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Chatterjee A, Ambrose K, Canaday DH, Delair S, Ezike N, Huber VC, Jhaveri R, Nyquist AC, Sporer A, Varman M, Vivekanandan R, Wojcik R, Jandhyala R. The association between influenza vaccine effectiveness and egg-based manufacturing technology: literature review and US expert consensus. Curr Med Res Opin 2024; 40:335-343. [PMID: 38054898 DOI: 10.1080/03007995.2023.2284386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Influenza is associated with significant disease burden in the US and is currently best controlled by vaccination programs. Influenza vaccine effectiveness (VE) is low and may be reduced by several factors, including egg adaptations. Although non-egg-based influenza vaccines reportedly have greater VE in egg-adapted seasons, evidence for egg adaptations' reduction of VE is indirect and dissociated, apart from two previous European consensuses. METHODS This study replicated the methodology used in a 2020 literature review and European consensus, providing an updated review and consensus opinion of 10 US experts on the evidence for a mechanistic basis for reduction of VE due to egg-based manufacturing methods. A mechanistic basis was assumed if sufficient evidence was found for underlying principles proposed to give rise to such an effect. Evidence for each principle was brought forward from the 2020 review and identified here by structured literature review and expert panel. Experts rated the strength of support for each principle and a mechanistic basis for reduction of VE due to egg-based influenza vaccine manufacture in a consensus method (consensus for strong/very strong evidence = ≥ 3.5 on 5-point Likert scale). RESULTS Experts assessed 251 references (from previous study: 185; this study: 66). The majority of references for all underlying principles were rated as strong or very strong supporting evidence (52-86%). Global surveillance, WHO candidate vaccine virus selection, and manufacturing stages involving eggs were identified as most likely to impact influenza VE. CONCLUSION After review of extensive evidence for reduction of VE due to egg-based influenza vaccine manufacture, influenza experts in the US joined those in Europe in unanimous agreement for a mechanistic basis for the effect. Vaccine providers and administrators should consider use of non-egg-based influenza vaccine manufacture to reduce the risk of egg adaptations and likely impact on VE.
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Affiliation(s)
- Archana Chatterjee
- Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | | | | | | | | | | | - Ravi Jhaveri
- Feinberg School of Medicine, Northwestern, IL, USA
| | | | | | | | | | | | - Ravi Jandhyala
- Medialis Ltd, Milton Keynes, UK
- King's College London, London, UK
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Lin CH, Tam HMH, Yang CY, Hsieh FC, Wang JL, Yang CC, Hsu HW, Liu HP, Wu HY. Evolution of the coronavirus spike protein in the full-length genome and defective viral genome under diverse selection pressures. J Gen Virol 2023; 104:001920. [PMID: 37997889 PMCID: PMC10768696 DOI: 10.1099/jgv.0.001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 11/25/2023] Open
Abstract
How coronaviruses evolve by altering the structures of their full-length genome and defective viral genome (DVG) under dynamic selection pressures has not been studied. In this study, we aimed to experimentally identify the dynamic evolutionary patterns of the S protein sequence in the full-length genome and DVG under diverse selection pressures, including persistence, innate immunity and antiviral drugs. The evolutionary features of the S protein sequence in the full-length genome and in the DVG under diverse selection pressures are as follows: (i) the number of nucleotide (nt) mutations does not necessarily increase with the number of selection pressures; (ii) certain types of selection pressure(s) can lead to specific nt mutations; (iii) the mutated nt sequence can be reverted to the wild-type nt sequence under the certain type of selection pressure(s); (iv) the DVG can also undergo mutations and evolve independently of the full-length genome; and (v) DVG species are regulated during evolution under diverse selection pressures. The various evolutionary patterns of the S protein sequence in the full-length genome and DVG identified in this study may contribute to coronaviral fitness under diverse selection pressures.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hon-Man-Herman Tam
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Feng-Cheng Hsieh
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Long Wang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan, ROC
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chun-Chun Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hsuan-Wei Hsu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hao-Ping Liu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan, ROC
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Garjani A, Chegini AM, Salehi M, Tabibzadeh A, Yousefi P, Razizadeh MH, Esghaei M, Esghaei M, Rohban MH. Forecasting influenza hemagglutinin mutations through the lens of anomaly detection. Sci Rep 2023; 13:14944. [PMID: 37696867 PMCID: PMC10495359 DOI: 10.1038/s41598-023-42089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/05/2023] [Indexed: 09/13/2023] Open
Abstract
The influenza virus hemagglutinin is an important part of the virus attachment to the host cells. The hemagglutinin proteins are one of the genetic regions of the virus with a high potential for mutations. Due to the importance of predicting mutations in producing effective and low-cost vaccines, solutions that attempt to approach this problem have recently gained significant attention. A historical record of mutations has been used to train predictive models in such solutions. However, the imbalance between mutations and preserved proteins is a big challenge for the development of such models that need to be addressed. Here, we propose to tackle this challenge through anomaly detection (AD). AD is a well-established field in Machine Learning (ML) that tries to distinguish unseen anomalies from normal patterns using only normal training samples. By considering mutations as anomalous behavior, we could benefit existing rich solutions in this field that have emerged recently. Such methods also fit the problem setup of extreme imbalance between the number of unmutated vs. mutated training samples. Motivated by this formulation, our method tries to find a compact representation for unmutated samples while forcing anomalies to be separated from the normal ones. This helps the model to learn a shared unique representation between normal training samples as much as possible, which improves the discernibility and detectability of mutated samples from the unmutated ones at the test time. We conduct a large number of experiments on four publicly available datasets, consisting of three different hemagglutinin protein datasets, and one SARS-CoV-2 dataset, and show the effectiveness of our method through different standard criteria.
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Affiliation(s)
- Ali Garjani
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | | | - Mohammadreza Salehi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Alireza Tabibzadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Parastoo Yousefi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Moein Esghaei
- Cognitive Neuroscience Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Nabakooza G, Galiwango R, Frost SDW, Kateete DP, Kitayimbwa JM. Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review. Microorganisms 2022; 10:900. [PMID: 35630344 PMCID: PMC9145646 DOI: 10.3390/microorganisms10050900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa's benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa's contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
| | - Ronald Galiwango
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
- African Center of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala 256, Uganda
| | - Simon D W Frost
- Microsoft Research, Redmond, 14820 NE 36th Street, Washington, DC 98052, USA
- London School of Hygiene & Tropical Medicine (LSHTM), University of London, Keppel Street, Bloomsbury, London WC1E7HT, UK
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
| | - John M Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
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Lin CH, Yang CY, Ou SC, Wang M, Lo CY, Tsai TL, Wu HY. The Impacts of Antivirals on the Coronavirus Genome Structure and Subsequent Pathogenicity, Virus Fitness and Antiviral Design. Biomedicines 2020; 8:E376. [PMID: 32987828 PMCID: PMC7601523 DOI: 10.3390/biomedicines8100376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/29/2023] Open
Abstract
With the global threat of SARS-CoV-2, much effort has been focused on treatment and disease control. However, how coronaviruses react to the treatments and whether the surviving viruses have altered their characteristics are also unanswered questions with medical importance. To this end, bovine coronavirus (BCoV), which is in the same genus as SARS-CoV-2, was used as a test model and the findings were as follows. With the treatment of antiviral remdesivir, the selected BCoV variant with an altered genome structure developed resistance, but its pathogenicity was not increased in comparison to that of wild type (wt) BCoV. Under the selection pressure of innate immunity, the genome structure was also altered; however, neither resistance developed nor pathogenicity increased for the selected BCoV variant. Furthermore, both selected BCoV variants showed a better efficiency in adapting to alternative host cells than wt BCoV. In addition, the previously unidentified feature that the spike protein was a common target for mutations under different antiviral treatments might pose a problem for vaccine development because spike protein is a common target for antibody and vaccine designs. The findings derived from this fundamental research may contribute to the disease control and treatments against coronaviruses, including SARS-CoV-2.
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Affiliation(s)
- Ching-Hung Lin
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Cheng-Yao Yang
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Shan-Chia Ou
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Meilin Wang
- Department of Microbiology and Immunology, Chung Shan Medical University, Taichung 40201, Taiwan;
| | - Chen-Yu Lo
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Tsung-Lin Tsai
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
| | - Hung-Yi Wu
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan; (C.-H.L.); (C.-Y.Y.); (C.-Y.L.); (T.-L.T.)
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The impact of candidate influenza virus and egg-based manufacture on vaccine effectiveness: Literature review and expert consensus. Vaccine 2020; 38:6047-6056. [PMID: 32600916 DOI: 10.1016/j.vaccine.2020.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Influenza is associated with significant morbidity and mortality worldwide. Whilst vaccination is key for the prevention of influenza infection, there are many factors which may contribute to reduced vaccine effectiveness, including antigenic evolution via both antigenic drift and egg-adaptations. Due to the currently dissociated and indirect evidence supporting both the occurrence of these two phenomena in the egg-based manufacturing process and their effects on vaccine effectiveness, this topic remains a subject of debate. OBJECTIVE To review the evidence and level of agreement in expert opinion supporting a mechanistic basis for reduced vaccine effectiveness due to egg-based manufacturing, using an expert consensus-based methodology and literature reviews. METHODS Ten European influenza specialists were recruited to the expert panel. The overall research question was deconstructed into four component principles, which were examined in series using a novel, online, two-stage assessment of proportional group awareness and consensus. The first stage independently generated a list of supporting references for each component principle via literature searches and expert assessments. In the second stage, a summary of each reference was circulated amongst the experts, who rated their agreement that each reference supported the component principle on a 5-point Likert scale. Finally, the panel were asked if they agreed that, as a whole, the evidence supported a mechanistic basis for reduced vaccine effectiveness due to egg-based manufacturing. RESULTS All component principles were reported to have a majority of strong or very strong supporting evidence (70-90%). CONCLUSIONS On reviewing the evidence for all component principles, experts unanimously agreed that there is a mechanistic basis for reduced vaccine effectiveness resulting from candidate influenza virus variation due to egg-based manufacturing, particularly in the influenza A/H3N2 strain. Experts pointed to surveillance, candidate vaccine virus selection and manufacturing stages involving eggs as the most likely to impact vaccine effectiveness.
