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Virus Adaptation Following Experimental Infection of Chickens with a Domestic Duck Low Pathogenic Avian Influenza Isolate from the 2017 USA H7N9 Outbreak Identifies Polymorphic Mutations in Multiple Gene Segments. Viruses 2021; 13:v13061166. [PMID: 34207098 PMCID: PMC8234733 DOI: 10.3390/v13061166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
In March 2017, highly pathogenic (HP) and low pathogenic (LP) avian influenza virus (AIV) subtype H7N9 were detected from poultry farms and backyard birds in several states in the southeast United States. Because interspecies transmission is a known mechanism for evolution of AIVs, we sought to characterize infection and transmission of a domestic duck-origin H7N9 LPAIV in chickens and genetically compare the viruses replicating in the chickens to the original H7N9 clinical field samples used as inoculum. The results of the experimental infection demonstrated virus replication and transmission in chickens, with overt clinical signs of disease and shedding through both oral and cloacal routes. Unexpectedly, higher levels of virus shedding were observed in some cloacal swabs. Next generation sequencing (NGS) analysis identified numerous non-synonymous mutations at the consensus level in the polymerase genes (i.e., PA, PB1, and PB2) and the hemagglutinin (HA) receptor binding site in viruses recovered from chickens, indicating possible virus adaptation in the new host. For comparison, NGS analysis of clinical samples obtained from duck specimen collected during the outbreak indicated three polymorphic sides in the M1 segment and a minor population of viruses carrying the D139N (21.4%) substitution in the NS1 segment. Interestingly, at consensus level, A/duck/Alabama (H7N9) had isoleucine at position 105 in NP protein, similar to HPAIV (H7N9) but not to LPAIV (H7N9) isolated from the same 2017 influenza outbreak in the US. Taken together, this work demonstrates that the H7N9 viruses could readily jump between avian species, which may have contributed to the evolution of the virus and its spread in the region.
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Ding X, Qin L, Meng J, Peng Y, Wu A, Jiang T. Progress and Challenge in Computational Identification of Influenza Virus Reassortment. Virol Sin 2021; 36:1273-1283. [PMID: 34037948 DOI: 10.1007/s12250-021-00392-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
Genomic reassortment is an important evolutionary mechanism for influenza viruses. In this process, the novel viruses acquire new characteristics by the exchange of the intact gene segments among multiple influenza virus genomes, which may cause flu endemics and epidemics within or even across hosts. Due to the safety and ethical limitations of the experimental studies on influenza virus reassortment, numerous computational researches on the influenza virus reassortment have been done with the explosion of the influenza virus genomic data. A great amount of computational methods and bioinformatics databases were developed to facilitate the identification of influenza virus reassortments. In this review, we summarized the progress and challenge of the bioinformatics research on influenza virus reassortment, which can guide the researchers to investigate the influenza virus reassortment events reasonably and provide valuable insight to develop the related computational identification tools.
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Affiliation(s)
- Xiao Ding
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Luyao Qin
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Jing Meng
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Yousong Peng
- College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082, China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. .,Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China.
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Yin R, Zhang Y, Zhou X, Kwoh CK. Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks. J Bioinform Comput Biol 2021; 18:2040002. [PMID: 32336247 DOI: 10.1142/s0219720020400028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics due to rapid viral evolution. Vaccines are used to prevent influenza infections but the composition of the influenza vaccines have to be updated regularly to ensure its efficacy. Computational tools and analyses have become increasingly important in guiding the process of vaccine selection. By constructing time-series training samples with splittings and embeddings, we develop a computational method for predicting suitable strains as the recommendation of the influenza vaccines using recurrent neural networks (RNNs). The Encoder-decoder architecture of RNN model enables us to perform sequence-to-sequence prediction. We employ this model to predict the prevalent sequence of the H3N2 viruses sampled from 2006 to 2017. The identity between our predicted sequence and recommended vaccines is greater than 98% and the Pepitope<0.2 indicates their antigenic similarity. The multi-step vaccine prediction further demonstrates the robustness of our method which achieves comparable results in contrast to single step prediction. The results show significant matches of the recommended vaccine strains to the circulating strains. We believe it would facilitate the process of vaccine selection and surveillance of seasonal influenza epidemics.
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Affiliation(s)
- Rui Yin
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Xinrui Zhou
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
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Abstract
The HA protein of influenza A viruses is the major viral antigen. In this study, we simultaneously introduced mutations at 17 amino acid positions of an H5 HA expected to affect antigenicity. Viruses with ≥13 amino acid changes in HA were viable, and some had altered antigenic properties. H5 HA can therefore accommodate many mutations in regions that affect antigenicity. The substantial plasticity of H5 HA may facilitate the emergence of novel antigenic variants. Since the emergence of highly pathogenic avian influenza viruses of the H5 subtype, the major viral antigen, hemagglutinin (HA), has undergone constant evolution, resulting in numerous genetic and antigenic (sub)clades. To explore the consequences of amino acid changes at sites that may affect the antigenicity of H5 viruses, we simultaneously mutated 17 amino acid positions of an H5 HA by using a synthetic gene library that, theoretically, encodes all combinations of the 20 amino acids at the 17 positions. All 251 mutant viruses sequenced possessed ≥13 amino acid substitutions in HA, demonstrating that the targeted sites can accommodate a substantial number of mutations. Selection with ferret sera raised against H5 viruses of different clades resulted in the isolation of 39 genotypes. Further analysis of seven variants demonstrated that they were antigenically different from the parental virus and replicated efficiently in mammalian cells. Our data demonstrate the substantial plasticity of the influenza virus H5 HA protein, which may lead to novel antigenic variants.
