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Hatuwal B, Goel V, Deliberto TJ, Lowe J, Emch M, Webby RJ, Wan XF. Spatial patterns of influenza A virus spread across compartments in commercial swine farms in the United States. Emerg Microbes Infect 2024:2400530. [PMID: 39221652 DOI: 10.1080/22221751.2024.2400530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
AbstractMultiple genetic variants of H1 and H3 influenza A viruses (IAVs) circulate concurrently in US swine farms. Understanding the spatial transmission patterns of IAVs among these farms is crucial for developing effective control strategies and mitigating the emergence of novel IAVs. In this study, we analyzed 1,909 IAV genomic sequences from 785 US swine farms, representing 33 farming systems across 12 states, primarily in the Midwest from 2004 to 2023. Bayesian phylogeographic analyses were performed to identify the dispersal patterns of both H1 and H3 virus genetic lineages and to elucidate their spatial migration patterns within and between different systems. Our results showed that both intra-system and inter-system migrations occurred between the swine farms, with intra-system migrations being more frequent. However, migration rates for H1 and H3 IAVs were similar between intra-system and inter-system migration events. Spatial migration patterns aligned with expected pig movement across different compartments of swine farming systems. Sow-Farms were identified as key sources of viruses, with bi-directional migration observed between these farms and other parts of the system, including Wean-to-Finish and Gilt-Development-Units. High intra-system migration was detected across farms in the same region, while spread to geographically distant intra- and inter- system farms was less frequently. These findings suggest that prioritizing resources towards systems frequently confronting influenza problems and targeting pivotal source farms, such as sow farms, could be an effective strategy for controlling influenza in US commercial swine operations.
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Affiliation(s)
- Bijaya Hatuwal
- Center for Influenza and Emerging Diseases, University of Missouri, Columbia, MO 652011, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Varun Goel
- Department of Epidemiology, University of North Carolina School, Chapel Hill, NC 27127, USA
| | - Thomas J Deliberto
- US Department of Agriculture Animal and Plant Health Inspection Service, Fort Collins, Colorado, USA
| | - Jim Lowe
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Michael Emch
- Department of Epidemiology, University of North Carolina School, Chapel Hill, NC 27127, USA
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard J Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 63141, USA
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Diseases, University of Missouri, Columbia, MO 652011, USA
- Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO 65211, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
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2
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Carlock MA, Ross TM. A computationally optimized broadly reactive hemagglutinin vaccine elicits neutralizing antibodies against influenza B viruses from both lineages. Sci Rep 2023; 13:15911. [PMID: 37741893 PMCID: PMC10517972 DOI: 10.1038/s41598-023-43003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023] Open
Abstract
Influenza B viruses (IBV) can cause severe disease and death much like influenza A viruses (IAV), with a disproportionate number of infections in children. Despite moving to a quadrivalent vaccine to include strains from both the B/Victoria and B/Yamagata lineages, vaccine effectiveness rates continue to be variable and low in many past seasons. To develop more effective influenza B virus vaccines, three novel IBV hemagglutinin (HA) vaccines were designed using a computationally optimized broadly reactive antigen (COBRA) methodology. These IBV HA proteins were expressed on the surface of a virus-like particle (VLP) and used to vaccinate ferrets that were pre-immune to historical B/Victoria or B/Yamagata lineage viruses. Ferrets vaccinated with B-COBRA HA vaccines had neutralizing antibodies with high titer HAI titer against all influenza B viruses regardless of pre-immunization history. Conversely, VLPs expressing wild-type IBV HA antigens preferentially boosted titers against viruses from the same lineage and there was little-to-no seroprotective antibodies detected in ferrets with mismatched IBV pre-immune infections. Overall, a single IBV HA developed using the COBRA methodology elicited protective broadly-reactive antibodies against current and future drifted IBVs from both lineages.
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Affiliation(s)
- Michael A Carlock
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
- Global Vaccine Development, Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.
- Department of Infectious Diseases, University of Georgia, Athens, GA, USA.
- Global Vaccine Development, Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, USA.
- Department of Infection Biology, Lehner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Global Vaccine Development, Florida Research and Innovation Center, Cleveland Clinic, 9801 SW Discovery Way, Port Saint Lucie, FL, 34987, USA.
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3
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Varghese PM, Kishore U, Rajkumari R. Innate and adaptive immune responses against Influenza A Virus: Immune evasion and vaccination strategies. Immunobiology 2022; 227:152279. [DOI: 10.1016/j.imbio.2022.152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
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Tsybalova LM, Stepanova LA, Ramsay ES, Vasin AV. Influenza B: Prospects for the Development of Cross-Protective Vaccines. Viruses 2022; 14:1323. [PMID: 35746794 PMCID: PMC9228933 DOI: 10.3390/v14061323] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/09/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
In this review, we analyze the epidemiological and ecological features of influenza B, one of the most common and severe respiratory infections. The review presents various strategies for cross-protective influenza B vaccine development, including recombinant viruses, virus-like particles, and recombinant proteins. We provide an overview of viral proteins as cross-protective vaccine targets, along with other updated broadly protective vaccine strategies. The importance of developing such vaccines lies not only in influenza B prevention, but also in the very attractive prospect of eradicating the influenza B virus in the human population.
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Affiliation(s)
- Liudmila M. Tsybalova
- Smorodintsev Research Institute of Influenza, Prof. Popova Str., 15/17, 197376 St. Petersburg, Russia; (L.A.S.); (E.S.R.); or (A.V.V.)
| | - Liudmila A. Stepanova
- Smorodintsev Research Institute of Influenza, Prof. Popova Str., 15/17, 197376 St. Petersburg, Russia; (L.A.S.); (E.S.R.); or (A.V.V.)
| | - Edward S. Ramsay
- Smorodintsev Research Institute of Influenza, Prof. Popova Str., 15/17, 197376 St. Petersburg, Russia; (L.A.S.); (E.S.R.); or (A.V.V.)
| | - Andrey V. Vasin
- Smorodintsev Research Institute of Influenza, Prof. Popova Str., 15/17, 197376 St. Petersburg, Russia; (L.A.S.); (E.S.R.); or (A.V.V.)
- Research Institute of Influenza named after A.A. Smorodintsev, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St. Petersburg, Russia
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5
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Antigenic escape selects for the evolution of higher pathogen transmission and virulence. Nat Ecol Evol 2022; 6:51-62. [PMID: 34949816 PMCID: PMC9671278 DOI: 10.1038/s41559-021-01603-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022]
Abstract
Despite the propensity for complex and non-equilibrium dynamics in nature, eco-evolutionary analytical theory typically assumes that populations are at equilibria. In particular, pathogens often show antigenic escape from host immune defences, leading to repeated epidemics, fluctuating selection and diversification, but we do not understand how this impacts the evolution of virulence. We model the impact of antigenic drift and escape on the evolution of virulence in a generalized pathogen and apply a recently introduced oligomorphic methodology that captures the dynamics of the mean and variance of traits, to show analytically that these non-equilibrium dynamics select for the long-term persistence of more acute pathogens with higher virulence. Our analysis predicts both the timings and outcomes of antigenic shifts leading to repeated epidemics and predicts the increase in variation in both antigenicity and virulence before antigenic escape. There is considerable variation in the degree of antigenic escape that occurs across pathogens and our results may help to explain the difference in virulence between related pathogens including, potentially, human influenzas. Furthermore, it follows that these pathogens will have a lower R0, with clear implications for epidemic behaviour, endemic behaviour and control. More generally, our results show the importance of examining the evolutionary consequences of non-equilibrium dynamics.
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Sreenivasan CC, Sheng Z, Wang D, Li F. Host Range, Biology, and Species Specificity of Seven-Segmented Influenza Viruses-A Comparative Review on Influenza C and D. Pathogens 2021; 10:1583. [PMID: 34959538 PMCID: PMC8704295 DOI: 10.3390/pathogens10121583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 02/06/2023] Open
Abstract
Other than genome structure, influenza C (ICV), and D (IDV) viruses with seven-segmented genomes are biologically different from the eight-segmented influenza A (IAV), and B (IBV) viruses concerning the presence of hemagglutinin-esterase fusion protein, which combines the function of hemagglutinin and neuraminidase responsible for receptor-binding, fusion, and receptor-destroying enzymatic activities, respectively. Whereas ICV with humans as primary hosts emerged nearly 74 years ago, IDV, a distant relative of ICV, was isolated in 2011, with bovines as the primary host. Despite its initial emergence in swine, IDV has turned out to be a transboundary bovine pathogen and a broader host range, similar to influenza A viruses (IAV). The receptor specificities of ICV and IDV determine the host range and the species specificity. The recent findings of the presence of the IDV genome in the human respiratory sample, and high traffic human environments indicate its public health significance. Conversely, the presence of ICV in pigs and cattle also raises the possibility of gene segment interactions/virus reassortment between ICV and IDV where these viruses co-exist. This review is a holistic approach to discuss the ecology of seven-segmented influenza viruses by focusing on what is known so far on the host range, seroepidemiology, biology, receptor, phylodynamics, species specificity, and cross-species transmission of the ICV and IDV.
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Affiliation(s)
- Chithra C. Sreenivasan
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (C.C.S.); (D.W.)
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA;
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (C.C.S.); (D.W.)
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA; (C.C.S.); (D.W.)