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Li L, Chang D, Han L, Zhang X, Zaia J, Wan XF. Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A(H1N1) virus using mutations and variations in glycosylation of Hemagglutinin. BMC Bioinformatics 2020; 21:182. [PMID: 32393178 PMCID: PMC7216668 DOI: 10.1186/s12859-020-3527-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determined by both protein sequence and N-linked glycosylation of influenza glycoproteins, especially hemagglutinin (HA). The currently available computational methods are only considered features in protein sequence but not N-linked glycosylation. RESULTS A multi-task learning sparse group least absolute shrinkage and selection operator (LASSO) (MTL-SGL) regression method was developed and applied to derive two types of predominant features including protein sequence and N-linked glycosylation in hemagglutinin (HA) affecting variations in serologic data for human and swine H1N1 IAVs. Results suggested that mutations and changes in N-linked glycosylation sites are associated with the rise of antigenic variants of H1N1 IAVs. Furthermore, the implicated mutations are predominantly located at five reported antibody-binding sites, and within or close to the HA receptor binding site. All of the three N-linked glycosylation sites (i.e. sequons NCSV at HA 54, NHTV at HA 125, and NLSK at HA 160) identified by MTL-SGL to determine antigenic changes were experimentally validated in the H1N1 antigenic variants using mass spectrometry analyses. Compared with conventional sparse learning methods, MTL-SGL achieved a lower prediction error and higher accuracy, indicating that grouped features and MTL in the MTL-SGL method are not only able to handle serologic data generated from multiple reagents, supplies, and protocols, but also perform better in genetic sequence-based antigenic quantification. CONCLUSIONS In summary, the results of this study suggest that mutations and variations in N-glycosylation in HA caused antigenic variations in H1N1 IAVs and that the sequence-based antigenicity predictive model will be useful in understanding antigenic evolution of IAVs.
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Affiliation(s)
- Lei Li
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Deborah Chang
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Lei Han
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.,Tencent AI Lab, Shenzhen, China
| | - Xiaojian Zhang
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA.,MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA. .,Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, USA. .,MU Center for Research on Influenza Systems Biology (CRISB), University of Missouri, Columbia, MO, USA. .,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Department of Electrical Engineering & Computer Science, College of Engineering, University of Missouri, Columbia, MO, USA. .,MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA.
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Ryt-Hansen P, Pedersen AG, Larsen I, Kristensen CS, Krog JS, Wacheck S, Larsen LE. Substantial Antigenic Drift in the Hemagglutinin Protein of Swine Influenza A Viruses. Viruses 2020; 12:E248. [PMID: 32102230 PMCID: PMC7077184 DOI: 10.3390/v12020248] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
The degree of antigenic drift in swine influenza A viruses (swIAV) has historically been regarded as minimal compared to that of human influenza A virus strains. However, as surveillance activities on swIAV have increased, more isolates have been characterized, revealing a high level of genetic and antigenic differences even within the same swIAV lineage. The objective of this study was to investigate the level of genetic drift in one enzootically infected swine herd over one year. Nasal swabs were collected monthly from sows (n = 4) and piglets (n = 40) in the farrowing unit, and from weaners (n = 20) in the nursery. Virus from 1-4 animals were sequenced per month. Analyses of the sequences revealed that the hemagglutinin (HA) gene was the main target for genetic drift with a substitution rate of 7.6 × 10-3 substitutions/site/year and evidence of positive selection. The majority of the mutations occurred in the globular head of the HA protein and in antigenic sites. The phylogenetic tree of the HA sequences displayed a pectinate typology, where only a single lineage persists and forms the ancestor for subsequent lineages. This was most likely caused by repeated selection of a single immune-escape variant, which subsequently became the founder of the next wave of infections.
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Affiliation(s)
- Pia Ryt-Hansen
- National Veterinary Institute, Technical University of Denmark, Kemitorvet Building 204, DK-2800 Kongens Lyngby, Denmark
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kemitorvet Building 208, DK-2800 Kongens Lyngby, Denmark;
| | - Inge Larsen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
| | | | - Jesper Schak Krog
- Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark;
| | - Silke Wacheck
- Ceva Santé Animale 10 Avenue de la Ballastière, 33500 Libourne, France;
| | - Lars Erik Larsen
- Dpt. of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 2, DK-1870 Frederiksberg C, Denmark; (I.L.); (L.E.L.)
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9
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Ryt-Hansen P, Pedersen AG, Larsen I, Krog JS, Kristensen CS, Larsen LE. Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination. PLoS One 2019; 14:e0224854. [PMID: 31725751 PMCID: PMC6855628 DOI: 10.1371/journal.pone.0224854] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Influenza A virus (IAV) is a highly contagious pathogen in pigs. Swine IAV (swIAV) infection causes respiratory disease and is thereby a challenge for animal health, animal welfare and the production economy. In Europe, the most widespread strategy for controlling swIAV is implementation of sow vaccination programs, to secure delivery of protective maternally derived antibodies (MDAs) to the newborn piglets. In this study we report a unique case, where a persistently swIAV (A/sw/Denmark/P5U4/2016(H1N1)) infected herd experienced an acute outbreak with a new swIAV subtype (A/sw/Denmark/HB4280U1/2017(H1N2)) and subsequently decided to implement a mass sow vaccination program. Clinical registrations, nasal swabs and blood samples were collected from four different batches of pigs before and after vaccination. Virus isolation, sequencing of the virus strain and hemagglutinin inhibition (HI) tests were performed on samples collected before and during the outbreak and after implementation of mass sow vaccination. After implementation of the sow mass vaccination, the time of infection was delayed and the viral load significantly decreased. An increased number of pigs, however, tested positive at two consecutive sampling times indicating prolonged shedding. In addition, a significantly smaller proportion of the 10–12 weeks old pigs were seropositive by the end of the study, indicating an impaired induction of antibodies against swIAV in the presence of MDAs. Sequencing of the herd strains revealed major differences in the hemagglutinin gene of the strain isolated before- and during the acute outbreak despite that, the two strains belonged to the same HA lineage. The HI tests confirmed a limited degree of cross-reaction between the two strains. Furthermore, the sequencing results of the hemagglutinin gene obtained before and after implementation of mass sow vaccination revealed an increased substitution rate and an increase in positively selected sites in the globular head of the hemagglutinin after vaccination.
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Affiliation(s)
- Pia Ryt-Hansen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inge Larsen
- University of Copenhagen, Dpt. of Veterinary and Animal Sciences, Frederiksberg C, Denmark
| | - Jesper Schak Krog
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lars Erik Larsen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- University of Copenhagen, Dpt. of Veterinary and Animal Sciences, Frederiksberg C, Denmark
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Banerjee R, Roy A, Ahmad F, Das S, Basak S. Evolutionary patterning of hemagglutinin gene sequence of 2009 H1N1 pandemic. J Biomol Struct Dyn 2016; 29:733-42. [PMID: 22208275 DOI: 10.1080/07391102.2012.10507411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The 2009 H1N1 swine flu is the first pandemic in decades. Infectivity of the influenza virus for human host depends largely on its ability to evade antibodies specific for viral protein called hemagglutinin (HA) that mediates attachment to the host. In the present study we analysed large number of HA gene sequences available in Flu Database maintained at NCBI. Our sequence based analysis clearly demonstrates that the amino acid usage pattern may dramatically change during the course of evolution, and there exists a clear link between a particular pattern of amino acid usage of HA genes and its potential to become infectious. Structural studies revealed how binding efficiency between the HA and sialic acid may alter the pandemic potential of infection. Our work highlights the evolutionary significance and biochemical basis of the selective advantage of certain amino acids of HA in 2009 and provides a link between the characteristics changes in HA protein and their potential to pronounce a global menace to public health.
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Affiliation(s)
- Rachana Banerjee
- Department of Bio-Physics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Kolkata, India
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11
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Civetta A, Ostapchuk DCM, Nwali B. Genome Hotspots for Nucleotide Substitutions and the Evolution of Influenza A (H1N1) Human Strains. Genome Biol Evol 2016; 8:986-93. [PMID: 26988249 PMCID: PMC4860693 DOI: 10.1093/gbe/evw061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In recent years a number of studies have brought attention to the role of positive selection during the evolution of antigenic escape by influenza strains. Particularly, the identification of positively selected sites within antigenic domains of viral surface proteins has been used to suggest that the evolution of viral–host receptor binding specificity is driven by selection. Here we show that, following the 1918 outbreak, the antigenic sites of the hemagglutinin (HA) viral surface protein and the stalk region of neuraminidase became substitution hotspots. The hotspots show similar patterns of nucleotide substitution bias at synonymous and nonsynonymous sites. Such bias imposes directionality in amino acid replacements that can influence signals of selection at antigenic sites. Our results suggest that the high accumulation of substitutions within the antigenic sites of HA can explain not only cases of antigenic escape by antigenic drift but also lead to occasional episodes of viral extinction.
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Affiliation(s)
- Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba R3B 2G3, Canada
| | | | - Basil Nwali
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba R3B 2G3, Canada Department of Biochemistry, Ebonyi State University, Abakaliki, Nigeria
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Kannan S, Kolandaivel P. Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs. J Biomol Struct Dyn 2015; 34:272-89. [PMID: 25893548 DOI: 10.1080/07391102.2015.1027737] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The purpose of this work was to study the binding properties of two pandemic influenza A virus 1918 H1N1 (SC1918) and 2009 H1N1 (CA09) hemagglutinin (HA) with avian and human receptors. The quantum chemical calculations have been performed to analyze the interactions of 130 loop, 190 helix, 220 loop region, and conserved residues 95,145,153-155, of pandemic viruses' HA with sialo-trisaccharide receptor of avian and human using density functional theory. The HA's residues Tyr 95, Ala 138, Gln 191, Arg 220, and Asp 225 from the above regions have stronger interaction with avian receptor. The residues Thr 136, Trp 153, His 183, and Asp 190 of HA are important and play a significant role to bind with human receptor. The residues Tyr 95, Ala 138, Lys 145, Trp 153, Gln 192, and Gln 226 of HA of CA09 virus have found more interaction energies with human than avian receptors. Due to mutations in the active residues of HA of CA09 virus comparing with SC1918, the binding capabilities of HA with human have been increased. The molecular dynamics simulation was made to understand the different dynamical properties of HA and molecular interactions between HA of these two viruses with sialo-trisaccharide receptors of avian and human receptors. The interaction energy of HA of CA09 virus with human receptor decreases due to the human receptor far away from conserved residue region of HA protein. This reveals that the conserved residues particularly Lys 145 play major contribution to interaction with human receptor in HA of CA09 virus.
