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Wu H, Zhou HY, Zheng H, Wu A. Towards Understanding and Identification of Human Viral Co-Infections. Viruses 2024; 16:673. [PMID: 38793555 PMCID: PMC11126107 DOI: 10.3390/v16050673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Viral co-infections, in which a host is infected with multiple viruses simultaneously, are common in the human population. Human viral co-infections can lead to complex interactions between the viruses and the host immune system, affecting the clinical outcome and posing challenges for treatment. Understanding the types, mechanisms, impacts, and identification methods of human viral co-infections is crucial for the prevention and control of viral diseases. In this review, we first introduce the significance of studying human viral co-infections and summarize the current research progress and gaps in this field. We then classify human viral co-infections into four types based on the pathogenic properties and species of the viruses involved. Next, we discuss the molecular mechanisms of viral co-infections, focusing on virus-virus interactions, host immune responses, and clinical manifestations. We also summarize the experimental and computational methods for the identification of viral co-infections, emphasizing the latest advances in high-throughput sequencing and bioinformatics approaches. Finally, we highlight the challenges and future directions in human viral co-infection research, aiming to provide new insights and strategies for the prevention, control, diagnosis, and treatment of viral diseases. This review provides a comprehensive overview of the current knowledge and future perspectives on human viral co-infections and underscores the need for interdisciplinary collaboration to address this complex and important topic.
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Affiliation(s)
- Hui Wu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Hang-Yu Zhou
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211100, China;
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
- State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
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Retrospective Assessment of the Antigenic Similarity of Egg-Propagated and Cell Culture-Propagated Reference Influenza Viruses as Compared with Circulating Viruses across Influenza Seasons 2002-2003 to 2017-2018. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17155423. [PMID: 32731417 PMCID: PMC7432082 DOI: 10.3390/ijerph17155423] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/24/2020] [Accepted: 07/25/2020] [Indexed: 11/17/2022]
Abstract
Suboptimal vaccine effectiveness against seasonal influenza is a significant public health concern, partly explained by antigenic differences between vaccine viruses and viruses circulating in the environment. Haemagglutinin mutations within vaccine viruses acquired during serial passage in eggs have been identified as a source of antigenic variation between vaccine and circulating viruses. This study retrospectively compared the antigenic similarity of circulating influenza isolates with egg- and cell-propagated reference viruses to assess any observable trends over a 16-year period. Using annual and interim reports published by the Worldwide Influenza Centre, London, for the 2002-2003 to 2017-2018 influenza seasons, we assessed the proportions of circulating viruses which showed antigenic similarity to reference viruses by season. Egg-propagated reference viruses were well matched against circulating viruses for A/H1N1 and B/Yamagata. However, A/H3N2 and B/Victoria cell-propagated reference viruses appeared to be more antigenically similar to circulating A/H3N2 and B/Victoria viruses than egg-propagated reference viruses. These data support the possibility that A/H3N2 and B/Victoria viruses are relatively more prone to egg-adaptive mutation. Cell-propagated A/H3N2 and B/Victoria reference viruses were more antigenically similar to circulating A/H3N2 and B/Victoria viruses over a 16-year period than were egg-propagated reference viruses.
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Chen L, Xiong J, Peng L, Yang P, Yu H, Yan Q, Cheng Y, Zhao G, Chen Y, Jiang Q, Xiong C. Sequence analysis of reassortants within H3N2 subtype influenza A virus circulated in Hong Kong, 2014-2017. Travel Med Infect Dis 2019; 33:101510. [PMID: 31698043 DOI: 10.1016/j.tmaid.2019.101510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 09/16/2019] [Accepted: 11/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Liang Chen
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiasheng Xiong
- College of Marine Science, Shandong University, Weihai, China
| | - Li Peng
- Shanghai Key Laboratory of Meteorology and Health, Shanghai, China
| | - Pengfei Yang
- Huai'an Center for Disease Control and Prevention, Huai'an, China
| | - Hao Yu
- Hongze Center for Disease Control and Prevention, Hongze, China
| | - Qingli Yan
- Huai'an Center for Disease Control and Prevention, Huai'an, China
| | - Yan Cheng
- Hongze Center for Disease Control and Prevention, Hongze, China
| | - Genming Zhao
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Qingwu Jiang
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Chenglong Xiong
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China; School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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Jacquot M, Rao PP, Yadav S, Nomikou K, Maan S, Jyothi YK, Reddy N, Putty K, Hemadri D, Singh KP, Maan NS, Hegde NR, Mertens P, Biek R. Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot. Virus Evol 2019; 5:vez027. [PMID: 31392031 PMCID: PMC6680063 DOI: 10.1093/ve/vez027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
For segmented viruses, rapid genomic and phenotypic changes can occur through the process of reassortment, whereby co-infecting strains exchange entire segments creating novel progeny virus genotypes. However, for many viruses with segmented genomes, this process and its effect on transmission dynamics remain poorly understood. Here, we assessed the consequences of reassortment for selection on viral diversity through time using bluetongue virus (BTV), a segmented arbovirus that is the causative agent of a major disease of ruminants. We analysed ninety-two BTV genomes isolated across four decades from India, where BTV diversity, and thus opportunities for reassortment, are among the highest in the world. Our results point to frequent reassortment and segment turnover, some of which appear to be driven by selective sweeps and serial hitchhiking. Particularly, we found evidence for a recent selective sweep affecting segment 5 and its encoded NS1 protein that has allowed a single variant to essentially invade the full range of BTV genomic backgrounds and serotypes currently circulating in India. In contrast, diversifying selection was found to play an important role in maintaining genetic diversity in genes encoding outer surface proteins involved in virus interactions (VP2 and VP5, encoded by segments 2 and 6, respectively). Our results support the role of reassortment in driving rapid phenotypic change in segmented viruses and generate testable hypotheses for in vitro experiments aiming at understanding the specific mechanisms underlying differences in fitness and selection across viral genomes.