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Fitness Barriers Limit Reversion of a Proofreading-Deficient Coronavirus. J Virol 2019; 93:JVI.00711-19. [PMID: 31341046 PMCID: PMC6798108 DOI: 10.1128/jvi.00711-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/05/2019] [Indexed: 12/28/2022] Open
Abstract
Coronaviruses encode an exoribonuclease (ExoN) that is important for viral replication, fitness, and virulence, yet coronaviruses with a defective ExoN (ExoN-AA) have not reverted under diverse experimental conditions. In this study, we identify multiple impediments to MHV-ExoN-AA reversion. We show that ExoN-AA reversion is possible but evolutionarily unfavorable. Instead, compensatory mutations outside ExoN-AA motif I are more accessible and beneficial than partial reversion. We also show that coevolution between replicase proteins over long-term passage partially compensates for ExoN-AA motif I but renders the virus inhospitable to a reverted ExoN. Our results reveal the evolutionary basis for the genetic stability of ExoN-inactivating mutations, illuminate complex functional and evolutionary relationships between coronavirus replicase proteins, and identify potential mechanisms for stabilization of ExoN-AA coronavirus mutants. The 3′-to-5′ exoribonuclease in coronavirus (CoV) nonstructural protein 14 (nsp14-ExoN) mediates RNA proofreading during genome replication. ExoN catalytic residues are arranged in three motifs: I (DE), II (E), and III (D). Alanine replacement of the motif I residues (AA-E-D; four nucleotide substitutions) in murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV yields viable mutants with impaired replication and fitness, increased mutation rates, and attenuated virulence in vivo. Despite these impairments, MHV- and SARS-CoV ExoN motif I AA mutants (ExoN-AA) have not reverted at motif I in diverse in vitro and in vivo environments, suggesting that profound fitness barriers prevent motif I reversion. To test this hypothesis, we engineered MHV-ExoN-AA with 1, 2, or 3 nucleotide mutations along genetic pathways to AA-to-DE reversion. We show that engineered intermediate revertants were viable but had no increased replication or competitive fitness compared to that of MHV-ExoN-AA. In contrast, a low-passage-number (passage 10 [P10]) MHV-ExoN-AA showed increased replication and competitive fitness without reversion of ExoN-AA. Finally, engineered reversion of ExoN-AA to ExoN-DE in the presence of ExoN-AA passage-adaptive mutations resulted in significant fitness loss. These results demonstrate that while reversion is possible, at least one alternative adaptive pathway is more rapidly advantageous than intermediate revertants and may alter the genetic background to render reversion detrimental to fitness. Our results provide an evolutionary rationale for lack of ExoN-AA reversion, illuminate potential multiprotein replicase interactions and coevolution, and support future studies aimed at stabilizing attenuated CoV ExoN-AA mutants. IMPORTANCE Coronaviruses encode an exoribonuclease (ExoN) that is important for viral replication, fitness, and virulence, yet coronaviruses with a defective ExoN (ExoN-AA) have not reverted under diverse experimental conditions. In this study, we identify multiple impediments to MHV-ExoN-AA reversion. We show that ExoN-AA reversion is possible but evolutionarily unfavorable. Instead, compensatory mutations outside ExoN-AA motif I are more accessible and beneficial than partial reversion. We also show that coevolution between replicase proteins over long-term passage partially compensates for ExoN-AA motif I but renders the virus inhospitable to a reverted ExoN. Our results reveal the evolutionary basis for the genetic stability of ExoN-inactivating mutations, illuminate complex functional and evolutionary relationships between coronavirus replicase proteins, and identify potential mechanisms for stabilization of ExoN-AA coronavirus mutants.
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Lyons DM, Lauring AS. Mutation and Epistasis in Influenza Virus Evolution. Viruses 2018; 10:E407. [PMID: 30081492 PMCID: PMC6115771 DOI: 10.3390/v10080407] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 12/25/2022] Open
Abstract
Influenza remains a persistent public health challenge, because the rapid evolution of influenza viruses has led to marginal vaccine efficacy, antiviral resistance, and the annual emergence of novel strains. This evolvability is driven, in part, by the virus's capacity to generate diversity through mutation and reassortment. Because many new traits require multiple mutations and mutations are frequently combined by reassortment, epistatic interactions between mutations play an important role in influenza virus evolution. While mutation and epistasis are fundamental to the adaptability of influenza viruses, they also constrain the evolutionary process in important ways. Here, we review recent work on mutational effects and epistasis in influenza viruses.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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Tewawong N, Prachayangprecha S, Vichiwattana P, Korkong S, Klinfueng S, Vongpunsawad S, Thongmee T, Theamboonlers A, Poovorawan Y. Assessing Antigenic Drift of Seasonal Influenza A(H3N2) and A(H1N1)pdm09 Viruses. PLoS One 2015; 10:e0139958. [PMID: 26440103 PMCID: PMC4594909 DOI: 10.1371/journal.pone.0139958] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/18/2015] [Indexed: 12/03/2022] Open
Abstract
Under selective pressure from the host immune system, antigenic epitopes of influenza virus hemagglutinin (HA) have continually evolved to escape antibody recognition, termed antigenic drift. We analyzed the genomes of influenza A(H3N2) and A(H1N1)pdm09 virus strains circulating in Thailand between 2010 and 2014 and assessed how well the yearly vaccine strains recommended for the southern hemisphere matched them. We amplified and sequenced the HA gene of 120 A(H3N2) and 81 A(H1N1)pdm09 influenza virus samples obtained from respiratory specimens and calculated the perfect-match vaccine efficacy using the pepitope model, which quantitated the antigenic drift in the dominant epitope of HA. Phylogenetic analysis of the A(H3N2) HA1 genes classified most strains into genetic clades 1, 3A, 3B, and 3C. The A(H3N2) strains from the 2013 and 2014 seasons showed very low to moderate vaccine efficacy and demonstrated antigenic drift from epitopes C and A to epitope B. Meanwhile, most A(H1N1)pdm09 strains from the 2012–2014 seasons belonged to genetic clades 6A, 6B, and 6C and displayed the dominant epitope mutations at epitopes B and E. Finally, the vaccine efficacy for A(H1N1)pdm09 (79.6–93.4%) was generally higher than that of A(H3N2). These findings further confirmed the accelerating antigenic drift of the circulating influenza A(H3N2) in recent years.