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Affiliation(s)
- S Kannan
- a Department of Physics , Bharathiar University , Coimbatore 641 046 , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore 641 046 , India
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Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans. J Virol 2015; 89:5427-40. [PMID: 25741011 DOI: 10.1128/jvi.03636-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Although a large number of immune epitopes have been identified in the influenza A virus (IAV) hemagglutinin (HA) protein using various experimental systems, it is unclear which are involved in protective immunity to natural infection in humans. We developed a data mining approach analyzing natural H1N1 human isolates to identify HA protein regions that may be targeted by the human immune system and can predict the evolution of IAV. We identified 16 amino acid sites experiencing diversifying selection during the evolution of prepandemic seasonal H1N1 strains and found that 11 sites were located in experimentally determined B-cell/antibody (Ab) epitopes, including three distinct neutralizing Caton epitopes: Sa, Sb, and Ca2 [A. J. Caton, G. G. Brownlee, J. W. Yewdell, and W. Gerhard, Cell 31:417-427, 1982, http://dx.doi.org/10.1016/0092-8674(82)90135-0]. We predicted that these diversified epitope regions would be the targets of mutation as the 2009 H1N1 pandemic (pH1N1) lineage evolves in response to the development of population-level protective immunity in humans. Using a chi-squared goodness-of-fit test, we identified 10 amino acid sites that significantly differed between the pH1N1 isolates and isolates from the recent 2012-2013 and 2013-2014 influenza seasons. Three of these sites were located in the same diversified B-cell/Ab epitope regions as identified in the analysis of prepandemic sequences, including Sa and Sb. As predicted, hemagglutination inhibition (HI) assays using human sera from subjects vaccinated with the initial pH1N1 isolate demonstrated reduced reactivity against 2013-2014 isolates. Taken together, these results suggest that diversifying selection analysis can identify key immune epitopes responsible for protective immunity to influenza virus in humans and thereby predict virus evolution. IMPORTANCE The WHO estimates that approximately 5 to 10% of adults and 20 to 30% of children in the world are infected by influenza virus each year. While an adaptive immune response helps eliminate the virus following acute infection, the virus rapidly evolves to evade the established protective memory immune response, thus allowing for the regular seasonal cycles of influenza virus infection. The analytical approach described here, which combines an analysis of diversifying selection with an integration of immune epitope data, has allowed us to identify antigenic regions that contribute to protective immunity and are therefore the key targets of immune evasion by the virus. This information can be used to determine when sequence variations in seasonal influenza virus strains have affected regions responsible for protective immunity in order to decide when new vaccine formulations are warranted.
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Adaptive evolution of a novel avian-origin influenza A/H7N9 virus. Genomics 2014; 104:545-53. [PMID: 25449177 DOI: 10.1016/j.ygeno.2014.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 10/25/2014] [Accepted: 10/29/2014] [Indexed: 11/21/2022]
Abstract
In China, the recent outbreak of novel influenza A/H7N9 virus has been assumed to be severe, and it may possibly turn brutal in the near future. In order to develop highly protective vaccines and drugs for the A/H7N9 virus, it is critical to find out the selection pressure of each amino acid site. In the present study, six different statistical methods consisting of four independent codon-based maximum likelihood (CML) methods, one hierarchical Bayesian (HB) method and one branch-site (BS) method, were employed to determine if each amino acid site of A/H7N9 virus is under natural selection pressure. Functions for both positively and negatively selected sites were inferred by annotating these sites with experimentally verified amino acid sites. Comprehensively, the single amino acid site 627 of PB2 protein was inferred as positively selected and it function was identified as a T-cell epitope (TCE). Among the 26 negatively selected amino acid sites of PB2, PB1, PA, HA, NP, NA, M1 and NS2 proteins, only 16 amino acid sites were identified to be involved in TCEs. In addition, 7 amino acid sites including, 608 and 609 of PA, 480 of NP, and 24, 25, 109 and 205 of M1, were identified to be involved in both B-cell epitopes (BCEs) and TCEs. Conversely, the function of positions 62 of PA, and, 43 and 113 of HA was unknown. In conclusion, the seven amino acid sites engaged in both BCEs and TCEs were identified as highly suitable targets, as these sites will be predicted to play a principal role in inducing strong humoral and cellular immune responses against A/H7N9 virus.
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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The mechanism of poly-galloyl-glucoses preventing Influenza A virus entry into host cells. PLoS One 2014; 9:e94392. [PMID: 24718639 PMCID: PMC3981784 DOI: 10.1371/journal.pone.0094392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 03/14/2014] [Indexed: 12/18/2022] Open
Abstract
Hemagglutinin (HA) is essential for Influenza A virus infection, but its diversity of subtypes presents an obstacle to developing broad-spectrum HA inhibitors. In this study, we investigated the molecular mechanisms by which poly-galloyl glucose (pGG) analogs inhibit influenza hemagglutinin (HA) in vitro and in silico. We found that (1) star-shaped pGG analogs exhibit HA-inhibition activity by interacting with the conserved structural elements of the receptor binding domain (RBD); (2) HA inhibition depends on the number of galloyl substituents in a pGG analog; the best number is four; and when PGG binds with two HA trimers at their conserved receptor binding domains (loop 130, loop 220, and 190-α-helix), PGG acts as a molecular glue by aggregating viral particles so as to prevent viral entry into host cells (this was revealed via an in silico simulation on the binding of penta-galloyl-glucose (PGG) with HA). pGGs are also effective on a broad-spectrum influenza A subtypes (including H1, H3, H5, H7); this suggests that pGG analogs can be applied to most influenza A subtypes as a prophylactic against influenza viral infections.
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Apiwat C, Wiriyachaiporn N, Maneeprakorn W, Dharakul T, Thepthai C, Puthavathana P, Siritantikorn S, Horthongkham N. Simultaneous discrimination and detection of influenza A(H1N1)pdm09 and seasonal influenza A viruses using a rapid immunogold biosensor. Arch Virol 2014; 159:1603-11. [PMID: 24402634 DOI: 10.1007/s00705-013-1974-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/30/2013] [Indexed: 11/28/2022]
Abstract
A rapid immunogold biosensor for the simultaneous discrimination of influenza A(H1N1)pdm09 and seasonal influenza A viruses was developed successfully. Monoclonal antibodies (mAbs) that were specific for the hemagglutinin protein of the A(H1N1)pdm09 virus were produced, and the best mAb pairs were selected. Using an mAb that was specific for the influenza A nucleoprotein, a rapid immunogold biosensor for the discrimination and detection of A(H1N1)pdm09/seasonal influenza viruses was developed. When tested with 72 virus isolates, the system achieved 100 % detection of the A(H1N1)pdm09 virus without cross-reactivity against seasonal influenza A (H1, H3 subtypes) and B viruses, parainfluenza viruses, respiratory syncytial viruses, and adenoviruses. The detection limits for A(H1N1)pdm09 and seasonal strains were 5 × 10(2)-7.5 × 10(3) and 1 × 10(3)-7.5 × 10(5) TCID50/mL, respectively. When tested with 49 clinical specimens, the specificity was high (100 %). The sensitivity for the detection of A(H1N1)pdm09 and seasonal strains was 90 % and 100 %, respectively, which correlated with the results of real-time reverse transcription polymerase chain reaction as a reference method. The ability of the system to detect and discriminate the A(H1N1)pdm09 strain from the seasonal strains suggests that this method may be beneficial for investigation of outbreaks and diagnostic applications. Furthermore, this method might be a useful platform for developing a rapid diagnostic system for the simultaneous discrimination of other influenza virus subtypes during future outbreaks.
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Affiliation(s)
- Chayachon Apiwat
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani, 12120, Thailand
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Moreno A, Gabanelli E, Sozzi E, Lelli D, Chiapponi C, Ciccozzi M, Zehender G, Cordioli P. Different evolutionary trends of swine H1N2 influenza viruses in Italy compared to European viruses. Vet Res 2013; 44:112. [PMID: 24289094 PMCID: PMC4176092 DOI: 10.1186/1297-9716-44-112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/19/2013] [Indexed: 12/22/2022] Open
Abstract
European H1N2 swine influenza viruses (EU H1N2SIVs) arose from multiple reassortment events among human H1N1, human H3N2, and avian influenza viruses. We investigated the evolutionary dynamics of 53 Italian H1N2 strains by comparing them with EU H1N2 SIVs. Hemagglutinin (HA) phylogeny revealed Italian strains fell into four groups: Group A and B (41 strains) had a human H1 similar to EU H1N2SIVs, which probably originated in 1986. However Group B (38 strains) formed a subgroup that had a two-amino acid deletion at positions 146/147 in HA. Group C (11 strains) contained an avian H1 that probably originated in 1996, and Group D (1 strain) had an H1 characteristic of the 2009 pandemic strain. Neuraminidase (NA) phylogeny suggested a series of genomic reassortments had occurred. Group A had an N2 that originated from human H3N2 in the late 1970s. Group B had different human N2 that most likely arose from a reassortment with the more recent human H3N2 virus, which probably occurred in 2000. Group C had an avian-like H1 combined with an N2 gene from one of EU H1N2SIVs, EU H3N2SIVs or Human H3N2. Group D was part of the EU H3N2SIVs clade. Although selection pressure for HA and NA was low, several positively selected sites were identified in both proteins, some of which were antigenic, suggesting selection influenced the evolution of SIV. The data highlight different evolutionary trends between European viruses and currently circulating Italian B strains and show the establishment of reassortant strains involving human viruses in Italian pigs.
