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Timin AS, Muslimov AR, Petrova AV, Lepik KV, Okilova MV, Vasin AV, Afanasyev BV, Sukhorukov GB. Hybrid inorganic-organic capsules for efficient intracellular delivery of novel siRNAs against influenza A (H1N1) virus infection. Sci Rep 2017; 7:102. [PMID: 28273907 PMCID: PMC5427965 DOI: 10.1038/s41598-017-00200-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
The implementation of RNAi technology into the clinical practice has been significantly postponing due to the issues regarding to the delivery of naked siRNA predominantly to target cells. Here we report the approach to enhance the efficiency of siRNA delivery by encapsulating the siRNA into new carrier systems which are obtained via the combination of widely used layer-by-layer technique and in situ modification by sol-gel chemistry. We used three types of siRNAs (NP-717, NP-1155 and NP-1496) in encapsulated form as new therapeutic agents against H1N1 influenza virus infection. By employing the hybrid microcontainers for the siRNA encapsulation we demonstrate the reduction of viral nucleoprotein (NP) level and inhibition of influenza virus production in infected cell lines (MDCK and A549). The obtained hybrid carriers based on assembled biodegradable polyelectrolytes and sol-gel coating possess several advantages such as a high cell uptake efficiency, low toxicity, efficient intracellular delivery of siRNAs and the protection of siRNAs from premature degradation before reaching the target cells. These findings underpin a great potential of versatile microencapsulation technology for the development of anti-viral RNAi delivery systems against influenza virus infection.
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Affiliation(s)
- Alexander S Timin
- RASA center in Tomsk, Tomsk Polytechnic University, Lenin Avenue, 30, 634050, Tomsk, Russian Federation.
| | - Albert R Muslimov
- First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, Saint-Petersburg, Russian Federation
- RASA center in St. Petersburg, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation
| | - Aleksandra V Petrova
- Research Institute of Influenza, Popova str., 15/17, 197376, Saint-Petersburg, Russian Federation
| | - Kirill V Lepik
- First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, Saint-Petersburg, Russian Federation
| | - Maria V Okilova
- First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, Saint-Petersburg, Russian Federation
| | - Andrey V Vasin
- Research Institute of Influenza, Popova str., 15/17, 197376, Saint-Petersburg, Russian Federation
- Department of Molecular Biology, Peter The Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251, St. Petersburg, Russian Federation
| | - Boris V Afanasyev
- First I. P. Pavlov State Medical University of St. Petersburg, Lev Tolstoy str., 6/8, 197022, Saint-Petersburg, Russian Federation
| | - Gleb B Sukhorukov
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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202
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A universal computational model for predicting antigenic variants of influenza A virus based on conserved antigenic structures. Sci Rep 2017; 7:42051. [PMID: 28165025 PMCID: PMC5292743 DOI: 10.1038/srep42051] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/06/2017] [Indexed: 11/08/2022] Open
Abstract
Rapid determination of the antigenicity of influenza A virus could help identify the antigenic variants in time. Currently, there is a lack of computational models for predicting antigenic variants of some common hemagglutinin (HA) subtypes of influenza A viruses. By means of sequence analysis, we demonstrate here that multiple HA subtypes of influenza A virus undergo similar mutation patterns of HA1 protein (the immunogenic part of HA). Further analysis on the antigenic variation of influenza A virus H1N1, H3N2 and H5N1 showed that the amino acid residues' contribution to antigenic variation highly differed in these subtypes, while the regional bands, defined based on their distance to the top of HA1, played conserved roles in antigenic variation of these subtypes. Moreover, the computational models for predicting antigenic variants based on regional bands performed much better in the testing HA subtype than those did based on amino acid residues. Therefore, a universal computational model, named PREDAV-FluA, was built based on the regional bands to predict the antigenic variants for all HA subtypes of influenza A viruses. The model achieved an accuracy of 0.77 when tested with avian influenza H9N2 viruses. It may help for rapid identification of antigenic variants in influenza surveillance.
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203
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Bravo-Vasquez N, Karlsson EA, Jimenez-Bluhm P, Meliopoulos V, Kaplan B, Marvin S, Cortez V, Freiden P, Beck MA, Hamilton-West C, Schultz-Cherry S. Swine Influenza Virus (H1N2) Characterization and Transmission in Ferrets, Chile. Emerg Infect Dis 2017; 23:241-251. [PMID: 28098524 PMCID: PMC5324791 DOI: 10.3201/eid2302.161374] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phylogenetic analysis of the influenza hemagglutinin gene (HA) has suggested that commercial pigs in Chile harbor unique human seasonal H1-like influenza viruses, but further information, including characterization of these viruses, was unavailable. We isolated influenza virus (H1N2) from a swine in a backyard production farm in Central Chile and demonstrated that the HA gene was identical to that in a previous report. Its HA and neuraminidase genes were most similar to human H1 and N2 viruses from the early 1990s and internal segments were similar to influenza A(H1N1)pdm09 virus. The virus replicated efficiently in vitro and in vivo and transmitted in ferrets by respiratory droplet. Antigenically, it was distinct from other swine viruses. Hemagglutination inhibition analysis suggested that antibody titers to the swine Chilean H1N2 virus were decreased in persons born after 1990. Further studies are needed to characterize the potential risk to humans, as well as the ecology of influenza in swine in South America.
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Affiliation(s)
| | | | - Pedro Jimenez-Bluhm
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Victoria Meliopoulos
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Bryan Kaplan
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Shauna Marvin
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Valerie Cortez
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Pamela Freiden
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
| | - Melinda A. Beck
- University of Chile, Santiago, Chile (N. Bravo-Vasquez, C. Hamilton-West)
- St. Jude Children’s Research Hospital, Memphis, Tennessee, USA (E.A. Karlsson, P. Jimenez-Bluhm, V. Meliopoulos, B. Kaplan, S. Marvin, V. Cortez, P. Freiden, S. Schultz-Cherry)
- University of North Carolina, Chapel Hill, North Carolina, USA (M.A. Beck)
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204
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Oong XY, Ng KT, Tan JL, Chan KG, Kamarulzaman A, Chan YF, Sam IC, Tee KK. Whole-Genome Phylogenetic Analysis of Influenza B/Phuket/3073/2013-Like Viruses and Unique Reassortants Detected in Malaysia between 2012 and 2014. PLoS One 2017; 12:e0170610. [PMID: 28129386 PMCID: PMC5271328 DOI: 10.1371/journal.pone.0170610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/06/2017] [Indexed: 11/19/2022] Open
Abstract
Reassortment of genetic segments between and within influenza B lineages (Victoria and Yamagata) has been shown to generate novel reassortants with unique genetic characteristics. Based on hemagglutinin (HA) and neuraminidase (NA) genes, recent surveillance study has identified reassortment properties in B/Phuket/3073/2013-like virus, which is currently used in the WHO-recommended influenza vaccine. To understand the potential reassortment patterns for all gene segments, four B/Phuket/3073/2013-like viruses and two unique reassortants (one each from Yamagata and Victoria) detected in Malaysia from 2012-2014 were subjected to whole-genome sequencing. Each gene was phylogenetically classified into lineages, clades and sub-clades. Three B/Phuket/3073/2013-like viruses from Yamagata lineage were found to be intra-clade reassortants, possessing PA and NA genes derived from Stockholm/12-like sub-clade, while the remaining genes from Wisconsin/01-like sub-clade (both sub-clades were within Yamagata Clade 3/Yam-3). However, the other B/Phuket/3073/2013-like virus had NS gene that derived from Stockholm/12-like sub-clade instead of Wisconsin/01-like sub-clade. One inter-clade reassortant had Yamagata Clade 2/Yam-2-derived HA and NP, and its remaining genes were Yam-3-derived. Within Victoria Clade 1/Vic-1 in Victoria lineage, one virus had intra-clade reassortment properties: HA and PB2 from Vic-1B sub-clade, MP and NS from a unique sub-clade "Vic-1C", and the remaining genes from Vic-1A sub-clade. Although random reassortment event may generate unique reassortants, detailed phylogenetic classification of gene segments showed possible genetic linkage between PA and NA genes in B/Phuket/3073/2013-like viruses, which requires further investigation. Understanding on reassortment patterns in influenza B evolution may contribute to future vaccine design.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Joon Ling Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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205
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Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct 2017; 12:1. [PMID: 28095902 PMCID: PMC5240389 DOI: 10.1186/s13062-016-0172-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. Results I describe a new approach that uses a null model based on experimental measurements of a gene’s site-specific amino-acid preferences generated by deep mutational scanning in the lab. This null model makes it possible to identify both diversifying selection for repeated amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. Conclusions As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual protein sites, approaches like the one here can improve our ability to identify many interesting forms of selection in natural sequences. Reviewers This article was reviewed by Sebastian Maurer-Stroh, Olivier Tenaillon, and Tal Pupko. All three reviewers are members of the Biology Direct editorial board. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, 98109, WA, USA.
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206
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Karnbunchob N, Omori R, Tessmer HL, Ito K. Tracking the Evolution of Polymerase Genes of Influenza A Viruses during Interspecies Transmission between Avian and Swine Hosts. Front Microbiol 2017; 7:2118. [PMID: 28082971 PMCID: PMC5183616 DOI: 10.3389/fmicb.2016.02118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Human influenza pandemics have historically been caused by reassortant influenza A viruses using genes from human and avian viruses. This genetic reassortment between human and avian viruses has been known to occur in swine during viral circulation, as swine are capable of circulating both avian and human viruses. Therefore, avian-to-swine transmission of viruses plays an important role in the emergence of new pandemic strains. The amino acids at several positions on PB2, PB1, and PA are known to determine the host range of influenza A viruses. In this paper, we track viral transmission between avian and swine to investigate the evolution on polymerase genes associated with their hosts. We traced viral transmissions between avian and swine hosts by using nucleotide sequences of avian viruses and swine viruses registered in the NCBI GenBank. Using BLAST and the reciprocal best hits technique, we found 32, 33, and 30 pairs of avian and swine nucleotide sequences that may be associated with avian-to-swine transmissions for PB2, PB1, and PA genes, respectively. Then, we examined the amino acid substitutions involved in these sporadic transmissions. On average, avian-to-swine transmission pairs had 5.47, 3.73, and 5.13 amino acid substitutions on PB2, PB1, and PA, respectively. However, amino acid substitutions were distributed over the positions, and few positions showed common substitutions in the multiple transmission events. Statistical tests on the number of repeated amino acid substitutions suggested that no specific positions on PB2 and PA may be required for avian viruses to infect swine. We also found that avian viruses that transmitted to swine tend to process I478V substitutions on PB2 before interspecies transmission events. Furthermore, most mutations occurred after the interspecies transmissions, possibly due to selective viral adaptation to swine.