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Affiliation(s)
- Nipaporn Tewawong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Slinporn Prachayangprecha
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Preeyaporn Vichiwattana
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sumeth Korkong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thanunrat Thongmee
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiradee Theamboonlers
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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8
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change. J Mol Graph Model 2014; 53:48-58. [DOI: 10.1016/j.jmgm.2014.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 11/19/2022]
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10
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Durviaux S, Treanor J, Beran J, Duval X, Esen M, Feldman G, Frey SE, Launay O, Leroux-Roels G, McElhaney JE, Nowakowski A, Ruiz-Palacios GM, van Essen GA, Oostvogels L, Devaster JM, Walravens K. Genetic and antigenic typing of seasonal influenza virus breakthrough cases from a 2008-2009 vaccine efficacy trial. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:271-9. [PMID: 24371255 PMCID: PMC3957665 DOI: 10.1128/cvi.00544-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/16/2013] [Indexed: 01/07/2023]
Abstract
Estimations of the effectiveness of vaccines against seasonal influenza virus are guided by comparisons of the antigenicities between influenza virus isolates from clinical breakthrough cases with strains included in a vaccine. This study examined whether the prediction of antigenicity using a sequence analysis of the hemagglutinin (HA) gene-encoded HA1 domain is a simpler alternative to using the conventional hemagglutination inhibition (HI) assay, which requires influenza virus culturing. Specimens were taken from breakthrough cases that occurred in a trivalent influenza virus vaccine efficacy trial involving >43,000 participants during the 2008-2009 season. A total of 498 influenza viruses were successfully subtyped as A(H3N2) (380 viruses), A(H1N1) (29 viruses), B(Yamagata) (23 viruses), and B(Victoria) (66 viruses) from 603 PCR- or culture-confirmed specimens. Unlike the B strains, most A(H3N2) (377 viruses) and all A(H1N1) viruses were classified as homologous to the respective vaccine strains based on their HA1 domain nucleic acid sequence. HI titers relative to the respective vaccine strains and PCR subtyping were determined for 48% (182/380) of A(H3N2) and 86% (25/29) of A(H1N1) viruses. Eighty-four percent of the A(H3N2) and A(H1N1) viruses classified as homologous by sequence were matched to the respective vaccine strains by HI testing. However, these homologous A(H3N2) and A(H1N1) viruses displayed a wide range of relative HI titers. Therefore, although PCR is a sensitive diagnostic method for confirming influenza virus cases, HA1 sequence analysis appeared to be of limited value in accurately predicting antigenicity; hence, it may be inappropriate to classify clinical specimens as homologous or heterologous to the vaccine strain for estimating vaccine efficacy in a prospective clinical trial.
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Affiliation(s)
| | - John Treanor
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jiri Beran
- Vaccination and Travel Medicine Centre, Poliklinika 2, Hradec Kralove, Czech Republic
| | - Xavier Duval
- Hôpital Bichat Claude Bernard, C.I.C. Bichat GH BICHAT, Paris, France
| | - Meral Esen
- Institut für Tropenmedizin, Tübingen, Germany
| | - Gregory Feldman
- S. Carolina Pharmaceutical Research, Spartanburg, South Carolina, USA
| | - Sharon E. Frey
- Saint Louis University Medical Center, St. Louis, Missouri, USA
| | - Odile Launay
- Université Paris-Descartes, Assistance-Publique Hôpitaux de Paris, Hôpital Cochin, CIC de Vaccinologie Cochin-Pasteur, Paris, France
| | - Geert Leroux-Roels
- Centre for Vaccinology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Janet E. McElhaney
- Health Sciences North and Advanced Medical Research Institute of Canada, Sudbury, Ontario, Canada
| | - Andrzej Nowakowski
- Family Medicine Centre, Lubartów, Poland
- Department of Gynaecology and Oncologic Gynaecology, Military Institute of Medicine, Warsaw, Poland
| | - Guillermo M. Ruiz-Palacios
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, Mexico City, Mexico
| | - Gerrit A. van Essen
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lidia Oostvogels
- GlaxoSmithKline Vaccines, Parc de la Noire Epine, Wavre, Belgium
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Eshaghi A, Duvvuri VR, Li A, Patel SN, Bastien N, Li Y, Low DE, Gubbay JB. Genetic characterization of seasonal influenza A (H3N2) viruses in Ontario during 2010-2011 influenza season: high prevalence of mutations at antigenic sites. Influenza Other Respir Viruses 2013; 8:250-7. [PMID: 24313991 PMCID: PMC4186474 DOI: 10.1111/irv.12219] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The direct effect of antigenic site mutations in influenza viruses on antigenic drift and vaccine effectiveness is poorly understood. OBJECTIVE To investigate the genetic and antigenic characteristics of human influenza A (H3N2) viruses circulating in Ontario during the early 2010-2011 winter season. STUDY DESIGN We sequenced the hemagglutinin (HA) and neuraminidase (NA) genes from 41 A(H3N2) viruses detected in nasopharyngeal specimens. Strain typing was performed by hemagglutination inhibition (HI) assay. Molecular and phylogenetic tree analyses were conducted. RESULTS HA and NA genes showed high similarity to the 2010-2011 vaccine strain, A/Perth/16/2009 (H3N2)-like virus (97·7-98·5% and 98·7-99·5% amino acid (AA) identity, respectively). Compared to A/Perth/16/2009 strain, HA gene mutations were documented at 28 different AA positions across all five H3 antigenic sites, with a range of 5-11 mutations in individual viruses. Thirty-six (88%) viruses had 8 AA substitutions in common; none of these had reduced HI titer. Among Ontario isolates, 11 antigenic site AAs were positively selected with an increase in glycosylation sites. CONCLUSION The presence of antigenic site mutations with high frequency among 2010-2011 influenza H3N2 isolates confirms ongoing adaptive H3N2 evolution. These may represent early phylogenetic changes that could cause antigenic drift with further mutations. Clinical relevance of antigenic site mutations not causing drift in HI assays is unknown and requires further investigation. In addition, viral sequencing information will assist with vaccine strain planning and may facilitate early detection of vaccine escape.