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Affiliation(s)
- Ana Moreno
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via Bianchi, 9, 25124 Brescia, Italy
| | - Elena Gabanelli
- Laboratory of Infectious Diseases and Tropical Medicine, University of Milan, Ospedale Luigi Sacco Azienda Ospedaliera Polo Universitario, Via G.B. Grassi, 74, 20157 Milan, Italy
| | - Enrica Sozzi
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via Bianchi, 9, 25124 Brescia, Italy
| | - Davide Lelli
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via Bianchi, 9, 25124 Brescia, Italy
| | - Chiara Chiapponi
- Diagnostic Laboratory, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via dei Mercati, 13A, 43100 Parma, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic, and Immunomediated Disease, National Institute of Health, V.le Regina Elena, 299, 00161 Rome, Italy
| | - Gianguglielmo Zehender
- Laboratory of Infectious Diseases and Tropical Medicine, University of Milan, Ospedale Luigi Sacco Azienda Ospedaliera Polo Universitario, Via G.B. Grassi, 74, 20157 Milan, Italy
| | - Paolo Cordioli
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via Bianchi, 9, 25124 Brescia, Italy
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Gopinath SC, Kumar PK. Aptamers that bind to the hemagglutinin of the recent pandemic influenza virus H1N1 and efficiently inhibit agglutination. Acta Biomater 2013; 9:8932-41. [PMID: 23791676 DOI: 10.1016/j.actbio.2013.06.016] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/04/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
Abstract
Influenza virus hemagglutinin (HA) mediates both receptor (glycan) binding and membrane fusion for cell entry and has been the basis for typing influenza A viruses. In this study we have selected RNA aptamers (D-12 and D-26) that specifically target the HA protein of the recent pandemic influenza virus pdmH1N1 (A/California/07/2009). Among the selected aptamers the D-26 aptamer showed higher affinity for the HA of pdmH1N1 and was able to distinguish HA derived from other sub-types of influenza A viruses. The affinity of the D-26 aptamer was further improved upon incorporation of 2'-fluoropyrimidines to a level of 67 fM. Furthermore, the high affinity D-12 and D-26 aptamers were tested for their ability to interfere with HA-glycan interactions using a chicken red blood cell (RBC) agglutination assay. At a concentration of 200 nM the D-26 aptamer completely abolished the agglutination of RBCs, whereas D-12 only did so at 400 nM. These studies suggest that the selected aptamer D-26 not only has a higher affinity and specificity for the HA of pdmH1N1 but also has a better ability to efficiently interfere with HA-glycan interactions compared with the D-12 aptamer. The D-26 aptamer warrants further study regarding its application in developing topical virucidal products against the pdmH1N1 virus and also in surveillance of the pdmH1N1 influenza virus.
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Khandaker I, Suzuki A, Kamigaki T, Tohma K, Odagiri T, Okada T, Ohno A, Otani K, Sawayama R, Kawamura K, Okamoto M, Oshitani H. Molecular evolution of the hemagglutinin and neuraminidase genes of pandemic (H1N1) 2009 influenza viruses in Sendai, Japan, during 2009-2011. Virus Genes 2013; 47:456-466. [PMID: 24078044 PMCID: PMC3834170 DOI: 10.1007/s11262-013-0980-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/07/2013] [Indexed: 01/17/2023]
Abstract
Analyzing the evolutionary pattern of the influenza A(H1N1)pdm09 strain in different regions is important for understanding its diversification. We therefore conducted this study to elucidate the genetic variability and molecular evolution of the influenza A(H1N1)pdm09 strains that circulated during the 2009-2010 and 2010-2011 influenza seasons in Sendai, Japan. Nasopharyngeal swab specimens were collected from patients with influenza-like illnesses who visited outpatient clinics in Sendai City, Japan, from September 2009 to April 2011. A total of 75 isolates were selected from September 2009 to April 2011 to analyze the genetic changes in the entire hemagglutinin 1 (HA1) segment of the HA gene and the neuraminidase (NA) gene based on sequence analysis. Bayesian coalescent Markov chain Monte Carlo analyses of HA1 and NA gene sequences were performed for further analysis. High sequence identities were observed for HA1 and NA in influenza A(H1N1)pdm09, displaying 99.06 and 99.33 % nucleotide identities, respectively, with the A(H1N1)pdm09 vaccine strain A/California/07/2009. The substitution rates of nucleotides for HA1 in the 2009-2010 and 2010-2011 were 1.5 × 10-3 and 1.6 × 10-3 substitutions per site per year, respectively. Phylogenetic tree analysis demonstrated that Sendai isolates were clustered into global clade 7, which is characterized by an S203T mutation in the HA1 gene. Moreover, two distinct circulation clusters were present in the 2010-2011 season. Mutations were present in antigenic or receptor-binding domains of the HA1 segment, including A141V, S143G, S183P, S185T, and S203T. The Bayesian skyline plot model illustrated a steady rate for the maintenance of genetic diversity, followed by a slight increase in the later part of the 2010-2011 season. Selection analysis revealed that the HA1 (position 197) and NA (position 46) sites were under positive selection; however, no known mutation conferring resistance to NA inhibitors such as H275Y was observed. The effect on control of the influenza A(H1N1)pdm09 virus, including vaccine strain selection, requires continuous monitoring of the strain by genetic surveillance.
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Affiliation(s)
- Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kentaro Tohma
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Takashi Odagiri
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Takashi Okada
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Ayumu Ohno
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kanako Otani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Rumi Sawayama
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kazuhisa Kawamura
- Kawamura Pediatric Clinic, 2-22-27, Saiwaicho, Miyagino-Ku, Sendai, Miyagi 983-0836 Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
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El Moussi A, Pozo F, Ben Hadj Kacem MA, Ledesma J, Cuevas MT, Casas I, Slim A. Virological Surveillance of Influenza Viruses during the 2008-09, 2009-10 and 2010-11 Seasons in Tunisia. PLoS One 2013; 8:e74064. [PMID: 24069267 PMCID: PMC3777972 DOI: 10.1371/journal.pone.0074064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/29/2013] [Indexed: 12/03/2022] Open
Abstract
Background The data contribute to a better understanding of the circulation of influenza viruses especially in North-Africa. Objective The objective of this surveillance was to detect severe influenza cases, identify their epidemiological and virological characteristics and assess their impact on the healthcare system. Method We describe in this report the findings of laboratory-based surveillance of human cases of influenza virus and other respiratory viruses' infection during three seasons in Tunisia. Results The 2008–09 winter influenza season is underway in Tunisia, with co-circulation of influenza A/H3N2 (56.25%), influenza A(H1N1) (32.5%), and a few sporadic influenza B viruses (11.25%). In 2010–11 season the circulating strains are predominantly the 2009 pandemic influenza A(H1N1)pdm09 (70%) and influenza B viruses (22%). And sporadic viruses were sub-typed as A/H3N2 and unsubtyped influenza A, 5% and 3%, respectively. Unlike other countries, highest prevalence of influenza B virus Yamagata-like lineage has been reported in Tunisia (76%) localised into the clade B/Bangladesh/3333/2007. In the pandemic year, influenza A(H1N1)pdm09 predominated over other influenza viruses (95%). Amino acid changes D222G and D222E were detected in the HA gene of A(H1N1)pdm09 virus in two severe cases, one fatal case and one mild case out of 50 influenza A(H1N1)pdm09 viruses studied. The most frequently reported respiratory virus other than influenza in three seasons was RSV (45.29%). Conclusion This article summarises the surveillance and epidemiology of influenza viruses and other respiratory viruses, showing how rapid improvements in influenza surveillance were feasible by connecting the existing structure in the health care system for patient records to electronic surveillance system for reporting ILI cases.
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Affiliation(s)
- Awatef El Moussi
- Unit Virology, Microbiology Laboratory, National Influenza Centre, Charles Nicolle's Hospital, Tunis, Tunisia
- * E-mail:
| | - Francisco Pozo
- Influenza and Respiratory Viruses Unit, National Influenza Centre, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mohamed Ali Ben Hadj Kacem
- Unit Virology, Microbiology Laboratory, National Influenza Centre, Charles Nicolle's Hospital, Tunis, Tunisia
| | - Juan Ledesma
- Influenza and Respiratory Viruses Unit, National Influenza Centre, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Maria Teresa Cuevas
- Influenza and Respiratory Viruses Unit, National Influenza Centre, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Inmaculada Casas
- Influenza and Respiratory Viruses Unit, National Influenza Centre, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Amine Slim
- Unit Virology, Microbiology Laboratory, National Influenza Centre, Charles Nicolle's Hospital, Tunis, Tunisia
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Yusuf M, Konc J, Sy Bing C, Trykowska Konc J, Ahmad Khairudin NB, Janezic D, Wahab HA. Structurally conserved binding sites of hemagglutinin as targets for influenza drug and vaccine development. J Chem Inf Model 2013; 53:2423-36. [PMID: 23980878 DOI: 10.1021/ci400421e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ProBiS is a new method to identify the binding site of protein through local structural alignment against the nonredundant Protein Data Bank (PDB), which may result in unique findings compared to the energy-based, geometry-based, and sequence-based predictors. In this work, binding sites of Hemagglutinin (HA), which is an important target for drugs and vaccines in influenza treatment, have been revisited by ProBiS. For the first time, the identification of conserved binding sites by local structural alignment across all subtypes and strains of HA available in PDB is presented. ProBiS finds three distinctive conserved sites on HA's structure (named Site 1, Site 2, and Site 3). Compared to other predictors, ProBiS is the only one that accurately defines the receptor binding site (Site 1). Apart from that, Site 2, which is located slightly above the TBHQ binding site, is proposed as a potential novel conserved target for membrane fusion inhibitor. Lastly, Site 3, located around Helix A at the stem domain and recently targeted by cross-reactive antibodies, is predicted to be conserved in the latest H7N9 China 2013 strain as well. The further exploration of these three sites provides valuable insight in optimizing the influenza drug and vaccine development.