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Affiliation(s)
- Nipawit Karnbunchob
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido UniversitySapporo, Japan; Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
| | - Heidi L Tessmer
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University Sapporo, Japan
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University Sapporo, Japan
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207
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Lu L, Leigh Brown AJ, Lycett SJ. Quantifying predictors for the spatial diffusion of avian influenza virus in China. BMC Evol Biol 2017; 17:16. [PMID: 28086751 PMCID: PMC5237338 DOI: 10.1186/s12862-016-0845-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/08/2016] [Indexed: 11/18/2022] Open
Abstract
Background Avian influenza virus (AIV) causes both severe outbreaks and endemic disease among poultry and has caused sporadic human infections in Asia, furthermore the routes of transmission in avian species between geographic regions can be numerous and complex. Using nucleotide sequences from the internal protein coding segments of AIV, we performed a Bayesian phylogeographic study to uncover regional routes of transmission and factors predictive of the rate of viral diffusion within China. Results We found that the Central area and Pan-Pearl River Delta were the two main sources of AIV diffusion, while the East Coast areas especially the Yangtze River delta, were the major targets of viral invasion. Next we investigated the extent to which economic, agricultural, environmental and climatic regional data was predictive of viral diffusion by fitting phylogeographic discrete trait models using generalised linear models. Conclusions Our results highlighted that the economic-agricultural predictors, especially the poultry population density and the number of farm product markets, are the key determinants of spatial diffusion of AIV in China; high human density and freight transportation are also important predictors of high rates of viral transmission; Climate features (e.g. temperature) were correlated to the viral invasion in the destination to some degree; while little or no impacts were found from natural environment factors (such as surface water coverage). This study uncovers the risk factors and enhances our understanding of the spatial dynamics of AIV in bird populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0845-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lu Lu
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Andrew J Leigh Brown
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Samantha J Lycett
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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208
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Bourret V, Lyall J, Frost SDW, Teillaud A, Smith CA, Leclaire S, Fu J, Gandon S, Guérin JL, Tiley LS. Adaptation of avian influenza virus to a swine host. Virus Evol 2017; 3:vex007. [PMID: 28458917 PMCID: PMC5399929 DOI: 10.1093/ve/vex007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence of pathogenic RNA viruses into new hosts can have dramatic consequences for both livestock and public health. Here we characterize the viral genetic changes that were observed in a previous study which experimentally adapted a field isolate of duck influenza virus to swine respiratory cells. Both pre-existing and de novo mutations were selected during this adaptation. We compare the in vitro growth dynamics of the adapted virus with those of the original strain as well as all possible reassortants using reverse genetics. This full factorial design showed that viral gene segments are involved in complex epistatic interactions on virus fitness, including negative and sign epistasis. We also identify two point mutations at positions 67 and 113 of the HA2 subunit of the hemagglutinin protein conferring a fast growth phenotype on the naïve avian virus in swine cells. These HA2 mutations enhance the pH dependent, HA-mediated membrane fusion. A global H1 maximum-likelihood phylogenetic analysis, combined with comprehensive ancestry reconstruction and tests for directional selection, confirmed the field relevance of the mutation at position 113 of HA2. Most notably, this mutation was associated with the establishment of the H1 'avian-like' swine influenza lineage, regarded as the most likely to cause the next influenza pandemic in humans. This multidisciplinary approach to study the genetics of viral adaptation provides unique insights on the underlying processes leading to influenza emergence in a new host species, and identifies specific targets for future surveillance and functional studies.
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Affiliation(s)
- Vincent Bourret
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Jon Lyall
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angélique Teillaud
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Catherine A Smith
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Leclaire
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - JinQi Fu
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sylvain Gandon
- Centre d’Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Jean-Luc Guérin
- Université de Toulouse, INP, ENVT, Toulouse, France
- INRA, UMR 1225, IHAP, Toulouse, France
| | - Laurence S Tiley
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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209
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Construction of Multilevel Structure for Avian Influenza Virus System Based on Granular Computing. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5404180. [PMID: 28191464 PMCID: PMC5278516 DOI: 10.1155/2017/5404180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/01/2016] [Accepted: 12/14/2016] [Indexed: 12/03/2022]
Abstract
Exploring the genetic structure of influenza viruses attracts the attention in the field of molecular ecology and medical genetics, whose epidemics cause morbidity and mortality worldwide. The rapid variations in RNA strand and changes of protein structure of the virus result in low-accuracy subtyping identification and make it difficult to develop effective drugs and vaccine. This paper constructs the evolutionary structure of avian influenza virus system considering both hemagglutinin and neuraminidase protein fragments. An optimization model was established to determine the rational granularity of the virus system for exploring the intrinsic relationship among the subtypes based on the fuzzy hierarchical evaluation index. Thus, an algorithm was presented to extract the rational structure. Furthermore, to reduce the systematic and computational complexity, the granular signatures of virus system were identified based on the coarse-grained idea and then its performance was evaluated through a designed classifier. The results showed that the obtained virus signatures could approximate and reflect the whole avian influenza virus system, indicating that the proposed method could identify the effective virus signatures. Once a new molecular virus is detected, it is efficient to identify the homologous virus hierarchically.
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210
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Nshogozabahizi JC, Dench J, Aris-Brosou S. Widespread Historical Contingency in Influenza Viruses. Genetics 2017; 205:409-420. [PMID: 28049709 PMCID: PMC5223518 DOI: 10.1534/genetics.116.193979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/04/2016] [Indexed: 11/18/2022] Open
Abstract
In systems biology and genomics, epistasis characterizes the impact that a substitution at a particular location in a genome can have on a substitution at another location. This phenomenon is often implicated in the evolution of drug resistance or to explain why particular "disease-causing" mutations do not have the same outcome in all individuals. Hence, uncovering these mutations and their locations in a genome is a central question in biology. However, epistasis is notoriously difficult to uncover, especially in fast-evolving organisms. Here, we present a novel statistical approach that replies on a model developed in ecology and that we adapt to analyze genetic data in fast-evolving systems such as the influenza A virus. We validate the approach using a two-pronged strategy: extensive simulations demonstrate a low-to-moderate sensitivity with excellent specificity and precision, while analyses of experimentally validated data recover known interactions, including in a eukaryotic system. We further evaluate the ability of our approach to detect correlated evolution during antigenic shifts or at the emergence of drug resistance. We show that in all cases, correlated evolution is prevalent in influenza A viruses, involving many pairs of sites linked together in chains; a hallmark of historical contingency. Strikingly, interacting sites are separated by large physical distances, which entails either long-range conformational changes or functional tradeoffs, for which we find support with the emergence of drug resistance. Our work paves a new way for the unbiased detection of epistasis in a wide range of organisms by performing whole-genome scans.
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Affiliation(s)
| | - Jonathan Dench
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ontario K1N 6N5, Canada
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211
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Maljkovic Berry I, Melendrez MC, Li T, Hawksworth AW, Brice GT, Blair PJ, Halsey ES, Williams M, Fernandez S, Yoon IK, Edwards LD, Kuschner R, Lin X, Thomas SJ, Jarman RG. Frequency of influenza H3N2 intra-subtype reassortment: attributes and implications of reassortant spread. BMC Biol 2016; 14:117. [PMID: 28034300 PMCID: PMC5200972 DOI: 10.1186/s12915-016-0337-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence suggests that influenza reassortment not only contributes to the emergence of new human pandemics but also plays an important role in seasonal influenza epidemics, disease severity, evolution, and vaccine efficacy. We studied this process within 2091 H3N2 full genomes utilizing a combination of the latest reassortment detection tools and more conventional phylogenetic analyses. RESULTS We found that the amount of H3N2 intra-subtype reassortment depended on the number of sampled genomes, occurred with a steady frequency of 3.35%, and was not affected by the geographical origins, evolutionary patterns, or previous reassortment history of the virus. We identified both single reassortant genomes and reassortant clades, each clade representing one reassortment event followed by successful spread of the reassorted variant in the human population. It was this spread that was mainly responsible for the observed high presence of H3N2 intra-subtype reassortant genomes. The successfully spread variants were generally sampled within one year of their formation, highlighting the risk of their rapid spread but also presenting an opportunity for their rapid detection. Simultaneous spread of several different reassortant lineages was observed, and despite their limited average lifetime, second and third generation reassortment was detected, as well as reassortment between viruses belonging to different vaccine-associated clades, likely displaying differing antigenic properties. Some of the spreading reassortants remained confined to certain geographical regions, while others, sharing common properties in amino acid positions of the HA, NA, and PB2 segments, were found throughout the world. CONCLUSIONS Detailed surveillance of seasonal influenza reassortment patterns and variant properties may provide unique information needed for prediction of spread and construction of future influenza vaccines.
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Affiliation(s)
| | | | - Tao Li
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Anthony W Hawksworth
- Operational Infectious Diseases Directorate, Naval Health Research Center, San Diego, CA, USA
| | - Gary T Brice
- Operational Infectious Diseases Directorate, Naval Health Research Center, San Diego, CA, USA
| | - Patrick J Blair
- Operational Infectious Diseases Directorate, Naval Health Research Center, San Diego, CA, USA
| | | | | | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - In-Kyu Yoon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Present Address: International Vaccine Institute, Seoul, Republic of Korea
| | - Leslie D Edwards
- Office of Medical Services, US Department of State, Washington, DC, USA
| | - Robert Kuschner
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiaoxu Lin
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Jiménez-Bluhm P, Karlsson EA, Ciuoderis KA, Cortez V, Marvin SA, Hamilton-West C, Schultz-Cherry S, Osorio JE. Avian H11 influenza virus isolated from domestic poultry in a Colombian live animal market. Emerg Microbes Infect 2016; 5:e121. [PMID: 27924808 PMCID: PMC5180366 DOI: 10.1038/emi.2016.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 01/29/2023]
Abstract
Live animal markets (LAMs) are an essential source of food and trade in Latin American countries; however, they can also serve as ‘hotbeds' for the emergence and potential spillover of avian influenza viruses (AIV). Despite extensive knowledge of AIV in Asian LAMs, little is known about the prevalence South American LAMs. To fill this gap in knowledge, active surveillance was carried out at the major LAM in Medellin, Colombia between February and September 2015. During this period, overall prevalence in the market was 2.67% and a North American origin H11N2 AIV most similar to a virus isolated from Chilean shorebirds asymptomatically spread through multiple bird species in the market resulting in 17.0% positivity at peak of infection. Phenotypically, the H11 viruses displayed no known molecular markers associated with increased virulence in birds or mammals, had α2,3-sialic acid binding preference, and caused minimal replication in vitro and little morbidity in vivo. However, the Colombian H11N2 virus replicated and transmitted effectively in chickens explaining the spread throughout the market. Genetic similarity to H11 viruses isolated from North and South American shorebirds suggest that the LAM occurrence may have resulted from a wild bird to domestic poultry spillover event. The ability to spread in domestic poultry as well as potential for human infection by H11 viruses highlight the need for enhanced AIV surveillance in South America in both avian species and humans.
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Affiliation(s)
- Pedro Jiménez-Bluhm
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erik A Karlsson
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Karl A Ciuoderis
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Valerie Cortez
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shauna A Marvin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christopher Hamilton-West
- Faculty of Veterinary Science, Department of Preventive Medicine, University of Chile, Santiago 8820808, Chile
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jorge E Osorio
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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213
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Chen H, Zhou X, Zheng J, Kwoh CK. Rules of co-occurring mutations characterize the antigenic evolution of human influenza A/H3N2, A/H1N1 and B viruses. BMC Med Genomics 2016; 9:69. [PMID: 28117657 PMCID: PMC5260787 DOI: 10.1186/s12920-016-0230-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The human influenza viruses undergo rapid evolution (especially in hemagglutinin (HA), a glycoprotein on the surface of the virus), which enables the virus population to constantly evade the human immune system. Therefore, the vaccine has to be updated every year to stay effective. There is a need to characterize the evolution of influenza viruses for better selection of vaccine candidates and the prediction of pandemic strains. Studies have shown that the influenza hemagglutinin evolution is driven by the simultaneous mutations at antigenic sites. Here, we analyze simultaneous or co-occurring mutations in the HA protein of human influenza A/H3N2, A/H1N1 and B viruses to predict potential mutations, characterizing the antigenic evolution. METHODS We obtain the rules of mutation co-occurrence using association rule mining after extracting HA1 sequences and detect co-mutation sites under strong selective pressure. Then we predict the potential drifts with specific mutations of the viruses based on the rules and compare the results with the "observed" mutations in different years. RESULTS The sites under frequent mutations are in antigenic regions (epitopes) or receptor binding sites. CONCLUSIONS Our study demonstrates the co-occurring site mutations obtained by rule mining can capture the evolution of influenza viruses, and confirms that cooperative interactions among sites of HA1 protein drive the influenza antigenic evolution.
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Affiliation(s)
- Haifen Chen
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore
| | - Xinrui Zhou
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Biopolis, 138672, Singapore, Singapore
| | - Chee-Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore, Singapore.