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Tohma K, Saito M, Pajuelo MJ, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale. Emerg Microbes Infect 2021; 10:1717-1730. [PMID: 34376124 PMCID: PMC8425682 DOI: 10.1080/22221751.2021.1967706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/08/2021] [Indexed: 11/03/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis. Human noroviruses present >30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Monica J. Pajuelo
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cara J Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | | | - Robert H. Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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Mittal N, Sengupta N, Malladi SK, Reddy P, Bhat M, Rajmani RS, Sedeyn K, Saelens X, Dutta S, Varadarajan R. Protective Efficacy of Recombinant Influenza Hemagglutinin Ectodomain Fusions. Viruses 2021; 13:v13091710. [PMID: 34578291 PMCID: PMC8473191 DOI: 10.3390/v13091710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
In current seasonal influenza vaccines, neutralizing antibody titers directed against the hemagglutinin surface protein are the primary correlate of protection. These vaccines are, therefore, quantitated in terms of their hemagglutinin content. Adding other influenza surface proteins, such as neuraminidase and M2e, to current quadrivalent influenza vaccines would likely enhance vaccine efficacy. However, this would come with increased manufacturing complexity and cost. To address this issue, as a proof of principle, we have designed genetic fusions of hemagglutinin ectodomains from H3 and H1 influenza A subtypes. These recombinant H1-H3 hemagglutinin ectodomain fusions could be transiently expressed at high yield in mammalian cell culture using Expi293F suspension cells. Fusions were trimeric, and as stable in solution as their individual trimeric counterparts. Furthermore, the H1-H3 fusion constructs were antigenically intact based on their reactivity with a set of conformation-specific monoclonal antibodies. H1-H3 hemagglutinin ectodomain fusion immunogens, when formulated with the MF59 equivalent adjuvant squalene-in-water emulsion (SWE), induced H1 and H3-specific humoral immune responses equivalent to those induced with an equimolar mixture of individually expressed H1 and H3 ectodomains. Mice immunized with these ectodomain fusions were protected against challenge with heterologous H1N1 (Bel/09) and H3N2 (X-31) mouse-adapted viruses with higher neutralizing antibody titers against the H1N1 virus. Use of such ectodomain-fused immunogens would reduce the number of components in a vaccine formulation and allow for the inclusion of other protective antigens to increase influenza vaccine efficacy.
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MESH Headings
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Cross Protection/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/administration & dosage
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Mice
- Mice, Inbred BALB C
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/prevention & control
- Vaccine Efficacy
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
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Affiliation(s)
- Nidhi Mittal
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Nayanika Sengupta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Sameer Kumar Malladi
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Poorvi Reddy
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India; (P.R.); (M.B.)
| | - Madhuraj Bhat
- Mynvax Private Limited, ES12, Entrepreneurship Centre, SID, Indian Institute of Science, Bengaluru 560012, India; (P.R.); (M.B.)
| | - Raju S. Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (K.S.); (X.S.)
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; (K.S.); (X.S.)
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
| | - Raghavan Varadarajan
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bengaluru 560012, India; (N.M.); (N.S.); (S.K.M.); (R.S.R.); (S.D.)
- Correspondence: ; Tel.: +91-80-22932612; Fax: +91-80-23600535
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9
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Bajic G, Harrison SC. Antibodies That Engage the Hemagglutinin Receptor-Binding Site of Influenza B Viruses. ACS Infect Dis 2021; 7:1-5. [PMID: 33274930 DOI: 10.1021/acsinfecdis.0c00726] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We describe cross-reactive human antibodies recognizing influenza B viruses spanning nearly 80 years of antigenic drift. Structures show that they engage the receptor-binding site (RBS) of the viral hemagglutinin with strong similarities to their influenza A counterparts, despite structural differences between the RBS of influenza A and B. Our data show that these antibodies readily cross-react with both influenza B Victoria and Yamagata lineages. We also note that all antibodies are encoded by IGHV3-9/IGK1-33. Future research will provide insight into the prevalence of these antibodies in the human population.
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Affiliation(s)
- Goran Bajic
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, United States
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10
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Shu B, Kirby MK, Warnes C, Sessions WM, Davis WG, Liu J, Wilson MM, Lindstrom S, Wentworth DE, Barnes JR. Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. ACTA ACUST UNITED AC 2021; 25. [PMID: 33063654 PMCID: PMC7565853 DOI: 10.2807/1560-7917.es.2020.25.41.1900652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background During the 2016/17 influenza season, influenza B/VIC lineage variant viruses emerged with two (K162N163) or three (K162N163D164) amino acid (aa) deletions in the haemagglutinin (HA) protein. There are currently five antigenically distinct HA proteins expressed by co-circulating influenza B viruses: B/YAM, B/VIC V1A (no deletion), B/VIC V1A-2DEL (2 aa deletion) and two antigenically distinguishable groups of B/VIC V1A-3DEL (3 aa deletion). The prevalence of these viruses differs across geographical regions, making it critical to have a sensitive, rapid diagnostic assay that detects and distinguishes these influenza B variant viruses during surveillance. Aim Our objective was to develop a real-time RT-PCR (rRT-PCR) assay for detection and discrimination of influenza B/VIC lineage variant viruses. Methods We designed a diagnostic assay with one pair of conserved primers and three probes specific to each genetic group. We used propagated influenza B/VIC variant viruses and clinical specimens to assess assay performance. Results This rRT-PCR assay detects and distinguishes the influenza B/VIC V1A, B/VIC V1A-2DEL, and B/VIC V1A-3DEL variant viruses, with no cross-reactivity. This assay can be run as a multiplex reaction, allowing for increased testing efficiency and reduced cost. Conclusion Coupling this assay with the Centers for Disease Control and Prevention’s Human Influenza Virus Real-Time RT-PCR Diagnostic Panel Influenza B Lineage Genotyping Kit results in rapid detection and characterisation of circulating influenza B viruses. Detailed surveillance information on these distinct influenza B variant viruses will provide insight into their prevalence and geographical distribution and could aid in vaccine recommendations.
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Affiliation(s)
- Bo Shu
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Marie K Kirby
- Battelle Memorial Institute, Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Christine Warnes
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Wendy M Sessions
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - William G Davis
- Battelle Memorial Institute, Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Ji Liu
- Chickasaw Nation Industries, Inc., Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Malania M Wilson
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Stephen Lindstrom
- Respiratory Virus Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, United States
| | - David E Wentworth
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - John R Barnes
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
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11
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Duev-Cohen A, Isaacson B, Berhani O, Charpak-Amikam Y, Friedman N, Drori Y, Mandelboim M, Mandelboim O. Altered NKp46 Recognition and Elimination of Influenza B Viruses. Viruses 2020; 13:v13010034. [PMID: 33375516 PMCID: PMC7824211 DOI: 10.3390/v13010034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/23/2022] Open
Abstract
Every year, millions of people worldwide are infected with influenza, causing enormous health and economic problems. The most common type of influenza is influenza A. It is known that Natural Killer (NK) cells play an important role in controlling influenza A infection, mostly through the recognition of the viral protein hemagglutinin (HA) by the activating receptor, NKp46. In contrast, little is known regarding NK cell recognition of influenza B viruses, even though they are responsible for a third of all pediatric influenza deaths and are therefore included in the seasonal vaccine each year. Here we show that NKp46 also recognizes influenza B viruses. We show that NKp46 binds the HA protein of influenza B in a sialic acid-dependent manner, and identified the glycosylated residue in NKp46, which is critical for this interaction. We discovered that this interaction has a binding affinity approximately seven times lower than NKp46 binding of influenza A’s HA. Finally, we demonstrated, using mice deficient for the mouse orthologue of NKp46, named NCR1, that NKp46 is not important for influenza B elimination. These findings enable us to better understand the interactions between the different influenza viruses and NK cells that are known to be crucial for viral elimination.
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Affiliation(s)
- Alexandra Duev-Cohen
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel; (A.D.-C.); (B.I.); (O.B.); (Y.C.-A.)
| | - Batya Isaacson
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel; (A.D.-C.); (B.I.); (O.B.); (Y.C.-A.)
| | - Orit Berhani
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel; (A.D.-C.); (B.I.); (O.B.); (Y.C.-A.)
| | - Yoav Charpak-Amikam
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel; (A.D.-C.); (B.I.); (O.B.); (Y.C.-A.)
| | - Nehemya Friedman
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 5265601, Israel; (N.F.); (Y.D.); (M.M.)
| | - Yaron Drori
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 5265601, Israel; (N.F.); (Y.D.); (M.M.)
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan 5265601, Israel; (N.F.); (Y.D.); (M.M.)
| | - Ofer Mandelboim
- The Concern Foundation Laboratories at the Lautenberg Center for Immunology and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel; (A.D.-C.); (B.I.); (O.B.); (Y.C.-A.)
- Correspondence:
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12
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HA1 (Hemagglutinin) quantitation for influenza A H1N1 and H3N2 high yield reassortant vaccine candidate seed viruses by RP-UPLC. Vaccine 2020; 39:545-553. [PMID: 33341306 DOI: 10.1016/j.vaccine.2020.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/20/2020] [Accepted: 12/01/2020] [Indexed: 11/23/2022]
Abstract
The only effective measure to decrease morbidity and mortality caused by the influenza virus in the human population is worldwide vaccination. Vaccination produces neutralizing antibodies that target the HA1 subunit of the HA (hemagglutinin) protein and are strain specific. The effectiveness of new influenza vaccines are linked to two factors, the correct prediction of the circulating strains in the population in a particular season and the concentration of the HA1 protein in the vaccine formulation. With the advent of the licensing of quadrivalent vaccines, pharmaceutical manufacturers are under considerable pressure due to time constraints and dedicated resources to deliver 194-198 million doses (2020-2021 U.S. market) of vaccine. Considering the valuable resources needed to produce the influenza vaccine in a timely manner, the efficient quantitation of the HA1 protein (the main component in the influenza vaccine) is required. Currently the only method approved by regulatory agencies for quantitation of the HA antigen in vaccines is the single radial immunodiffusion assay (SRID), an antibody dependent assay that is not time efficient. Time efficient methods that are antibody independent e.g. reverse phase-high performance liquid chromatography (RP-HPLC) or size exclusion-HPLC (SE-HPLC) are available. An improved method implementing reverse phase-ultra performance liquid chromatography (RP-UPLC) has been developed to quantitate the HA1 protein antigen present in the high yield reassortant vaccine seed viruses from influenza A H1N1 and H3N2 subtypes harvested from inoculated embryonated chicken eggs. This method differentiates between high yield and lower yielding reassortants in order to select the best vaccine candidate seed virus with the highest growth 'in ovo'. This direct capability to monitor the HA1 concentration of potential reassortant seed viruses and to choose the best yielding HA influenza reassortant when faced with multiple viral seed candidates provides a major advantage on the industrial scale to the influenza vaccine process.