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Affiliation(s)
- Muhammad Yusuf
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Pulau Pinang, Malaysia
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Arunachalam R. Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches. Genetica 2013; 141:143-55. [DOI: 10.1007/s10709-013-9713-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/18/2013] [Indexed: 12/17/2022]
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24
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Bulimo WD, Achilla RA, Majanja J, Mukunzi S, Wadegu M, Osunna F, Mwangi J, Njiri J, Wangui J, Nyambura J, Obura B, Mitei K, Omariba D, Segecha S, Nderitu M, Odindo A, Adega C, Kiponda J, Mupa R, Munyazi F, Kissinger G, Mwakuzimu M, Kamola D, Muhidin E, Kamau D, Kairithia S, Koech M, Sang A, Onge'ta L, Schnabel DC. Molecular characterization and phylogenetic analysis of the hemagglutinin 1 protein of human influenza A virus subtype H1N1 circulating in Kenya during 2007-2008. J Infect Dis 2013; 206 Suppl 1:S46-52. [PMID: 23169971 DOI: 10.1093/infdis/jis586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Among influenza viruses, type A viruses exhibit the greatest genetic diversity, infect the widest range of host species, and cause the vast majority of cases of severe disease in humans, including cases during the great pandemics. The hemagglutinin 1 (HA1) domain of the HA protein contains the highest concentration of epitopes and, correspondingly, experiences the most intense positive selection pressure. OBJECTIVES We sought to isolate and genetically characterize influenza A virus subtype H1N1 (A[H1N1]) circulating in Kenya during 2007-2008, using the HA1 protein. METHODS Nasopharyngeal swab specimens were collected from patients aged ≥ 2 months who presented to 8 healthcare facilities in Kenya with influenza-like illness. We tested specimens for seasonal influenza A viruses, using real-time reverse-transcription polymerase chain reaction (RT-PCR). Viruses were subtyped using subtype-specific primers. Specimens positive for seasonal A(H1N1) were inoculated onto Madin-Darby canine kidney cells for virus isolation. Viral RNAs were extracted from isolates, and the HA1 gene was amplified by RT-PCR, followed by nucleotide sequencing. Nucleotide sequences were assembled using BioEdit and translated into amino acid codes, using DS Gene, version 1.5. Multiple sequence alignments were performed using MUSCLE, version 3.6, and phylogenetic analysis was performed using MrBayes software. RESULTS We found that, similar to A/Brisbane/59/2007 (H1N1)-like virus, which was included in the southern hemisphere vaccine for the 2009 influenza season, all 2007 Kenyan viruses had D39N, R77K, T132V, K149R, and E277K amino acid substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus, a component of the southern hemisphere vaccine for the 2008 influenza season. However, the majority of 2008 viruses from Kenya also had R192K and R226Q substitutions, compared with A/Solomon Islands/3/2006 (H1N1)-like virus. These 2 changes occurred at the receptor binding site. The majority of the 2008 Kenyan isolates contained N187S, G189N, and A193T mutations, which differed from A/Brisbane/59/2007 (H1N1)-like virus. The A193T substitution is involved in binding the sialic acid receptor. Phylogenetically, the 2008 Kenyan isolates grouped into 2 clusters. The main cluster contained viruses with N187S and A193T changes; residue 187 is involved in receptor binding, whereas residue 193 is at antigenic site Sb. CONCLUSION Overall, the major genetic variations that occurred in seasonal A(H1) viruses either affected receptor binding or altered epitopes at the immunodominant sites. These genetic variations in seasonal A(H1N1) isolated in Kenya during 2007-2008 highlight the importance of continuing surveillance and characterization of emerging drift variants of influenza virus in Africa.
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Affiliation(s)
- Wallace D Bulimo
- US Army Medical Research Unit-Kenya, Village Market, 00621 Nairobi, Kenya.
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25
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Zehender G, Pariani E, Piralla A, Lai A, Gabanelli E, Ranghiero A, Ebranati E, Amendola A, Campanini G, Rovida F, Ciccozzi M, Galli M, Baldanti F, Zanetti AR. Reconstruction of the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during the pandemic and post-pandemic phases. PLoS One 2012; 7:e47517. [PMID: 23152755 PMCID: PMC3494699 DOI: 10.1371/journal.pone.0047517] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/12/2012] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to reconstruct the evolutionary dynamics of the A(H1N1)pdm09 influenza virus in Italy during two epidemic seasons (2009/2010 and 2010/2011) in the light of the forces driving the evolution of the virus. Nearly six thousands respiratory specimens were collected from patients with influenza-like illness within the framework of the Italian Influenza Surveillance Network, and the A(H1N1)pdm09 hemagglutinin (HA) gene was amplified and directly sequenced from 227 of these. Phylodynamic and phylogeographical analyses were made using a Bayesian Markov Chain Monte Carlo method, and codon-specific positive selection acting on the HA coding sequence was evaluated. The global and local phylogenetic analyses showed that all of the Italian sequences sampled in the post-pandemic (2010/2011) season grouped into at least four highly significant Italian clades, whereas those of the pandemic season (2009/2010) were interspersed with isolates from other countries at the tree root. The time of the most recent common ancestor of the strains circulating in the pandemic season in Italy was estimated to be between the spring and summer of 2009, whereas the Italian clades of the post-pandemic season originated in the spring of 2010 and showed radiation in the summer/autumn of the same year; this was confirmed by a Bayesian skyline plot showing the biphasic growth of the effective number of infections. The local phylogeography analysis showed that the first season of infection originated in Northern Italian localities with high density populations, whereas the second involved less densely populated localities, in line with a gravity-like model of geographical dispersion. Two HA sites, codons 97 and 222, were under positive selection. In conclusion, the A(H1N1)pdm09 virus was introduced into Italy in the spring of 2009 by means of multiple importations. This was followed by repeated founder effects in the post-pandemic period that originated specific Italian clades.
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Affiliation(s)
- Gianguglielmo Zehender
- Dipartimento di Scienze Cliniche e Biomediche Luigi Sacco, Sezione di Malattie Infettive, Università degli Studi di Milano, Milan, Italy.
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Shapshak P, Chiappelli F, Somboonwit C, Sinnott J. The Influenza Pandemic of 2009. Mol Diagn Ther 2012; 15:63-81. [DOI: 10.1007/bf03256397] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Parry RP, Tettmar KI, Hoschler K, Brailsford SR, Samuel D, Ashford M, Maclennan S, Williamson LM, Tedder RS. Strategies for screening blood donors to source convalescent H1N1v plasma for intervention therapy. Vox Sang 2012; 103:107-12. [PMID: 22404076 DOI: 10.1111/j.1423-0410.2012.01599.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVES During the 1918, pandemic blood components were successfully used to treat severe influenza pneumonia. A Proof of Principle trial investigating the clinical benefit of convalescent plasma was proposed in the 2009 H1N1v epidemic with the aim of screening donors for high titre antibody in order to stockpile plasma packs to be used for treatment for severe pneumonia. MATERIALS AND METHODS Serum samples were collected from donors. IgG antibody capture format enzyme-linked immunoassays using recombinant proteins (GACELISAs) were compared with microneutralization (MN) and haemagglutination inhibition (HAI). The influence of age and history of influenza-like illness (ILI) on the detection of high titre antibody was examined. RESULTS 1598 unselected donor sera collected in October and December 2009 were tested by HAI. The HAI and demographic data defined a possible strategy for selective donor screening. One of the GACELISAs was highly specific for recent infection but showed lower sensitivity than HAI. CONCLUSIONS During the 2009 pandemic screening 17- to 30-year-old donors by HAI delivered around 10% with high antibody levels. The ELISA using a short recombinant H1N1v HA detected fewer reactives but was more specific for high titre antibody (≥1:256). Screening strategies are proposed based on using HAI on serum or GACELISA on plasma.
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Affiliation(s)
- R P Parry
- Virus Reference Department, Health Protection Agency, London, UK.
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28
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Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1. Comput Biol Chem 2012; 36:23-30. [DOI: 10.1016/j.compbiolchem.2011.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 12/02/2011] [Accepted: 12/21/2011] [Indexed: 11/19/2022]
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Evidence for N-glycan shielding of antigenic sites during evolution of human influenza A virus hemagglutinin. J Virol 2012; 86:3446-51. [PMID: 22258255 DOI: 10.1128/jvi.06147-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
After the emergence of influenza A viruses in the human population, the number of N-glycosylation sites (NGS) in the globular head region of hemagglutinin (HA) has increased continuously for several decades. It has been speculated that the addition of NGS to the globular head region of HA has conferred selective advantages to the virus by preventing the binding of antibodies (Ab) to antigenic sites (AS). Here, the effect of N-glycosylation on the binding of Ab to AS in human influenza A virus subtype H3N2 (A/H3N2) was examined by inferring natural selection at AS and other sites (NAS) that are located close to and distantly from the NGS in the three-dimensional structure of HA through a comparison of the rates of synonymous (d(S)) and nonsynonymous (d(N)) substitutions. When positions 63, 122, 126, 133, 144, and 246 in the globular head region of HA were non-NGS, the d(N)/d(S) was >1 and positive selection was detected at the AS located near these positions. However, the d(N)/d(S) value decreased and the evidence of positive selection disappeared when these positions became NGS. In contrast, d(N)/d(S) at the AS distantly located from the positions mentioned above and at the NAS of any location were generally <1 and did not decrease when these positions changed from non-NGS to NGS. These results suggest that the attachment of N-glycans to the NGS in the globular head region of HA prevented the binding of Ab to AS in the evolutionary history of human A/H3N2 virus.
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Mir MA, Lal RB, Sullender W, Singh Y, Garten R, Krishnan A, Broor S. Genetic diversity of HA1 domain of hemagglutinin gene of pandemic influenza H1N1pdm09 viruses in New Delhi, India. J Med Virol 2012; 84:386-93. [DOI: 10.1002/jmv.23205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Stöhr K, Bucher D, Colgate T, Wood J. Influenza virus surveillance, vaccine strain selection, and manufacture. Methods Mol Biol 2012; 865:147-62. [PMID: 22528158 DOI: 10.1007/978-1-61779-621-0_9] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
As outlined in other chapters, the influenza virus, existing laboratory diagnostic abilities, and disease epidemiology have several peculiarities that impact on the timing and processes for the annual production of influenza vaccines. The chapter provides an overview on the key biological and other factors that influence vaccine production. They are the reason for an "annual circle race" beginning with global influenza surveillance during the influenza season in a given year to the eventual supply of vaccines 12 months later in time before the next seasonal outbreak and so on. As influenza vaccines are needed for the Northern and Southern Hemisphere outbreaks in fall and spring, respectively, global surveillance and vaccine production has become a year round business. Its highlights are the WHO recommendations on vaccine strains in February and September and the eventual delivery of vaccine doses in time before the coming influenza season. In between continues vaccine strain and epidemiological surveillance, preparation of new high growth reassortments, vaccine seed strain preparation and development of standardizing reagents, vaccine bulk production, fill-finishing and vaccine release, and in some regions, clinical trials for regulatory approval.
