1
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Liu L, Chen G, Huang S, Wen F. Receptor Binding Properties of Neuraminidase for influenza A virus: An Overview of Recent Research Advances. Virulence 2023; 14:2235459. [PMID: 37469130 PMCID: PMC10361132 DOI: 10.1080/21505594.2023.2235459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Influenza A viruses (IAVs) pose a serious risk to both human and animal health. IAVs' receptor binding characteristics account for a major portion of their host range and tissue tropism. While the function of neuraminidase (NA) in promoting the release of progeny virus is well-known, its role in the virus entry process remains poorly understood. Studies have suggested that certain subtypes of NA can act as receptor-binding proteins, either alone or in conjunction with haemagglutinin (HA). An important distinction is that NA from the avian influenza virus have a second sialic acid-binding site (2SBS) that is preserved in avian strains but missing in human or swine strains. Those observations suggest that the 2SBS may play a key role in the adaptation of the avian influenza virus to mammalian hosts. In this review, we provide an update of the recent research advances in the receptor-binding role of NA and highlight its underestimated importance during the early stages of the IAV life cycle. By doing so, we aim to provide new insights into the mechanisms underlying IAV host adaptation and pathogenesis.
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Affiliation(s)
- Lian Liu
- School of Medicine, Foshan University, Foshan, China
| | - Gaojie Chen
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Shujian Huang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Feng Wen
- School of Life Science and Engineering, Foshan University, Foshan, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China
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2
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Leeks A, Bono LM, Ampolini EA, Souza LS, Höfler T, Mattson CL, Dye AE, Díaz-Muñoz SL. Open questions in the social lives of viruses. J Evol Biol 2023; 36:1551-1567. [PMID: 37975507 PMCID: PMC11281779 DOI: 10.1111/jeb.14203] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 11/19/2023]
Abstract
Social interactions among viruses occur whenever multiple viral genomes infect the same cells, hosts, or populations of hosts. Viral social interactions range from cooperation to conflict, occur throughout the viral world, and affect every stage of the viral lifecycle. The ubiquity of these social interactions means that they can determine the population dynamics, evolutionary trajectory, and clinical progression of viral infections. At the same time, social interactions in viruses raise new questions for evolutionary theory, providing opportunities to test and extend existing frameworks within social evolution. Many opportunities exist at this interface: Insights into the evolution of viral social interactions have immediate implications for our understanding of the fundamental biology and clinical manifestation of viral diseases. However, these opportunities are currently limited because evolutionary biologists only rarely study social evolution in viruses. Here, we bridge this gap by (1) summarizing the ways in which viruses can interact socially, including consequences for social evolution and evolvability; (2) outlining some open questions raised by viruses that could challenge concepts within social evolution theory; and (3) providing some illustrative examples, data sources, and conceptual questions, for studying the natural history of social viruses.
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Affiliation(s)
- Asher Leeks
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Quantitative Biology Institute, Yale University, New Haven, Connecticut, USA
| | - Lisa M. Bono
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Elizabeth A. Ampolini
- Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lucas S. Souza
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Thomas Höfler
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Courtney L. Mattson
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
| | - Anna E. Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Samuel L. Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California, USA
- Genome Center, University of California Davis, Davis, California, USA
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3
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Abstract
The neuraminidase (NA) of influenza A and B viruses plays a distinct role in viral replication and has a highly conserved catalytic site. Numerous sialic (neuraminic) acid analogs that competitively bind to the NA active site and potently inhibit enzyme activity have been synthesized and tested. Four NA inhibitors are now licensed in various parts of the world (zanamivir, oseltamivir, peramivir, and laninamivir) to treat influenza A and B infections. NA changes, naturally occurring or acquired under selective pressure, have been shown to reduce drug binding, thereby affecting the effectiveness of NA inhibitors. Drug resistance and other drawbacks have prompted the search for the next-generation NA-targeting therapeutics. One of the promising approaches is the identification of monoclonal antibodies (mAbs) targeting the conserved NA epitopes. Anti-NA mAbs demonstrate Fab-based antiviral activity supplemented with Fc-mediated immune effector functions. Antiviral Fc-conjugates offer another cutting-edge strategy that is based on a multimodal mechanism of action. These novel antiviral agents are composed of a small-molecule NA inhibitor and an Fc-region that simultaneously engages the immune system. The significant advancements made in recent years further support the value of NA as an attractive target for the antiviral development.