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214
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Genesis, Evolution and Prevalence of H5N6 Avian Influenza Viruses in China. Cell Host Microbe 2016; 20:810-821. [PMID: 27916476 DOI: 10.1016/j.chom.2016.10.022] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/27/2016] [Accepted: 10/28/2016] [Indexed: 12/30/2022]
Abstract
Constant surveillance of live poultry markets (LPMs) is currently the best way to predict and identify emerging avian influenza viruses (AIVs) that pose a potential threat to public health. Through surveillance of LPMs from 16 provinces and municipalities in China during 2014-2016, we identified 3,174 AIV-positive samples and isolated and sequenced 1,135 AIVs covering 31 subtypes. Our analysis shows that H5N6 has replaced H5N1 as one of the dominant AIV subtypes in southern China, especially in ducks. Phylogenetic analysis reveals that H5N6 arose from reassortments of H5 and H6N6 viruses, with the hemagglutinin and neuraminidase combinations being strongly lineage specific. H5N6 viruses constitute at least 34 distinct genotypes derived from various evolutionary pathways. Notably, genotype G1.2 virus, with internal genes from the chicken H9N2/H7N9 gene pool, was responsible for at least five human H5N6 infections. Our findings highlight H5N6 AIVs as potential threats to public health and agriculture.
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215
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Hatcher EL, Zhdanov SA, Bao Y, Blinkova O, Nawrocki EP, Ostapchuck Y, Schäffer AA, Brister JR. Virus Variation Resource - improved response to emergent viral outbreaks. Nucleic Acids Res 2016; 45:D482-D490. [PMID: 27899678 PMCID: PMC5210549 DOI: 10.1093/nar/gkw1065] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 10/28/2016] [Indexed: 02/01/2023] Open
Abstract
The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can select sequences based on standardized gene, protein and metadata terms. Once sequences are selected, a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety of user directed activities. This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource.
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Affiliation(s)
- Eneida L Hatcher
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sergey A Zhdanov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yiming Bao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri Ostapchuck
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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216
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Biological characterization of highly pathogenic avian influenza H5N1 viruses that infected humans in Egypt in 2014-2015. Arch Virol 2016; 162:687-700. [PMID: 27864633 DOI: 10.1007/s00705-016-3137-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/26/2016] [Indexed: 01/25/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 influenza viruses emerged as a human pathogen in 1997 with expected potential to undergo sustained human-to-human transmission and pandemic viral spread. HPAI H5N1 is endemic in Egyptian poultry and has caused sporadic human infection. The first outbreak in early 2006 was caused by clade 2.2 viruses that rapidly evolved genetically and antigenically. A sharp increase in the number of human cases was reported in Egypt in the 2014/2015 season. In this study, we analyzed and characterized three isolates of HPAI H5N1 viruses isolated from infected humans in Egypt in 2014/2015. Phylogenetic analysis demonstrated that the nucleotide sequences of eight segments of the three isolates were clustered with those of members of clade 2.2.1.2. We also found that the human isolates from 2014/2015 had a slight, non-significant difference in their affinity for human-like sialic acid receptors. In contrast, they showed significant differences in their replication kinetics in MDCK, MDCK-SIAT, and A549 cells as well as in embryonated chicken eggs. An antiviral bioassay study revealed that all of the isolates were susceptible to amantadine. Therefore, further investigation and monitoring is required to correlate the genetic and/or antigenic changes of the emerging HPAI H5N1 viruses with possible alteration in their characteristics and their potential to become a further threat to public health.
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217
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Isakova-Sivak I, Korenkov D, Smolonogina T, Tretiak T, Donina S, Rekstin A, Naykhin A, Shcherbik S, Pearce N, Chen LM, Bousse T, Rudenko L. Comparative studies of infectivity, immunogenicity and cross-protective efficacy of live attenuated influenza vaccines containing nucleoprotein from cold-adapted or wild-type influenza virus in a mouse model. Virology 2016; 500:209-217. [PMID: 27829176 DOI: 10.1016/j.virol.2016.10.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/23/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
This study sought to improve an existing live attenuated influenza vaccine (LAIV) by including nucleoprotein (NP) from wild-type virus rather than master donor virus (MDV). H7N9 LAIV reassortants with 6:2 (NP from MDV) and 5:3 (NP from wild-type virus) genome compositions were compared with regard to their growth characteristics, induction of humoral and cellular immune responses in mice, and ability to protect mice against homologous and heterologous challenge viruses. Although, in general, the 6:2 reassortant induced greater cell-mediated immunity in C57BL6 mice than the 5:3 vaccine, mice immunized with the 5:3 LAIV were better protected against heterologous challenge. The 5:3 LAIV-induced CTLs also had better in vivo killing activity against target cells loaded with the NP366 epitope of recent influenza viruses. Modification of the genome of reassortant vaccine viruses by incorporating the NP gene from wild-type viruses represents a simple strategy to improve the immunogenicity and cross-protection of influenza vaccines.
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Affiliation(s)
| | - Daniil Korenkov
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | | | - Tatiana Tretiak
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Svetlana Donina
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Andrey Rekstin
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Anatoly Naykhin
- Institute of Experimental Medicine, Saint Petersburg, Russia
| | | | - Nicholas Pearce
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Li-Mei Chen
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tatiana Bousse
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Larisa Rudenko
- Institute of Experimental Medicine, Saint Petersburg, Russia
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218
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Sheikh QM, Gatherer D, Reche PA, Flower DR. Towards the knowledge-based design of universal influenza epitope ensemble vaccines. Bioinformatics 2016; 32:3233-3239. [PMID: 27402904 PMCID: PMC5079473 DOI: 10.1093/bioinformatics/btw399] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/14/2016] [Accepted: 06/18/2016] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. RESULTS To exemplify our approach we designed two epitope ensemble vaccines comprising highly conserved and experimentally verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96 and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97 and 88% coverage of observed subtypes. AVAILABILITY AND IMPLEMENTATION http://imed.med.ucm.es/Tools/episopt.html CONTACT: d.r.flower@aston.ac.uk.
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Affiliation(s)
- Qamar M Sheikh
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Derek Gatherer
- Division of Biomedical & Life Sciences, Faculty of Health & Medicine, Lancaster University, Lancaster LA1 4YW, UK
| | - Pedro A Reche
- Facultad de Medicina, Departamento de Microbiologia I, Universidad Complutense de Madrid, Madrid, Spain
| | - Darren R Flower
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
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219
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Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw130. [PMID: 27694207 PMCID: PMC5045858 DOI: 10.1093/database/baw130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
Abstract
The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated. The 3DFlu database contains well annotated HA representatives: 1192 models and 263 crystallographic structures. The relations between these proteins are defined using different metrics and are visualized as a network in the provided web interface. Moreover structural and sequence comparison of the proteins can be explored. Metadata information (e.g. protein identifier, IVA strain, year and location of infection) can enhance the exploration of the presented data. With our database researchers gain a useful tool for the exploration of high quality HA models, viewing and comparing changes in the HA viral subtypes at several information levels (sequence, structure, ESP). The complete and integrated view of those relations might be useful to determine the efficiency of transmission, pathogenicity and for the investigation of evolutionary tendencies of the influenza virus. Database URL: http://nucleus3d.cent.uw.edu.pl/influenza
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Affiliation(s)
- Giovanni Mazzocco
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Migdał
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Jan P Radomski
- Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
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220
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Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochem J 2016; 473:4327-4348. [PMID: 27694388 DOI: 10.1042/bcj20160651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.
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221
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Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity. J Virol 2016; 90:9263-84. [PMID: 27489273 PMCID: PMC5044859 DOI: 10.1128/jvi.01205-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Two alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types. Exemplar reassortant viruses also replicated to similar titers in mice, although mice infected with viruses with the avian virus-derived segment 8s had reduced weight loss compared to that achieved in mice infected with the A/Puerto Rico/8/1934 (H1N1) parent. In vitro, the viruses coped similarly with type I interferons. Temporal proteomics analysis of cellular responses to infection showed that the avian virus-derived NS segments provoked lower levels of expression of interferon-stimulated genes in cells than wild type-derived NS segments. Thus, neither the A nor the B allele of avian virus-derived NS segments necessarily attenuates virus replication in a mammalian host, although the alleles can attenuate disease. Phylogenetic analyses identified 32 independent incursions of an avian virus-derived A allele into mammals, whereas 6 introductions of a B allele were identified. However, A-allele isolates from birds outnumbered B-allele isolates, and the relative rates of Aves-to-Mammalia transmission were not significantly different. We conclude that while the introduction of an avian virus segment 8 into mammals is a relatively rare event, the dogma of the B allele being especially restricted is misleading, with implications in the assessment of the pandemic potential of avian influenza viruses. IMPORTANCE Influenza A virus (IAV) can adapt to poultry and mammalian species, inflicting a great socioeconomic burden on farming and health care sectors. Host adaptation likely involves multiple viral factors. Here, we investigated the role of IAV segment 8. Segment 8 has evolved into two distinct clades: the A and B alleles. The B-allele genes have previously been suggested to be restricted to avian virus species. We introduced a selection of avian virus A- and B-allele segment 8s into human H1N1 and H3N2 virus backgrounds and found that these reassortant viruses were fully competent in mammalian host systems. We also analyzed the currently available public data on the segment 8 gene distribution and found surprisingly little evidence for specific avian host restriction of the B-clade segment. We conclude that B-allele segment 8 genes are, in fact, capable of supporting infection in mammals and that they should be considered during the assessment of the pandemic risk of zoonotic influenza A viruses.
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222
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Romero-Beltran L, Baker SF, Puerto-Solís M, González-Losa R, Conde-Ferraez L, Alvarez-Sánchez LC, Martínez-Sobrido L, Ayora-Talavera G. Mutations at highly conserved residues in influenza A(H1N1)pdm09 virus affect neuraminidase activity. Virus Res 2016; 225:1-9. [PMID: 27596738 DOI: 10.1016/j.virusres.2016.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/17/2016] [Accepted: 09/02/2016] [Indexed: 01/16/2023]
Abstract
Influenza virus neuraminidase (NA) plays a pivotal role during viral growth since its sialidase activity allows the efficient release of nascent virions from infected cells. Consequently, mutations in the NA catalytic site affecting sialic acid (SA) cleavage may influence the biological properties of influenza viruses. This study reports two amino acid substitutions (N386K and P431S) in the NA of the influenza A(H1N1)pdm09 virus that emerged in 2009 in Mexico. The NA sialidase activity to cleave SA-like substrates, and viral growth were examined and the mutant viruses had various deficiencies. NA mutations N386K and P431S together or separately, and in the presence or absence of H275Y were further evaluated using recombinant influenza A/California/04/2009 (pH1N1) viruses containing single, double, or triple mutations. Viral growth was reduced in the presence of mutation P431S alone or combined with N386K and/or H275Y. Substrates hydrolysis was reduced when recombinant pH1N1 viruses were analyzed by NA inhibitory assays. Moreover, elution assays with guinea pig red blood cells indicated an unbalanced hemagglutinin (HA):NA functionality. Altogether, our data underline the functional significance of mutations at highly conserved sites in influenza virus NA glycoprotein and the occurrence of permissive mutations to compensate virus viability in vitro.