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Affiliation(s)
- Klaus Stöhr
- Novartis Vaccines and Diagnostics, Cambridge, MA, USA.
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32
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Chang SS, Huang HJ, Chen CYC. High performance screening, structural and molecular dynamics analysis to identify H1 inhibitors from TCM Database@Taiwan. MOLECULAR BIOSYSTEMS 2011; 7:3366-74. [PMID: 22012120 DOI: 10.1039/c1mb05320e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New-type oseltamivir-resistant H1N1 influenza viruses have been a major threat to human health since the 2009 flu pandemic. To resolve the drug resistance issue, we aimed to identify a new type of inhibitors against H1 from traditional Chinese medicine (TCM) by employing the world's largest TCM database () for virtual screening and molecular dynamics (MD). From the virtual screening results, sodium (+)-isolaricireinol-2 alpha-sulfate, sodium 3,4-dihydroxy-5-methoxybenzoic acid methyl ester-4-sulfate, sodium (E)-7-hydroxy-1,7-bis(4-hydroxyphenyl)hept-5-ene-3S-sulfonate, and 3-methoxytyramine-betaxanthin were identified as potential drug-like compounds. MD simulation of the binding poses with the key residues Asp103 and Glu83, as well as other binding site residues, identified higher numbers of hydrogen bonds than N-Acetyl-D-Glucosamine (NAG), the natural ligand of the esterase domain in H1. Ionic bonds, salt bridges, and electrostatic energy also contribute to binding stability. Key binding residues include Lys71, Glu83, Asp103, and Arg238. Structural moieties promoting H-bond or salt bridge formations at these locations greatly contribute to a stable ligand-protein complex. An available sodium atom for ionic interactions with Asp103 can further stabilize the ligands. Based on virtual screening, MD simulation, and interaction energy evaluation, TCM candidates demonstrate good potential as novel H1 inhibitors. In addition, the identified stabilizing features can provide insights for designing highly stable H1 inhibitors.
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Affiliation(s)
- Su-Sen Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
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33
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Masoodi TA, Shaik NA, Shafi G, Munshi A, Ahamed AK, Masoodi ZA. Comparative analysis of hemagglutinin of 2009 H1N1 influenza A pandemic indicates its evolution to 1918 H1N1 pandemic. Gene 2011; 491:200-4. [PMID: 22001408 DOI: 10.1016/j.gene.2011.09.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 09/05/2011] [Accepted: 09/24/2011] [Indexed: 11/17/2022]
Abstract
To gain insight into the possible origin of the hemagglutinin of 2009 outbreak, we performed its comparative analysis with hemagglutinin of influenza viral strains from 2005 to 2008 and the past pandemics of 1977, 1968, 1957 and 1918. This insilico analysis showed a maximum sequence similarity between 2009 and 1918 pandemics. Primary structure analysis, antigenic and glycosylation site analyses revealed that this protein has evolved from 1918 pandemic. Phylogenetic analysis of HA amino acid sequence of 2009 influenza A(H1N1) viruses indicated that this virus possesses a distinctive evolutionary trait with 1918 influenza A virus. Although the disordered sequences are different among all the isolates, the disordered positions and sequences between 2009 and 1918 isolates show a greater similarity. Thus these analyses contribute to the evidence of the evolution of 2009 pandemic from 1918 influenza pandemic. This is the first computational evolutionary analysis of HA protein of 2009 H1N1 pandemic.
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Affiliation(s)
- Tariq Ahmad Masoodi
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Rodríguez-Sánchez B, Alonso M, Catalán P, Sánchez Conde M, González-Candelas F, Giannella M, Bouza E, de Viedma DG. Genotyping of a nosocomial outbreak of pandemic influenza A/H1N1 2009. J Clin Virol 2011; 52:129-32. [DOI: 10.1016/j.jcv.2011.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 05/19/2011] [Accepted: 07/01/2011] [Indexed: 11/26/2022]
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Abstract
As all the enveloped viruses, the entry of influenza viruses includes a number of steps in host cell infection. This chapter summarizes the current knowledge of the entry pathway and the role of the fusion protein of influenza virus, hemagglutinin, in this process. Hemagglutinin (HA) is a trimeric glycoprotein that is present in multiple copies in the membrane envelope of influenza virus. HA contains a fusion peptide, a receptor binding site, a metastable structural motif, and the transmembrane domain. The first step of influenza virus entry is the recognition of the host cell receptor molecule, terminal α-sialic acid, by HA. This multivalent attachment by multiple copies of trimetric HA triggers endocytosis of influenza virus that is contained in the endosome. The endosome-trapped virus traffics via a unidirectional pathway to near the nucleus. At this location, the interior pH of the endosome becomes acidic that induces a dramatic conformational change in HA to insert the fusion peptide into the host membrane, induce juxtaposition of the two membranes, and form a fusion pore that allows the release of the genome segments of influenza virus. HA plays a key role in the entire entry pathway. Inhibitors of virus entry are potentially effective antiviral drugs of influenza viruses.
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Affiliation(s)
- Michael G. Rossmann
- grid.169077.e0000000419372197Dept. Biological Sciences, Purdue University, W. State St. 915, West Lafayette, 47907-2054 Indiana USA
| | - Venigalla B. Rao
- grid.39936.360000000121746686Dept. Biology, Catholic University of America, Washington, 20064 District of Columbia USA
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Tse H, Kao RYT, Wu WL, Lim WWL, Chen H, Yeung MY, Woo PCY, Sze KH, Yuen KY. Structural basis and sequence co-evolution analysis of the hemagglutinin protein of pandemic influenza A/H1N1 (2009) virus. Exp Biol Med (Maywood) 2011; 236:915-25. [PMID: 21727184 DOI: 10.1258/ebm.2011.010264] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Severe pandemic influenza A H1N1 (2009) infection, especially in the lower respiratory tract, is often associated with the virus carrying a D222G substitution in the hemagglutinin (HA) protein of the virus. The mechanism for this association has not been fully explored. In the in vitro binding assay, it was found that clinical isolates carrying D222G substitution exhibit higher binding avidity to 2,3-linked sialic acids than the wild-type virus. The receptor binding pocket of the pandemic influenza (H1N1) HA was found to be smaller than those of other influenza A strains, allowing tighter binding of the virus with the receptor, yet also inducing steric stress for the binding. Our homology modeling and molecular docking calculations implicated that residue 222 may affect the positioning of the conserved Q223 residue, hence modulating flexibility of the binding pocket and steric hindrance during receptor binding. The molecular property of residue 222 can also directly influence the 'lysine fence' via the polarity of the amino acid residue where D222G substitution will enhance the electrostatic interactions between the receptor and the protein. The potential importance of residue 222 was illustrated by evolutionary analysis, which showed that this site is under intense selection pressure during adaptation of the virus to human host. Our findings provide a useful reference for follow-up studies in monitoring the ongoing evolution of the pandemic influenza A H1N1 (2009) virus.
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Affiliation(s)
- Herman Tse
- Department of Microbiology and State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong
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Chen J, Sun Y. Variation in the analysis of positively selected sites using nonsynonymous/synonymous rate ratios: an example using influenza virus. PLoS One 2011; 6:e19996. [PMID: 21629696 PMCID: PMC3101217 DOI: 10.1371/journal.pone.0019996] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 04/08/2011] [Indexed: 11/24/2022] Open
Abstract
Sites in a gene showing the nonsynonymous/synonymous rate ratio (ω) >1 have been frequently identified to be under positive selection. To examine the performance of such analysis, sites of the ω ratio >1 in the HA1 gene of H3N2 subtype human influenza viruses were identified from seven overlapping sequence data sets in this study. Our results showed that the sites of the ω ratio >1 were of significant variation among the data sets even though they targeted similar clusters, indicating that the analysis is likely to be either of low sensitivity or of low specificity in identifying sites under positive selection. Most (43/45) of the sites showing ω >1 calculated from at least one data set are involved in B-cell epitopes which cover less than a half sites in the protein, suggesting that the analysis is likely to be of low sensitivity rather than of low specificity. It was further found that the analysis sensitivity could not be enhanced by including more sequences or covering longer time intervals. Previously some reports also likely identified only a portion of the sites under positive selection in the viral gene using the ω ratio. Low sensitivity of the analysis may result from that some sites under positive selection in the gene are also under negative (purifying) selection simultaneously for functional constrains, and so their ω ratios could be <1. Theoretically, the sites under the two opposite selection forces at the same time favor only certain nonsynonymous changes, e.g. those changing the antigenicity of the gene and maintaining the gene function. This study also suggested that sometimes we can identify more sites under positive selection using the ω ratio by integrating the positively selected sites estimated from multiple data sets.
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Affiliation(s)
- Jiming Chen
- China Animal Health and Epidemiology Center, Qingdao, China.
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38
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Li W, Shi W, Qiao H, Ho SYW, Luo A, Zhang Y, Zhu C. Positive selection on hemagglutinin and neuraminidase genes of H1N1 influenza viruses. Virol J 2011; 8:183. [PMID: 21507270 PMCID: PMC3094300 DOI: 10.1186/1743-422x-8-183] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 04/21/2011] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Since its emergence in March 2009, the pandemic 2009 H1N1 influenza A virus has posed a serious threat to public health. To trace the evolutionary path of these new pathogens, we performed a selection-pressure analysis of a large number of hemagglutinin (HA) and neuraminidase (NA) gene sequences of H1N1 influenza viruses from different hosts. RESULTS Phylogenetic analysis revealed that both HA and NA genes have evolved into five distinct clusters, with further analyses indicating that the pandemic 2009 strains have experienced the strongest positive selection. We also found evidence of strong selection acting on the seasonal human H1N1 isolates. However, swine viruses from North America and Eurasia were under weak positive selection, while there was no significant evidence of positive selection acting on the avian isolates. A site-by-site analysis revealed that the positively selected sites were located in both of the cleaved products of HA (HA1 and HA2), as well as NA. In addition, the pandemic 2009 strains were subject to differential selection pressures compared to seasonal human, North American swine and Eurasian swine H1N1 viruses. CONCLUSIONS Most of these positively and/or differentially selected sites were situated in the B-cell and/or T-cell antigenic regions, suggesting that selection at these sites might be responsible for the antigenic variation of the viruses. Moreover, some sites were also associated with glycosylation and receptor-binding ability. Thus, selection at these positions might have helped the pandemic 2009 H1N1 viruses to adapt to the new hosts after they were introduced from pigs to humans. Positive selection on position 274 of NA protein, associated with drug resistance, might account for the prevalence of drug-resistant variants of seasonal human H1N1 influenza viruses, but there was no evidence that positive selection was responsible for the spread of the drug resistance of the pandemic H1N1 strains.