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Affiliation(s)
- Maude Jacquot
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Pavuluri P Rao
- Ella Foundation, Genome Valley Hyderabad, Hyderabad, Telangana, India
| | - Sarita Yadav
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sushila Maan
- College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Y Krishna Jyothi
- Veterinary Biological and Research Institute, Vijayawada, Andhra Pradesh, India
| | - Narasimha Reddy
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Kalyani Putty
- PVNR Telangana Veterinary University, Hyderabad, Telangana, India
| | - Divakar Hemadri
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Karam P Singh
- Centre for Animal Disease Research and Diagnosis, Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Narender Singh Maan
- College of Veterinary Sciences, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Nagendra R Hegde
- Ella Foundation, Genome Valley Hyderabad, Hyderabad, Telangana, India
| | - Peter Mertens
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.,The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative Medicine, Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Chen Q, Zhu J. Detecting virus-specific effects on post-infection temporal gene expression. BMC Bioinformatics 2019; 20:129. [PMID: 30925863 PMCID: PMC6439963 DOI: 10.1186/s12859-019-2653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Different types of viruses have different envelope proteins, and may have their shared or distinctive host-virus interactions which result in various post-infection effects in humans and animals. These effects often do not appear at once but take time to unfold. To characterize the virus-specific effects, we applied a Multivariate Polynomial Time-dependent Genetic Association (MPTGA) method, previously proposed for detecting differences in temporal gene expression traits, to test for the differences in mouse lung transcriptome response to infection of different subtypes of influenza A viruses. Results We compared two methods: the Multivariate Polynomial Time-dependent Genetic Association (MPTGA) method, and the conventional modified t-test, to study the virus-specific effects on mouse lung gene expression. Both methods found H3N2 to be the most different virus among the three viruses tested, with the largest number of genes with H3N2-specific effects. However, the MPTGA method demonstrated much higher power of detection, and the detected genes with virus-specific effects showed better biological relevance. Conclusions Transcriptome response to virus infection is dynamic. MPTGA which leverages temporal gene expression traits showed increased power in detecting biologically relevant virus-specific effects comparing with conventional t-test method.
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Affiliation(s)
- Quan Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. .,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA. .,Sema4, a Mount Sinai venture, Stamford, 06902, CT, USA.
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Elliott ST, Keaton AA, Chu JD, Reed CC, Garman B, Patel A, Yan J, Broderick KE, Weiner DB. A Synthetic Micro-Consensus DNA Vaccine Generates Comprehensive Influenza A H3N2 Immunity and Protects Mice Against Lethal Challenge by Multiple H3N2 Viruses. Hum Gene Ther 2018; 29:1044-1055. [PMID: 30062926 PMCID: PMC6152850 DOI: 10.1089/hum.2018.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Influenza A H3N2 viruses circulate globally, leading to substantial morbidity and mortality. Commercially available, antigen-matched influenza vaccines must be updated frequently to match dynamic sequence variability in immune epitopes, especially within viral influenza A H3N2 hemagglutinin (H3). In an effort to create comprehensive immune responses against H3N2, four micro-consensus antigens were designed to mimic the sequence and antigenic diversity of H3. Synthetic plasmid DNA constructs were developed to express each micro-consensus immunogen and combined into a multi-antigen DNA vaccine cocktail, pH3HA. Facilitated delivery of pH3HA via intramuscular electroporation in mice induced comprehensive, potent humoral responses against diverse seasonal H3N2 viruses that circulated between 1968 and the present. Vaccination with pH3HA also induced an antigen-specific cellular cytokine response. Mice immunized with pH3HA were protected against lethal challenge using two distinct H3N2 viruses, highlighting the heterologous protection afforded by synthetic micro-consensus immunogens. These findings warrant further study of the DNA vaccine micro-consensus platform for broad protection against influenza viruses.
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Affiliation(s)
| | - Amelia A. Keaton
- The Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania
| | - Jacqueline D. Chu
- The Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania
| | | | | | - Ami Patel
- The Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania
| | - Jian Yan
- Inovio Pharmaceuticals, Plymouth Meeting, Pennsylvania
| | | | - David B. Weiner
- The Wistar Institute of Anatomy and Biology, Philadelphia, Pennsylvania.,Correspondence: Dr. David B. Weiner, The Wistar Institute of Anatomy and Biology, 3601 Spruce Street, Philadelphia, PA, 19104.