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Affiliation(s)
- Alireza Eshaghi
- Ontario Agency for Health Protection and Promotion, Toronto, ON, Canada
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12
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Suzuki Y. Detection of positive selection eliminating effects of structural constraints in hemagglutinin of H3N2 human influenza A virus. INFECTION GENETICS AND EVOLUTION 2013; 16:93-8. [PMID: 23403095 DOI: 10.1016/j.meegid.2013.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 11/19/2022]
Abstract
In the evolutionary studies of proteins, the average effect of natural selection operating on amino acid mutations may be examined by comparing the numbers of synonymous (dS) and nonsynonymous (dN) substitutions that have accumulated during the same time period. In this method, destabilizing mutations occurring across protein molecules may interfere with detection of natural selection, particularly positive selection, operating on other mutations. Here an attempt to detect positive selection eliminating effects of structural constraints is demonstrated using hemagglutinin (HA) of H3N2 human influenza A virus as an example. Compatible and incompatible amino acids were inferred at each site from the computational analysis of three-dimensional structure using the thermodynamic stability as an indicator, and natural selection was examined by comparing dS and dN among compatible amino acids. In the analysis of 2701 nucleotide sequences for the entire coding region of HA, the new method identified twice as many positively selected amino acid sites as the ordinary method (16 and 4 sites in the former method without and with correction for multiple testing, respectively, and 8 and 2 sites in the latter method). Positively selected sites were involved in epitopes, receptor-binding pocket, epistasis, and stabilization, which appeared to be biologically reasonable. Nevertheless, there still appeared to be several problems, which may largely render this method conservative. It may be effective to analyze many densely sampled sequences in this method.
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Affiliation(s)
- Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya-shi, Aichi-ken 467-8501, Japan.
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13
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Zinder D, Bedford T, Gupta S, Pascual M. The roles of competition and mutation in shaping antigenic and genetic diversity in influenza. PLoS Pathog 2013; 9:e1003104. [PMID: 23300455 PMCID: PMC3536651 DOI: 10.1371/journal.ppat.1003104] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 11/10/2012] [Indexed: 01/05/2023] Open
Abstract
Influenza A (H3N2) offers a well-studied, yet not fully understood, disease in terms of the interactions between pathogen population dynamics, epidemiology and genetics. A major open question is why the virus population is globally dominated by a single and very recently diverged (2-8 years) lineage. Classically, this has been modeled by limiting the generation of new successful antigenic variants, such that only a small subset of progeny acquire the necessary mutations to evade host immunity. An alternative approach was recently suggested by Recker et al. in which a limited number of antigenic variants are continuously generated, but most of these are suppressed by pre-existing host population immunity. Here we develop a framework spanning the regimes described above to explore the impact of rates of mutation and levels of competition on phylodynamic patterns. We find that the evolutionary dynamics of the subtype H3N2 influenza is most easily generated within this framework when it is mutation limited as well as being under strong immune selection at a number of epitope regions of limited diversity.
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Affiliation(s)
- Daniel Zinder
- University of Michigan, Department of Computational Medicine and Bioinformatics, Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, United States of America
| | - Trevor Bedford
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Sunetra Gupta
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Mercedes Pascual
- University of Michigan, Department of Computational Medicine and Bioinformatics, Department of Ecology and Evolutionary Biology, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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14
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Nobusawa E, Omagari K, Nakajima S, Nakajima K. Reactivity of human convalescent sera with influenza virus hemagglutinin protein mutants at antigenic site A. Microbiol Immunol 2012; 56:99-106. [PMID: 22309642 DOI: 10.1111/j.1348-0421.2012.00412.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How the antibodies of individual convalescent human sera bind to each amino acid residue at the antigenic sites of hemagglutinin (HA) of influenza viruses, and how the antigenic drift strains of influenza viruses are selected by human sera, is not well understood. In our previous study, it was found by a binding assay with a chimeric HA between A/Kamata/14/91 (Ka/91) and A/Aichi/2/68 that convalescent human sera, following Ka/91 like (H3N2) virus infection, bind to antigenic site A of Ka/91 HA. Here using chimeric HAs possessing single amino acid substitutions at site A, it was determined how those human sera recognize each amino acid residue at antigenic site A. It was found that the capacity of human sera to recognize amino acid substitutions at site A differs from one person to another and that some amino acid substitutions result in all convalescent human sera losing their binding capacity. Among these amino acid substitutions, certain ones might be selected by chance, thus creating successive antigenic drift. Phylogenetic analysis of the drift strains of Ka/91 showed amino acid substitutions at positions 133, 135 and 145 were on the main stream of the phylogenetic tree. Indeed, all of the investigated convalescent sera failed to recognize one of them.
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Affiliation(s)
- Eri Nobusawa
- Department of Virology, Nagoya City University Graduate School of Medical Science, Nagoya City, Aichi, Japan.