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13
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Nath Neerukonda S, Vassell R, Weiss CD. Neutralizing Antibodies Targeting the Conserved Stem Region of Influenza Hemagglutinin. Vaccines (Basel) 2020; 8:E382. [PMID: 32664628 PMCID: PMC7563823 DOI: 10.3390/vaccines8030382] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/02/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022] Open
Abstract
Influenza continues to be a public health threat despite the availability of annual vaccines. While vaccines are generally effective at inducing strain-specific immunity, they are sub-optimal or ineffective when drifted or novel pandemic strains arise due to sequence changes in the major surface glycoprotein hemagglutinin (HA). The discovery of a large number of antibodies targeting the highly conserved stem region of HAs that are capable of potently neutralizing a broad range of virus strains and subtypes suggests new ways to protect against influenza. The structural characterization of HA stem epitopes and broadly neutralizing antibody paratopes has enabled the design of novel proteins, mini-proteins, and peptides targeting the HA stem, thus providing a foundation for the design of new vaccines. In this narrative, we comprehensively review the current knowledge about stem-directed broadly neutralizing antibodies and the structural features contributing to virus neutralization.
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Affiliation(s)
| | | | - Carol D. Weiss
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (S.N.N.); (R.V.)
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14
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Li Y, Wang L, Si H, Yu Z, Tian S, Xiang R, Deng X, Liang R, Jiang S, Yu F. Influenza virus glycoprotein-reactive human monoclonal antibodies. Microbes Infect 2020; 22:263-271. [PMID: 32569735 PMCID: PMC7303604 DOI: 10.1016/j.micinf.2020.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 11/05/2022]
Abstract
Influenza continues to be a significant public health challenge. Two glycoproteins on the surface of influenza virus, hemagglutinin and neuraminidase, play a prominent role in the process of influenza virus infection and release. Monoclonal antibodies targeting glycoproteins can effectively prevent the spread of the virus. In this review, we summarized currently reported human monoclonal antibodies targeting glycoproteins of influenza A and B viruses.
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Affiliation(s)
- Yanbai Li
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Helong Si
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhengsen Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shijun Tian
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Rong Xiang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China.
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15
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Valesano AL, Fitzsimmons WJ, McCrone JT, Petrie JG, Monto AS, Martin ET, Lauring AS. Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts. J Virol 2020; 94:e01710-19. [PMID: 31801858 PMCID: PMC7022338 DOI: 10.1128/jvi.01710-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Influenza B virus (IBV) undergoes seasonal antigenic drift more slowly than influenza A virus, but the reasons for this difference are unclear. While the evolutionary dynamics of influenza viruses play out globally, they are fundamentally driven by mutation, reassortment, drift, and selection at the level of individual hosts. These processes have recently been described for influenza A virus, but little is known about the evolutionary dynamics of IBV during individual infections and transmission events. Here, we define the within-host evolutionary dynamics of IBV by sequencing virus populations from naturally infected individuals enrolled in a prospective, community-based cohort over 8,176 person-seasons of observation. Through analysis of high depth-of-coverage sequencing data from samples from 91 individuals with influenza B, we find that IBV accumulates lower genetic diversity than previously observed for influenza A virus during acute infections. Consistent with studies of influenza A viruses, the within-host evolution of IBVs is characterized by purifying selection and the general absence of widespread positive selection of within-host variants. Analysis of shared genetic diversity across 15 sequence-validated transmission pairs suggests that IBV experiences a tight transmission bottleneck similar to that of influenza A virus. These patterns of local-scale evolution are consistent with the lower global evolutionary rate of IBV.IMPORTANCE The evolution of influenza virus is a significant public health problem and necessitates the annual evaluation of influenza vaccine formulation to keep pace with viral escape from herd immunity. Influenza B virus is a serious health concern for children, in particular, yet remains understudied compared to influenza A virus. Influenza B virus evolves more slowly than influenza A virus, but the factors underlying this are not completely understood. We studied how the within-host diversity of influenza B virus relates to its global evolution by sequencing viruses from a community-based cohort. We found that influenza B virus populations have lower within-host genetic diversity than influenza A virus and experience a tight genetic bottleneck during transmission. Our work provides insights into the varying dynamics of influenza viruses in human infection.
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Affiliation(s)
- Andrew L Valesano
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, USA
| | - William J Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joshua G Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Arnold S Monto
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Emily T Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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16
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A Complex Dance: Measuring the Multidimensional Worlds of Influenza Virus Evolution and Anti-Influenza Immune Responses. Pathogens 2019; 8:pathogens8040238. [PMID: 31731815 PMCID: PMC6963821 DOI: 10.3390/pathogens8040238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 11/17/2022] Open
Abstract
The human antibody response to influenza virus infection or vaccination is as complicated as it is essential for protection against flu. The constant antigenic changes of the virus to escape human herd immunity hinder the yearly selection of vaccine strains since it is hard to predict which virus strains will circulate for the coming flu season. A "universal" influenza vaccine that could induce broad cross-influenza subtype protection would help to address this issue. However, the human antibody response is intricate and often obscure, with factors such as antigenic seniority or original antigenic sin (OAS), and back-boosting ensuring that each person mounts a unique immune response to infection or vaccination with any new influenza virus strain. Notably, the effects of existing antibodies on cross-protective immunity after repeated vaccinations are unclear. More research is needed to characterize the mechanisms at play, but traditional assays such as hemagglutinin inhibition (HAI) and microneutralization (MN) are excessively limited in scope and too resource-intensive to effectively meet this challenge. In the past ten years, new multiple dimensional assays (MDAs) have been developed to help overcome these problems by simultaneously measuring antibodies against a large panel of influenza hemagglutinin (HA) proteins with a minimal amount of sample in a high throughput way. MDAs will likely be a powerful tool for accelerating the study of the humoral immune response to influenza vaccination and the development of a universal influenza vaccine.
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17
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Broadly Cross-Reactive, Nonneutralizing Antibodies against Influenza B Virus Hemagglutinin Demonstrate Effector Function-Dependent Protection against Lethal Viral Challenge in Mice. J Virol 2019; 93:JVI.01696-18. [PMID: 30626682 DOI: 10.1128/jvi.01696-18] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/24/2018] [Indexed: 11/20/2022] Open
Abstract
Protection from influenza virus infection is canonically associated with antibodies that neutralize the virus by blocking the interaction between the viral hemagglutinin and host cell receptors. However, protection can also be conferred by other mechanisms, including antibody-mediated effector functions. Here, we report the characterization of 22 broadly cross-reactive, nonneutralizing antibodies specific for influenza B virus hemagglutinin. The majority of these antibodies recognized influenza B viruses isolated over the period of 73 years and bind the conserved stalk domain of the hemagglutinin. A proportion of the characterized antibodies protected mice from both morbidity and mortality after challenge with a lethal dose of influenza B virus. Activity in an antibody-dependent cell-mediated cytotoxicity reporter assay correlated strongly with protection, suggesting that Fc-dependent effector function determines protective efficacy. The information regarding mechanism of action and epitope location stemming from our characterization of these antibodies will inform the design of urgently needed vaccines that could induce broad protection against influenza B viruses.IMPORTANCE While broadly protective antibodies against the influenza A virus hemagglutinin have been well studied, very limited information is available for antibodies that broadly recognize influenza B viruses. Similarly, the development of a universal or broadly protective influenza B virus vaccine lags behind the development of such a vaccine for influenza A virus. More information about epitope location and mechanism of action of broadly protective influenza B virus antibodies is required to inform vaccine development. In addition, protective antibodies could be a useful tool to treat or prevent influenza B virus infection in pediatric cohorts or in a therapeutic setting in immunocompromised individuals in conjugation with existing treatment avenues.
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18
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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19
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de Vries RD, Nieuwkoop NJ, van der Klis FRM, Koopmans MPG, Krammer F, Rimmelzwaan GF. Primary Human Influenza B Virus Infection Induces Cross-Lineage Hemagglutinin Stalk-Specific Antibodies Mediating Antibody-Dependent Cellular Cytoxicity. J Infect Dis 2017; 217:3-11. [PMID: 29294018 PMCID: PMC5853962 DOI: 10.1093/infdis/jix546] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) and influenza B virus (IBV) cause substantial morbidity and mortality during annual epidemics. Two distinct lineages of IBV are distinguished, based on variation in hemagglutinin (HA): B/Victoria/2/87-like (B/Vic) and B/Yamagata/16/88-like (B/Yam). Here, we show that, in humans, primary IBV infection with either lineage induces HA-specific antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies. IBV infection induced antibodies specific to the HA head and stalk, but only HA stalk-specific antibodies mediated ADCC efficiently and displayed cross-reactivity with IBV of both lineages. This corresponds to recent findings that 2 points of contact between the effector and target cell (ie, HA and sialic acid, respectively, and the fragment crystallizable [Fc] domain and Fcγ receptor IIIα, respectively) are required for efficient ADCC activity and that antibodies specific for the receptor-binding site located in the head domain of HA therefore fail to mediate ADCC. Potentially, ADCC-mediating antibodies directed to the HA stalk of IBV contribute to cross-protective immunity to IBV of both lineages.