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Tongo M, de Oliveira T, Martin DP. Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation. Virus Evol 2018; 4:vey015. [PMID: 29942655 PMCID: PMC6007327 DOI: 10.1093/ve/vey015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recombination between different HIV-1 group M (HIV-1M) subtypes is a major contributor to the ongoing genetic diversification of HIV-1M. However, it remains unclear whether the different genome regions of recombinants are randomly inherited from the different subtypes. To elucidate this, we analysed the distribution within 82 circulating and 201 unique recombinant forms (CRFs/URFs), of genome fragments derived from HIV-1M Subtypes A, B, C, D, F, and G and CRF01_AE. We found that viruses belonging to the analysed HIV-1M subtypes and CRF01_AE contributed certain genome fragments more frequently during recombination than other fragments. Furthermore, we identified statistically significant hot-spots of Subtype A sequence inheritance in genomic regions encoding portions of Gag and Nef, Subtype B in Pol, Tat and Env, Subtype C in Vif, Subtype D in Pol and Env, Subtype F in Gag, Subtype G in Vpu-Env and Nef, and CRF01_AE inheritance in Vpu and Env. The apparent non-randomness in the frequencies with which different subtypes have contributed specific genome regions to known HIV-1M recombinants is consistent with selection strongly impacting the survival of inter-subtype recombinants. We propose that hotspots of genomic region inheritance are likely to demarcate the locations of subtype-specific adaptive genetic variations.
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Affiliation(s)
- Marcel Tongo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal (UKZN), 719 Umbilo Road, Durban 4001, South Africa
- Center of Research for Emerging and Re-Emerging Diseases (CREMER), Institute of Medical Research and Study of Medicinal Plants (IMPM), Yaoundé, Cameroon
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal (UKZN), 719 Umbilo Road, Durban 4001, South Africa
| | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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8
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Goldstein EJ, Harvey WT, Wilkie GS, Shepherd SJ, MacLean AR, Murcia PR, Gunson RN. Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses. Microb Genom 2017; 4. [PMID: 29310750 PMCID: PMC5857367 DOI: 10.1099/mgen.0.000137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.
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Affiliation(s)
- Emily J Goldstein
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - William T Harvey
- 2Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Gavin S Wilkie
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Samantha J Shepherd
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Alasdair R MacLean
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Pablo R Murcia
- 3Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Rory N Gunson
- 1West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, UK
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Abstract
Influenza is an RNA virus that causes mild to severe respiratory symptoms in humans and other hosts. Every year approximately half a million people around the world die from seasonal Influenza. But this number is substantially larger in the case of pandemics, with the most dramatic instance being the 1918 “Spanish flu” that killed more than 50 million people worldwide. In the last few years, thousands of Influenza genomic sequences have become publicly available, including the 1918 pandemic strain and many isolates from non-human hosts. Using these data and developing adequate bioinformatic and statistical tools, some of the major questions surrounding Influenza evolution are becoming tractable. Are the mutations and reassortments random? What are the patterns behind the virus's evolution? What are the necessary and sufficient conditions for a virus adapted to one host to infect a different host? Why is Influenza seasonal? In this review, we summarize some of the recent progress in understanding the evolution of the virus.
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Affiliation(s)
- Raul Rabadan
- Institute for Advanced Study, Einstein Dr., Princeton, NJ 08540, U.S.A
| | - Harlan Robins
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, U.S.A
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10
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Fitness cost of reassortment in human influenza. PLoS Pathog 2017; 13:e1006685. [PMID: 29112968 PMCID: PMC5675378 DOI: 10.1371/journal.ppat.1006685] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2. For the surface proteins hemagglutinin and neuraminidase, reassortant variants with a mean distance of at least 3 nucleotides to their parent strains get established at a rate of about 10−2 in units of the neutral point mutation rate. Our inference is based on a new method to map reassortment events from joint genealogies of multiple genome segments, which is tested by extensive simulations. We show that intra-lineage reassortment processes are, on average, under substantial negative selection that increases in strength with increasing sequence distance between the parent strains. The deleterious effects of reassortment manifest themselves in two ways: there are fewer reassortment events than expected from a null model of neutral reassortment, and reassortant strains have fewer descendants than their non-reassortant counterparts. Our results suggest that influenza evolves under ubiquitous epistasis across proteins, which produces fitness barriers against reassortment even between co-circulating strains within one lineage. The genome of the human influenza virus consists of 8 disjoint RNA polymer segments. These segments can undergo reassortment: when two viruses co-infect a host cell, they can produce viral offspring with a new combination of segments. In this paper, we show that reassortment within a given influenza lineage induces a fitness cost that increases in strength with increasing genetic distance of the parent viruses. Our finding suggests that evolution continuously produces viral proteins whose fitness depends on each other; reassortment reduces fitness by breaking up successful combinations of proteins. Thus, selection across proteins constrains viral evolution within a given lineage, and it may be an important factor in defining a viral species.