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15
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Yoshioka A, Takematsu K, Kurisaki I, Fukuzawa K, Mochizuki Y, Nakano T, Nobusawa E, Nakajima K, Tanaka S. Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1048-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations. J Mol Graph Model 2011; 30:110-9. [DOI: 10.1016/j.jmgm.2011.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 11/22/2022]
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17
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Naturally occurring antibodies in humans can neutralize a variety of influenza virus strains, including H3, H1, H2, and H5. J Virol 2011; 85:11048-57. [PMID: 21865387 DOI: 10.1128/jvi.05397-11] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza A viruses are classified into 16 subtypes according to the serotypes of hemagglutinin (HA). It is generally thought that neutralizing antibodies (Abs) are not broadly cross-reactive among HA subtypes. We examined the repertoire of neutralizing Abs against influenza viruses in humans. B lymphocytes were collected from donors by apheresis, and Ab libraries were constructed by using phage-display technology. Anti-HA clones were isolated by screening with H3N2 viruses. Their binding activity was examined, and four kinds of Abs showing broad strain specificity were identified from one donor. Two of the Abs, F045-092 and F026-427, were extensively analyzed. They neutralized not only H3N2 but also H1N1, H2N2, and H5N1 viruses, although the activities were largely varied. Flow cytometry suggested that they have the ability to bind to HA and HA1 artificially expressed on the cell surface. They show hemagglutination inhibition activity and do not compete with C179, an Ab thought to bind to the stalk region. F045-092 competes with Abs that recognize sites A and B for binding to HA. Furthermore, the serine at residue 136 in site A could be a part of the epitope. Thus, it is likely that F045-092 and F026-427 bind to a conserved epitope in the head region formed by HA1. Interestingly, while the V(H)1-69 gene can encode MAbs against the HA stem that are group 1 specific, F045-092 and its relatives that recognize the head region also use V(H)1-69. The possible epitope recognized by these clones is discussed.
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18
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Okada J, Ohshima N, Kubota-Koketsu R, Iba Y, Ota S, Takase W, Yoshikawa T, Ishikawa T, Asano Y, Okuno Y, Kurosawa Y. Localization of epitopes recognized by monoclonal antibodies that neutralized the H3N2 influenza viruses in man. J Gen Virol 2010; 92:326-35. [PMID: 21068214 PMCID: PMC3081080 DOI: 10.1099/vir.0.026419-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through extensive isolation of neutralizing mAbs against H3N2 influenza viruses representing the in vivo repertoire in a human donor, we examined the relationships between antigenic drift of influenza virus and protective antibodies generated in an infected individual. The majority of mAbs isolated from a donor born in 1960 were divided into three major groups with distinct strain specificity: 1968-1973, 1977-1993 and 1997-2003. In the present study, we developed a new method that allowed us to comprehensively determine the location of epitopes recognized by many mAbs. Original haemagglutinins (HAs) of several strains and chimaeric variants, in which one of the seven sites (A, B1, B2, C1, C2, D or E) was replaced by some other strain-derived sequence, were artificially expressed on the cell surface. The binding activity of mAbs to the HAs was examined by flow cytometry. By using this method, we determined the location of epitopes recognized by 98 different mAbs. Clones that neutralize the 1968-1973 strains bind to site B2/D, A or A/B1. While sites C, E and B were recognized by clones that neutralized the 1977-1993 strains, the majority of these clones bind to site C. Clones that neutralize the 1997-2003 strains bind to site B, A/B1, A/B2 or E/C2.
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Affiliation(s)
- Jun Okada
- Division of Antibody Project, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
- Institute for Antibody Ltd, Toyoake, Aichi 470-1192, Japan
| | - Nobuko Ohshima
- 21st Century COE Research Center, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshitaka Iba
- Division of Antibody Project, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Sayuri Ota
- 21st Century COE Research Center, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Wakana Takase
- 21st Century COE Research Center, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, School of Medicine, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Toyokazu Ishikawa
- The Research Foundation for Microbial Diseases, Osaka University, Kannonji, Kagawa 768-0061, Japan
| | - Yoshizo Asano
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinobu Okuno
- The Research Foundation for Microbial Diseases, Osaka University, Kannonji, Kagawa 768-0061, Japan
| | - Yoshikazu Kurosawa
- Division of Antibody Project, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
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Sawada T, Fedorov DG, Kitaura K. Role of the Key Mutation in the Selective Binding of Avian and Human Influenza Hemagglutinin to Sialosides Revealed by Quantum-Mechanical Calculations. J Am Chem Soc 2010; 132:16862-72. [DOI: 10.1021/ja105051e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Toshihiko Sawada
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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20
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Mochizuki Y, Yamashita K, Fukuzawa K, Takematsu K, Watanabe H, Taguchi N, Okiyama Y, Tsuboi M, Nakano T, Tanaka S. Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA). Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Takematsu K, Fukuzawa K, Omagari K, Nakajima S, Nakajima K, Mochizuki Y, Nakano T, Watanabe H, Tanaka S. Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding. J Phys Chem B 2009; 113:4991-4. [DOI: 10.1021/jp810997c] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazutomo Takematsu
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Kaori Fukuzawa
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Katsumi Omagari
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Setsuko Nakajima
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Katsuhisa Nakajima
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Yuji Mochizuki
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Tatsuya Nakano
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Hirofumi Watanabe
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
| | - Shigenori Tanaka
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan, Mizuho Information & Research Institute Inc., 2-3 Kanda Nishiki-Cho, Chiyoda-ku, Tokyo 101-8442, Japan, Department of Virology, Medical School, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan, Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan,
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Ito M, Nagai M, Hayakawa Y, Komae H, Murakami N, Yotsuya S, Asakura S, Sakoda Y, Kida H. Genetic Analyses of an H3N8 Influenza Virus Isolate, Causative Strain of the Outbreak of Equine Influenza at the Kanazawa Racecourse in Japan in 2007. J Vet Med Sci 2008; 70:899-906. [PMID: 18840963 DOI: 10.1292/jvms.70.899] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In August 2007, an outbreak of equine influenza occurred among vaccinated racehorses with Japanese commercial equine influenza vaccine at Kanazawa Racecourse in Ishikawa prefecture in Japan. Apparent symptoms were pyrexia (38.2-41.0 degrees C) and nasal discharge with or without coughing, although approximately half of the infected horses were subclinical. All horses had been shot with a vaccine that contained two inactivated H3N8 influenza virus strains [A/equine/La Plata/93 (La Plata/93) of American lineage and A/equine/Avesta/93 (Avesta/93) of European lineage] and an H7N7 strain (A/equine/Newmarket/1/77). Influenza virus, A/equine/Kanazawa/1/2007 (H3N8) (Kanazawa/07), was isolated from one of the nasal swab samples of diseased horses. Phylogenetic analysis indicated that Kanazawa/07 was classified into the American sublineage Florida. In addition, four amino acid substitutions were found in the antigenic sites B and E in the HA1 subunit protein of Kanazawa/07 in comparison with that of La Plata/93. Hemagglutination-inhibition (HI) test using 16 serum samples from recovering horses revealed that 1.4- to 8-fold difference in titers between Kanazawa/07 and either of the vaccine strains. The present findings suggest that Japanese commercial inactivated vaccine contributed to reducing the morbidity rate and manifestation of the clinical signs of horses infected with Kanazawa/07 that may be antigenically different from the vaccine strains.