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Affiliation(s)
- Larisa Gubareva
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
| | - Teena Mohan
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30329-4027, USA
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4
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Dolan PT, Taguwa S, Rangel MA, Acevedo A, Hagai T, Andino R, Frydman J. Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells. eLife 2021; 10:e61921. [PMID: 33491648 PMCID: PMC7880689 DOI: 10.7554/elife.61921] [Citation(s) in RCA: 12] [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: 08/08/2020] [Accepted: 01/24/2021] [Indexed: 01/11/2023] Open
Abstract
Dengue virus (DENV) cycles between mosquito and mammalian hosts. To examine how DENV populations adapt to these different host environments, we used serial passage in human and mosquito cell lines and estimated fitness effects for all single-nucleotide variants in these populations using ultra-deep sequencing. This allowed us to determine the contributions of beneficial and deleterious mutations to the collective fitness of the population. Our analysis revealed that the continuous influx of a large burden of deleterious mutations counterbalances the effect of rare, host-specific beneficial mutations to shape the path of adaptation. Beneficial mutations preferentially map to intrinsically disordered domains in the viral proteome and cluster to defined regions in the genome. These phenotypically redundant adaptive alleles may facilitate host-specific DENV adaptation. Importantly, the evolutionary constraints described in our simple system mirror trends observed across DENV and Zika strains, indicating it recapitulates key biophysical and biological constraints shaping long-term viral evolution.
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Affiliation(s)
- Patrick T Dolan
- Stanford University, Department of BiologyStanfordUnited States
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Shuhei Taguwa
- Stanford University, Department of BiologyStanfordUnited States
| | | | - Ashley Acevedo
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel AvivIsrael
| | - Raul Andino
- University of California, Microbiology and Immunology, San FranciscoSan FranciscoUnited States
| | - Judith Frydman
- Stanford University, Department of BiologyStanfordUnited States
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5
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Wille M, Holmes EC. The Ecology and Evolution of Influenza Viruses. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038489. [PMID: 31871237 DOI: 10.1101/cshperspect.a038489] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The patterns and processes of influenza virus evolution are of fundamental importance, underpinning such traits as the propensity to emerge in new host species and the ability to rapidly generate antigenic variation. Herein, we review key aspects of the ecology and evolution of influenza viruses. We begin with an exploration of the origins of influenza viruses within the orthomyxoviruses, showing how our perception of the evolutionary history of these viruses has been transformed with metagenomic sequencing. We then outline the diversity of virus subtypes in different species and the processes by which these viruses have emerged in new hosts, with a particular focus on the role played by segment reassortment. We then turn our attention to documenting the spread and phylodynamics of seasonal influenza A and B viruses in human populations, including the drivers of antigenic evolution, and finish with a discussion of virus diversity and evolution at the scale of individual hosts.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney 2006, Australia
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6
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Gentles LE, Wan H, Eichelberger MC, Bloom JD. Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Viruses 2020; 12:v12060597. [PMID: 32486222 PMCID: PMC7354634 DOI: 10.3390/v12060597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
Influenza virus infection elicits antibodies against the receptor-binding protein hemagglutinin (HA) and the receptor-cleaving protein neuraminidase (NA). Because HA is essential for viral entry, antibodies targeting HA often potently neutralize the virus in single-cycle infection assays. However, antibodies against NA are not potently neutralizing in such assays, since NA is dispensable for single-cycle infection. Here we show that a modified influenza virus that depends on NA for receptor binding is much more sensitive than a virus with receptor-binding HA to neutralization by some anti-NA antibodies. Specifically, a virus with a receptor-binding G147R N1 NA and a binding-deficient HA is completely neutralized in single-cycle infections by an antibody that binds near the NA active site. Infection is also substantially inhibited by antibodies that bind NA epitopes distant from the active site. Finally, we demonstrate that this modified virus can be used to efficiently select mutations in NA that escape antibody binding, a task that can be laborious with typical influenza viruses that are not well neutralized by anti-NA antibodies. Thus, viruses dependent on NA for receptor binding allow for sensitive in vitro detection of antibodies binding near the catalytic site of NA and enable the selection of viral escape mutants.