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Affiliation(s)
| | - Steven F Baker
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | | | | | | | - Leidi C Alvarez-Sánchez
- Laboratorio de Virología, Universidad Autonoma de Yucatan, Mexico; Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, USA
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223
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Broad Spectrum Anti-Influenza Agents by Inhibiting Self-Association of Matrix Protein 1. Sci Rep 2016; 6:32340. [PMID: 27573445 PMCID: PMC5004101 DOI: 10.1038/srep32340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/02/2016] [Indexed: 02/04/2023] Open
Abstract
The matrix protein 1 (M1) of influenza A virus (IAV) exists as a three-dimensional oligomeric structure in mature virions with high sequence conservation across different IAV subtypes, which makes it a potential broad spectrum antiviral target. We hypothesized that impairing self-association of M1 through a small molecule 'wedge', which avidly binds to an M1-M1 interface, would result in a completely new class of anti-influenza agents. To establish this proof-of-principle, we performed virtual screening on a library of >70,000 commercially available small molecules that resulted in several plausible 'wedges'. Biophysical studies showed that the best molecule bound the M1 protein potently and weakened M1-M1 self-association. Most importantly, the agent reduced the thickness of the M1 layer in mature virions and inhibited in ovo propagation of multiple IAV strains including H1N1, pandemic H1N1, H3N2 and H5N1, which supports the "wedge" hypothesis. These results demonstrate that M1 is a promising druggable target for the discovery of a completely new line of broad spectrum anti-IAV agents.
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224
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Incorporating structure context of HA protein to improve antigenicity calculation for influenza virus A/H3N2. Sci Rep 2016; 6:31156. [PMID: 27498613 PMCID: PMC4976332 DOI: 10.1038/srep31156] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/11/2016] [Indexed: 11/25/2022] Open
Abstract
The rapid and consistent mutation of influenza requires frequent evaluation of antigenicity variation among newly emerged strains, during which several in-silico methods have been reported to facilitate the assays. In this paper, we designed a structure-based antigenicity scoring model instead of those sequence-based previously published. Protein structural context was adopted to derive the antigenicity-dominant positions, as well as the physic-chemical change of local micro-environment in correlation with antigenicity change. Then a position specific scoring matrix (PSSM) profile and local environmental change over above positions were integrated to predict the antigenicity variance. Independent testing showed a high accuracy of 0.875, and sensitivity of 0.986, with a significant ability to discover antigenic-escaping strains. When applying this model to the historical data, global and regional antigenic drift events can be successfully detected. Furthermore, two well-known vaccine failure events were clearly suggested. Therefore, this structure-context model may be particularly useful to identify those to-be-failed vaccine strains, in addition to suggest potential new vaccine strains.
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225
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Kim SM, Kim YI, Pascua PNQ, Choi YK. Avian Influenza A Viruses: Evolution and Zoonotic Infection. Semin Respir Crit Care Med 2016; 37:501-11. [PMID: 27486732 PMCID: PMC7171714 DOI: 10.1055/s-0036-1584953] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although efficient human-to-human transmission of avian influenza virus has yet to be seen, in the past two decades avian-to-human transmission of influenza A viruses has been reported. Influenza A/H5N1, in particular, has repeatedly caused human infections associated with high mortality, and since 1998 the virus has evolved into many clades of variants with significant antigenic diversity. In 2013, three (A/H7N9, A/H6N1, and A/H10N8) novel avian influenza viruses (AIVs) breached the animal-human host species barrier in Asia. In humans, roughly 35% of A/H7N9-infected patients succumbed to the zoonotic infection, and two of three A/H10N8 human infections were also lethal; however, neither of these viruses cause influenza-like symptoms in poultry. While most of these cases were associated with direct contact with infected poultry, some involved sustained human-to-human transmission. Thus, these events elicited concern regarding potential AIV pandemics. This article reviews the human incursions associated with AIV variants and the potential role of pigs as an intermediate host that may hasten AIV evolution. In addition, we discuss the known influenza A virus virulence and transmission factors and their evaluation in animal models. With the growing number of human AIV infections, constant vigilance for the emergence of novel viruses is of utmost importance. In addition, careful characterization and pathobiological assessment of these novel variants will help to identify strains of particular concern for future pandemics.
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Affiliation(s)
- Se Mi Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Young-Il Kim
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Philippe Noriel Q Pascua
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
| | - Young Ki Choi
- Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
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226
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Kim K, Kim Y. Population genetic processes affecting the mode of selective sweeps and effective population size in influenza virus H3N2. BMC Evol Biol 2016; 16:156. [PMID: 27487769 PMCID: PMC4972962 DOI: 10.1186/s12862-016-0727-8] [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] [Received: 02/22/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022] Open
Abstract
Background Human influenza virus A/H3N2 undergoes rapid adaptive evolution in response to host immunity. Positively selected amino acid substitutions have been detected mainly in the hemagglutinin (HA) segment. The genealogical tree of HA sequences sampled over several decades comprises a long trunk and short side branches, which indicates small effective population size. Various studies have reproduced this unique genealogical structure by modeling recurrent positive selection. However, it has not been clearly demonstrated whether recurrent selective sweeps alone can explain the limited level of genetic diversity observed in the HA of H3N2. In addition, the variation-reducing impacts of other evolutionary processes – background selection and complex demography – relative to that of positive selection have never been explicitly evaluated. Results In this paper, using computer simulation of a viral population evolving under recurrent selective sweeps we demonstrate that positive selection alone, if it occurs at a rate estimated by previous studies, cannot lead to such a small effective population size. Genetic hitchhiking fails to completely wipe out pre-existing variation because soft, rather than hard, selective sweeps prevail under realistic parameters of mutation rate and population size. We find that antigenic-cluster-transition substitutions in HA occur as hard sweeps. This indicates that the effective population size under which those mutations arise must be much smaller than the actual population size due to other evolutionary forces before selective sweeps further reduce it. We thus examine the effects of background selection and metapopulation dynamics in reducing the effective population size, using parameter values that reproduce other aspects of molecular evolution in H3N2. When either process is incorporated in recurrent selective sweep simulation, selective sweeps are mostly hard and the observed level of synonymous diversity is obtained with large census population size. Conclusions Background selection and metapopulation dynamics have greater variation reducing power than recurrent positive selection under realistic parameters in H3N2. Therefore, these evolutionary processes are likely to play crucial roles in reducing the effective population size of H3N2 viruses and thus explaining the characteristic shape of H3N2 genealogy. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0727-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kangchon Kim
- Interdisciplinary Program of EcoCreative, Ewha Womans University, Ewhayeodae-gil 52, Seodaemun-gu, Seoul, 120-750, South Korea
| | - Yuseob Kim
- Interdisciplinary Program of EcoCreative, Ewha Womans University, Ewhayeodae-gil 52, Seodaemun-gu, Seoul, 120-750, South Korea. .,Department of Life Sciences, Ewha Womans University, Ewhayeodae-gil 52, Seodaemun-gu, Seoul, 120-750, South Korea.
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227
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Khaliq Z, Leijon M, Belák S, Komorowski J. Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes. BMC Genomics 2016; 17:529. [PMID: 27473048 PMCID: PMC4966792 DOI: 10.1186/s12864-016-2919-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 07/07/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The underlying strategies used by influenza A viruses (IAVs) to adapt to new hosts while crossing the species barrier are complex and yet to be understood completely. Several studies have been published identifying singular genomic signatures that indicate such a host switch. The complexity of the problem suggested that in addition to the singular signatures, there might be a combinatorial use of such genomic features, in nature, defining adaptation to hosts. RESULTS We used computational rule-based modeling to identify combinatorial sets of interacting amino acid (aa) residues in 12 proteins of IAVs of H1N1 and H3N2 subtypes. We built highly accurate rule-based models for each protein that could differentiate between viral aa sequences coming from avian and human hosts. We found 68 host-specific combinations of aa residues, potentially associated to host adaptation on HA, M1, M2, NP, NS1, NEP, PA, PA-X, PB1 and PB2 proteins of the H1N1 subtype and 24 on M1, M2, NEP, PB1 and PB2 proteins of the H3N2 subtypes. In addition to these combinations, we found 132 novel singular aa signatures distributed among all proteins, including the newly discovered PA-X protein, of both subtypes. We showed that HA, NA, NP, NS1, NEP, PA-X and PA proteins of the H1N1 subtype carry H1N1-specific and HA, NA, PA-X, PA, PB1-F2 and PB1 of the H3N2 subtype carry H3N2-specific signatures. M1, M2, PB1-F2, PB1 and PB2 of H1N1 subtype, in addition to H1N1 signatures, also carry H3N2 signatures. Similarly M1, M2, NP, NS1, NEP and PB2 of H3N2 subtype were shown to carry both H3N2 and H1N1 host-specific signatures (HSSs). CONCLUSIONS To sum it up, we computationally constructed simple IF-THEN rule-based models that could distinguish between aa sequences of avian and human IAVs. From the rules we identified HSSs having a potential to affect the adaptation to specific hosts. The identification of combinatorial HSSs suggests that the process of adaptation of IAVs to a new host is more complex than previously suggested. The present study provides a basis for further detailed studies with the aim to elucidate the molecular mechanisms providing the foundation for the adaptation process.
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Affiliation(s)
- Zeeshan Khaliq
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Mikael Leijon
- Department of Virology, Parasitology and Immunobiology (VIP), National Veterinary Institute (SVA), Uppsala, Sweden.,OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden
| | - Sándor Belák
- OIE Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine, Ulls väg 2B and 26, SE-756 89, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health (BVF), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Science for Life Laboratory, Uppsala University, SE-751 24, Uppsala, Sweden. .,Institute of Computer Science, Polish Academy of Sciences, 01-248, Warszawa, Poland.
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228
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Prediction of influenza B vaccine effectiveness from sequence data. Vaccine 2016; 34:4610-4617. [PMID: 27473305 DOI: 10.1016/j.vaccine.2016.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 07/01/2016] [Accepted: 07/12/2016] [Indexed: 11/22/2022]
Abstract
Influenza is a contagious respiratory illness that causes significant human morbidity and mortality, affecting 5-15% of the population in a typical epidemic season. Human influenza epidemics are caused by types A and B, with roughly 25% of human cases due to influenza B. Influenza B is a single-stranded RNA virus with a high mutation rate, and both prior immune history and vaccination put significant pressure on the virus to evolve. Due to the high rate of viral evolution, the influenza B vaccine component of the annual influenza vaccine is updated, roughly every other year in recent years. To predict when an update to the vaccine is needed, an estimate of expected vaccine effectiveness against a range of viral strains is required. We here introduce a method to measure antigenic distance between the influenza B vaccine and circulating viral strains. The measure correlates well with effectiveness of the influenza B component of the annual vaccine in humans between 1979 and 2014. We discuss how this measure of antigenic distance may be used in the context of annual influenza vaccine design and prediction of vaccine effectiveness.
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229
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Gutiérrez AH, Loving C, Moise L, Terry FE, Brockmeier SL, Hughes HR, Martin WD, De Groot AS. In Vivo Validation of Predicted and Conserved T Cell Epitopes in a Swine Influenza Model. PLoS One 2016; 11:e0159237. [PMID: 27411061 PMCID: PMC4943726 DOI: 10.1371/journal.pone.0159237] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/29/2016] [Indexed: 01/10/2023] Open
Abstract
Swine influenza is a highly contagious respiratory viral infection in pigs that is responsible for significant financial losses to pig farmers annually. Current measures to protect herds from infection include: inactivated whole-virus vaccines, subunit vaccines, and alpha replicon-based vaccines. As is true for influenza vaccines for humans, these strategies do not provide broad protection against the diverse strains of influenza A virus (IAV) currently circulating in U.S. swine. Improved approaches to developing swine influenza vaccines are needed. Here, we used immunoinformatics tools to identify class I and II T cell epitopes highly conserved in seven representative strains of IAV in U.S. swine and predicted to bind to Swine Leukocyte Antigen (SLA) alleles prevalent in commercial swine. Epitope-specific interferon-gamma (IFNγ) recall responses to pooled peptides and whole virus were detected in pigs immunized with multi-epitope plasmid DNA vaccines encoding strings of class I and II putative epitopes. In a retrospective analysis of the IFNγ responses to individual peptides compared to predictions specific to the SLA alleles of cohort pigs, we evaluated the predictive performance of PigMatrix and demonstrated its ability to distinguish non-immunogenic from immunogenic peptides and to identify promiscuous class II epitopes. Overall, this study confirms the capacity of PigMatrix to predict immunogenic T cell epitopes and demonstrate its potential for use in the design of epitope-driven vaccines for swine. Additional studies that match the SLA haplotype of animals with the study epitopes will be required to evaluate the degree of immune protection conferred by epitope-driven DNA vaccines in pigs.