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Affiliation(s)
- Rory D de Vries
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Nella J Nieuwkoop
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Fiona R M van der Klis
- Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Guus F Rimmelzwaan
- Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
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20
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Fitness cost of reassortment in human influenza. PLoS Pathog 2017; 13:e1006685. [PMID: 29112968 PMCID: PMC5675378 DOI: 10.1371/journal.ppat.1006685] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10−2 in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage. The genome of the human influenza virus consists of 8 disjoint RNA polymer segments. These segments can undergo reassortment: when two viruses co-infect a host cell, they can produce viral offspring with a new combination of segments. In this paper, we show that reassortment within a given influenza lineage induces a fitness cost that increases in strength with increasing genetic distance of the parent viruses. Our finding suggests that evolution continuously produces viral proteins whose fitness depends on each other; reassortment reduces fitness by breaking up successful combinations of proteins. Thus, selection across proteins constrains viral evolution within a given lineage, and it may be an important factor in defining a viral species.
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21
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Skowronski DM, Chambers C, De Serres G, Sabaiduc S, Winter AL, Dickinson JA, Gubbay JB, Fonseca K, Drews SJ, Charest H, Martineau C, Krajden M, Petric M, Bastien N, Li Y. Age-Related Differences in Influenza B Infection by Lineage in a Community-Based Sentinel System, 2010-2011 to 2015-2016, Canada. J Infect Dis 2017; 216:697-702. [PMID: 28934439 PMCID: PMC5853978 DOI: 10.1093/infdis/jix393] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022] Open
Abstract
Age-related differences in influenza B lineage detection were explored in the community-based Canadian Sentinel Practitioner Surveillance Network (SPSN) from 2010–2011 to 2015–2016. Whereas >80% of B(Victoria) cases were <40 years old, B(Yamagata) cases showed a bimodal age distribution with 27% who were <20 years old and 61% who were 30–64 years old, but with a notable gap in cases between 20 and 29 years old (4%). Overall, the median age was 20 years lower for B(Victoria) vs B(Yamagata) cases (20 vs 40 years; P < .01). Additional phylodynamic and immuno-epidemiological research is needed to understand age-related variation in influenza B risk by lineage, with potential implications for prevention and control across the lifespan.
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Affiliation(s)
- Danuta M Skowronski
- British Columbia Centre for Disease Control.,University of British Columbia, Vancouver
| | | | - Gaston De Serres
- Institut National de Santé Publique du Québec.,Laval University.,Centre Hospitalier Universitaire de Québec, Québec City
| | | | | | | | | | - Kevin Fonseca
- University of Calgary, Alberta.,Alberta Provincial Laboratory, Calgary
| | - Steven J Drews
- Alberta Provincial Laboratory, Edmonton.,University of Alberta, Edmonton
| | | | | | - Mel Krajden
- British Columbia Centre for Disease Control.,University of British Columbia, Vancouver
| | | | - Nathalie Bastien
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Yan Li
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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22
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Morris DE, Cleary DW, Clarke SC. Secondary Bacterial Infections Associated with Influenza Pandemics. Front Microbiol 2017; 8:1041. [PMID: 28690590 PMCID: PMC5481322 DOI: 10.3389/fmicb.2017.01041] [Citation(s) in RCA: 316] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/24/2017] [Indexed: 12/16/2022] Open
Abstract
Lower and upper respiratory infections are the fourth highest cause of global mortality (Lozano et al., 2012). Epidemic and pandemic outbreaks of respiratory infection are a major medical concern, often causing considerable disease and a high death toll, typically over a relatively short period of time. Influenza is a major cause of epidemic and pandemic infection. Bacterial co/secondary infection further increases morbidity and mortality of influenza infection, with Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus reported as the most common causes. With increased antibiotic resistance and vaccine evasion it is important to monitor the epidemiology of pathogens in circulation to inform clinical treatment and development, particularly in the setting of an influenza epidemic/pandemic.
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Affiliation(s)
- Denise E. Morris
- Infectious Disease Epidemiology Group, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, Institute for Life Sciences, University of Southampton, University Hospital Southampton Foundation NHS TrustSouthampton, United Kingdom
| | - David W. Cleary
- Infectious Disease Epidemiology Group, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, Institute for Life Sciences, University of Southampton, University Hospital Southampton Foundation NHS TrustSouthampton, United Kingdom
| | - Stuart C. Clarke
- Infectious Disease Epidemiology Group, Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, Institute for Life Sciences, University of Southampton, University Hospital Southampton Foundation NHS TrustSouthampton, United Kingdom
- Global Health Research Institute, University of SouthamptonSouthampton, United Kingdom
- NIHR Southampton Respiratory Biomedical Research UnitSouthampton, United Kingdom
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23
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Wu NC, Wilson IA. A Perspective on the Structural and Functional Constraints for Immune Evasion: Insights from Influenza Virus. J Mol Biol 2017. [PMID: 28648617 DOI: 10.1016/j.jmb.2017.06.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Influenza virus evolves rapidly to constantly escape from natural immunity. Most humoral immune responses to influenza virus target the hemagglutinin (HA) glycoprotein, which is the major antigen on the surface of the virus. The HA is composed of a globular head domain for receptor binding and a stem domain for membrane fusion. The major antigenic sites of HA are located in the globular head subdomain, which is highly tolerant of amino acid substitutions and continual addition of glycosylation sites. Nonetheless, the evolution of the receptor-binding site and the stem region on HA is severely constrained by their functional roles in engaging the host receptor and in mediating membrane fusion, respectively. Here, we review how broadly neutralizing antibodies (bnAbs) exploit these evolutionary constraints to protect against diverse influenza strains. We also discuss the emerging role of other epitopes that are conserved only in subsets of viruses. This rapidly increasing knowledge of the evolutionary biology, immunology, structural biology, and virology of influenza virus is invaluable for development and design of more universal influenza vaccines and novel therapeutics.
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Affiliation(s)
- Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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24
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Seleka M, Treurnicht FK, Tempia S, Hellferscee O, Mtshali S, Cohen AL, Buys A, McAnerney JM, Besselaar TG, Pretorius M, von Gottberg A, Walaza S, Cohen C, Madhi SA, Venter M. Epidemiology of influenza B/Yamagata and B/Victoria lineages in South Africa, 2005-2014. PLoS One 2017; 12:e0177655. [PMID: 28542324 PMCID: PMC5444647 DOI: 10.1371/journal.pone.0177655] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/01/2017] [Indexed: 12/29/2022] Open
Abstract
Background Studies describing the epidemiology of influenza B lineages in South Africa are lacking. Methods We conducted a prospective study to describe the circulation of influenza B/Victoria and B/Yamagata lineages among patients of all ages enrolled in South Africa through three respiratory illness surveillance systems between 2005 and 2014: (i) the Viral Watch (VW) program enrolled outpatients with influenza-like illness (ILI) from private healthcare facilities during 2005–2014; (ii) the influenza-like illnesses program enrolled outpatients in public healthcare clinics (ILI/PHC) during 2012–2014; and (iii) the severe acute respiratory illnesses (SARI) program enrolled inpatients from public hospitals during 2009–2014. Influenza B viruses were detected by virus isolation during 2005 to 2009 and by real-time reverse transcription polymerase chain reaction from 2009–2014. Clinical and epidemiological characteristics of patients hospitalized with SARI and infected with different influenza B lineages were also compared using unconditional logistic regression. Results Influenza viruses were detected in 22% (8,706/39,804) of specimens from patients with ILI or SARI during 2005–2014, of which 24% (2,087) were positive for influenza B. Influenza B viruses predominated in all three surveillance systems in 2010. B/Victoria predominated prior to 2011 (except 2008) whereas B/Yamagata predominated thereafter (except 2012). B lineages co-circulated in all seasons, except in 2013 and 2014 for SARI and ILI/PHC surveillance. Among influenza B-positive SARI cases, the detection of influenza B/Yamagata compared to influenza B/Victoria was significantly higher in individuals aged 45–64 years (adjusted odds ratio [aOR]: 4.2; 95% confidence interval [CI]: 1.1–16.5) and ≥65 years (aOR: 12.2; 95% CI: 2.3–64.4) compared to children aged 0–4 years, but was significantly lower in HIV-infected patients (aOR: 0.4; 95% CI: 0.2–0.9). Conclusion B lineages co-circulated in most seasons except in 2013 and 2014. Hospitalized SARI cases display differential susceptibility for the two influenza B lineages, with B/Victoria being more prevalent among children and HIV-infected persons.
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Affiliation(s)
- Mpho Seleka
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Florette K. Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- * E-mail:
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johanneburg, South Africa
| | - Senzo Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Adam L. Cohen
- Global Influenza Program, World Health Organization (WHO), Geneva, Switzerland
| | - Amelia Buys
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Johanna M. McAnerney
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Terry G. Besselaar
- Global Influenza Program, World Health Organization (WHO), Geneva, Switzerland
| | - Marthi Pretorius
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johanneburg, South Africa
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shabir A. Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Services (NHLS), Johannesburg, South Africa
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonoses Research Unit, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
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25
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Atkinson KV, Bishop LA, Rhodes G, Salez N, McEwan NR, Hegarty MJ, Robey J, Harding N, Wetherell S, Lauder RM, Pickup RW, Wilkinson M, Gatherer D. Influenza C in Lancaster, UK, in the winter of 2014-2015. Sci Rep 2017; 7:46578. [PMID: 28406194 PMCID: PMC5390268 DOI: 10.1038/srep46578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
Influenza C is not included in the annual seasonal influenza vaccine, and has historically been regarded as a minor respiratory pathogen. However, recent work has highlighted its potential role as a cause of pneumonia in infants. We performed nasopharyngeal or nasal swabbing and/or serum sampling (n = 148) in Lancaster, UK, over the winter of 2014-2015. Using enzyme-linked immunosorbent assay (ELISA), we obtain seropositivity of 77%. By contrast, only 2 individuals, both asymptomatic adults, were influenza C-positive by polymerase chain reaction (PCR). Deep sequencing of nasopharyngeal samples produced partial sequences for 4 genome segments in one of these patients. Bayesian phylogenetic analysis demonstrated that the influenza C genome from this individual is evolutionarily distant to those sampled in recent years and represents a novel genome constellation, indicating that it may be a product of a decades-old reassortment event. Although we find no evidence that influenza C was a significant respiratory pathogen during the winter of 2014-2015 in Lancaster, we confirm previous observations of seropositivity in the majority of the population. (170 words).