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Affiliation(s)
- Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, Japan
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23
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Yano T, Nobusawa E, Nagy A, Nakajima S, Nakajima K. Effects of single-point amino acid substitutions on the structure and function neuraminidase proteins in influenza A virus. Microbiol Immunol 2008; 52:216-23. [PMID: 18426396 DOI: 10.1111/j.1348-0421.2008.00034.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In order to clarify the effect of amino acid substitutions on the structure and function of the neuraminidase (NA) protein of influenza A virus, we introduced single-point amino acid substitutions into the NA protein of the A/Tokyo/3/67 (H2N2) strain using PCR-based random mutation. The rate of tolerant random one amino acid substitutions in the NA protein was 47%. Rates of tolerant substitutions for the stalk and for the surface and inner portion of the head region of the NA protein were 79, 54, and 19%, respectively. Deleterious changes, such as those causing the NA protein to stop at the Golgi/endoplasmic reticulum, were scattered throughout the protein. On the other hand, the ratio of mutations with which the NA protein lost neuraminidase activity, but was transported to the cell surface, decreased in proportion to the distance from the structural center of enzyme active site. In order to investigate the effect of accumulated amino acid substitutions on the structural character of the N2NA protein during evolution, the same amino acid substitutions were introduced by site-directed mutagenesis at 23 homologous positions on N2 proteins of A/Tokyo/3/67, A/Bangkok/15/85 (H3N2), and A/Mie/1/2004 (H3N2). The results showed a shift, or discordance, in tolerance at some of the positions. An increase in discordance was correlated with the interval in years between virus strains, and the discordance rate was estimated to be 0.6-0.7% per year.
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Affiliation(s)
- Takuya Yano
- Department of Virology, Medical School, Nagoya City University, Nagoya, Japan
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24
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Tobin GJ, Trujillo JD, Bushnell RV, Lin G, Chaudhuri AR, Long J, Barrera J, Pena L, Grubman MJ, Nara PL. Deceptive imprinting and immune refocusing in vaccine design. Vaccine 2008; 26:6189-99. [PMID: 18852005 DOI: 10.1016/j.vaccine.2008.09.080] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
A large number of the world's most widespread and problematic pathogens evade host immune responses by inducing strain-specific immunity to immunodominant epitopes with high mutation rates capable of altering antigenic profiles. The immune system appears to be decoyed into reacting to these immunodominant epitopes that offer little cross protection between serotypes or subtypes. For example, during HIV-1 infection, the immune system reacts strongly to the V1, V2, and/or V3 loops of the surface envelope glycoprotein but not to epitopes that afford broad protection against strain variants. Similarly, the host mounts strain-specific immunity to immunodominant epitopes of the influenza hemagglutinin (HA) protein. A large number of pathogens appear to exploit this weakness in the host immune system by focusing antigenic attention upon highly variable epitopes while avoiding surveillance toward more highly conserved receptor binding sites or other essential functional domains. Because the propensity of the immune system to react against immunodominant strain-specific epitopes appears to be genetically hard-wired, the phenomenon has been termed "deceptive imprinting." In this review, the authors describe observations related to deceptive imprinting in multiple systems and propose strategies for overcoming this phenomenon in the design of vaccines capable of inducing protection against highly variable pathogens.
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Affiliation(s)
- Gregory J Tobin
- Biological Mimetics, Inc., 124 Byte Drive Frederick, MD 21702, USA.
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Mochizuki Y, Yamashita K, Murase T, Nakano T, Fukuzawa K, Takematsu K, Watanabe H, Tanaka S. Large scale FMO-MP2 calculations on a massively parallel-vector computer. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.03.090] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Nakajima S, Nakajima K, Nobusawa E, Zhao J, Tanaka S, Fukuzawa K. Comparison of epitope structures of H3HAs through protein modeling of influenza A virus hemagglutinin: mechanism for selection of antigenic variants in the presence of a monoclonal antibody. Microbiol Immunol 2008; 51:1179-87. [PMID: 18094536 DOI: 10.1111/j.1348-0421.2007.tb04013.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Starting with nine plaques of influenza A/Kamata/14/91(H3N2) virus, we selected mutants in the presence of monoclonal antibody 203 (mAb203). In total, amino acid substitutions were found at nine positions (77, 80, 131, 135, 141, 142, 143, 144 and 146), which localized in the antigenic site A of the hemagglutinin (HA). The escape mutants differed in the extent to which they had lost binding to mAb203. HA protein with substitutions of some amino acid residues created by site-directed mutagenesis in the escape mutants retained the ability to bind to mAb203. Changes in the amino acid character affecting charge or hydrophobicity accounted for the binding capacity to the antibody of the HA with most of the substitutions in the escape mutants and binding-positive mutants. However, the effect of some amino acid substitutions remained unexplained. A three-dimensional model of the 1991 HA was constructed and used to analyze substituted amino acids in these mutants for the accessible surface hydrophobic and hydrophilic characters. One amino acid substitution in an escape mutant and another amino acid substitution in a binding-positive mutant seemed to be explained by the changes noted on this model.