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MESH Headings
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Epitopes/immunology
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/metabolism
- Influenza, Human/immunology
- Influenza, Human/virology
- Neuraminidase/metabolism
- Neutralization Tests
- Orthomyxoviridae/genetics
- Orthomyxoviridae/immunology
- Orthomyxoviridae/metabolism
- RNA, Viral/genetics
- Receptors, Virus/metabolism
- Sequence Analysis, RNA
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Affiliation(s)
- Lauren E. Gentles
- Division of Basic Sciences Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA;
- Department of Microbiology, University of Washington, 1705 NE Pacific St., Seattle, WA 98195-7735, USA
| | - Hongquan Wan
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Maryna C. Eichelberger
- Division of Biological Standards and Quantity Control, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Jesse D. Bloom
- Division of Basic Sciences Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA;
- Department of Microbiology, University of Washington, 1705 NE Pacific St., Seattle, WA 98195-7735, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Correspondence:
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7
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Brown JC, Barclay WS, Galiano M, Harvey R. Passage of influenza A/H3N2 viruses in human airway cells removes artefactual variants associated with neuraminidase-mediated binding. J Gen Virol 2020; 101:456-466. [PMID: 31702542 PMCID: PMC7414449 DOI: 10.1099/jgv.0.001348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022] Open
Abstract
Serological assays with modern influenza A/H3N2 viruses have become problematic due to the progressive reduction in the ability of viruses of this subtype to bind and agglutinate red blood cells (RBCs). This is due to reduced ability of the viral haemagglutinin (HA) glycoprotein to bind to the sialic acid-containing receptors presented by these cells. Additionally, as a result of reduced HA-mediated binding in cell culture, modern A/H3N2 viruses often acquire compensatory mutations during propagation that enable binding of cellular receptors through their neuraminidase (NA) surface protein. Viruses that have acquired this NA-mediated binding agglutinate RBCs through their NA, confusing the results of serological assays designed to assess HA antigenicity. Here we confirm with a large dataset that the acquisition of mutations that confer NA binding of RBCs is a culture artefact, and demonstrate that modern A/H3N2 isolates with acquired NA-binding mutations revert to a clinical-like NA sequence after a single passage in human airway epithelial (HAE) cells.
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Affiliation(s)
- Jonathan C. Brown
- National Institute for Biological Standards and Control, Potters Bar, UK
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Monica Galiano
- Public Health England, London, UK
- Present address: WHO Collaborating Centre for Reference and Research on Influenza, Francis Crick Institute, London, UK
| | - Ruth Harvey
- National Institute for Biological Standards and Control, Potters Bar, UK
- Present address: WHO Collaborating Centre for Reference and Research on Influenza, Francis Crick Institute, London, UK
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8
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Xue KS, Bloom JD. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nat Genet 2020; 51:1298-1301. [PMID: 30804564 DOI: 10.1038/s41588-019-0349-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Katherine S Xue
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jesse D Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
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9
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Díaz-Muñoz SL. Uncovering Virus-Virus Interactions by Unifying Approaches and Harnessing High-Throughput Tools. mSystems 2019; 4:e00121-19. [PMID: 31164405 PMCID: PMC6584877 DOI: 10.1128/msystems.00121-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 01/05/2023] Open
Abstract
Virus-host interactions have received much attention in virology. Virus-virus interactions can occur when >1 virus infects a host and can be deemed social when one virus affects the fitness of another virus, as in the well-known case of superinfection exclusion. Coinfection and subsequent social interactions can change viral pathogenicity, host range, and genetic composition, with implications for human health and viral evolution. I propose that this field can be advanced by bringing new perspectives into virology (e.g., social evolution theory) and uniting disciplinary divides within virology (classical, host-focused, and ecoevolutionary). The development of novel high-throughput tools that meld molecular and evolutionary approaches can harness viral diversity as an experimental asset to understand complex viral social interactions. A greater knowledge of virus-virus interactions will lead to the reformulation of basic concepts of virology and advances in applied virology, with new treatments that harness interactions between viruses to fight viral and bacterial infections.