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11
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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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Newly Emergent Highly Pathogenic H5N9 Subtype Avian Influenza A Virus. J Virol 2015; 89:8806-15. [PMID: 26085150 DOI: 10.1128/jvi.00653-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The novel H7N9 avian influenza virus (AIV) was demonstrated to cause severe human respiratory infections in China. Here, we examined poultry specimens from live bird markets linked to human H7N9 infection in Hangzhou, China. Metagenomic sequencing revealed mixed subtypes (H5, H7, H9, N1, N2, and N9). Subsequently, AIV subtypes H5N9, H7N9, and H9N2 were isolated. Evolutionary analysis showed that the hemagglutinin gene of the novel H5N9 virus originated from A/Muscovy duck/Vietnam/LBM227/2012 (H5N1), which belongs to clade 2.3.2.1. The neuraminidase gene of the novel H5N9 virus originated from human-infective A/Hangzhou/1/2013 (H7N9). The six internal genes were similar to those of other H5N1, H7N9, and H9N2 virus strains. The virus harbored the PQRERRRKR/GL motif characteristic of highly pathogenic AIVs at the HA cleavage site. Receptor-binding experiments demonstrated that the virus binds α-2,3 sialic acid but not α-2,6 sialic acid. Identically, pathogenicity experiments also showed that the virus caused low mortality rates in mice. This newly isolated H5N9 virus is a highly pathogenic reassortant virus originating from H5N1, H7N9, and H9N2 subtypes. Live bird markets represent a potential transmission risk to public health and the poultry industry. IMPORTANCE This investigation confirms that the novel H5N9 subtype avian influenza A virus is a reassortant strain originating from H5N1, H7N9, and H9N2 subtypes and is totally different from the H5N9 viruses reported before. The novel H5N9 virus acquired a highly pathogenic H5 gene and an N9 gene from human-infecting subtype H7N9 but caused low mortality rates in mice. Whether this novel H5N9 virus will cause human infections from its avian host and become a pandemic subtype is not known yet. It is therefore imperative to assess the risk of emergence of this novel reassortant virus with potential transmissibility to public health.
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Zhang XS, Pebody R, De Angelis D, White PJ, Charlett A, McCauley JW. The Possible Impact of Vaccination for Seasonal Influenza on Emergence of Pandemic Influenza via Reassortment. PLoS One 2014; 9:e114637. [PMID: 25494180 PMCID: PMC4262424 DOI: 10.1371/journal.pone.0114637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 11/12/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One pathway through which pandemic influenza strains might emerge is reassortment from coinfection of different influenza A viruses. Seasonal influenza vaccines are designed to target the circulating strains, which intuitively decreases the prevalence of coinfection and the chance of pandemic emergence due to reassortment. However, individual-based analyses on 2009 pandemic influenza show that the previous seasonal vaccination may increase the risk of pandemic A(H1N1) pdm09 infection. In view of pandemic influenza preparedness, it is essential to understand the overall effect of seasonal vaccination on pandemic emergence via reassortment. METHODS AND FINDINGS In a previous study we applied a population dynamics approach to investigate the effect of infection-induced cross-immunity on reducing such a pandemic risk. Here the model was extended by incorporating vaccination for seasonal influenza to assess its potential role on the pandemic emergence via reassortment and its effect in protecting humans if a pandemic does emerge. The vaccination is assumed to protect against the target strains but only partially against other strains. We find that a universal seasonal vaccine that provides full-spectrum cross-immunity substantially reduces the opportunity of pandemic emergence. However, our results show that such effectiveness depends on the strength of infection-induced cross-immunity against any novel reassortant strain. If it is weak, the vaccine that induces cross-immunity strongly against non-target resident strains but weakly against novel reassortant strains, can further depress the pandemic emergence; if it is very strong, the same kind of vaccine increases the probability of pandemic emergence. CONCLUSIONS Two types of vaccines are available: inactivated and live attenuated, only live attenuated vaccines can induce heterosubtypic immunity. Current vaccines are effective in controlling circulating strains; they cannot always help restrain pandemic emergence because of the uncertainty of the oncoming reassortant strains, however. This urges the development of universal vaccines for prevention of pandemic influenza.
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Affiliation(s)
- Xu-Sheng Zhang
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
- * E-mail:
| | - Richard Pebody
- Respiratory Diseases Department, Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - Daniela De Angelis
- Statistics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
- Medical Research Council Biostatistics Unit, University Forvie Site, Cambridge, United Kingdom
| | - Peter J. White
- Modelling and Economics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
- NIHR Health Protection Research Unit in Modelling Methodology, Department of Infectious Disease Epidemiology, Imperial College School of Public Health, London, United Kingdom
| | - Andre Charlett
- Statistics Unit, Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
| | - John W. McCauley
- Medical Research Council National Institute for Medical Research, Mill Hill, London, United Kingdom
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Escalera-Zamudio M, Nelson MI, Cobián Güemes AG, López-Martínez I, Cruz-Ortiz N, Iguala-Vidales M, García ER, Barrera-Badillo G, Díaz-Quiñonez JA, López S, Arias CF, Isa P. Molecular epidemiology of influenza A/H3N2 viruses circulating in Mexico from 2003 to 2012. PLoS One 2014; 9:e102453. [PMID: 25075517 PMCID: PMC4116128 DOI: 10.1371/journal.pone.0102453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America.