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Affiliation(s)
- Kate V Atkinson
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK
- Present address: University College London Hospitals NHS Foundation Trust, London, UK
| | - Lisa A Bishop
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK
- Royal Lancaster Infirmary, Ashton Road, Lancaster, LA1 4RP, UK
| | - Glenn Rhodes
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4AP, UK
| | - Nicolas Salez
- UMR_D 190, Emergence des Pathologies Virales, Aix-Marseille University, 27 Bd Jean Moulin, Marseille cedex 05, 13005, France
| | - Neil R McEwan
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Matthew J Hegarty
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Julie Robey
- Queen Square Medical Practice, 2 Queen Square, Lancaster, LA1 1RP, UK
| | - Nicola Harding
- Queen Square Medical Practice, 2 Queen Square, Lancaster, LA1 1RP, UK
| | - Simon Wetherell
- Queen Square Medical Practice, 2 Queen Square, Lancaster, LA1 1RP, UK
| | - Robert M Lauder
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK
| | - Roger W Pickup
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4AP, UK
| | - Mark Wilkinson
- Royal Lancaster Infirmary, Ashton Road, Lancaster, LA1 4RP, UK
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster, LA1 4YT, UK.
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26
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Chai N, Swem LR, Park S, Nakamura G, Chiang N, Estevez A, Fong R, Kamen L, Kho E, Reichelt M, Lin Z, Chiu H, Skippington E, Modrusan Z, Stinson J, Xu M, Lupardus P, Ciferri C, Tan MW. A broadly protective therapeutic antibody against influenza B virus with two mechanisms of action. Nat Commun 2017; 8:14234. [PMID: 28102191 PMCID: PMC5253702 DOI: 10.1038/ncomms14234] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/12/2016] [Indexed: 01/12/2023] Open
Abstract
Influenza B virus (IBV) causes annual influenza epidemics around the world. Here we use an in vivo plasmablast enrichment technique to isolate a human monoclonal antibody, 46B8 that neutralizes all IBVs tested in vitro and protects mice against lethal challenge of all IBVs tested when administered 72 h post infection. 46B8 demonstrates a superior therapeutic benefit over Tamiflu and has an additive antiviral effect in combination with Tamiflu. 46B8 binds to a conserved epitope in the vestigial esterase domain of hemagglutinin (HA) and blocks HA-mediated membrane fusion. After passage of the B/Brisbane/60/2008 virus in the presence of 46B8, we isolated three resistant clones, all harbouring the same mutation (Ser301Phe) in HA that abolishes 46B8 binding to HA at low pH. Interestingly, 46B8 is still able to protect mice against lethal challenge of the mutant viruses, possibly owing to its ability to mediate antibody-dependent cellular cytotoxicity (ADCC). Influenza B virus (IBV) co-circulates with influenza A virus to cause annual epidemics. Here, Chai et al. isolate a human monoclonal antibody that binds to a conserved epitope in the viral HA protein, neutralizes IBV strains in vitro, and protects mice against IBV infection.
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Affiliation(s)
- Ning Chai
- Department of Infectious Diseases, Genentech, South San Francisco, California 94080, USA
| | - Lee R Swem
- Department of Infectious Diseases, Genentech, South San Francisco, California 94080, USA
| | - Summer Park
- Department of Translational Immunology, Genentech, South San Francisco, California 94080, USA
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, South San Francisco, California 94080, USA
| | - Nancy Chiang
- Department of Antibody Engineering, Genentech, South San Francisco, California 94080, USA
| | - Alberto Estevez
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Rina Fong
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Lynn Kamen
- Department of BioAnalytical Sciences, Genentech, South San Francisco, California 94080, USA
| | - Elviza Kho
- Department of BioAnalytical Sciences, Genentech, South San Francisco, California 94080, USA
| | - Mike Reichelt
- Department of Pathology, Genentech, South San Francisco, California 94080, USA
| | - Zhonghua Lin
- Department of Translational Immunology, Genentech, South San Francisco, California 94080, USA
| | - Henry Chiu
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California 94080, USA
| | - Elizabeth Skippington
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, California 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, South San Francisco, California 94080, USA
| | - Min Xu
- Department of Translational Immunology, Genentech, South San Francisco, California 94080, USA
| | - Patrick Lupardus
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech, South San Francisco, California 94080, USA
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27
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Furuse Y, Matsuzaki Y, Nishimura H, Oshitani H. Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses. Viruses 2016; 8:E321. [PMID: 27898037 PMCID: PMC5192382 DOI: 10.3390/v8120321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022] Open
Abstract
Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 9808575, Japan.
| | - Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata 9909585, Japan.
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 9838520, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai 9808575, Japan.
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28
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Horthongkham N, Athipanyasilp N, Pattama A, Kaewnapan B, Sornprasert S, Srisurapanont S, Kantakamalakul W, Amaranond P, Sutthent R. Epidemiological, Clinical and Virological Characteristics of Influenza B Virus from Patients at the Hospital Tertiary Care Units in Bangkok during 2011-2014. PLoS One 2016; 11:e0158244. [PMID: 27387488 PMCID: PMC4936745 DOI: 10.1371/journal.pone.0158244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/12/2016] [Indexed: 11/19/2022] Open
Abstract
Influenza B virus, which causes acute respiratory infections, has increased in prevalence in recent years. Based on the nucleotide sequence of the hemagglutinin (HA) gene, influenza B virus can be divided into two lineages, Victoria and Yamagata, that co-circulate during the influenza season. However, analysis of the potential association between the clinical and virological characteristic and the lineage of influenza B viruses isolated in Thailand was lacking. To investigate influenza B virus genetically and determine its neuraminidase (NA) inhibitor susceptibility phenotype, a total of 6920 nasopharyngeal-wash samples were collected from patients with influenza-like illness between the years 2011 and 2014 and were screened for influenza B virus by real-time PCR. Of these samples, 3.1% (216/6920) were confirmed to contain influenza B viruses, and 110 of these influenza viruses were randomly selected for nucleotide sequence analysis of the HA and NA genes. Phylogenetic analysis of the HA sequences showed clustering into various clades: Yamagata clade 3 (11/110, 10%), Yamagata clade 2 (71/110, 64.5%), and Victoria clade 1 (28/110, 25.5%). The analysis of clinical characteristic demonstrated that the Victoria lineage was significantly associated with the duration of hospitalization, number of deceased cases, pneumonia, secondary bacterial infection and underlying disease. When combined with phylogenetic analysis of the NA sequences, four samples showed viruses with reassortant sequences between the Victoria and Yamagata lineages. Statistical analysis of the clinical outcomes and demographic data for the reassortant strains did not differ from those of the other strains in circulation. Oseltamivir-resistant influenza B viruses were not detected. Our findings indicated the co-circulation of the Victoria and Yamagata lineages over the past four cold seasons in Bangkok. We also demonstrated differences in the clinical symptoms between these lineages.
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Affiliation(s)
- Navin Horthongkham
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Niracha Athipanyasilp
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Archiraya Pattama
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Bualan Kaewnapan
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suthatta Sornprasert
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Surangrat Srisurapanont
- Department of Pathology, Faculty of Medicine, Srinakharinwirot University, Bangkok, Thailand
| | - Wannee Kantakamalakul
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Palanee Amaranond
- Department of Blood transfusion, Faculty of Allied Health Science, Chulalongkorn University, Bangkok, Thailand
| | - Ruengpung Sutthent
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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29
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Chiu SS, Feng S, Chan KH, Lo JYC, Chan ELY, So LY, Cowling BJ, Peiris JSM. Hospital-based vaccine effectiveness against influenza B lineages, Hong Kong, 2009-14. Vaccine 2016; 34:2164-9. [PMID: 27013437 DOI: 10.1016/j.vaccine.2016.03.032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/07/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND We estimated vaccine effectiveness (VE) against pediatric influenza B hospitalizations in Hong Kong year round between November 2001 and October 2014. METHODS We conducted a test-negative year-round study, enrolling children 6 months to 17 years of age admitted to two hospitals in Hong Kong with a febrile acute respiratory infection. Children were tested for influenza A and B. Conditional logistic regression was used to estimate overall and lineage-specific vaccine effectiveness comparing influenza vaccination history of the trivalent influenza vaccine (TIV) among patients testing positive for influenza B versus negative for influenza A and B, adjusting for age and sex and matching by calendar week of recruitment. RESULTS Of the 6013 children included in the analysis, 262 tested positive for influenza B. Vaccination coverage was low: 6.5% in the influenza B positive children when compared with 8.8% in children who tested negative for both influenza A and B (p=0.248). Overall, VE was 47.6% (95% CI: 10.0, 69.4%) against influenza B hospitalization despite variable co-circulation of both lineages in all years. VE for Victoria-like virus calculated from 3 years when the vaccine was lineage-matched was 59.1% (95% CI: 6.2, 82.2%). Lineage-matched VE for Yamagata-like virus was -8.8% (95% CI: -215.4, 62.5%) in a clade mismatch season. With wide confidence intervals, we were unable to demonstrate cross-lineage protection: VE against the mismatched B/Yamagata-like virus was 9.5% (95% CI: -240.4, 76.0%) in 2011/12 and against mismatched B/Victoria-like virus in 2013/14 was 42.7% (95% CI: -368.6, 93.0%). CONCLUSIONS TIV conferred an overall VE of 47.6% (95% CI: 10.0, 69.4%) against influenza B hospitalization in children despite variable co-circulation of both lineages in all years. Lineage-matched VE for Yamagata-like virus was poor and may be related to clade mismatch. Cross-lineage protection was not observed.