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Affiliation(s)
- Andres H. Gutiérrez
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, United States of America
| | - Crystal Loving
- Virus and Prion Diseases Research Unit, NADC, USDA ARS, Ames, IA, United States of America
| | - Leonard Moise
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, United States of America
- EpiVax Inc., Providence, RI, United States of America
| | | | - Susan L. Brockmeier
- Virus and Prion Diseases Research Unit, NADC, USDA ARS, Ames, IA, United States of America
| | - Holly R. Hughes
- Virus and Prion Diseases Research Unit, NADC, USDA ARS, Ames, IA, United States of America
| | | | - Anne S. De Groot
- Institute for Immunology and Informatics, Department of Cell and Molecular Biology, University of Rhode Island, Providence, RI, United States of America
- EpiVax Inc., Providence, RI, United States of America
- * E-mail:
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230
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Kanrai P, Mostafa A, Madhugiri R, Lechner M, Wilk E, Schughart K, Ylösmäki L, Saksela K, Ziebuhr J, Pleschka S. Identification of specific residues in avian influenza A virus NS1 that enhance viral replication and pathogenicity in mammalian systems. J Gen Virol 2016; 97:2135-2148. [PMID: 27405649 DOI: 10.1099/jgv.0.000542] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reassortment of their segmented genomes allows influenza A viruses (IAV) to gain new characteristics, which potentially enable them to cross the species barrier and infect new hosts. Improved replication was observed for reassortants of the strictly avian IAV A/FPV/Rostock/34 (FPV, H7N1) containing the NS segment from A/Goose/Guangdong/1/1996 (GD, H5N1), but not for reassortants containing the NS segment of A/Mallard/NL/12/2000 (MA, H7N3). The NS1 of GD and MA differ only in 8 aa positions. Here, we show that efficient replication of FPV-NSMA-derived mutants was linked to the presence of a single substitution (D74N) and more prominently to a triple substitution (P3S+R41K+D74N) in the NS1MA protein. The substitution(s) led to (i) increased virus titres, (ii) larger plaque sizes and (iii) increased levels and faster kinetics of viral mRNA and protein accumulation in mammalian cells. Interestingly, the NS1 substitutions did not affect viral growth characteristics in avian cells. Furthermore, we show that an FPV mutant with N74 in the NS1 (already possessing S3+K41) is able to replicate and cause disease in mice, demonstrating a key role of NS1 in the adaptation of avian IAV to mammalian hosts. Our data suggest that (i) adaptation to mammalian hosts does not necessarily compromise replication in the natural (avian) host and (ii) very few genetic changes may pave the way for zoonotic transmission. The study reinforces the need for close surveillance and characterization of circulating avian IAV to identify genetic signatures that indicate a potential risk for efficient transmission of avian strains to mammalian hosts.
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Affiliation(s)
- Pumaree Kanrai
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Ahmed Mostafa
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
- Center of Scientific Excellence for Influenza Viruses, National Research Center (NRC), 12311 Dokki, Giza, Egypt
| | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Marcus Lechner
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Esther Wilk
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Klaus Schughart
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Leena Ylösmäki
- Department of Virology, University of Helsinki, PO Box 21 (Haartmaninkatu 3) 00014, Finland
| | - Kalle Saksela
- Department of Virology, University of Helsinki, PO Box 21 (Haartmaninkatu 3) 00014, Finland
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
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231
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Kobayashi Y, Dadonaite B, van Doremalen N, Suzuki Y, Barclay WS, Pybus OG. Computational and molecular analysis of conserved influenza A virus RNA secondary structures involved in infectious virion production. RNA Biol 2016; 13:883-94. [PMID: 27399914 DOI: 10.1080/15476286.2016.1208331] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
As well as encoding viral proteins, genomes of RNA viruses harbor secondary and tertiary RNA structures that have been associated with functions essential for successful replication and propagation. Here, we identified stem-loop structures that are extremely conserved among 1,884 M segment sequences of influenza A virus (IAV) strains from various subtypes and host species using computational and evolutionary methods. These structures were predicted within the 3' and 5' ends of the coding regions of M1 and M2, respectively, where packaging signals have been previously proposed to exist. These signals are thought to be required for the incorporation of a single copy of 8 different negative-strand RNA segments (vRNAs) into an IAV particle. To directly test the functionality of conserved stem-loop structures, we undertook reverse genetic experiments to introduce synonymous mutations designed to disrupt secondary structures predicted at 3 locations and found them to attenuate infectivity of recombinant virus. In one mutant, predicted to disrupt stem loop structure at nucleotide positions 219-240, attenuation was more evident at increased temperature and was accompanied by an increase in the production of defective virus particles. Our results suggest that the conserved secondary structures predicted in the M segment are involved in the production of infectious viral particles during IAV replication.
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Affiliation(s)
- Yuki Kobayashi
- a Nihon University Veterinary Research Center , Fujisawa , Kanagawa , Japan.,b Department of Zoology , University of Oxford , Oxford , UK
| | - Bernadeta Dadonaite
- c Section of Virology, Department of Medicine, Imperial College London , London , UK
| | - Neeltje van Doremalen
- c Section of Virology, Department of Medicine, Imperial College London , London , UK.,d Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Hamilton , MT , USA
| | - Yoshiyuki Suzuki
- e Graduate School of Natural Sciences, Nagoya City University , Nagoya , Japan
| | - Wendy S Barclay
- c Section of Virology, Department of Medicine, Imperial College London , London , UK
| | - Oliver G Pybus
- b Department of Zoology , University of Oxford , Oxford , UK
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232
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Ramey AM, Kim Torchetti M, Poulson RL, Carter D, Reeves AB, Link P, Walther P, Lebarbenchon C, Stallknecht DE. Evidence for wild waterfowl origin of H7N3 influenza A virus detected in captive-reared New Jersey pheasants. Arch Virol 2016; 161:2519-26. [PMID: 27372454 DOI: 10.1007/s00705-016-2947-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
In August 2014, a low-pathogenic H7N3 influenza A virus was isolated from pheasants at a New Jersey gamebird farm and hunting preserve. In this study, we use phylogenetic analyses and calculations of genetic similarity to gain inference into the genetic ancestry of this virus and to identify potential routes of transmission. Results of maximum-likelihood (ML) and maximum-clade-credibility (MCC) phylogenetic analyses provide evidence that A/pheasant/New Jersey/26996-2/2014 (H7N3) had closely related H7 hemagglutinin (HA) and N3 neuraminidase (NA) gene segments as compared to influenza A viruses circulating among wild waterfowl in the central and eastern USA. The estimated time of the most recent common ancestry (TMRCA) between the pheasant virus and those most closely related from wild waterfowl was early 2013 for both the H7 HA and N3 NA gene segments. None of the viruses from waterfowl identified as being most closely related to A/pheasant/New Jersey/26996-2/2014 at the HA and NA gene segments in ML and MCC phylogenetic analyses shared ≥99 % nucleotide sequence identity for internal gene segment sequences. This result indicates that specific viral strains identified in this study as being closely related to the HA and NA gene segments of A/pheasant/New Jersey/26996-2/2014 were not the direct predecessors of the etiological agent identified during the New Jersey outbreak. However, the recent common ancestry of the H7 and N3 gene segments of waterfowl-origin viruses and the virus isolated from pheasants suggests that viral diversity maintained in wild waterfowl likely played an important role in the emergence of A/pheasant/New Jersey/26996-2/2014.
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Affiliation(s)
- Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska, 99508, USA.
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, P.O. Box 844, Ames, Iowa, 50010, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
| | - Deborah Carter
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
| | - Andrew B Reeves
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska, 99508, USA
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, 2000 Quail Drive, Room 436, Baton Rouge, Louisiana, 70808, USA
| | - Patrick Walther
- US Fish and Wildlife Service, Texas Chenier Plain Refuge Complex, 4017 FM 563, P.O. Box 278, Anahuac, Texas, 77514, USA
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Saint Denis, Réunion
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
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233
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McWhite CD, Meyer AG, Wilke CO. Sequence amplification via cell passaging creates spurious signals of positive adaptation in influenza virus H3N2 hemagglutinin. Virus Evol 2016; 2:vew026. [PMID: 27713835 PMCID: PMC5049878 DOI: 10.1093/ve/vew026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical influenza A virus isolates are frequently not sequenced directly. Instead, a majority of these isolates (~70% in 2015) are first subjected to passaging for amplification, most commonly in non-human cell culture. Here, we find that this passaging leaves distinct signals of adaptation, which can confound evolutionary analyses of the viral sequences. We find distinct patterns of adaptation to Madin-Darby (MDCK) and monkey cell culture absent from unpassaged hemagglutinin sequences. These patterns also dominate pooled datasets not separated by passaging type, and they increase in proportion to the number of passages performed. By contrast, MDCK-SIAT1 passaged sequences seem mostly (but not entirely) free of passaging adaptations. Contrary to previous studies, we find that using only internal branches of influenza virus phylogenetic trees is insufficient to correct for passaging artifacts. These artifacts can only be safely avoided by excluding passaged sequences entirely from subsequent analysis. We conclude that future influenza virus evolutionary analyses should appropriately control for potentially confounding effects of passaging adaptations.
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Affiliation(s)
- Claire D. McWhite
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin,
Austin, TX 78712, USA
| | - Austin G. Meyer
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Center for Computational Biology and Bioinformatics, The University of Texas
at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin,
Austin, TX 78712, USA
| | - Claus O. Wilke
- Center for Systems and Synthetic Biology and Institute for Cellular and
Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Center for Computational Biology and Bioinformatics, The University of Texas
at Austin, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas at Austin,
Austin, TX 78712, USA
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234
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Mena I, Nelson MI, Quezada-Monroy F, Dutta J, Cortes-Fernández R, Lara-Puente JH, Castro-Peralta F, Cunha LF, Trovão NS, Lozano-Dubernard B, Rambaut A, van Bakel H, García-Sastre A. Origins of the 2009 H1N1 influenza pandemic in swine in Mexico. eLife 2016; 5. [PMID: 27350259 PMCID: PMC4957980 DOI: 10.7554/elife.16777] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade. DOI:http://dx.doi.org/10.7554/eLife.16777.001 In 2009 a new influenza virus jumped from pigs to humans and spread very rapidly, causing an initial outbreak in Mexico and becoming a global pandemic in just a few months. Although the most straightforward explanation is that the virus originated in swine in Mexico, several studies suggested that this was unlikely because key genetic components of the virus had never been detected in the Americas. Determining the source of the disease is critical for predicting and preparing for future influenza pandemics. Mena, Nelson et al. sought to better characterize the genetic diversity of influenza viruses in Mexican swine by obtaining the entire genetic sequences of 58 viruses collected from swine in Mexico, including some from previously unsampled regions in central Mexico. The sequences revealed extensive diversity among the influenza viruses circulating in Mexican swine. Several viruses included genetic segments that originated from viruses from Eurasia (the landmass containing Europe and Asia) and had not previously been detected in the Americas. The new sequences contained key genetic components of the 2009 pandemic virus. Furthermore, the sequences suggest that viruses with a similar genetic composition to the 2009 pandemic virus have been circulating in pigs in central-west Mexico for more than a decade. Thus, this region is the most likely source of the virus that started the 2009 pandemic. Mena, Nelson et al. also found that the movement of viruses from Eurasia and the United States into Mexico closely follows the direction of the global trade of live swine. This highlights the critical role that animal trading plays in bringing together diverse viruses from different continents, which can then combine and generate new pandemic viruses. A potential next step is to perform experiments that investigate how well the swine viruses can replicate and pass between different animal models. Comparing the results of such experiments with the findings presented by Mena, Nelson et al. could identify factors that make the viruses more likely to spread to humans and produce a pandemic. DOI:http://dx.doi.org/10.7554/eLife.16777.002
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Affiliation(s)
- Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States
| | | | - Jayeeta Dutta
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | | | | | | | - Luis F Cunha
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Nídia S Trovão
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium
| | | | - Andrew Rambaut
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Harm van Bakel
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, United States
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235
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Yang HT, Yang H, Chiang JH, Wang SJ. Translating genomic sequences into antibody efficacy and safety against influenza toward clinical trial outcomes: a case study. Drug Discov Today 2016; 21:1664-1671. [PMID: 27319290 DOI: 10.1016/j.drudis.2016.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/26/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022]
Abstract
Antibodies (Abs) are regarded as a newly emerging form of therapeutics that can provide passive protection against influenza. Although the application of genomics in clinics has increased dramatically, the number of therapeutics available for the treatment of many diseases remains insufficient. To translate genomics into medicines, we established a computational workflow to reconstruct 3D structures of hemagglutinin [HA, antigen (Ag)] and Ab for modeling Ab-HA interactions, based on their protein sequences. This platform was capable of testing the validity of bioinformatics predictions against viral neutralization titers for four Abs: CH65, CR8020, C05, and 5J8. By considering off-target effects, CR8020, the only successful candidate in clinical trials, was prospectively identified. Our approach could facilitate the discovery of Ab drugs against infectious diseases.