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Affiliation(s)
- Samuel L Díaz-Muñoz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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10
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Gong YN, Tsao KC, Chen GW, Wu CJ, Chen YH, Liu YC, Yang SL, Huang YC, Shih SR. Population dynamics at neuraminidase position 151 of influenza A (H1N1)pdm09 virus in clinical specimens. J Gen Virol 2019; 100:752-759. [PMID: 30994443 DOI: 10.1099/jgv.0.001258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Influenza A virus mutates rapidly, allowing it to escape natural and vaccine-induced immunity. Neuraminidase (NA) is a surface protein capable of cleaving the glycosidic linkages of neuraminic acids to release newly formed virions from infected cells. Genetic variants within a viral population can influence the emergence of pandemic viruses as well as drug susceptibility and vaccine effectiveness. In the present study, 55 clinical specimens from patients infected with the 2009 pandemic influenza A/H1N1 virus, abbreviated as A(H1N1)pdm09, during the 2015-2016 outbreak season in Taiwan were collected. Whole genomes were obtained through next-generation sequencing. Based on the published sequences from A(H1N1)pdm09 strains worldwide, a mixed population of two distinct variants at NA position 151 was revealed. We initially reasoned that such a mixed population may have emerged during cell culture. However, additional investigations confirmed that these mixed variants were detectable in the specimens of patients. To further investigate the role of the two NA-151 variants in a dynamic population, a reverse genetics system was employed to generate recombinant A(H1N1)pdm09 viruses. It was observed that the mixture of the two distinct variants was characterized by a higher replication rate compared to the recombinant viruses harbouring a single variant. Moreover, an NA inhibition assay revealed that a high frequency of the minor NA-151 variant in A(H1N1)pdm09 was associated with a reduced susceptibility to NA inhibitors. We conclude that two distinct NA-151 variants can be identified in patient specimens and that such variants may increase viral replication and NA activity.
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Affiliation(s)
- Yu-Nong Gong
- 1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
| | - Kuo-Chien Tsao
- 1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,3Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
| | - Guang-Wu Chen
- 1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC.,4Department of Computer Science and Information Engineering, School of Electrical and Computer Engineering, College of Engineering, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Chung-Jung Wu
- 1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Yi-Hsiang Chen
- 1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Yi-Chun Liu
- 2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
| | - Shu-Li Yang
- 2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC.,3Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Yhu-Chering Huang
- 5Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC.,6College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Shin-Ru Shih
- 2Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC.,7Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan, ROC.,1Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,3Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC
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11
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Wen F, Wan XF. Influenza Neuraminidase: Underrated Role in Receptor Binding. Trends Microbiol 2019; 27:477-479. [PMID: 30930001 DOI: 10.1016/j.tim.2019.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 01/08/2023]
Abstract
Influenza virus neuraminidase cleaves sialic acid groups from cell glycoproteins, enabling release of the virus from host cells. Neuraminidase also contributes to virus binding to the sialic acid groups of cell glycoproteins, which could complement the receptor-binding function of hemagglutinin, enhancing enzymatic activities of neuraminidase, and facilitate virus infection.
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Affiliation(s)
- Feng Wen
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Xiu-Feng Wan
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA.
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12
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Matsumoto S, Chong Y, Kang D, Ikematsu H. High genetic stability in MDCK-SIAT1 passaged human influenza viruses. J Infect Chemother 2019; 25:222-224. [DOI: 10.1016/j.jiac.2018.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/12/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
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13
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Shirogane Y, Watanabe S, Yanagi Y. Cooperation between different variants: A unique potential for virus evolution. Virus Res 2019; 264:68-73. [PMID: 30822430 DOI: 10.1016/j.virusres.2019.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/25/2019] [Indexed: 02/05/2023]
Abstract
RNA viruses exist as quasispecies containing many variants within their populations because of the error prone nature of viral RNA-dependent RNA polymerases. Quasispecies are not a simple collection of individual variants. Instead, internal interactions among variants provide quasispecies with unique evolvability. An example is 'cooperation' between wild-type and defective measles viruses, in which co-existence of a wild-type and a mutant genome produces a new phenotype. Such internal interactions presuppose efficient co-transmission of multiple genomes to the same cell, which is achieved by polyploid virions of some virus families or by a high multiplicity of infection. Recent studies have revealed that multiple viral genomes can also be transmitted simultaneously ('bloc transmission') by other mechanisms, strengthening the concept of internal interactions among viral quasispecies. Elucidation of the mechanisms of virus evolution, including internal interactions and bloc transmission, may provide rational strategies to solve such important problems of virus infections as drug-resistance, immune evasion, and acquisition of the new tropism and host range.
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Affiliation(s)
- Yuta Shirogane
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
| | - Shumpei Watanabe
- Department of Microbiology, Faculty of Veterinary Medicine, Okayama University of Science, Ehime, 794-0085, Japan
| | - Yusuke Yanagi
- Department of Virology, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan.