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Affiliation(s)
- Susan S Chiu
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
| | - Shuo Feng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Janice Y C Lo
- Public Health Laboratory Services Branch, Centre for Health Protection, Department of Health, China
| | - Eunice L Y Chan
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lok-Yee So
- Department of Pediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - J S Malik Peiris
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China; Centre of Influenza Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
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30
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Oong XY, Ng KT, Lam TTY, Pang YK, Chan KG, Hanafi NS, Kamarulzaman A, Tee KK. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014. PLoS One 2015; 10:e0136254. [PMID: 26313754 PMCID: PMC4552379 DOI: 10.1371/journal.pone.0136254] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/01/2015] [Indexed: 12/16/2022] Open
Abstract
Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore throat. This study describes the evolution of influenza B viruses in Malaysia and highlights the importance of continuous surveillance for better vaccination policy in this region.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tommy Tsan-Yuk Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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31
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Hua S, Li X, Liu M, Cheng Y, Peng Y, Huang W, Tan M, Wei H, Guo J, Wang D, Wu A, Shu Y, Jiang T. Antigenic variation of the human influenza A (H3N2) virus during the 2014-2015 winter season. SCIENCE CHINA-LIFE SCIENCES 2015. [PMID: 26219513 DOI: 10.1007/s11427-015-4899-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human influenza A (H3N2) virus dominated the 2014-2015 winter season in many countries and caused massive morbidity and mortality because of its antigenic variation. So far, very little is known about the antigenic patterns of the recent H3N2 virus. By systematically mapping the antigenic relationships of H3N2 strains isolated since 2010, we discovered that two groups with obvious antigenic divergence, named SW13 (A/Switzerland/9715293/2013-like strains) and HK14 (A/Hong Kong/5738/2014-like strains), co-circulated during the 2014-2015 winter season. HK14 group co-circulated with SW13 in Europe and the United States during this season, while there were few strains of HK14 in mainland China, where SW13 has dominated since 2012. Furthermore, we found that substitutions near the receptor-binding site on hemagglutinin played an important role in the antigenic variation of both the groups. These findings provide a comprehensive understanding of the recent antigenic evolution of H3N2 virus and will aid in the selection of vaccine strains.
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Affiliation(s)
- Sha Hua
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - XiYan Li
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - Mi Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - YanHui Cheng
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - YouSong Peng
- College of Information Science and Engineering, Hunan University, Changsha, 410082, China
| | - WeiJuan Huang
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - MinJu Tan
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - HeJiang Wei
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - JunFeng Guo
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - DaYan Wang
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China
| | - AiPing Wu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,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.
| | - YueLong Shu
- National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, 102206, China.
| | - TaiJiao Jiang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Information Science and Engineering, Hunan University, Changsha, 410082, China. .,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.
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32
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Current and emerging cell culture manufacturing technologies for influenza vaccines. BIOMED RESEARCH INTERNATIONAL 2015; 2015:504831. [PMID: 25815321 PMCID: PMC4359798 DOI: 10.1155/2015/504831] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 01/08/2023]
Abstract
Annually, influenza virus infects millions of people worldwide. Vaccination programs against seasonal influenza infections require the production of hundreds of million doses within a very short period of time. The influenza vaccine is currently produced using a technology developed in the 1940s that relies on replicating the virus in embryonated hens' eggs. The monovalent viral preparation is inactivated and purified before being formulated in trivalent or tetravalent influenza vaccines. The production process has depended on a continuous supply of eggs. In the case of pandemic outbreaks, this mode of production might be problematic because of a possible drastic reduction in the egg supply and the low flexibility of the manufacturing process resulting in a lack of supply of the required vaccine doses in a timely fashion. Novel production systems using mammalian or insect cell cultures have emerged to overcome the limitations of the egg-based production system. These industrially well-established production systems have been primarily selected for a faster and more flexible response to pandemic threats. Here, we review the most important cell culture manufacturing processes that have been developed in recent years for mass production of influenza vaccines.
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33
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Fluorescent immunochromatography for rapid and sensitive typing of seasonal influenza viruses. PLoS One 2015; 10:e0116715. [PMID: 25650570 PMCID: PMC4317186 DOI: 10.1371/journal.pone.0116715] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 12/13/2014] [Indexed: 02/03/2023] Open
Abstract
Lateral flow tests also known as Immunochromatography (IC) is an antigen-detection method conducted on a nitrocellulose membrane that can be completed in less than 20 min. IC has been used as an important rapid test for clinical diagnosis and surveillance of influenza viruses, but the IC sensitivity is relatively low (approximately 60%) and the limit of detection (LOD) is as low as 10³ pfu per reaction. Recently, we reported an improved IC assay using antibodies conjugated with fluorescent beads (fluorescent immunochromatography; FLIC) for subtyping H5 influenza viruses (FLIC-H5). Although the FLIC strip must be scanned using a fluorescent reader, the sensitivity (LOD) is significantly improved over that of conventional IC methods. In addition, the antibodies which are specific against the subtypes of influenza viruses cannot be available for the detection of other subtypes when the major antigenicity will be changed. In this study, we established the use of FLIC to type seasonal influenza A and B viruses (FLIC-AB). This method has improved sensitivity to 100-fold higher than that of conventional IC methods when we used several strains of influenza viruses. In addition, FLIC-AB demonstrated the ability to detect influenza type A and influenza type B viruses from clinical samples with high sensitivity and specificity (Type A: sensitivity 98.7% (74/75), specificity 100% (54/54), Type B: sensitivity 100% (90/90), specificity 98.2% (54/55) in nasal swab samples) in comparison to the results of qRT-PCR. And furthermore, FLIC-AB performs better in the detection of early stage infection (under 13h) than other conventional IC methods. Our results provide new strategies to prevent the early-stage transmission of influenza viruses in humans during both seasonal outbreaks and pandemics.
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Peters TR, Snively BM, Suerken CK, Blakeney E, Vannoy L, Poehling KA. Relative timing of influenza disease by age group. Vaccine 2014; 32:6451-6. [PMID: 25280434 PMCID: PMC4252244 DOI: 10.1016/j.vaccine.2014.09.047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/22/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022]
Abstract
A detailed understanding of influenza movement in communities during yearly epidemics is needed to inform improved influenza control programs. We sought to determine the relative timing of influenza presentation and symptom onset by age group and influenza strain. Prospective, laboratory-confirmed surveillance was performed over three moderate influenza seasons in emergency departments and inpatient settings of both medical centers in Winston-Salem, NC. Influenza disease presented first in school age children through community epidemics of influenza A(H1N1)pdm09 and influenza B, and first in persons 5-49 years old for influenza A(H3N2). This finding indicates that influenza prevention in persons 5-49 years of age may be particularly important in influenza epidemic control.
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Affiliation(s)
- Timothy R Peters
- Department of Pediatrics, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
| | - Beverly M Snively
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
| | - Cynthia K Suerken
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
| | - Elizabeth Blakeney
- Department of Pediatrics, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
| | - Lauren Vannoy
- Department of Pediatrics, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
| | - Katherine A Poehling
- Department of Pediatrics, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA; Department of Pediatrics and Epidemiology and Prevention, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA.
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35
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Sakurai A, Takayama K, Nomura N, Yamamoto N, Sakoda Y, Kobayashi Y, Kida H, Shibasaki F. Multi-colored immunochromatography using nanobeads for rapid and sensitive typing of seasonal influenza viruses. J Virol Methods 2014; 209:62-8. [PMID: 25218175 DOI: 10.1016/j.jviromet.2014.08.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/19/2014] [Accepted: 08/28/2014] [Indexed: 12/09/2022]
Abstract
Immunochromatography (IC) is an antigen-detection assay that plays an important role in the rapid diagnosis of influenza viruses because of its rapid turnaround and ease of use. Despite the usefulness of IC, the limit of detection of common IC kits is as high as 10(3)-10(4) plaque forming units (pfu) per reaction, resulting in their limited sensitivities. Early diagnosis within 24h would provide more appropriate timing of treatment. In this study, a multi-colored NanoAct™ bead IC was established to detect seasonal influenza viruses. This method has approximately 10-fold higher sensitivity than that of colloidal gold or colored latex bead IC assays, and does not require specific instruments. More notably, NanoAct™ bead IC can distinguish influenza A and B viruses from clinical samples with a straightforward readout composed of colored lines. Our results will provide new strategies for the diagnosis, treatment, and a chance to survey of influenza viruses in developing countries and in the field research.
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Affiliation(s)
- Akira Sakurai
- Department of Molecular Medical Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | | | - Namiko Nomura
- Department of Molecular Medical Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Naoki Yamamoto
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, N18 W9, Kita-ku, Sapporo 060-0818, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, N18 W9, Kita-ku, Sapporo 060-0818, Japan
| | | | - Hiroshi Kida
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, N18 W9, Kita-ku, Sapporo 060-0818, Japan
| | - Futoshi Shibasaki
- Department of Molecular Medical Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.
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Sun J, Kudahl UJ, Simon C, Cao Z, Reinherz EL, Brusic V. Large-scale analysis of B-cell epitopes on influenza virus hemagglutinin - implications for cross-reactivity of neutralizing antibodies. Front Immunol 2014; 5:38. [PMID: 24570677 PMCID: PMC3916768 DOI: 10.3389/fimmu.2014.00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/22/2014] [Indexed: 11/13/2022] Open
Abstract
Influenza viruses continue to cause substantial morbidity and mortality worldwide. Fast gene mutation on surface proteins of influenza virus result in increasing resistance to current vaccines and available antiviral drugs. Broadly neutralizing antibodies (bnAbs) represent targets for prophylactic and therapeutic treatments of influenza. We performed a systematic bioinformatics study of cross-reactivity of neutralizing antibodies (nAbs) against influenza virus surface glycoprotein hemagglutinin (HA). This study utilized the available crystal structures of HA complexed with the antibodies for the analysis of tens of thousands of HA sequences. The detailed description of B-cell epitopes, measurement of epitope area similarity among different strains, and estimation of antibody neutralizing coverage provide insights into cross-reactivity status of existing nAbs against influenza virus. We have developed a method to assess the likely cross-reactivity potential of bnAbs for influenza strains, either newly emerged or existing. Our method catalogs influenza strains by a new concept named discontinuous peptide, and then provide assessment of cross-reactivity. Potentially cross-reactive strains are those that share 100% identity with experimentally verified neutralized strains. By cataloging influenza strains and their B-cell epitopes for known bnAbs, our method provides guidance for selection of representative strains for further experimental design. The knowledge of sequences, their B-cell epitopes, and differences between historical influenza strains, we enhance our preparedness and the ability to respond to the emerging pandemic threats.