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Affiliation(s)
- Wenfu Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weifeng Shi
- UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland
| | - Huijie Qiao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon YW Ho
- School of Biological Sciences, University of Sydney, Sydney NSW 2006, Australia
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanzhou Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Furuse Y, Oshitani H. Evolution of the influenza A virus untranslated regions. INFECTION GENETICS AND EVOLUTION 2011; 11:1150-4. [PMID: 21515407 DOI: 10.1016/j.meegid.2011.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/31/2011] [Accepted: 04/08/2011] [Indexed: 01/28/2023]
Abstract
In case of the influenza virus, untranslated regions are considered to possess plural functions. The specific packaging model suggests that each of eight segments contains a unique "packaging signal", situated within the untranslated region and coding regions at the 5' and 3' ends of the genomic RNA. In addition to packaging signal, UTRs play key roles in polyadenylation and signals for genomic replication. In the present study, we report the evolutionary characteristics of untranslated regions of influenza virus. We analyzed 574 sequences of the human influenza A (H3N2) virus. The sequence of the untranslated region is highly conserved. Our analysis produced several observations regarding the untranslated region: (1) it has an extremely low divergence; (2) its evolutionary speed is not associated with the protein(s) it encodes; (3) its evolutionary rate is smaller than that of the open reading frame. We revealed the evolutionary characteristics of the untranslated region; this is the first study on the non-coding region of the influenza virus from the perspective of evolutionary molecular biology. In the future, clarifying the detailed mechanisms of packaging as well as the function of the RNA sequence in the untranslated region will increase the understanding of viral life cycles and evolution.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryou-machi Aoba-ku, Sendai 980-8575, Japan
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The role of swine as “mixing vessel” for interspecies transmission of the influenza A subtype H1N1: A simultaneous Bayesian inference of phylogeny and ancestral hosts. INFECTION GENETICS AND EVOLUTION 2011; 11:437-41. [DOI: 10.1016/j.meegid.2010.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 11/30/2010] [Accepted: 12/01/2010] [Indexed: 11/18/2022]
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Graham M, Liang B, Van Domselaar G, Bastien N, Beaudoin C, Tyler S, Kaplen B, Landry E, Li Y. Nationwide molecular surveillance of pandemic H1N1 influenza A virus genomes: Canada, 2009. PLoS One 2011; 6:e16087. [PMID: 21249207 PMCID: PMC3017559 DOI: 10.1371/journal.pone.0016087] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 12/06/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In April 2009, a novel triple-reassortant swine influenza A H1N1 virus ("A/H1N1pdm"; also known as SOIV) was detected and spread globally as the first influenza pandemic of the 21(st) century. Sequencing has since been conducted at an unprecedented rate globally in order to monitor the diversification of this emergent virus and to track mutations that may affect virus behavior. METHODOLOGY/PRINCIPAL FINDINGS By Sanger sequencing, we determined consensus whole-genome sequences for A/H1N1pdm viruses sampled nationwide in Canada over 33 weeks during the 2009 first and second pandemic waves. A total of 235 virus genomes sampled from unique subjects were analyzed, providing insight into the temporal and spatial trajectory of A/H1N1pdm lineages within Canada. Three clades (2, 3, and 7) were identifiable within the first two weeks of A/H1N1pdm appearance, with clades 5 and 6 appearing thereafter; further diversification was not apparent. Only two viral sites displayed evidence of adaptive evolution, located in hemagglutinin (HA) corresponding to D222 in the HA receptor-binding site, and to E374 at HA2-subunit position 47. Among the Canadian sampled viruses, we observed notable genetic diversity (1.47 x 10⁻³ amino acid substitutions per site) in the gene encoding PB1, particularly within the viral genomic RNA (vRNA)-binding domain (residues 493-757). This genome data set supports the conclusion that A/H1N1pdm is evolving but not excessively relative to other H1N1 influenza A viruses. Entropy analysis was used to investigate whether any mutated A/H1N1pdm protein residues were associated with infection severity; however no virus genotypes were observed to trend with infection severity. One virus that harboured heterozygote coding mutations, including PB2 D567D/G, was attributed to a severe and potentially mixed infection; yet the functional significance of this PB2 mutation remains unknown. CONCLUSIONS/SIGNIFICANCE These findings contribute to enhanced understanding of Influenza A/H1N1pdm viral dynamics.
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Affiliation(s)
- Morag Graham
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
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Baldanti F, Campanini G, Piralla A, Rovida F, Braschi A, Mojoli F, Iotti G, Belliato M, Conaldi PG, Arcadipane A, Pariani E, Zanetti A, Minoli L, Emmi V. Severe outcome of influenza A/H1N1/09v infection associated with 222G/N polymorphisms in the haemagglutinin: a multicentre study. Clin Microbiol Infect 2010; 17:1166-9. [PMID: 20946414 DOI: 10.1111/j.1469-0691.2010.03403.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In a multicentre study, influenza A/H1N1/09v 222G/N variants were more frequently detected in patients admitted to the intensive-care unit for invasive mechanical ventilation or extracorporeal membrane oxygenation (10/23; 43.5%) than in patients hospitalized in other units (2/27; 7.4%) and community patients (0/81; 0.0%) (p <0.01). A significantly higher virus load (p 0.02) in the lower vs the upper respiratory tract was observed. Predominance of 222G/N variants in the lower respiratory tract (40% of total virus population) vs the upper respiratory tract (10%) was shown by clonal analysis of haemagglutinin sequences in paired nasal swab and bronchoalveolar lavage samples. The time from illness onset to sampling was significantly longer in patients with severe infection vs community patients (p <0.001). It was concluded that the 222G/N variants showed increased virulence; mutant variants were probably selected in individual patients; and the longer duration of illness might have favoured the emergence of adaptive mutations through multiple replication cycles.
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Affiliation(s)
- F Baldanti
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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Wolf YI, Nikolskaya A, Cherry JL, Viboud C, Koonin E, Lipman DJ. Projection of seasonal influenza severity from sequence and serological data. PLOS CURRENTS 2010; 2:RRN1200. [PMID: 21152078 PMCID: PMC2998708 DOI: 10.1371/currents.rrn1200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/06/2010] [Indexed: 11/25/2022]
Abstract
Severity of seasonal influenza A epidemics is related to the antigenic novelty of the predominant viral strains circulating each year. Support for a strong correlation between epidemic severity and antigenic drift comes from infectious challenge experiments on vaccinated animals and human volunteers, field studies of vaccine efficacy, prospective studies of subjects with laboratory-confirmed prior infections, and analysis of the connection between drift and severity from surveillance data. We show that, given data on the antigenic and sequence novelty of the hemagglutinin protein of clinical isolates of H3N2 virus from a season along with the corresponding data from prior seasons, we can accurately predict the influenza severity for that season. This model therefore provides a framework for making projections of the severity of the upcoming season using assumptions based on viral isolates collected in the current season. Our results based on two independent data sets from the US and Hong Kong suggest that seasonal severity is largely determined by the novelty of the hemagglutinin protein although other factors, including mutations in other influenza genes, co-circulating pathogens and weather conditions, might also play a role. These results should be helpful for the control of seasonal influenza and have implications for improvement of influenza surveillance.
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Affiliation(s)
- Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
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Das pandemische H1N1-Influenzavirus/2009. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2010; 53:1231-7. [DOI: 10.1007/s00103-010-1166-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Souza TML, Salluh JIF, Bozza FA, Mesquita M, Soares M, Motta FC, Pitrowsky MT, de Lourdes Oliveira M, Mishin VP, Gubareva LV, Whitney A, Rocco SA, Gonçalves VMC, Marques VP, Velasco E, Siqueira MM. H1N1pdm influenza infection in hospitalized cancer patients: clinical evolution and viral analysis. PLoS One 2010; 5:e14158. [PMID: 21152402 PMCID: PMC2994772 DOI: 10.1371/journal.pone.0014158] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Accepted: 10/27/2010] [Indexed: 12/17/2022] Open
Abstract
Background The novel influenza A pandemic virus (H1N1pdm) caused considerable morbidity and mortality worldwide in 2009. The aim of the present study was to evaluate the clinical course, duration of viral shedding, H1N1pdm evolution and emergence of antiviral resistance in hospitalized cancer patients with severe H1N1pdm infections during the winter of 2009 in Brazil. Methods We performed a prospective single-center cohort study in a cancer center in Rio de Janeiro, Brazil. Hospitalized patients with cancer and a confirmed diagnosis of influenza A H1N1pdm were evaluated. The main outcome measures in this study were in-hospital mortality, duration of viral shedding, viral persistence and both functional and molecular analyses of H1N1pdm susceptibility to oseltamivir. Results A total of 44 hospitalized patients with suspected influenza-like illness were screened. A total of 24 had diagnosed H1N1pdm infections. The overall hospital mortality in our cohort was 21%. Thirteen (54%) patients required intensive care. The median age of the studied cohort was 14.5 years (3–69 years). Eighteen (75%) patients had received chemotherapy in the previous month, and 14 were neutropenic at the onset of influenza. A total of 10 patients were evaluated for their duration of viral shedding, and 5 (50%) displayed prolonged viral shedding (median 23, range = 11–63 days); however, this was not associated with the emergence of a resistant H1N1pdm virus. Viral evolution was observed in sequentially collected samples. Conclusions Prolonged influenza A H1N1pdm shedding was observed in cancer patients. However, oseltamivir resistance was not detected. Taken together, our data suggest that severely ill cancer patients may constitute a pandemic virus reservoir with major implications for viral propagation.