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Affiliation(s)
- Setsuko Nakajima
- Department of Virology, Medical School, Nagoya City University, Mizuho-ku, Aichi, Japan.
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27
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Genetic and epidemiological analysis of influenza virus epidemics in Taiwan during 2003 to 2006. J Clin Microbiol 2008; 46:1426-34. [PMID: 18256223 DOI: 10.1128/jcm.01560-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic characterization of Taiwanese influenza A and B viruses on the basis of analyses of pairwise amino acid variations, genetic clustering, and phylogenetics was performed. A total of 548, 2,123, and 1,336 sequences of the HA1 genes of influenza A virus subtypes H1 and H3 and influenza B virus, respectively, collected during 2003 to 2006 from an island-wide surveillance network were determined. Influenza A virus H3 showed activity during all periods, although it was dominant only in the winters of 2002-2003 and 2003-2004. Instead, influenza B virus and influenza A virus H1 were dominant in the winters of 2004-2005 and 2005-2006, respectively. Additionally, two influenza A virus H3 peaks were found in the summers of 2004 and 2005. From clustering analysis, similar characteristics of high sequence diversity and short life spans for the influenza A virus H1 and H3 clusters were observed, despite their distinct seasonal patterns. In contrast, clusters with longer life spans and fewer but larger clusters were found among the influenza B viruses. We also noticed that more amino acid changes at antigenic sites, especially at sites B and D in the H3 viruses, were found in 2003 and 2004 than in the following 2 years. The only epidemic of the H1 viruses, which occurred in the winter of 2005-2006, was caused by two genetically distinct lineages, and neither of them showed apparent antigenic changes compared with the antigens of the vaccine strain. For the influenza B viruses, the multiple dominant lineages of Yamagata-like strains with large genetic variations observed reflected the evolutionary pressure caused by the Yamagata-like vaccine strain. On the other hand, only one dominant lineage of Victoria-like strains circulated from 2004 to 2006.
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28
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Du X, Wang Z, Wu A, Song L, Cao Y, Hang H, Jiang T. Networks of genomic co-occurrence capture characteristics of human influenza A (H3N2) evolution. Genome Res 2007; 18:178-87. [PMID: 18032723 DOI: 10.1101/gr.6969007] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The recent availability of full genomic sequence data for a large number of human influenza A (H3N2) virus isolates over many years provides us an opportunity to analyze human influenza virus evolution by considering all gene segments simultaneously. However, such analysis requires development of new computational models that can capture the complex evolutionary features over the entire genome. By analyzing nucleotide co-occurrence over the entire genome of human H3N2 viruses, we have developed a network model to describe H3N2 virus evolutionary patterns and dynamics. The network model effectively captures the evolutionary antigenic features of H3N2 virus at the whole-genome level and accurately describes the complex evolutionary patterns between individual gene segments. Our analyses show that the co-occurring nucleotide modules apparently underpin the dynamics of human H3N2 evolution and that amino acid substitutions corresponding to nucleotide co-changes cluster preferentially in known antigenic regions of the viral HA. Therefore, our study demonstrates that nucleotide co-occurrence networks represent a powerful method for tracking influenza A virus evolution and that cooperative genomic interaction is a major force underlying influenza virus evolution.
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Affiliation(s)
- Xiangjun Du
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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Prediction of Mutations Initiated by Internal Power in H3N2 Hemagglutinins of Influenza A Virus from North America. Int J Pept Res Ther 2007. [DOI: 10.1007/s10989-007-9104-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Watabe T, Kishino H, de Oliveira Martins L, Kitazoe Y. A likelihood-based index of protein protein binding affinities with application to influenza HA escape from antibodies. Mol Biol Evol 2007; 24:1627-38. [PMID: 17478433 PMCID: PMC7107539 DOI: 10.1093/molbev/msm079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In many biological systems, proteins interact with other organic molecules to produce indispensable functions, in which molecular recognition phenomena are essential. Proteins have kept or gained their functions during molecular evolution. Their functions seem to be flexible, and a few amino acid substitutions sometimes cause drastic changes in function. In order to monitor and predict such drastic changes in the early stages in target populations, we need to identify patterns of structural changes during molecular evolution causing decreases or increases in the binding affinity of protein complexes. In previous work, we developed a likelihood-based index to quantify the degree to which a sequence fits a given structure. This index was named the sequence-structure fitness (SSF) and is calculated empirically based on amino acid preferences and pairwise interactions in the structural environment present in template structures. In the present work, we used the SSF to develop an index to measure the binding affinity of protein-protein complexes defined as the log likelihood ratio, contrasting the fitness of the sequences to the structure of the complex and that of the uncomplexed proteins. We applied the developed index to the complexes formed between influenza A hemagglutinin (HA) and four antibodies. The antibody-antigen binding region of HA is under strong selection pressure by the host immune system. Hence, examination of the long-term adaptation of HA to the four antibodies could reveal the strategy of the molecular evolution of HA. Two antibodies cover the HA receptor-binding region, while the other two bind away from the receptor-binding region. By focusing on branches with a significant decline in binding ability, we could detect key amino acid replacements and investigate the mechanism via conditional probabilities. The contrast between the adaptations to the two types of antibodies suggests that the virus adapts to the immune system at the cost of structural change.