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Affiliation(s)
- Jing Sun
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
| | - Ulrich J Kudahl
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Center for Biological Sequence Analysis, Technical University of Denmark , Lyngby , Denmark
| | - Christian Simon
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Center for Biological Sequence Analysis, Technical University of Denmark , Lyngby , Denmark
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University , Shanghai , China
| | - Ellis L Reinherz
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA ; Laboratory of Immunobiology, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA , USA ; Department of Medicine, Harvard Medical School , Boston, MA , USA
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37
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Sheng Z, Ran Z, Wang D, Hoppe AD, Simonson R, Chakravarty S, Hause BM, Li F. Genomic and evolutionary characterization of a novel influenza-C-like virus from swine. Arch Virol 2014; 159:249-55. [PMID: 23942954 PMCID: PMC5714291 DOI: 10.1007/s00705-013-1815-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/30/2013] [Indexed: 10/26/2022]
Abstract
We recently described the isolation of a novel influenza virus from swine exhibiting respiratory disease in the United States that is distantly related to human influenza C virus. Based on genetic, biochemical and morphological analysis, the virus was provisionally classified as C/swine/Oklahoma/1334/2011 (C/OK). To further understand the genetics and evolution of this novel pathogen, we performed a comprehensive analysis of its sequence and phylogeny. The results demonstrated that C/OK and human influenza C viruses share a conserved array of predicted functional domains in the viral RNA genome replication and viral entry machinery but vary at key functional sites. Furthermore, our evolutionary analysis showed that homologous genes of C/OK and human influenza C viruses diverged from each other an estimated several hundred to several thousand years ago. Taken together, the findings described in this study support and extend our previous observations that C/OK is a genetically and evolutionarily distinct influenza virus in the family Orthomyxoviridae.
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Affiliation(s)
- Zizhang Sheng
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, 57007, USA
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Dela-Moss LI, Moss WN, Turner DH. Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C. BMC Res Notes 2014; 7:22. [PMID: 24405943 PMCID: PMC3895672 DOI: 10.1186/1756-0500-7-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/02/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Influenza B and C are single-stranded RNA viruses that cause yearly epidemics and infections. Knowledge of RNA secondary structure generated by influenza B and C will be helpful in further understanding the role of RNA structure in the progression of influenza infection. FINDINGS All available protein-coding sequences for influenza B and C were analyzed for regions with high potential for functional RNA secondary structure. On the basis of conserved RNA secondary structure with predicted high thermodynamic stability, putative structures were identified that contain splice sites in segment 8 of influenza B and segments 6 and 7 of influenza C. The sequence in segment 6 also contains three unused AUG start codon sites that are sequestered within a hairpin structure. CONCLUSIONS When added to previous studies on influenza A, the results suggest that influenza splicing may share common structural strategies for regulation of splicing. In particular, influenza 3' splice sites are predicted to form secondary structures that can switch conformation to regulate splicing. Thus, these RNA structures present attractive targets for therapeutics aimed at targeting one or the other conformation.
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Affiliation(s)
- Lumbini I Dela-Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
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Auksornkitti V, Kamprasert N, Thongkomplew S, Suwannakarn K, Theamboonlers A, Samransamruajkij R, Poovorawan Y. Molecular characterization of human respiratory syncytial virus, 2010-2011: identification of genotype ON1 and a new subgroup B genotype in Thailand. Arch Virol 2013; 159:499-507. [DOI: 10.1007/s00705-013-1773-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
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Differing epidemiological dynamics of influenza B virus lineages in Guangzhou, southern China, 2009-2010. J Virol 2013; 87:12447-56. [PMID: 24027322 DOI: 10.1128/jvi.01039-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The epidemiological and evolutionary dynamics of the two cocirculating lineages of influenza B virus, Victoria and Yamagata, are poorly understood, especially in tropical or subtropical areas of Southeast Asia. We performed a phylogenetic analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of influenza B viruses isolated in Guangzhou, a southern Chinese city, during 2009 to 2010 and compared the demographic and clinical features of infected patients. We identified multiple viral introductions of Victoria strains from both Chinese and international sources, which formed two phylogenetically and antigenically distinct clades (Victoria 1 and 2), some of which persisted between seasons. We identified one dominant Yamagata introduction from outside China during 2009. Our phylogenetic analysis reveals the occurrence of reassortment events among the Victoria and Yamagata lineages and also within the Victoria lineage. We found no significant difference in clinical severity by influenza B lineage, with the exceptions that (i) the Yamagata lineage infected older people than either Victoria lineage and (ii) fewer upper respiratory tract infections were caused by the Victoria 2 than the Victoria 1 clade. Overall, our study reveals the complex epidemiological dynamics of different influenza B lineages within a single geographic locality and has implications for vaccination policy in southern China.
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41
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Burnham AJ, Baranovich T, Govorkova EA. Neuraminidase inhibitors for influenza B virus infection: efficacy and resistance. Antiviral Res 2013; 100:520-34. [PMID: 24013000 DOI: 10.1016/j.antiviral.2013.08.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/17/2013] [Accepted: 08/25/2013] [Indexed: 01/28/2023]
Abstract
Many aspects of the biology and epidemiology of influenza B viruses are far less studied than for influenza A viruses, and one of these aspects is efficacy and resistance to the clinically available antiviral drugs, the neuraminidase (NA) inhibitors (NAIs). Acute respiratory infections are one of the leading causes of death in children and adults, and influenza is among the few respiratory infections that can be prevented and treated by vaccination and antiviral treatment. Recent data has suggested that influenza B virus infections are of specific concern to pediatric patients because of the increased risk of severe disease. Treatment of influenza B is a challenging task for the following reasons: This review presents current knowledge of the efficacy of NAIs for influenza B virus and antiviral resistance in clinical, surveillance, and experimental studies.
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Affiliation(s)
- Andrew J Burnham
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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42
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Velkov T. The specificity of the influenza B virus hemagglutinin receptor binding pocket: what does it bind to? J Mol Recognit 2013; 26:439-49. [DOI: 10.1002/jmr.2293] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/16/2013] [Accepted: 06/16/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Tony Velkov
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade; Parkville; 3052; Victoria; Australia
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43
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Yu K, Sheng ZZ, Huang B, Ma X, Li Y, Yuan X, Qin Z, Wang D, Chakravarty S, Li F, Song M, Sun H. Structural, antigenic, and evolutionary characterizations of the envelope protein of newly emerging Duck Tembusu Virus. PLoS One 2013; 8:e71319. [PMID: 23990944 PMCID: PMC3750017 DOI: 10.1371/journal.pone.0071319] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/04/2013] [Indexed: 11/19/2022] Open
Abstract
Since the first reported cases of ducks infected with a previously unknown flavivirus in eastern China in April 2010, the virus, provisionally designated Duck Tembusu Virus (DTMUV), has spread widely in domestic ducks in China and caused significant economic losses to poultry industry. In this study, we examined in detail structural, antigenic, and evolutionary properties of envelope (E) proteins of six DTMUV isolates spanning 2010–2012, each being isolated from individual farms with different geographical locations where disease outbreaks were documented. Structural analysis showed that E proteins of DTMUV and its closely related flavivirus (Japanese Encephalitis Virus) shared a conserved array of predicted functional domains and motifs. Among the six DTMUV strains, mutations were observed only at thirteen amino acid positions across three separate domains of the E protein. Interestingly, these genetic polymorphisms resulted in no detectable change in viral neutralization properties as demonstrated in a serum neutralization assay. Furthermore, phylogenetic analysis of the nucleotide sequences of the E proteins showed that viruses evolved into two distinct genotypes, termed as DTMUV.I and DTMUV.II, with II emerging as the dominant genotype. New findings described here shall give insights into the antigenicity and evolution of this new pathogen and provide guidance for further functional studies of the E protein for which no effective vaccine has yet been developed.