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Affiliation(s)
- Marina Escalera-Zamudio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | | | | | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail:
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15
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Genomewide analysis of reassortment and evolution of human influenza A(H3N2) viruses circulating between 1968 and 2011. J Virol 2013; 88:2844-57. [PMID: 24371052 DOI: 10.1128/jvi.02163-13] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Influenza A(H3N2) viruses became widespread in humans during the 1968 H3N2 virus pandemic and have been a major cause of influenza epidemics ever since. These viruses evolve continuously by reassortment and genomic evolution. Antigenic drift is the cause for the need to update influenza vaccines frequently. Using two data sets that span the entire period of circulation of human influenza A(H3N2) viruses, it was shown that influenza A(H3N2) virus evolution can be mapped to 13 antigenic clusters. Here we analyzed the full genomes of 286 influenza A(H3N2) viruses from these two data sets to investigate the genomic evolution and reassortment patterns. Numerous reassortment events were found, scattered over the entire period of virus circulation, but most prominently in viruses circulating between 1991 and 1998. Some of these reassortment events persisted over time, and one of these coincided with an antigenic cluster transition. Furthermore, selection pressures and nucleotide and amino acid substitution rates of all proteins were studied, including those of the recently discovered PB1-N40, PA-X, PA-N155, and PA-N182 proteins. Rates of nucleotide and amino acid substitutions were most pronounced for the hemagglutinin, neuraminidase, and PB1-F2 proteins. Selection pressures were highest in hemagglutinin, neuraminidase, matrix 1, and nonstructural protein 1. This study of genotype in relation to antigenic phenotype throughout the period of circulation of human influenza A(H3N2) viruses leads to a better understanding of the evolution of these viruses. IMPORTANCE Each winter, influenza virus infects approximately 5 to 15% of the world's population, resulting in significant morbidity and mortality. Influenza A(H3N2) viruses evolve continuously by reassortment and genomic evolution. This leads to changes in antigenic recognition (antigenic drift) which make it necessary to update vaccines against influenza A(H3N2) viruses frequently. In this study, the relationship of genetic evolution to antigenic change spanning the entire period of A(H3N2) virus circulation was studied for the first time. The results presented in this study contribute to a better understanding of genetic evolution in correlation with antigenic evolution of influenza A(H3N2) viruses.
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16
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Abstract
In February 2013, two patients living in Shanghai were admitted to the Shanghai Fifth Hospital with fever, cough and respiratory tract infection, followed by severe pneumonia, respiratory distress and multiorgan dysfunction(1). While the first patient, an 87-year-old man, did not present a history of exposure to live birds during the preceding 2 weeks, the second patient, a 27-year-old man,was a butcher at a market selling live birds. A 35-year-old female from the Anhui Province of China, the third patient who became infected, visited a chicken market a week before her symptoms started (2,3). All three patients died, and their infections did not appear to be epidemiologically linked (4).
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Affiliation(s)
- R A Stein
- Biochemistry and Molecular Pharmacology, New York University School of Medicine, 180 Varick Street, Room 643, New York, NY, USA. ,
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17
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Marshall N, Priyamvada L, Ende Z, Steel J, Lowen AC. Influenza virus reassortment occurs with high frequency in the absence of segment mismatch. PLoS Pathog 2013; 9:e1003421. [PMID: 23785286 PMCID: PMC3681746 DOI: 10.1371/journal.ppat.1003421] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/30/2013] [Indexed: 01/12/2023] Open
Abstract
Reassortment is fundamental to the evolution of influenza viruses and plays a key role in the generation of epidemiologically significant strains. Previous studies indicate that reassortment is restricted by segment mismatch, arising from functional incompatibilities among components of two viruses. Additional factors that dictate the efficiency of reassortment remain poorly characterized. Thus, it is unclear what conditions are favorable for reassortment and therefore under what circumstances novel influenza A viruses might arise in nature. Herein, we describe a system for studying reassortment in the absence of segment mismatch and exploit this system to determine the baseline efficiency of reassortment and the effects of infection dose and timing. Silent mutations were introduced into A/Panama/2007/99 virus such that high-resolution melt analysis could be used to differentiate all eight segments of the wild-type and the silently mutated variant virus. The use of phenotypically identical parent viruses ensured that all progeny were equally fit, allowing reassortment to be measured without selection bias. Using this system, we found that reassortment occurred efficiently (88.4%) following high multiplicity infection, suggesting the process is not appreciably limited by intracellular compartmentalization. That co-infection is the major determinant of reassortment efficiency in the absence of segment mismatch was confirmed with the observation that the proportion of viruses with reassortant genotypes increased exponentially with the proportion of cells co-infected. The number of reassortants shed from co-infected guinea pigs was likewise dependent on dose. With 106 PFU inocula, 46%–86% of viruses isolated from guinea pigs were reassortants. The introduction of a delay between infections also had a strong impact on reassortment and allowed definition of time windows during which super-infection led to reassortment in culture and in vivo. Overall, our results indicate that reassortment between two like influenza viruses is efficient but also strongly dependent on dose and timing of the infections. Reassortment is the process by which influenza viruses, which carry RNA genomes comprising eight segments, exchange genetic material. Reassortment of the genome segments of two differing influenza strains has the potential to vastly increase the diversity of circulating influenza viruses. Despite its importance to influenza virus evolution, the frequency with which reassortment occurs in a cell or an animal infected with two or more variant viruses is unclear. Toward determining how readily reassortment can occur, we assessed the incidence of reassortment during experimental infection in cultured cells and in guinea pigs. We found that reassortment can occur with high efficiency in both systems, but that that efficiency is dependent on i) the dose of each virus added to the cells or taken up by the host and ii) the relative timing with which each virus infects. These results suggest that influenza A virus reassortment may be more prevalent in nature than one might expect based on the results of surveillance studies.