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Affiliation(s)
- Hsih-Te Yang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan; Institute of Oral Medicine, National Cheng Kung University College of Medicine, Taiwan.
| | - Hong Yang
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Jung-Hsien Chiang
- Institute of Medical Informatics, Department of Computer Science and Information Engineering, National Cheng Kung University, Taiwan
| | - Shih-Jon Wang
- Department of Bioscience Technology, Chang Jung Christian University, Taiwan
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236
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Ramey AM, Reeves AB, TeSlaa JL, Nashold S, Donnelly T, Bahl J, Hall JS. Evidence for common ancestry among viruses isolated from wild birds in Beringia and highly pathogenic intercontinental reassortant H5N1 and H5N2 influenza A viruses. INFECTION GENETICS AND EVOLUTION 2016; 40:176-185. [DOI: 10.1016/j.meegid.2016.02.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/22/2016] [Accepted: 02/26/2016] [Indexed: 12/09/2022]
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237
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Vasin AV, Petrova AV, Egorov VV, Plotnikova MA, Klotchenko SA, Karpenko MN, Kiselev OI. The influenza A virus NS genome segment displays lineage-specific patterns in predicted RNA secondary structure. BMC Res Notes 2016; 9:279. [PMID: 27206548 PMCID: PMC4875733 DOI: 10.1186/s13104-016-2083-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 05/10/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Influenza A virus (IAV) is a segmented negative-sense RNA virus that causes seasonal epidemics and periodic pandemics in humans. Two regions (nucleotide positions 82-148 and 497-564) in the positive-sense RNA of the NS segment fold into a multi-branch loop or hairpin structures. RESULTS We studied 25,384 NS segment positive-sense RNA unique sequences of human and non-human IAVs in order to predict secondary RNA structures of the 82-148 and 497-564 regions using RNAfold software, and determined their host- and lineage-specific distributions. Hairpins prevailed in avian and avian-origin human IAVs, including H1N1pdm1918 and H5N1. In human and swine IAV hairpins distribution varied between evolutionary lineages. CONCLUSIONS These results suggest a possible functional role for these RNA secondary structures and the need for experimental evaluation of these structures in the influenza life cycle.
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Affiliation(s)
- A V Vasin
- Research Institute of Influenza, 197376, St-Petersburg, Russia. .,Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia.
| | - A V Petrova
- Research Institute of Influenza, 197376, St-Petersburg, Russia.,Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia
| | - V V Egorov
- Research Institute of Influenza, 197376, St-Petersburg, Russia
| | - M A Plotnikova
- Research Institute of Influenza, 197376, St-Petersburg, Russia
| | - S A Klotchenko
- Research Institute of Influenza, 197376, St-Petersburg, Russia
| | - M N Karpenko
- Peter the Great St-Petersburg Polytechnic University, 195251, St-Petersburg, Russia
| | - O I Kiselev
- Research Institute of Influenza, 197376, St-Petersburg, Russia
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238
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Bailey E, Long LP, Zhao N, Hall JS, Baroch JA, Nolting J, Senter L, Cunningham FL, Pharr GT, Hanson L, Slemons R, DeLiberto TJ, Wan XF. Antigenic Characterization of H3 Subtypes of Avian Influenza A Viruses from North America. Avian Dis 2016; 60:346-53. [PMID: 27309078 PMCID: PMC4911812 DOI: 10.1637/11086-041015-regr] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Besides humans, H3 subtypes of influenza A viruses (IAVs) can infect various animal hosts, including avian, swine, equine, canine, and sea mammal species. These H3 viruses are both antigenically and genetically diverse. Here, we characterized the antigenic diversity of contemporary H3 avian IAVs recovered from migratory birds in North America. Hemagglutination inhibition (HI) assays were performed on 37 H3 isolates of avian IAVs recovered from 2007 to 2011 using generated reference chicken sera. These isolates were recovered from samples taken in the Atlantic, Mississippi, Central, and Pacific waterfowl migration flyways. Antisera to all the tested H3 isolates cross-reacted with each other and, to a lesser extent, with those to H3 canine and H3 equine IAVs. Antigenic cartography showed that the largest antigenic distance among the 37 avian IAVs is about four units, and each unit corresponds to a 2 log 2 difference in the HI titer. However, none of the tested H3 IAVs cross-reacted with ferret sera derived from contemporary swine and human IAVs. Our results showed that the H3 avian IAVs we tested lacked significant antigenic diversity, and these viruses were antigenically different from those circulating in swine and human populations. This suggests that H3 avian IAVs in North American waterfowl are antigenically relatively stable.
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Affiliation(s)
- Elizabeth Bailey
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Li-Ping Long
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nan Zhao
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jeffrey S. Hall
- USGS National Wildlife Health Center, Madison, Wisconsin, 53711 USA
| | - John A. Baroch
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, Colorado, 80521 USA
| | - Jacqueline Nolting
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210 USA
| | - Lucy Senter
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Frederick L. Cunningham
- Mississippi Field Station, National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Mississippi State, Mississippi, 39762 USA
| | - G. Todd Pharr
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Larry Hanson
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Richard Slemons
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210 USA
| | - Thomas J. DeLiberto
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, Colorado, 80521 USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
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239
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Carter DM, Darby CA, Lefoley BC, Crevar CJ, Alefantis T, Oomen R, Anderson SF, Strugnell T, Cortés-Garcia G, Vogel TU, Parrington M, Kleanthous H, Ross TM. Design and Characterization of a Computationally Optimized Broadly Reactive Hemagglutinin Vaccine for H1N1 Influenza Viruses. J Virol 2016; 90:4720-4734. [PMID: 26912624 PMCID: PMC4836330 DOI: 10.1128/jvi.03152-15] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 02/19/2016] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED One of the challenges of developing influenza A vaccines is the diversity of antigenically distinct isolates. Previously, a novel hemagglutinin (HA) for H5N1 influenza was derived from a methodology termed computationally optimized broadly reactive antigen (COBRA). This COBRA HA elicited a broad antibody response against H5N1 isolates from different clades. We now report the development and characterization of a COBRA-based vaccine for both seasonal and pandemic H1N1 influenza virus isolates. Nine prototype H1N1 COBRA HA proteins were developed and tested in mice using a virus-like particle (VLP) format for the elicitation of broadly reactive, functional antibody responses and protection against viral challenge. These candidates were designed to recognize H1N1 viruses isolated within the last 30 years. In addition, several COBRA candidates were designed based on sequences of H1N1 viruses spanning the past 100 years, including modern pandemic H1N1 isolates. Four of the 9 H1N1 COBRA HA proteins (X1, X3, X6, and P1) had the broadest hemagglutination inhibition (HAI) activity against a panel of 17 H1N1 viruses. These vaccines were used in cocktails or prime-boost combinations. The most effective regimens that both elicited the broadest HAI response and protected mice against a pandemic H1N1 challenge were vaccines that contained the P1 COBRA VLP and either the X3 or X6 COBRA VLP vaccine. These mice had little or no detectable viral replication, comparable to that observed with a matched licensed vaccine. This is the first report describing a COBRA-based HA vaccine strategy that elicits a universal, broadly reactive, protective response against seasonal and pandemic H1N1 isolates. IMPORTANCE Universal influenza vaccine approaches have the potential to be paradigm shifting for the influenza vaccine field, with the goal of replacing the current standard of care with broadly cross-protective vaccines. We have used COBRA technology to develop an HA head-based strategy that elicits antibodies against many H1 strains that have undergone genetic drift and has potential as a "subtype universal" vaccine. Nine HA COBRA candidates were developed, and these vaccines were used alone, in cocktails or in prime-boost combinations. The most effective regimens elicited the broadest hemagglutination inhibition (HAI) response against a panel of H1N1 viruses isolated over the past 100 years. This is the first report describing a COBRA-based HA vaccine strategy that elicits a broadly reactive response against seasonal and pandemic H1N1 isolates.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Cell Line
- Disease Models, Animal
- Hemagglutination Inhibition Tests
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunization
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/ultrastructure
- Influenza Vaccines/immunology
- Influenza, Human/prevention & control
- Mice
- Models, Molecular
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/prevention & control
- Phylogeny
- Protein Binding/immunology
- Protein Conformation
- Protein Interaction Domains and Motifs
- Vaccines, Virus-Like Particle/immunology
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Affiliation(s)
- Donald M Carter
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Christopher A Darby
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Bradford C Lefoley
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
| | - Corey J Crevar
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, Florida, USA
| | | | | | | | | | | | | | | | | | - Ted M Ross
- Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA
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240
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Tambunan USF, Sipahutar FRP, Parikesit AA, Kerami D. Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions. Bioinform Biol Insights 2016; 10:27-35. [PMID: 27147821 PMCID: PMC4852757 DOI: 10.4137/bbi.s38378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/10/2016] [Accepted: 03/16/2016] [Indexed: 12/11/2022] Open
Abstract
From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Vaccine is the most effective immunologic intervention. In this study, we use the epitope-based vaccine design from hemagglutinin and neuraminidase of H5N1 Indonesian strain virus by using immunoinformatics approach in order to predict the binding of B-cell and T-cell epitopes (class I and class II human leukocyte antigen [HLA]). BCPREDS was used to predict the B-cell epitope. Propred, Propred I, netMHCpan, and netMHCIIpan were used to predict the T-cell epitope. Two B-cell epitopes of hemagglutinin candidates and one B-cell epitope of neuraminidase candidates were obtained to bind T-cell CD4(+) (class II HLA), and also five T-cell epitope hemagglutinin and four T-cell epitope neuraminidase were obtained to bind T-cell CD8(+) (class I HLA). The visualization of epitopes was done using MOE 2008.10. It shows that the binding affinity of epitope-HLA was based on minimum binding free energy (ΔG binding). Based on this result, visualization, and dynamic simulation, four hemagglutinin epitopes (MEKIVLLLA, CPYLGSPSF, KCQTPMGAI, and IGTSTLNQR) and two neuraminidase epitopes (NPNQKIITI and CYPDAGEIT) were computed as having the best binding affinity from HLA ligand. The results mentioned above are from in silico experiments and need to be validated using wet experiment.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Feimmy Ruth Pratiwi Sipahutar
- Bioinformatics Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Arli Aditya Parikesit
- Bioinformatics Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Djati Kerami
- Mathematics Computation Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
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241
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Peng Y, Yang L, Li H, Zou Y, Deng L, Wu A, Du X, Wang D, Shu Y, Jiang T. PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences. Bioinformatics 2016; 32:2526-7. [PMID: 27153622 DOI: 10.1093/bioinformatics/btw185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/01/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Timely surveillance of the antigenic dynamics of the influenza virus is critical for accurate selection of vaccine strains, which is important for effective prevention of viral spread and infection. RESULTS Here, we provide a computational platform, called PREDAC-H3, for antigenic surveillance of human influenza A(H3N2) virus based on the sequence of surface protein hemagglutinin (HA). PREDAC-H3 not only determines the antigenic variants and antigenic cluster (grouped for similar antigenicity) to which the virus belongs, based on HA sequences, but also allows visualization of the spatial distribution and temporal dynamics of antigenic clusters of viruses isolated from around the world, thus assisting in antigenic surveillance of human influenza A(H3N2) virus. AVAILABILITY AND IMPLEMENTATION It is publicly available from: http://biocloud.hnu.edu.cn/influ411/html/index.php CONTACTS : yshu@cnic.org.cn or taijiao@moon.ibp.ac.cn.