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MESH Headings
- Algorithms
- Amino Acids
- Antibodies, Monoclonal/immunology
- Antigenic Variation
- Binding Sites, Antibody
- Cell Line
- Crystallography, X-Ray
- Epitopes/immunology
- Gene Expression Regulation
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Hemagglutinins, Viral/genetics
- Hemagglutinins, Viral/immunology
- Hemagglutinins, Viral/metabolism
- Humans
- Influenza A virus/genetics
- Influenza A virus/metabolism
- Likelihood Functions
- Mutation
- Protein Binding
- Protein Conformation
- Receptors, Virus/metabolism
- beta-Lactamases/genetics
- beta-Lactamases/immunology
- beta-Lactamases/metabolism
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Affiliation(s)
- Teruaki Watabe
- Center of Medical Information Science, Kochi University, Kochi, Japan.
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Griffiths PD. Boom and bust from influenza. Rev Med Virol 2007; 17:63-5. [PMID: 17335119 DOI: 10.1002/rmv.536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Martella V, Elia G, Decaro N, Di Trani L, Lorusso E, Campolo M, Desario C, Parisi A, Cavaliere N, Buonavoglia C. An outbreak of equine influenza virus in vaccinated horses in Italy is due to an H3N8 strain closely related to recent North American representatives of the Florida sub-lineage. Vet Microbiol 2007; 121:56-63. [PMID: 17197135 DOI: 10.1016/j.vetmic.2006.11.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Revised: 11/15/2006] [Accepted: 11/20/2006] [Indexed: 11/19/2022]
Abstract
In December 2005, equine influenza virus infection was confirmed as the cause of clinical respiratory disease in vaccinated horses in Apulia, Italy. The infected horses had been vaccinated with a vaccine that contained strains representatives from both the European (A/eq/Suffolk/89) and American (A/eq/Newmarket/1/93) H3N8 influenza virus lineages, and the H7N7 strain A/eq/Praga/56. Genetic characterization of the hemagglutinin (HA) and neuraminidase (NA) genes of the virus from the outbreak, indicated that the isolate (A/eq/Bari/2005) was an H3N8 strain closely related to recent representatives (Kentucky/5/02-like) of the American sub-lineage Florida, that was introduced in Italy through movement of infected horses from a large outbreak described in 2003 in United Kingdom. Strain A/eq/Bari/2005 displayed 9 amino acid changes in the HA1 subunit protein with respect to the reference American strain A/eq/Newmarket/1/93 contained in the vaccine. Four changes were localized in the antigenic regions C-D and likely accounted for the vaccine failure.
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Affiliation(s)
- Vito Martella
- Department of Animal Health and Well-being, University of Bari, Valenzano, Bari, Italy.
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Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science 2007; 314:1898-903. [PMID: 17185596 DOI: 10.1126/science.1132745] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human influenza A (subtype H3N2) is characterized genetically by the limited standing diversity of its hemagglutinin and antigenically by clusters that emerge and replace each other within 2 to 8 years. By introducing an epidemiological model that allows for differences between the genetic and antigenic properties of the virus's hemagglutinin, we show that these patterns can arise from cluster-specific immunity alone. Central to the formulation is a genotype-to-phenotype mapping, based on neutral networks, with antigenic phenotypes, not genotypes, determining the degree of strain cross-immunity. The model parsimoniously explains well-known, as well as previously unremarked, features of interpandemic influenza dynamics and evolution. It captures the observed boom-and-bust pattern of viral evolution, with periods of antigenic stasis during which genetic diversity grows, and with episodic contraction of this diversity during cluster transitions.
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MESH Headings
- Amino Acid Substitution
- Antigenic Variation
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Computer Simulation
- Cross Reactions
- Disease Outbreaks
- Disease Susceptibility
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Evolution, Molecular
- Genotype
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunity, Herd
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/transmission
- Influenza, Human/virology
- Models, Biological
- Models, Statistical
- Phenotype
- Phylogeny
- Point Mutation
- Polymorphism, Genetic
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Affiliation(s)
- Katia Koelle
- Department of Ecology and Evolutionary Biology, 2019 Kraus Natural Science Building, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109-1048, USA.
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Wolf YI, Viboud C, Holmes EC, Koonin EV, Lipman DJ. Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct 2006; 1:34. [PMID: 17067369 PMCID: PMC1647279 DOI: 10.1186/1745-6150-1-34] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 10/26/2006] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance. RESULTS We performed phylogenetic analyses of the recently obtained large and relatively unbiased samples of the HA sequences from 1995-2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements - the same amino acid substitution occurring independently in different lineages - were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change; no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals. CONCLUSION We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation; in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains. REVIEWERS Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Lee.
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Edward C Holmes
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David J Lipman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Nakajima K, Nobusawa E, Nakajima S. [Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution]. Uirusu 2006; 56:91-8. [PMID: 17038817 DOI: 10.2222/jsv.56.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
During protein evolution the amino acid substitutions accumulate with time. However, the effect of accumulation of the amino acid substitutions to structural changes has not been estimated well. We will propose that the discordance of amino acid substitution on the HA protein of influenza A virus is useful for the assessment of structural changes during evolution. Discordance value can be obtained from the experimental data of tolerance or intolerance by introducing site directed mutagenesis at the homologous positions of two HA proteins holding the same amino acid residues. The value of discordance correlated to the number of amino acid differences among proteins. In the H3HA discordance rate was calculated to be 0.45% per one amino acid change. Furthermore, discordance of amino acid substitutions suggests that tolerable amino acid substitutions in different order have a probability of promoting irreversible divergence of the HA protein to different subtypes.
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Affiliation(s)
- Katsuhisa Nakajima
- Department of Virology, Medical School, Nagoya City University, 1-Kawasumi, Mizuho-cho, Mizhuo-ku, Nagoya 467, Japan.
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