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Affiliation(s)
- Nicolle Marshall
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, United States of America
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18
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Co-circulation of influenza A virus strains and emergence of pandemic via reassortment: the role of cross-immunity. Epidemics 2012; 5:20-33. [PMID: 23438428 DOI: 10.1016/j.epidem.2012.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/09/2012] [Accepted: 10/29/2012] [Indexed: 12/24/2022] Open
Abstract
Reassortment is an important evolutionary route for influenza A viruses to generate pandemic strains. The pre-requisite for reassortment to occur is co-infection of different influenza virus strains in the same host population. Empirical evidence suggests that co-circulation of influenza A virus strains is common and co-infection in patients has been reported. Whether a novel virus can successfully spread among a host population is determined by its life-history (infectivity and infectious period). It is also well known that different influenza A strains interfere through the immune response of human body cells. The reassortant virus strain generated from co-infections deviates dramatically in antigenic and genetic properties from its parental strains such that human populations have limited immunity against it. We consider a mathematical model which includes two strains of influenza virus within a standard SIR model and integrate life history and cross-immunity into the evolutionary dynamics of influenza virus. We assume that, following primary infection by one strain and recovery, individuals are susceptible to secondary infection by the other strain only but with reduced probability due to cross-immunity. Co-infection is included to examine how life-history and cross-immunity interplay to regulate the co-circulation and co-infection of different influenza A virus strains in human populations. Further, we introduce novel strains via reassortment and investigate how the opportunities of a reassortant strain developing into a pandemic are constrained by its life-history and the residual immunity within human populations. We find that though the probability of pandemic emergence via reassortment increases with transmissibility of reassortant strains and the rate of reassortment, the existence of cross-immunity acquired through previous infections or vaccination can greatly constrain pandemic emergence.
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19
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Lun AT, Wong JW, Downard KM. FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry. BMC Bioinformatics 2012; 13:208. [PMID: 22906155 PMCID: PMC3505172 DOI: 10.1186/1471-2105-13-208] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 08/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented. RESULTS The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain. CONCLUSIONS The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk.
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Affiliation(s)
- Aaron Tl Lun
- School of Molecular Bioscience G-08, The University of Sydney, Sydney, NSW, 2006, Australia
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20
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Shapshak P, Chiappelli F, Somboonwit C, Sinnott J. The Influenza Pandemic of 2009. Mol Diagn Ther 2012; 15:63-81. [DOI: 10.1007/bf03256397] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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21
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Radomski JP, Slonimski PP. Alignment free characterization of the influenza-A hemagglutinin genes by the ISSCOR method. C R Biol 2012; 335:180-93. [PMID: 22464426 DOI: 10.1016/j.crvi.2012.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/26/2011] [Accepted: 01/11/2012] [Indexed: 12/23/2022]
Abstract
Analyses and visualizations by the ISSCOR method of the influenza virus hemagglutinin genes of three different A-subtypes revealed some rather striking temporal (for A/H3N3), and spatial relationships (for A/H5N1) between groups of individual gene subsets. The application to the A/H1N1 set revealed also relationships between the seasonal H1, and the swine-like novel 2009 H1v variants in a quick and unambiguous manner. Based on these examples we consider the application of the ISSCOR method for analysis of large sets of homologous genes as a worthwhile addition to a toolbox of genomics-it allows a rapid diagnostics of trends, and possibly can even aid an early warning of newly emerging epidemiological threats.
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Affiliation(s)
- Jan P Radomski
- Interdisciplinary Center for Mathematical and Computational Modeling, Warsaw University, Warsaw, Poland.
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22
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Preexisting influenza-specific CD4+ T cells correlate with disease protection against influenza challenge in humans. Nat Med 2012; 18:274-80. [PMID: 22286307 DOI: 10.1038/nm.2612] [Citation(s) in RCA: 772] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 11/18/2011] [Indexed: 12/11/2022]
Abstract
Protective immunity against influenza virus infection is mediated by neutralizing antibodies, but the precise role of T cells in human influenza immunity is uncertain. We conducted influenza infection studies in healthy volunteers with no detectable antibodies to the challenge viruses H3N2 or H1N1. We mapped T cell responses to influenza before and during infection. We found a large increase in influenza-specific T cell responses by day 7, when virus was completely cleared from nasal samples and serum antibodies were still undetectable. Preexisting CD4+, but not CD8+, T cells responding to influenza internal proteins were associated with lower virus shedding and less severe illness. These CD4+ cells also responded to pandemic H1N1 (A/CA/07/2009) peptides and showed evidence of cytotoxic activity. These cells are an important statistical correlate of homotypic and heterotypic response and may limit severity of influenza infection by new strains in the absence of specific antibody responses. Our results provide information that may aid the design of future vaccines against emerging influenza strains.
