titers vs WT in vitro. In experimentally-infected mice, the mortality rates were 62.5%, 0% and 14.3% for the WT, I417T/Q313R and I427T viruses, respectively. There were about 2.5- and 2-Log reductions in mean lung viral titers on day 5 post-infection for the I427T/Q313R and I427T mutants, respectively, compared to WT. Results from simulations revealed that the I427T change indirectly altered the stability of the catalytic R368 residue of the NA enzyme causing its reduced binding to the substrate/inhibitor. This study demonstrates that the I427T/Q313R mutant, not only alters NAI susceptibility but also compromises NA properties and viral fitness, which could explain its infrequent detection in clinic.
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Affiliation(s)
- Véronique Tu
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Yacine Abed
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Xavier Barbeau
- Proteo and IBIS, Department of Chemistry, Faculty of Science and Engineering, Laval University, Québec City, QC, Canada
| | - Julie Carbonneau
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Clément Fage
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Patrick Lagüe
- Proteo and IBIS, Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, Laval University, Québec City, QC, Canada
| | - Guy Boivin
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada.
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12
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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.
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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.
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13
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Kurebayashi Y, Takahashi T, Tamoto C, Sahara K, Otsubo T, Yokozawa T, Shibahara N, Wada H, Minami A, Ikeda K, Suzuki T. High-Efficiency Capture of Drug Resistant-Influenza Virus by Live Imaging of Sialidase Activity. PLoS One 2016; 11:e0156400. [PMID: 27232333 PMCID: PMC4883822 DOI: 10.1371/journal.pone.0156400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/13/2016] [Indexed: 11/18/2022] Open
Abstract
Influenza A and B viruses possess a neuraminidase protein that shows sialidase activity. Influenza virus-specific neuraminidase inhibitors (NAIs) are commonly used for clinical treatment of influenza. However, some influenza A and B viruses that are resistant to NAIs have emerged in nature. NAI-resistant viruses have been monitored in public hygiene surveys and the mechanism underlying the resistance has been studied. Here, we describe a new assay for selective detection and isolation of an NAI-resistant virus in a speedy and easy manner by live fluorescence imaging of viral sialidase activity, which we previously developed, in order to achieve high-efficiency capture of an NAI-resistant virus. An NAI-resistant virus maintains sialidase activity even at a concentration of NAI that leads to complete deactivation of the virus. Infected cells and focuses (infected cell populations) of an oseltamivir-resistant virus were selectively visualized by live fluorescence sialidase imaging in the presence of oseltamivir, resulting in high-efficiency isolation of the resistant viruses. The use of a combination of other NAIs (zanamivir, peramivir, and laninamivir) in the imaging showed that the oseltamivir-resistant virus isolated in 2008 was sensitive to zanamivir and laninamivir but resistant to peramivir. Fluorescence imaging in the presence of zanamivir also succeeded in selective live-cell visualization of cells that expressed zanamivir-resistant NA. Fluorescence imaging of NAI-resistant sialidase activity will be a powerful method for study of the NAI resistance mechanism, for public monitoring of NAI-resistant viruses, and for development of a new NAI that shows an effect on various NAI-resistant mutations.
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Affiliation(s)
- Yuuki Kurebayashi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Tadanobu Takahashi
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Chihiro Tamoto
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Keiji Sahara
- Shizuoka Institute of Environment and Hygiene, Shizuoka-shi, Shizuoka, Japan
| | - Tadamune Otsubo
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, Kure-shi, Hiroshima, Japan
| | - Tatsuya Yokozawa
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Nona Shibahara
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
- Shizuoka City Institute of Environmental Sciences and Public Health, Shizuoka-shi, Shizuoka, Japan
| | - Hirohisa Wada
- Shizuoka City Institute of Environmental Sciences and Public Health, Shizuoka-shi, Shizuoka, Japan
| | - Akira Minami
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
| | - Kiyoshi Ikeda
- Department of Organic Chemistry, School of Pharmaceutical Sciences, Hiroshima International University, Kure-shi, Hiroshima, Japan
| | - Takashi Suzuki
- Department of Biochemistry, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka-shi, Shizuoka, Japan
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14
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Wilson BA, Garud NR, Feder AF, Assaf ZJ, Pennings PS. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens. Mol Ecol 2016; 25:42-66. [PMID: 26578204 PMCID: PMC4943078 DOI: 10.1111/mec.13474] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/28/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023]
Abstract
Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.