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Affiliation(s)
- Thiago Moreno L. Souza
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
- * E-mail: (TMLS); (MMS)
| | | | - Fernando A. Bozza
- Intensive Care Unit, Instituto de Pesquisas Evandro Chagas/Fiocruz, Rio de Janeiro, Brazil
| | - Milene Mesquita
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Márcio Soares
- Intensive Care Unit, Hospital do Câncer-I/INCA, Rio de Janeiro, Brazil
| | - Fernando C. Motta
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | | | - Maria de Lourdes Oliveira
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
| | - Vasiliy P. Mishin
- Influenza Division, National Center for Immunization and Respiratory Diseases/Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Larissa V. Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases/Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Anne Whitney
- Influenza Division, National Center for Immunization and Respiratory Diseases/Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Sandra Amaral Rocco
- Pediatric Intensive Care Unit, Hospital de Câncer-I/INCA, Rio de Janeiro, Brazil
| | - Vânia Maria C. Gonçalves
- Infection Control Committee and Infectious Diseases Department, Hospital de Câncer-I/INCA, Rio de Janeiro, Brazil
| | - Venceslaine Prado Marques
- Infection Control Committee and Infectious Diseases Department, Hospital de Câncer-I/INCA, Rio de Janeiro, Brazil
| | - Eduardo Velasco
- Infection Control Committee and Infectious Diseases Department, Hospital de Câncer-I/INCA, Rio de Janeiro, Brazil
| | - Marilda M. Siqueira
- Laboratório de vírus respiratórios e do sarampo, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, Brazil
- * E-mail: (TMLS); (MMS)
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Duvvuri VRSK, Moghadas SM, Guo H, Duvvuri B, Heffernan JM, Fisman DN, Wu GE, Wu J. Highly conserved cross-reactive CD4+ T-cell HA-epitopes of seasonal and the 2009 pandemic influenza viruses. Influenza Other Respir Viruses 2010; 4:249-58. [PMID: 20716156 PMCID: PMC4634651 DOI: 10.1111/j.1750-2659.2010.00161.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Please cite this paper as: Duvvuri et al. (2010) Highly conserved cross‐reactive CD4+ T‐cell HA‐epitopes of seasonal and the 2009 pandemic influenza viruses. Influenza and Other Respiratory Viruses 4(5), 249–258. Background The relatively mild nature of the 2009 influenza pandemic (nH1N1) highlights the overriding importance of pre‐existing immune memory. The absence of cross‐reactive antibodies to nH1N1 in most individuals suggests that such attenuation may be attributed to pre‐existing cellular immune responses to epitopes shared between nH1N1 virus and previously circulating strains of inter‐pandemic influenza A viruses. Results We sought to identify potential CD4+ T cell epitopes and predict the level of cross‐reactivity of responding T cells. By performing large‐scale major histocompatibility complex II analyses on Hemagglutinin (HA) proteins, we investigated the degree of T‐cell cross‐reactivity between seasonal influenza A (sH1N1, H3N2) from 1968 to 2009 and nH1N1 strains. Each epitope was examined against all the protein sequences that correspond to sH1N1, H3N2, and nH1N1. T‐cell cross‐reactivity was estimated to be 52%, and maximum conservancy was found between sH1N1 and nH1N1 with a significant correlation (P < 0·05). Conclusions Given the importance of cellular responses in kinetics of influenza infection in humans, our findings underscore the role of T‐cell assays for understanding the inter‐pandemic variability in severity and for planning treatment methods for emerging influenza viruses.
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Affiliation(s)
- Venkata R S K Duvvuri
- MITACS Centre for Disease Modeling, York Institute of Health Research, Toronto, Ontario, Canada
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Liu Y, Liu X, Fang J, Shen X, Chen W, Lin X, Li H, Tan W, Wang Y, Zhao P, Qi Z. Characterization of antibodies specific for hemagglutinin and neuraminidase proteins of the 1918 and 2009 pandemic H1N1 viruses. Vaccine 2010; 29:183-90. [PMID: 21055499 DOI: 10.1016/j.vaccine.2010.10.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Revised: 10/16/2010] [Accepted: 10/21/2010] [Indexed: 12/28/2022]
Abstract
Serologic studies have detected protective immunity against 2009 pandemic H1N1 influenza virus (H1N1-2009) in some people. However, further study of preexisting immunity has been complicated by the complexity of the human immunological background. Here, we immunized mice with HA- and NA-encoding plasmids. The cross-neutralizing activity of the anti-HA antisera and the effect of the anti-NA antisera on viral infectivity were evaluated using H1N1-1918- and 2009-pseudotyped particles (pps) and an H1N1-2009 isolate. Antibodies to H1N1-2009 HA (09HA) neutralized pps harboring 09HA or H1N1-1918 HA (18HA); similarly, antibodies to 18HA neutralized pps harboring 18HA or 09HA. Antibodies to 09HA and 18HA also neutralized the H1N1-2009 virus with high efficiency. Antibodies to H1N1-1918 NA (18NA) or H1N1-2009 NA (09NA) both enhanced the infectivity of pps harboring 09NA and 18NA. Although anti-09NA and -18NA antibodies significantly reduced cytopathic effects in multiple-cycle infection assays, conversely, these antibodies enhanced the infectivity of H1N1-2009 in single-cycle infection assays. Our study demonstrates the existence of cross-protection between antibodies against these two antigenically related virus strains and shows that anti-NA antibodies have a dual effect that requires reexamination of their role in human immunity.
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Affiliation(s)
- Yuan Liu
- Department of Microbiology, Shanghai Key Laboratory of Medical Biodefense, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, PR China
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Perales C, Lorenzo-Redondo R, López-Galíndez C, Martínez MA, Domingo E. Mutant spectra in virus behavior. Future Virol 2010. [DOI: 10.2217/fvl.10.61] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA viruses replicate as complex mutant spectra, also termed ‘mutant clouds’, known as viral quasispecies. While this is a widely observed viral population structure, it is less known that a number of biologically relevant features of this important group of viral pathogens depend on (or are strongly influenced by) the complexity and composition of mutant spectra. Among them, fitness increase or decrease depending on intrapopulation complementation or interference, selection triggered by memory genomes, pathogenic potential of viruses, disease evolution and the response to antiviral treatments. Quasispecies represent the recognition of complex behavior in viruses, and it is an oversimplification to equate such a population structure with the classic polymorphism of population biology. Darwinian principles acting on genome collectivities that replicate with high error rates provide a unique population structure prone to flexible and largely unpredictable behavior.
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Affiliation(s)
- Celia Perales
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, 1 Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Ramón Lorenzo-Redondo
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, Potter MA, Rosenfeld R, Wheaton WD, Wiringa AE, Bacon KM, Burke DS. Vaccination deep into a pandemic wave potential mechanisms for a "third wave" and the impact of vaccination. Am J Prev Med 2010; 39:e21-9. [PMID: 20965375 PMCID: PMC2975455 DOI: 10.1016/j.amepre.2010.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Revised: 04/30/2010] [Accepted: 07/02/2010] [Indexed: 01/12/2023]
Abstract
BACKGROUND In December 2009, when the H1N1 influenza pandemic appeared to be subsiding, public health officials and unvaccinated individuals faced the question of whether continued H1N1 immunization was still worthwhile. PURPOSE To delineate what combinations of possible mechanisms could generate a third pandemic wave and then explore whether vaccinating the population at different rates and times would mitigate the wave. METHODS As part of ongoing work with the Office of the Assistant Secretary for Preparedness and Response at the USDHHS during the H1N1 influenza pandemic, the University of Pittsburgh Models of Infectious Disease Agent Study team employed an agent-based computer simulation model of the Washington DC metropolitan region to delineate what mechanisms could generate a "third pandemic wave" and explored whether vaccinating the population at different rates and times would mitigate the wave. This model included explicit representations of the region's individuals, school systems, workplaces/commutes, households, and communities. RESULTS Three mechanisms were identified that could cause a third pandemic wave; substantially increased viral transmissibility from seasonal forcing (changing influenza transmission with changing environmental conditions, i.e., seasons) and progressive viral adaptation; an immune escape variant; and changes in social mixing from holiday school closures. Implementing vaccination for these mechanisms, even during the down-slope of the fall epidemic wave, significantly mitigated the third wave. Scenarios showed the gains from initiating vaccination earlier, increasing the speed of vaccination, and prioritizing population subgroups based on Advisory Committee on Immunization Practices recommendations. CONCLUSIONS Additional waves in an epidemic can be mitigated by vaccination even when an epidemic appears to be waning.
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Affiliation(s)
- Bruce Y Lee
- Department of Medicine, University of Pittsburgh, PA 15213, USA.
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Lee JI, Lee GC, Oh YH, Lee YK, Kim MY, Lee CH. Molecular characterization of partial-open reading frames 1a and 2 of the human astroviruses in South Korea. Virol J 2010; 7:221. [PMID: 20831802 PMCID: PMC2944169 DOI: 10.1186/1743-422x-7-221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 09/10/2010] [Indexed: 01/23/2023] Open
Abstract
Human astroviruses (HAstVs) are among the major causes of gastroenteritis in South Korea. In this study, the partial regions of the open reading frame (ORF) 1a and ORF2 genes of HAstVs from gastroenteritis patients in nine hospitals were sequenced, and the molecular characterization of the viruses was revealed. 89 partial nucleotide sequences of ORF1a and 88 partial nucleotide sequences of ORF2 were amplified from 120 stool specimens. Phylogenetic analysis showed that most of the nucleotide sequences of ORF1a and ORF2 were grouped with HAstV type 1 but had evolutionary genetic distance compared with the reference sequences, such as the HAstV-1 prototype, Dresden strain, and Oxford strain. According to the phylogenetic analysis, some nucleotide sequences including SE0506041, SE0506043, and SE0506058, showed the discrepancy of the genotypes, but there was no proof of recombination among the HAstV types. In conclusion, this study showed that the dominant HAstV isolated from the Seoul metropolitan area in 2004-2005 was HAstV type 1, and that Korean HAstV-1 had the genetic distance in evolution compared with the reference sequences of HAstVs. Lots of nucleotide sequences of the ORF1a and ORF2 genes of HAstV will be useful for studying for the control and prevention of HAstV gastroenteritis in South Korea.
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Affiliation(s)
- Jae In Lee
- Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
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