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23
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Wong KKY, Bull RA, Rockman S, Scott G, Stelzer-Braid S, Rawlinson W. Correlation of polymerase replication fidelity with genetic evolution of influenza A/Fujian/411/02(H3N2) viruses. J Med Virol 2011; 83:510-6. [PMID: 21264873 DOI: 10.1002/jmv.21991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Influenza virus evolves continuously through mutations presumed to result from evolutionary pressure driving viral replication. This study examined the relationship between the genetic evolution and replication fidelity of influenza viruses. Analysis of influenza sequences from National Centre for Biotechnology Information (NCBI) database revealed a gradual decrease in the rate of genetic evolution of A/Fujian/411/02(H3N2)-like variants after the emergence and predominance of the A/H3N2 Fujian strain in 2002. This decrease may be related to an increase in replication fidelity, which was investigated by assessing mutation frequencies of reassortant viruses carrying the PB1 segment of Fujian variants isolated between 2003 and 2005 in a sequencing-based plaque assay. The data revealed a threefold decrease in substitution per site of the reassortant viruses carrying the Fujian PB1 segments isolated in 2004-2005 compared with those circulating in 2003. The decrease in mutation frequency paralleled a decrease in genetic evolution of the Fujian variants from the NCBI database. This correlation implicates changes in the polymerase replication fidelity as contributing to altered genetic evolution of influenza viruses.
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Affiliation(s)
- Karen Ka Yin Wong
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney, Australia
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24
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Wong KKY, Bull RA, Stelzer-Braid S, Fennell M, Rawlinson W. Effect of reassortment on the nucleotide and amino acid changes of human A/H3N2 RNP subunits during 1998–2009. J Clin Virol 2011; 51:270-5. [DOI: 10.1016/j.jcv.2011.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Revised: 05/10/2011] [Accepted: 05/11/2011] [Indexed: 10/18/2022]
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Zhang J, Mamlouk AM, Martinetz T, Chang S, Wang J, Hilgenfeld R. PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. BMC Bioinformatics 2011; 12:248. [PMID: 21689434 PMCID: PMC3142226 DOI: 10.1186/1471-2105-12-248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 06/20/2011] [Indexed: 11/10/2022] Open
Abstract
Background Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome. Results Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed. Conclusions The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at http://www.biochem.uni-luebeck.de/public/software/phylomap.html
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Affiliation(s)
- Jiajie Zhang
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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26
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Hao W. Evidence of intra-segmental homologous recombination in influenza A virus. Gene 2011; 481:57-64. [PMID: 21571048 PMCID: PMC7127770 DOI: 10.1016/j.gene.2011.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 10/26/2022]
Abstract
The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza.
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Affiliation(s)
- Weilong Hao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada.
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27
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Ottmann M, Duchamp MB, Casalegno JS, Frobert E, Moulès V, Ferraris O, Valette M, Escuret V, Lina B. Novel influenza A(H1N1) 2009 in vitro reassortant viruses with oseltamivir resistance. Antivir Ther 2010; 15:721-6. [PMID: 20710053 DOI: 10.3851/imp1576] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND With the recent emergence of the novel A(H1N1) virus in 2009, the efficacy of available drugs, such as neuraminidase (NA) inhibitors, is of great concern for good patient care. Influenza viruses are known to be able to acquire resistance. In 2007, A(H1N1) viruses related to A/Brisbane/59/2007 (H1N1) (A[H1N1] Brisbane-like virus), which are naturally resistant to oseltamivir, emerged. Resistance to oseltamivir can be acquired either by spontaneous mutation in the NA (H275Y in N1), or by reassortment with a mutated NA. It is therefore crucial to determine the risk of pandemic A(H1N1) 2009 virus acquiring resistance against oseltamivir by reassortment. METHODS We estimated the capacity of reassortment between the A(H1N1) 2009 virus and an oseltamivir-resistant A(H1N1) Brisbane-like virus by in vitro coinfections of influenza-permissive cells. The screening and the analysis of reassortant viruses was performed by specific reverse transcriptase PCRs and by sequencing. RESULTS Out of 50 analysed reassortant viruses, two harboured the haemagglutinin (HA) segment from the pandemic A(H1N1) 2009 virus and the mutated NA originated from the A(H1N1) Brisbane-like virus. The replicating capacities of these viruses were measured, showing no difference as compared to the two parental strains, suggesting that acquisition of the mutated NA segment did not impair viral fitness in vitro. CONCLUSIONS Our results suggest that the novel A(H1N1) 2009 virus can acquire by in vitro genetic reassortment the H275Y mutated NA segment conferring resistance to oseltamivir.
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Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence. Proc Natl Acad Sci U S A 2010; 107:4687-92. [PMID: 20176961 DOI: 10.1073/pnas.0912807107] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spread of avian H5N1 influenza viruses around the globe has become a worldwide public health concern. To evaluate the pathogenic potential of reassortant viruses between currently cocirculating avian H5N1 and human H3N2 influenza viruses, we generated all the 254 combinations of reassortant viruses between A/chicken/South Kalimantan/UT6028/06 (SK06, H5N1) and A/Tokyo/Ut-Sk-1/07 (Tok07, H3N2) influenza viruses by reverse genetics. We found that the presence of Tok07 PB2 protein in the ribonucleoprotein (RNP) complex allowed efficient viral RNA transcription in a minigenome assay and that RNP activity played an essential role in the viability and replicative ability of the reassortant viruses. When the pathogenicity of 75 reassortant H5 viruses was tested in mice, 22 were more pathogenic than the parental SK06 virus, and three were extremely virulent. Strikingly, all 22 of these viruses obtained their PB2 segment from Tok07 virus. Further analysis showed that Tok07 PB1 alone lacked the ability to enhance the pathogenicity of the reassortant viruses but could do so by cooperating with Tok07 PB2. Our data demonstrate that reassortment between an avian H5N1 virus with low pathogenicity in mice and a human virus could result in highly pathogenic viruses and that the human virus PB2 segment functions in the background of an avian H5N1 virus, enhancing its virulence. Our findings highlight the importance of surveillance programs to monitor the emergence of human H5 reassortant viruses, especially those containing a PB2 segment of human origin.