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Affiliation(s)
| | | | | | - Zoe J. Assaf
- Department of GeneticsStanford UniversityStanfordCA94305USA
| | - Pleuni S. Pennings
- Department of BiologySan Francisco State UniversityRoom 520Hensill Hall1600 Holloway AveSan FranciscoCA94132USA
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15
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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. J Mol Biol 2015; 428:538-553. [PMID: 26656922 DOI: 10.1016/j.jmb.2015.11.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 11/22/2022]
Abstract
The therapeutic benefits of the neuraminidase (NA) inhibitor oseltamivir are dampened by the emergence of drug resistance mutations in influenza A virus (IAV). To investigate the mechanistic features that underlie resistance, we developed an approach to quantify the effects of all possible single-nucleotide substitutions introduced into important regions of NA. We determined the experimental fitness effects of 450 nucleotide mutations encoding positions both surrounding the active site and at more distant sites in an N1 strain of IAV in the presence and absence of oseltamivir. NA mutations previously known to confer oseltamivir resistance in N1 strains, including H275Y and N295S, were adaptive in the presence of drug, indicating that our experimental system captured salient features of real-world selection pressures acting on NA. We identified mutations, including several at position 223, that reduce the apparent affinity for oseltamivir in vitro. Position 223 of NA is located adjacent to a hydrophobic portion of oseltamivir that is chemically distinct from the substrate, making it a hotspot for substitutions that preferentially impact drug binding relative to substrate processing. Furthermore, two NA mutations, K221N and Y276F, each reduce susceptibility to oseltamivir by increasing NA activity without altering drug binding. These results indicate that competitive expansion of IAV in the face of drug pressure is mediated by a balance between inhibitor binding and substrate processing.
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16
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Heterosubtypic protection conferred by the human monoclonal antibody PN-SIA28 against influenza A virus lethal infections in mice. Antimicrob Agents Chemother 2015; 59:2647-53. [PMID: 25691648 DOI: 10.1128/aac.00118-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
PN-SIA28 is a human monoclonal antibody (Hu-MAb) targeting highly conserved epitopes within the stem portion of the influenza virus hemagglutinin (HA) (N. Clementi, et al, PLoS One 6:e28001, 2011, http://dx.doi.org/10.1371/journal.pone.0028001). Previous in vitro studies demonstrated PN-SIA28 neutralizing activities against phylogenetically divergent influenza A subtypes. In this study, the protective activity of PN-SIA28 was evaluated in mice inoculated with lethal influenza A/WSN/33 (H1N1), A/Quebec/144147/09 (H1N1)pdm09, and A/Victoria/3/75 (H3N2) viruses. At 24 h postinoculation (p.i.), animals received PN-SIA28 intraperitoneally (1 or 10 mg/kg of body weight) or 10 mg/kg of unrelated Hu-MAb (mock). Body weight loss and mortality rate (MR) were recorded for 14 days postinfection (p.i.). Lung viral titers (LVT) were determined at day 5 p.i. In A/WSN/33 (H1N1)-infected groups, all untreated and mock-receiving mice died, whereas MRs of 87.5% and 25% were observed in mice that received PN-SIA28 1 and 10 mg/kg, respectively. In influenza A(H1N1) pdm09-infected groups, an MR of 75% was recorded for untreated and mock-treated groups, whereas the PN-SIA28 1-mg/kg and 10-mg/kg groups had rates of 62.5% and 0%, respectively. In A/Victoria/3/75 (H3N2)-infected animals, untreated and mock-treated animals had MRs of 37.5% and 25%, respectively, and no mortalities were recorded after PN-SIA28 treatments. Accordingly, PN-SIA28 treatments significantly reduced weight losses and resulted in a ≥ 1-log reduction in LVT compared to the control in all infection groups. This study confirms that antibodies targeting highly conserved epitopes in the influenza HA stem region, like PN-SIA28, not only neutralize influenza A viruses of clinically relevant subtypes in vitro but also, more importantly, protect from a lethal influenza virus challenge in vivo.