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Affiliation(s)
- Kexiang Yu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhi-Zhang Sheng
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, United States of America
| | - Bing Huang
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiuli Ma
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yufeng Li
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaoyuan Yuan
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhuoming Qin
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Dan Wang
- Department of Health and Nutrition Sciences, South Dakota State University, Brookings, South Dakota, United States of America
| | - Suvobrata Chakravarty
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, United States of America
| | - Feng Li
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America
- * E-mail: (FL); (MS); (HS)
| | - Minxun Song
- Institute of Poultry Science, Shandong Academy of Agricultural Sciences, Jinan, China
- * E-mail: (FL); (MS); (HS)
| | - Huaichang Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- * E-mail: (FL); (MS); (HS)
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Paiva TM, Benega MA, Silva DBB, Santos KCO, Cruz AS, Hortenci MF, Barbieri MT, Monteiro MM, Barbosa HA, Carvalhanas TRMP. Evolutionary pattern of reemerging influenza B/Victoria lineage viruses in São Paulo, Brazil, 1996-2012: Implications for vaccine composition strategy. J Med Virol 2013; 85:1983-9. [PMID: 23926069 DOI: 10.1002/jmv.23684] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2013] [Indexed: 11/07/2022]
Abstract
Since the 1980s, 2 antigenically distinct influenza B lineages have cocirculated in the world: B/Victoria/2/87 (first appeared in the 1980s) and B/Yamagata/16/88 (became predominant in the 1990s). B/Victoria/2/87 isolates were geographically restricted to eastern Asia during 1991-2000. During 2000-2001 and 2001-2002, B/Victoria/2/87 isolates reemerged in North America, Europe, and South America, and then spread globally. During influenza virus surveillance, season 2002, an outbreak of acute respiratory illness, which quickly spread among the population, has been notified by public health authorities living in Araraquara, São Paulo, Brazil. Instituto Adolfo Lutz and Secretariat of Health of São Paulo state teams initiate an investigation towards to describe the pattern of infection in this population temporally and by age and to characterize the strains by virus isolation and hemagglutination inhibition assay. The outbreak lasted approximately 10 weeks; many cases occurred between mid-August and mid-September. Children younger than 13 years were the most affected; the elderly were mostly immune to infection. Analysis of the clinical respiratory samples helped in identifying the B/Hong Kong/330/2001 and B/Brisbane/32/2002 subtypes-recent variants of B/Victoria/02/88, a lineage restricted to Southeast Asia until 2001. The Araraquara outbreak confirms the reemergence of the B/Victoria viruses in South America and highlights the importance of monitoring local circulating strains, especially in light of the absence of cross-protection between antigenically distinct influenza lineages. Based on influenza virus surveillance, public health authorities worldwide should decide whether trivalent vaccines or quadrivalent vaccines (containing both influenza virus B lineages) are to be used in each country.
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Affiliation(s)
- T M Paiva
- Center of Respiratory Diseases, Adolfo Lutz Institute, São Paulo, Brazil.
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A comparison of the clinical and epidemiological characteristics of adult patients with laboratory-confirmed influenza A or B during the 2011-2012 influenza season in Korea: a multi-center study. PLoS One 2013; 8:e62685. [PMID: 23671624 PMCID: PMC3643978 DOI: 10.1371/journal.pone.0062685] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND During the 2011/2012 winter influenza season in the Republic of Korea, influenza A (H3N2) was the predominant virus in the first peak period of influenza activity during the second half of January 2012. On the other hand, influenza B was the predominant virus in the second peak period of influenza activity during the second half of March 2012. The objectives of this study were to compare the clinical and epidemiological characteristics of patients with laboratory-confirmed influenza A or influenza B. METHODOLOGY/PRINCIPAL FINDINGS We analyzed data from 2,129 adult patients with influenza-like illnesses who visited the emergency rooms of seven university hospitals in Korea from October 2011 to May 2012. Of 850 patients with laboratory-confirmed influenza, 656 (77.2%) had influenza A (H3N2), and 194 (22.8%) influenza B. Age, and the frequencies of cardiovascular disorders, diabetes, hypertension were significantly higher in patients with influenza A (H3N2) (P<0.05). The frequencies of leukopenia or thrombocytopenia in patients with influenza B at initial presentation were statistically higher than those in patients with influenza A (H3N2) (P<0.05). The rate of hospitalization, and length of hospital stay were statistically higher in patients with influenza A (H3N2) (P<0.05), and of the 79 hospitalized patients, the frequency of diabetes, hypertension, cases having at least one of the comorbid conditions, and the proportion of elderly were significantly higher in patients with influenza A (H3N2) (P<0.05). CONCLUSIONS The proportion of males to females and elderly population were significantly higher for influenza A (H3N2) patients group compared with influenza B group. Hypertension, diabetes, chronic lung diseases, cardiovascular disorders, and neuromuscular diseases were independently associated with hospitalization due to influenza. Physicians should assess and treat the underlying comorbid conditions as well as influenza viral infections for the appropriate management of patients with influenza.
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46
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Laursen NS, Wilson IA. Broadly neutralizing antibodies against influenza viruses. Antiviral Res 2013; 98:476-83. [PMID: 23583287 DOI: 10.1016/j.antiviral.2013.03.021] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/22/2013] [Accepted: 03/28/2013] [Indexed: 11/18/2022]
Abstract
Despite available antivirals and vaccines, influenza continues to be a major cause of mortality worldwide. Vaccination generally induces an effective, but strain-specific antibody response. As the virus continually evolves, new vaccines have to be administered almost annually when a novel strain becomes dominant. Furthermore, the sporadic emerging resistance to neuraminidase inhibitors among circulating strains suggests an urgent need for new therapeutic agents. Recently, several cross-reactive antibodies have been described, which neutralize an unprecedented spectrum of influenza viruses. These broadly neutralizing antibodies generally target conserved functional regions on the major influenza surface glycoprotein hemagglutinin (HA). The characterization of their neutralization breadth and epitopes on HA could stimulate the development of new antibody-based antivirals and broader influenza vaccines. This article forms part of a symposium in Antiviral Research on "Treatment of influenza: targeting the virus or the host."
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Affiliation(s)
- Nick S Laursen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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47
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Hause BM, Ducatez M, Collin EA, Ran Z, Liu R, Sheng Z, Armien A, Kaplan B, Chakravarty S, Hoppe AD, Webby RJ, Simonson RR, Li F. Isolation of a novel swine influenza virus from Oklahoma in 2011 which is distantly related to human influenza C viruses. PLoS Pathog 2013; 9:e1003176. [PMID: 23408893 PMCID: PMC3567177 DOI: 10.1371/journal.ppat.1003176] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 12/19/2012] [Indexed: 12/22/2022] Open
Abstract
Of the Orthomyxoviridae family of viruses, only influenza A viruses are thought to exist as multiple subtypes and has non-human maintenance hosts. In April 2011, nasal swabs were collected for virus isolation from pigs exhibiting influenza-like illness. Subsequent electron microscopic, biochemical, and genetic studies identified an orthomyxovirus with seven RNA segments exhibiting approximately 50% overall amino acid identity to human influenza C virus. Based on its genetic organizational similarities to influenza C viruses this virus has been provisionally designated C/Oklahoma/1334/2011 (C/OK). Phylogenetic analysis of the predicted viral proteins found that the divergence between C/OK and human influenza C viruses was similar to that observed between influenza A and B viruses. No cross reactivity was observed between C/OK and human influenza C viruses using hemagglutination inhibition (HI) assays. Additionally, screening of pig and human serum samples found that 9.5% and 1.3%, respectively, of individuals had measurable HI antibody titers to C/OK virus. C/OK virus was able to infect both ferrets and pigs and transmit to naive animals by direct contact. Cell culture studies showed that C/OK virus displayed a broader cellular tropism than a human influenza C virus. The observed difference in cellular tropism was further supported by structural analysis showing that hemagglutinin esterase (HE) proteins between two viruses have conserved enzymatic but divergent receptor-binding sites. These results suggest that C/OK virus represents a new subtype of influenza C viruses that currently circulates in pigs that has not been recognized previously. The presence of multiple subtypes of co-circulating influenza C viruses raises the possibility of reassortment and antigenic shift as mechanisms of influenza C virus evolution.
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Affiliation(s)
- Ben M. Hause
- Newport Laboratories, Worthington, Minnesota, United States of America
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
| | - Mariette Ducatez
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Emily A. Collin
- Newport Laboratories, Worthington, Minnesota, United States of America
| | - Zhiguang Ran
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America
| | - Runxia Liu
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America
| | - Zizhang Sheng
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, United States of America
| | - Anibal Armien
- Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Bryan Kaplan
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Suvobrata Chakravarty
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, United States of America
| | - Adam D. Hoppe
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, United States of America
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Randy R. Simonson
- Newport Laboratories, Worthington, Minnesota, United States of America
| | - Feng Li
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, United States of America
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota, United States of America
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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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49
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Lambe T. Novel viral vectored vaccines for the prevention of influenza. Mol Med 2012; 18:1153-60. [PMID: 22735755 PMCID: PMC3510293 DOI: 10.2119/molmed.2012.00147] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 06/19/2012] [Indexed: 01/29/2023] Open
Abstract
Influenza represents a substantial global healthcare burden, with annual epidemics resulting in 3-5 million cases of severe illness with a significant associated mortality. In addition, the risk of a virulent and lethal influenza pandemic has generated widespread and warranted concern. Currently licensed influenza vaccines are limited in their ability to induce efficacious and long-lasting herd immunity. In addition, and as evidenced by the H1N1 pandemic in 2009, there can be a significant delay between the emergence of a pandemic influenza and an effective, antibody-inducing vaccine. There is, therefore, a continued need for new, efficacious vaccines conferring cross-clade protection-obviating the need for biannual reformulation of seasonal influenza vaccines. Development of such a vaccine would yield enormous health benefits to society and also greatly reduce the associated global healthcare burden. There are a number of alternative influenza vaccine technologies being assessed both preclinically and clinically. In this review we discuss viral vectored vaccines, either recombinant live-attenuated or replication-deficient viruses, which are current lead candidates for inducing efficacious and long-lasting immunity toward influenza viruses. These alternate influenza vaccines offer real promise to deliver viable alternatives to currently deployed vaccines and more importantly may confer long-lasting and universal protection against influenza viral infection.
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Affiliation(s)
- Teresa Lambe
- Jenner Institute, University of Oxford, Oxford, United Kingdom.
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50
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Holmes EC, Garnett GP. Genes, trees and infections: Molecular evidence in epidemiology. Trends Ecol Evol 2012; 9:256-60. [PMID: 21236844 DOI: 10.1016/0169-5347(94)90291-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Molecular phylogenies constitute an important new way of tracking the progress of viral epidemics. The phylogenetic analysis of viral sequence data provides information on the origin, spread and maintenance of infections and can be used to reconstruct contact networks of infected individuals. Analysis of the branching structure of phylogenetic trees also allows inferences to be made about the rate of transmission and the distinction between endemic and epidemic infections, and provides estimates of the numbers of infected individuals.
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Affiliation(s)
- E C Holmes
- Dept of Zoology, University of Oxford, South Parks Road, Oxford, UK 0X1 3PS
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