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Abstract
Background The influenza A virus has two basic modes of evolution. Because of a high error rate in the process of replication by RNA polymerase, the viral genome drifts via accumulated mutations. The second mode of evolution is termed a shift, which results from the reassortment of the eight segments of this virus. When two different influenza viruses co‐infect the same host cell, new virions can be released that contain segments from both parental strains. This type of shift has been the source of at least two of the influenza pandemics in the 20th century (H2N2 in 1957 and H3N2 in 1968). Objectives The methods to measure these genetic shifts have not yet provided a quantitative answer to questions such as: what is the rate of genetic reassortment during a local epidemic? Are all possible reassortments equally likely or are there preferred patterns? Methods To answer these questions and provide a quantitative way to measure genetic shifts, a new method for detecting reassortments from nucleotide sequence data was created that does not rely upon phylogenetic analysis. Two different sequence databases were used: human H3N2 viruses isolated in New York State between 1995 and 2006, and human H3N2 viruses isolated in New Zealand between 2000 and 2005. Results Using this new method, we were able to reproduce all the reassortments found in earlier works, as well as detect, with very high confidence, many reassortments that were not detected by previous authors. We obtain a lower bound on the reassortment rate of 2–3 events per year, and find a clear preference for reassortments involving only one segment, most often hemagglutinin or neuraminidase. At a lower frequency several segments appear to reassort in vivo in defined groups as has been suggested previously in vitro. Conclusions Our results strongly suggest that the patterns of reassortment in the viral population are not random. Deciphering these patterns can be a useful tool in attempting to understand and predict possible influenza pandemics.
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Affiliation(s)
- Raul Rabadan
- Institute for Advanced Study, Einstein Dr, Princeton, NJ 08540, USA.
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30
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Different neuraminidase inhibitor susceptibilities of human H1N1, H1N2, and H3N2 influenza A viruses isolated in Germany from 2001 to 2005/2006. Antiviral Res 2009; 82:34-41. [DOI: 10.1016/j.antiviral.2009.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 12/15/2008] [Accepted: 01/22/2009] [Indexed: 11/20/2022]
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31
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Compatibility among polymerase subunit proteins is a restricting factor in reassortment between equine H7N7 and human H3N2 influenza viruses. J Virol 2008; 82:11880-8. [PMID: 18815312 DOI: 10.1128/jvi.01445-08] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reassortment is an important driving force for influenza virus evolution, and a better understanding of the factors that affect this process could improve our ability to respond to future influenza pandemics and epidemics. To identify factors that restrict the generation of reassortant viruses, we cotransfected human embryonic kidney cells with plasmids for the synthesis of viral RNAs of both A/equine/Prague/1/56 (Prague; H7N7) and A/Yokohama/2017/03 (Yokohama; H3N2) viruses together with the supporting protein expression plasmids. Of the possible 256 genotypes, we identified 29 genotypes in 120 randomly plaque-picked reassortants examined. Analyses of these reassortants suggested that the formation of functional ribonucleoprotein (RNP) complexes was a restricting factor, a finding that correlated with the activities of RNP complexes composed of different combinations of the proteins from the two viruses, as measured in a minigenome assay. For at least one nonfunctional RNP complex (i.e., Prague PB2, Prague PB1, Yokohama PA, and Prague NP), the lack of activity was due to the inability of the three polymerase subunit proteins to form a heterotrimer. Adaptation of viruses possessing a gene encoding a chimera of the PA proteins of the two viruses and the remaining genes from Prague virus resulted in compensatory mutations in the PB2 and/or PA protein. These results indicate substantial incompatibility among the gene products of the two test viruses, a critical role for the RNP complex in the generation of reassortant viruses, and a functional interaction of PB2 and PA.
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32
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Biere B, Schweiger B. Molekulare Analyse humaner Influenzaviren. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2008; 51:1050-60. [DOI: 10.1007/s00103-008-0634-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Manzoor R, Sakoda Y, Mweene A, Tsuda Y, Kishida N, Bai GR, Kameyama KI, Isoda N, Soda K, Naito M, Kida H. Phylogenic analysis of the M genes of influenza viruses isolated from free-flying water birds from their Northern Territory to Hokkaido, Japan. Virus Genes 2008; 37:144-52. [DOI: 10.1007/s11262-008-0248-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 06/03/2008] [Indexed: 10/21/2022]
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34
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Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC. The genomic and epidemiological dynamics of human influenza A virus. Nature 2008; 453:615-9. [PMID: 18418375 DOI: 10.1038/nature06945] [Citation(s) in RCA: 706] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 03/19/2008] [Indexed: 11/09/2022]
Abstract
The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions.
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Affiliation(s)
- Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3JT, UK.
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35
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Identification and characterization of a late AH1N2 human reassortant in France during the 2002–2003 influenza season. Virus Res 2008; 132:33-41. [DOI: 10.1016/j.virusres.2007.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 10/12/2007] [Accepted: 10/13/2007] [Indexed: 12/31/2022]
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