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17
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Behera AK, Basu S, Cherian SS. Molecular mechanism of the enhanced viral fitness contributed by secondary mutations in the hemagglutinin protein of oseltamivir resistant H1N1 influenza viruses: modeling studies of antibody and receptor binding. Gene 2014; 557:19-27. [PMID: 25479009 DOI: 10.1016/j.gene.2014.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 11/25/2022]
Abstract
The envelope protein hemagglutinin (HA) of influenza viruses is primarily associated with host antibody and receptor interactions. The HA protein is known to maintain a functional balance with neuraminidase (NA), the other major envelope protein. Prior to 2007-2008, human seasonal H1N1 viruses possessing the NA H274Y mutation, which confers oseltamivir resistance, generally had low growth capability. Subsequently, secondary mutations that compensate for the deleterious effect of the NA H274Y mutation have been identified. The molecular mechanism of how the defect could be counteracted by these secondary mutations is not fully understood. We studied here the effect of three such mutations (T86K, K144E and R192K) in the HA protein, which are located at either the HA receptor binding site or in the H1N1 antigenic sites. Molecular docking and dynamics studies showed that, of the three mutations, the R192K mutation could have mediated neutralizing antibody escape and decreased receptor binding affinity, either or both of which may have contributed to increased viral fitness. The study suggests the molecular basis of enhanced viral fitness induced by secondary mutations in the evolution of oseltamivir-resistant influenza strains.
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Affiliation(s)
- Abhisek Kumar Behera
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
| | - Sushmita Basu
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
| | - Sarah S Cherian
- Bioinformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, Post Box No. 11, Pune 411001, Maharashtra, India.
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18
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Duan S, Govorkova EA, Bahl J, Zaraket H, Baranovich T, Seiler P, Prevost K, Webster RG, Webby RJ. Epistatic interactions between neuraminidase mutations facilitated the emergence of the oseltamivir-resistant H1N1 influenza viruses. Nat Commun 2014; 5:5029. [PMID: 25297528 PMCID: PMC4197134 DOI: 10.1038/ncomms6029] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 08/19/2014] [Indexed: 01/06/2023] Open
Abstract
Oseltamivir-resistant H1N1 influenza viruses carrying the H275Y neuraminidase mutation predominated worldwide during the 2007–2009 seasons. While several neuraminidase substitutions were found to be necessary to counteract the adverse effects of H275Y, the order and impact of evolutionary events involved remain elusive. Here, we reconstruct H1N1 neuraminidase phylogeny during 1999–2009, estimate the timing and order of crucial amino acid changes, and evaluate their impact on the biological outcome of the H275Y mutation. Of the twelve neuraminidase substitutions that occurred during 1999–2009, five (chronologically, V234M, R222Q, K329E, D344N, H275Y, and D354G) are necessary for maintaining full neuraminidase function in the presence of the H275Y mutation by altering protein accumulation or enzyme affinity/activity. The sequential emergence and cumulative effects of these mutations clearly illustrate a role for epistasis in shaping the emergence and subsequent evolution of a drug-resistant virus population, which can be useful in understanding emergence of novel viral phenotypes of influenza.
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Affiliation(s)
- Susu Duan
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Elena A Govorkova
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Justin Bahl
- 1] School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, Texas 77030, USA [2] Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, 8 College Road, Singapore 169857, Singapore
| | - Hassan Zaraket
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Tatiana Baranovich
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Patrick Seiler
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Kristi Prevost
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Robert G Webster
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 330, Memphis, Tennessee 38105, USA
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19
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Emergence of H274Y oseltamivir-resistant A(H1N1) influenza viruses in Japan during the 2008–2009 season. J Clin Virol 2010; 47:23-8. [DOI: 10.1016/j.jcv.2009.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 11/04/2009] [Indexed: 11/23/2022]
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