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Affiliation(s)
- Yousong Peng
- College of Biology, Hunan University, Changsha, China College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Honglei Li
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Yuanqiang Zou
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China
| | - Lizong Deng
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
| | - Aiping Wu
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
| | - Xiangjun Du
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Taijiao Jiang
- College of Biology, Hunan University, Changsha, China Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, China
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242
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Thornburg NJ, Zhang H, Bangaru S, Sapparapu G, Kose N, Lampley RM, Bombardi RG, Yu Y, Graham S, Branchizio A, Yoder SM, Rock MT, Creech CB, Edwards KM, Lee D, Li S, Wilson IA, García-Sastre A, Albrecht RA, Crowe JE. H7N9 influenza virus neutralizing antibodies that possess few somatic mutations. J Clin Invest 2016; 126:1482-94. [PMID: 26950424 PMCID: PMC4811156 DOI: 10.1172/jci85317] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/21/2016] [Indexed: 01/08/2023] Open
Abstract
Avian H7N9 influenza viruses are group 2 influenza A viruses that have been identified as the etiologic agent for a current major outbreak that began in China in 2013 and may pose a pandemic threat. Here, we examined the human H7-reactive antibody response in 75 recipients of a monovalent inactivated A/Shanghai/02/2013 H7N9 vaccine. After 2 doses of vaccine, the majority of donors had memory B cells that secreted IgGs specific for H7 HA, with dominant responses against single HA subtypes, although frequencies of H7-reactive B cells ranged widely between donors. We isolated 12 naturally occurring mAbs with low half-maximal effective concentrations for binding, 5 of which possessed neutralizing and HA-inhibiting activities. The 5 neutralizing mAbs exhibited narrow breadth of reactivity with influenza H7 strains. Epitope-mapping studies using neutralization escape mutant analysis, deuterium exchange mass spectrometry, and x-ray crystallography revealed that these neutralizing mAbs bind near the receptor-binding pocket on HA. All 5 neutralizing mAbs possessed low numbers of somatic mutations, suggesting the clones arose from naive B cells. The most potent mAb, H7.167, was tested as a prophylactic treatment in a mouse intranasal virus challenge study, and systemic administration of the mAb markedly reduced viral lung titers.
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MESH Headings
- Adult
- Animals
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Binding Sites, Antibody/genetics
- Binding Sites, Antibody/immunology
- Epitope Mapping
- Epitopes/genetics
- Epitopes/immunology
- Female
- Humans
- Influenza A Virus, H7N9 Subtype/genetics
- Influenza A Virus, H7N9 Subtype/immunology
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Male
- Mice
- Middle Aged
- Mutation
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Affiliation(s)
- Natalie J. Thornburg
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
| | - Heng Zhang
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | | | - Gopal Sapparapu
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
| | | | | | | | | | | | | | - Sandra M. Yoder
- The Vanderbilt Vaccine Center and
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Michael T. Rock
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - C. Buddy Creech
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Kathryn M. Edwards
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Vaccine Research Program, Vanderbilt University, Nashville, Tennessee, USA
| | - David Lee
- Department of Medicine and Biomedical Sciences Graduate Program, School of Medicine, UCSD, San Diego, California, USA
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate Program, School of Medicine, UCSD, San Diego, California, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Adolfo García-Sastre
- Department of Microbiology
- Global Health and Emerging Pathogens Institute, and
- Department of Medicine, Division of Infectious Diseases at Icahn School of Medicine at Mount Sinai (ISMMS), New York, New York, USA
| | - Randy A. Albrecht
- Department of Microbiology
- Global Health and Emerging Pathogens Institute, and
| | - James E. Crowe
- The Vanderbilt Vaccine Center and
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, USA
- Departments of Pathology, Microbiology, and Immunology, and
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243
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Timmermans A, Melendrez MC, Se Y, Chuang I, Samon N, Uthaimongkol N, Klungthong C, Manasatienkij W, Thaisomboonsuk B, Tyner SD, Rith S, Horm VS, Jarman RG, Bethell D, Chanarat N, Pavlin J, Wongstitwilairoong T, Saingam P, El BS, Fukuda MM, Touch S, Sovann L, Fernandez S, Buchy P, Chanthap L, Saunders D. Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia. PLoS One 2016; 11:e0152529. [PMID: 27028323 PMCID: PMC4814059 DOI: 10.1371/journal.pone.0152529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/15/2016] [Indexed: 01/16/2023] Open
Abstract
Little is known about circulation of influenza and other respiratory viruses in remote populations along the Thai-Cambodia border in western Cambodia. We screened 586 outpatients (median age 5, range 1–77) presenting with influenza-like-illness (ILI) at 4 sentinel sites in western Cambodia between May 2010 and December 2012. Real-time reverse transcriptase (rRT) PCR for influenza was performed on combined nasal and throat specimens followed by viral culture, antigenic analysis, antiviral susceptibility testing and full genome sequencing for phylogenetic analysis. ILI-specimens negative for influenza were cultured, followed by rRT-PCR for enterovirus and rhinovirus (EV/RV) and EV71. Influenza was found in 168 cases (29%) and occurred almost exclusively in the rainy season from June to November. Isolated influenza strains had close antigenic and phylogenetic relationships, matching vaccine and circulating strains found elsewhere in Cambodia. Influenza vaccination coverage was low (<20%). Western Cambodian H1N1(2009) isolate genomes were more closely related to 10 earlier Cambodia isolates (94.4% genome conservation) than to 13 Thai isolates (75.9% genome conservation), despite sharing the majority of the amino acid changes with the Thai references. Most genes showed signatures of purifying selection. Viral culture detected only adenovirus (5.7%) and parainfluenza virus (3.8%), while non-polio enteroviruses (10.3%) were detected among 164 culture-negative samples including coxsackievirus A4, A6, A8, A9, A12, B3, B4 and echovirus E6 and E9 using nested RT-PCR methods. A single specimen of EV71 was found. Despite proximity to Thailand, influenza epidemiology of these western Cambodian isolates followed patterns observed elsewhere in Cambodia, continuing to support current vaccine and treatment recommendations from the Cambodian National Influenza Center. Amino acid mutations at non-epitope sites, particularly hemagglutinin genes, require further investigation in light of an increasingly important role of permissive mutations in influenza virus evolution. Further research about the burden of adenovirus and non-polio enteroviruses as etiologic agents in acute respiratory infections in Cambodia is also needed.
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Affiliation(s)
- Ans Timmermans
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Melanie C. Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Youry Se
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Ilin Chuang
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nou Samon
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Nichapat Uthaimongkol
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Stuart D. Tyner
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sareth Rith
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Viseth Srey Horm
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Delia Bethell
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Nitima Chanarat
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Julie Pavlin
- Deputy Director, Armed Forces Health Surveillance Center, Silver Spring, Maryland, United States of America
| | | | - Piyaporn Saingam
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - But Sam El
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Battambang, Cambodia
| | - Mark M. Fukuda
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sok Touch
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Ly Sovann
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Stefan Fernandez
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Philippe Buchy
- Virology Department, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lon Chanthap
- Department of Immunology, Armed Forces Research Institute of Medical Sciences, Phnom Penh, Cambodia
| | - David Saunders
- Department of Immunology, US Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
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244
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Ahmed SS, Volkmuth W, Duca J, Corti L, Pallaoro M, Pezzicoli A, Karle A, Rigat F, Rappuoli R, Narasimhan V, Julkunen I, Vuorela A, Vaarala O, Nohynek H, Pasini FL, Montomoli E, Trombetta C, Adams CM, Rothbard J, Steinman L. Antibodies to influenza nucleoprotein cross-react with human hypocretin receptor 2. Sci Transl Med 2016; 7:294ra105. [PMID: 26136476 DOI: 10.1126/scitranslmed.aab2354] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The sleep disorder narcolepsy is linked to the HLA-DQB1*0602 haplotype and dysregulation of the hypocretin ligand-hypocretin receptor pathway. Narcolepsy was associated with Pandemrix vaccination (an adjuvanted, influenza pandemic vaccine) and also with infection by influenza virus during the 2009 A(H1N1) influenza pandemic. In contrast, very few cases were reported after Focetria vaccination (a differently manufactured adjuvanted influenza pandemic vaccine). We hypothesized that differences between these vaccines (which are derived from inactivated influenza viral proteins) explain the association of narcolepsy with Pandemrix-vaccinated subjects. A mimic peptide was identified from a surface-exposed region of influenza nucleoprotein A that shared protein residues in common with a fragment of the first extracellular domain of hypocretin receptor 2. A significant proportion of sera from HLA-DQB1*0602 haplotype-positive narcoleptic Finnish patients with a history of Pandemrix vaccination (vaccine-associated narcolepsy) contained antibodies to hypocretin receptor 2 compared to sera from nonnarcoleptic individuals with either 2009 A(H1N1) pandemic influenza infection or history of Focetria vaccination. Antibodies from vaccine-associated narcolepsy sera cross-reacted with both influenza nucleoprotein and hypocretin receptor 2, which was demonstrated by competitive binding using 21-mer peptide (containing the identified nucleoprotein mimic) and 55-mer recombinant peptide (first extracellular domain of hypocretin receptor 2) on cell lines expressing human hypocretin receptor 2. Mass spectrometry indicated that relative to Pandemrix, Focetria contained 72.7% less influenza nucleoprotein. In accord, no durable antibody responses to nucleoprotein were detected in sera from Focetria-vaccinated nonnarcoleptic subjects. Thus, differences in vaccine nucleoprotein content and respective immune response may explain the narcolepsy association with Pandemrix.
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Affiliation(s)
- Syed Sohail Ahmed
- Global Clinical Sciences, Novartis Vaccines Srl, Siena 53100, Italy.
| | - Wayne Volkmuth
- Informatics and Information Technology, Atreca Inc., Redwood City, CA 94063, USA
| | - José Duca
- Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lorenzo Corti
- Formulation Analytics, Novartis Vaccines Srl, Siena 53100, Italy
| | - Michele Pallaoro
- Formulation Analytics, Novartis Vaccines Srl, Siena 53100, Italy
| | | | - Anette Karle
- Integrated Biologics Profiling Unit, Novartis Pharma AG, Basel 4057, Switzerland
| | - Fabio Rigat
- Quantitative Sciences, Novartis Vaccines Srl, Siena 53100, Italy
| | | | - Vas Narasimhan
- Development, Novartis Vaccines, Cambridge, MA 02139, USA
| | - Ilkka Julkunen
- National Institute for Health and Welfare (THL), Helsinki 00300, Finland. Virology, University of Turku, Turku 20520, Finland
| | - Arja Vuorela
- National Institute for Health and Welfare (THL), Helsinki 00300, Finland
| | - Outi Vaarala
- National Institute for Health and Welfare (THL), Helsinki 00300, Finland
| | - Hanna Nohynek
- National Institute for Health and Welfare (THL), Helsinki 00300, Finland
| | - Franco Laghi Pasini
- Internal Medicine, Policlinico Santa Maria alle Scotte, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy. Medical Science, Surgery, and Neuroscience, University of Siena, Siena 53100, Italy
| | - Emanuele Montomoli
- Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy. VisMederi Srl, Siena 53100, Italy
| | - Claudia Trombetta
- Molecular and Developmental Medicine, University of Siena, Siena 53100, Italy
| | - Christopher M Adams
- Stanford University Mass Spectrometry, Stanford University School of Medicine, Palo Alto, CA 94305 USA
| | - Jonathan Rothbard
- Immunology, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Lawrence Steinman
- Neurology and Neuroscience, Stanford University School of Medicine, Stanford, CA 94305, USA.
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245
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Xue KS, Hooper KA, Ollodart AR, Dingens AS, Bloom JD. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. eLife 2016; 5:e13974. [PMID: 26978794 PMCID: PMC4805539 DOI: 10.7554/elife.13974] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/19/2016] [Indexed: 01/21/2023] Open
Abstract
RNA viruses rapidly diversify into quasispecies of related genotypes. This genetic diversity has long been known to facilitate adaptation, but recent studies have suggested that cooperation between variants might also increase population fitness. Here, we demonstrate strong cooperation between two H3N2 influenza variants that differ by a single mutation at residue 151 in neuraminidase, which normally mediates viral exit from host cells. Residue 151 is often annotated as an ambiguous amino acid in sequenced isolates, indicating mixed viral populations. We show that mixed populations grow better than either variant alone in cell culture. Pure populations of either variant generate the other through mutation and then stably maintain a mix of the two genotypes. We suggest that cooperation arises because mixed populations combine one variant's proficiency at cell entry with the other's proficiency at cell exit. Our work demonstrates a specific cooperative interaction between defined variants in a viral quasispecies.
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Affiliation(s)
- Katherine S Xue
- Department of Genome Sciences, University of Washington, Seattle, United States.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kathryn A Hooper
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Anja R Ollodart
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Adam S Dingens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Molecular and Cellular Biology Program, University of Washington, Seattle, United States
| | - Jesse D Bloom
- Department of Genome Sciences, University of Washington, Seattle, United States.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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246
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Labonté K, Aris-Brosou S. Automatic detection of rate change in large data sets with an unsupervised approach: the case of influenza viruses. Genome 2016; 59:253-62. [PMID: 26966881 DOI: 10.1139/gen-2015-0163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Influenza viruses evolve at such a high rate that vaccine recommendations need to be changed, but not quite on a regular basis. This observation suggests that the rate of evolution of these viruses is not constant through time, which begs the question as to when such rate changes occur, if they do so independently of the host in which they circulate and (or) independently of their subtype. To address these outstanding questions, we introduce a novel heuristics, Mclust*, that is based on a two-tier clustering approach in a phylogenetic context to estimate (i) absolute rates of evolution and (ii) when rate change occurs. We employ the novel approach to compare the two influenza surface proteins, hemagglutinin and neuraminidase, that circulated in avian, human, and swine hosts between 1960 and 2014 in two subtypes: H3N2 and H1N1. We show that the algorithm performs well in most conditions, accounting for phylogenetic uncertainty by means of bootstrapping and scales up to analyze very large data sets. Our results show that our approach is robust to the time-dependent artifact of rate estimation, and confirm pervasive punctuated evolution across hosts and subtypes. As such, the novel approach can potentially detect when vaccine composition needs to be updated.
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Affiliation(s)
- Kasandra Labonté
- a Department of Biology, Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- a Department of Biology, Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, ON K1N 6N5, Canada.,b Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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247
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Abdelwhab EM, Hassan MK, Abdel-Moneim AS, Naguib MM, Mostafa A, Hussein ITM, Arafa A, Erfan AM, Kilany WH, Agour MG, El-Kanawati Z, Hussein HA, Selim AA, Kholousy S, El-Naggar H, El-Zoghby EF, Samy A, Iqbal M, Eid A, Ibraheem EM, Pleschka S, Veits J, Nasef SA, Beer M, Mettenleiter TC, Grund C, Ali MM, Harder TC, Hafez HM. Introduction and enzootic of A/H5N1 in Egypt: Virus evolution, pathogenicity and vaccine efficacy ten years on. INFECTION GENETICS AND EVOLUTION 2016; 40:80-90. [PMID: 26917362 DOI: 10.1016/j.meegid.2016.02.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/18/2016] [Accepted: 02/19/2016] [Indexed: 12/09/2022]
Abstract
It is almost a decade since the highly pathogenic H5N1 avian influenza virus (A/H5N1) of clade 2.2.1 was introduced to Egypt in 2005, most likely, via wild birds; marking the longest endemic status of influenza viruses in poultry outside Asia. The endemic A/H5N1 in Egypt still compromises the poultry industry, poses serious hazards to public health and threatens to become potentially pandemic. The control strategies adopted for A/H5N1 in Egyptian poultry using diverse vaccines in commercialized poultry neither eliminated the virus nor did they decrease its evolutionary rate. Several virus clades have evolved, a few of them disappeared and others prevailed. Disparate evolutionary traits in both birds and humans were manifested by accumulation of clade-specific mutations across viral genomes driven by a variety of selection pressures. Viruses in vaccinated poultry populations displayed higher mutation rates at the immunogenic epitopes, promoting viral escape and reducing vaccine efficiency. On the other hand, viruses isolated from humans displayed changes in the receptor binding domain, which increased the viral affinity to bind to human-type glycan receptors. Moreover, viral pathogenicity exhibited several patterns in different hosts. This review aims to provide an overview of the viral evolution, pathogenicity and vaccine efficacy of A/H5N1 in Egypt during the last ten years.
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Affiliation(s)
- E M Abdelwhab
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - M K Hassan
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - A S Abdel-Moneim
- Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt; Microbiology Department, Virology Division, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia
| | - M M Naguib
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany; National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - A Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Dokki, Giza 12311, Egypt; Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen 35392, Germany
| | - I T M Hussein
- Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - A Arafa
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - A M Erfan
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - W H Kilany
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - M G Agour
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt; Animal Health Research Institute, Dokki, 12618 Giza, Egypt
| | - Z El-Kanawati
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - H A Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - A A Selim
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - S Kholousy
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - H El-Naggar
- Veterinary Serum and Vaccine Research Institute, Abbasia, El-Sekka El-Beida St., PO Box 131, Cairo 11381, Egypt
| | - E F El-Zoghby
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - A Samy
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - M Iqbal
- Avian Influenza Group, The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, United Kingdom
| | - A Eid
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - E M Ibraheem
- Animal Health Research Institute, Dokki, 12618 Giza, Egypt
| | - S Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, Giessen 35392, Germany
| | - J Veits
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - S A Nasef
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt
| | - M Beer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - T C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - C Grund
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - M M Ali
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza 12618, Egypt; Animal Health Research Institute, Dokki, 12618 Giza, Egypt
| | - T C Harder
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - H M Hafez
- Institute of Poultry Diseases, Freie Universität Berlin, Königsweg 63, 14163 Berlin, Germany.
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248
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Abstract
Multiple divergent lineages challenge the design of cross-protective vaccines and highlight the need for additional surveillance. The evolutionary origins of the influenza A(H1N1)pdm09 virus that caused the first outbreak of the 2009 pandemic in Mexico remain unclear, highlighting the lack of swine surveillance in Latin American countries. Although Brazil has one of the largest swine populations in the world, influenza was not thought to be endemic in Brazil’s swine until the major outbreaks of influenza A(H1N1)pdm09 in 2009. Through phylogenetic analysis of whole-genome sequences of influenza viruses of the H1N1, H1N2, and H3N2 subtypes collected in swine in Brazil during 2009–2012, we identified multiple previously uncharacterized influenza viruses of human seasonal H1N2 and H3N2 virus origin that have circulated undetected in swine for more than a decade. Viral diversity has further increased in Brazil through reassortment between co-circulating viruses, including A(H1N1)pdm09. The circulation of multiple divergent hemagglutinin lineages challenges the design of effective cross-protective vaccines and highlights the need for additional surveillance.
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249
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Nguyen TH, Than VT, Thanh HD, Hung VK, Nguyen DT, Kim W. Intersubtype Reassortments of H5N1 Highly Pathogenic Avian Influenza Viruses Isolated from Quail. PLoS One 2016; 11:e0149608. [PMID: 26900963 PMCID: PMC4765837 DOI: 10.1371/journal.pone.0149608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/03/2016] [Indexed: 11/18/2022] Open
Abstract
H5N1 highly pathogenic avian influenza (HPAI) viruses are considered a threat to national animal industries, causing production losses and high mortality in domestic poultry. In recent years, quail has become a popular terrestrial poultry species raised for production of meat and eggs in Asia. In this study, to better understand the roles of quail in H5N1 viral evolution, two H5N1-positive samples, designated A/quail/Vietnam/CVVI-49/2010 (CVVI-49/2010) and A/quail/Vietnam/CVVI-50/2014 (CVVI-50/2014), were isolated from quail during H5N1 outbreaks in Vietnam, and their whole genome were analyzed. The phylogenetic analysis reveals new evolutionary variation in the worldwide H5N1 viruses. The quail HA genes were clustered into clades 1.1.1 (CVVI-49/2010) and clade 2.3.2.1c (CVVI-50/2014), which may have evolved from viruses circulating from chickens and/or ducks in Cambodia, mainland of China, Taiwan, Indonesia, and South Korea in recent years. Interestingly, the M2 gene of the CVVI-49/2010 strain contained amino acid substitutions at position 26L-I and 31S-N that are related to amantadine-resistance. In particular, the CVVI-50/2014 strain revealed evidence of multiple intersubtype reassortment events between virus clades 2.3.2.1c, 2.3.2.1b, and 2.3.2.1a. Data from this study supports the possible role of quail as an important intermediate host in avian influenza virus evolution. Therefore, additional surveillance is needed to monitor these HPAI viruses both serologically and virologically in quail.
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Affiliation(s)
- Tinh Huu Nguyen
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Van Thai Than
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Hien Dang Thanh
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Vu-Khac Hung
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Duc Tan Nguyen
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, South Korea
- * E-mail:
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250
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Limited Antigenic Diversity in Contemporary H7 Avian-Origin Influenza A Viruses from North America. Sci Rep 2016; 6:20688. [PMID: 26858078 PMCID: PMC4746648 DOI: 10.1038/srep20688] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/11/2016] [Indexed: 01/11/2023] Open
Abstract
Subtype H7 avian–origin influenza A viruses (AIVs) have caused at least 500 confirmed human infections since 2003 and culling of >75 million birds in recent years. Here we antigenically and genetically characterized 93 AIV isolates from North America (85 from migratory waterfowl [1976–2010], 7 from domestic poultry [1971–2012], and 1 from a seal [1980]). The hemagglutinin gene of these H7 viruses are separated from those from Eurasia. Gradual accumulation of nucleotide and amino acid substitutions was observed in the hemagglutinin of H7 AIVs from waterfowl and domestic poultry. Genotype characterization suggested that H7 AIVs in wild birds form diverse and transient internal gene constellations. Serologic analyses showed that the 93 isolates cross-reacted with each other to different extents. Antigenic cartography showed that the average antigenic distance among them was 1.14 units (standard deviation [SD], 0.57 unit) and that antigenic diversity among the H7 isolates we tested was limited. Our results suggest that the continuous genetic evolution has not led to significant antigenic diversity for H7 AIVs from North America. These findings add to our understanding of the natural history of IAVs and will inform public health decision-making regarding the threat these viruses pose to humans and poultry.
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