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14
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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15
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Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
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16
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Goodacre N, Devkota P, Bae E, Wuchty S, Uetz P. Protein-protein interactions of human viruses. Semin Cell Dev Biol 2018; 99:31-39. [PMID: 30031213 PMCID: PMC7102568 DOI: 10.1016/j.semcdb.2018.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 04/02/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
Abstract
Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understanding of viral infection mechanisms, disease etiology and the development of new drugs. In this review, we primarily survey human host-virus interaction data that are available from public databases following the standardized PSI-MS format. Notably, available host-virus protein interaction information is strongly biased toward a small number of virus families including herpesviridae, papillomaviridae, orthomyxoviridae and retroviridae. While we explore the reliability and relevance of these protein interactions we also survey the current knowledge about viruses functional and topological targets. Furthermore, we assess emerging frontiers of host-virus protein interaction research, focusing on protein interaction interfaces of hosts that are infected by different viruses and viruses that infect multiple hosts. Finally, we cover the current status of research that investigates the relationships of virus-targeted host proteins to other comorbidities as well as the influence of host-virus protein interactions on human metabolism.
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Affiliation(s)
- Norman Goodacre
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Prajwal Devkota
- Dept. of Computer Science, Univ. of Miami, Coral Gables, FL, 33146, USA
| | - Eunhae Bae
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Stefan Wuchty
- Dept. of Computer Science, Univ. of Miami, Coral Gables, FL, 33146, USA; Center for Computational Science, Univ. of Miami, Coral Gables, FL, 33146, USA; Dept. of Biology, Univ. of Miami, Coral Gables, FL, 33146, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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17
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Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation. mBio 2018; 9:mBio.00898-18. [PMID: 29970463 PMCID: PMC6030562 DOI: 10.1128/mbio.00898-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Human parainfluenza viruses cause a large burden of human respiratory illness. While much research relies upon viruses grown in cultured immortalized cells, human parainfluenza virus 3 (HPIV-3) evolves in culture. Cultured viruses differ in their properties compared to clinical strains. We present a genome-wide survey of HPIV-3 adaptations to culture using metagenomic next-generation sequencing of matched pairs of clinical samples and primary culture isolates (zero passage virus). Nonsynonymous changes arose during primary viral isolation, almost entirely in the genes encoding the two surface glycoproteins-the receptor binding protein hemagglutinin-neuraminidase (HN) or the fusion protein (F). We recovered genomes from 95 HPIV-3 primary culture isolates and 23 HPIV-3 strains directly from clinical samples. HN mutations arising during primary viral isolation resulted in substitutions at HN's dimerization/F-interaction site, a site critical for activation of viral fusion. Alterations in HN dimer interface residues known to favor infection in culture occurred within 4 days (H552 and N556). A novel cluster of residues at a different face of the HN dimer interface emerged (P241 and R242) and imply a role in HPIV-3-mediated fusion. Functional characterization of these culture-associated HN mutations in a clinical isolate background revealed acquisition of the fusogenic phenotype associated with cultured HPIV-3; the HN-F complex showed enhanced fusion and decreased receptor-cleaving activity. These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses.IMPORTANCE Human parainfluenza virus 3 is an important cause of morbidity and mortality among infants, the immunocompromised, and the elderly. Using deep genomic sequencing of HPIV-3-positive clinical material and its subsequent viral isolate, we discover a number of known and novel coding mutations in the main HPIV-3 attachment protein HN during brief exposure to immortalized cells. These mutations significantly alter function of the fusion complex, increasing fusion promotion by HN as well as generally decreasing neuraminidase activity and increasing HN-receptor engagement. These results show that viruses may evolve rapidly in culture even during primary isolation of the virus and before the first passage and reveal features of fitness for humans that are obscured by rapid adaptation to laboratory conditions.
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18
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Leeks A, Segredo-Otero EA, Sanjuán R, West SA. Beneficial coinfection can promote within-host viral diversity. Virus Evol 2018; 4:vey028. [PMID: 30288300 PMCID: PMC6166523 DOI: 10.1093/ve/vey028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In many viral infections, a large number of different genetic variants can coexist within a host, leading to more virulent infections that are better able to evolve antiviral resistance and adapt to new hosts. But how is this diversity maintained? Why do faster-growing variants not outcompete slower-growing variants, and erode this diversity? One hypothesis is if there are mutually beneficial interactions between variants, with host cells infected by multiple different viral genomes producing more, or more effective, virions. We modelled this hypothesis with both mathematical models and simulations, and found that moderate levels of beneficial coinfection can maintain high levels of coexistence, even when coinfection is relatively rare, and when there are significant fitness differences between competing variants. Rare variants are more likely to be coinfecting with a different variant, and hence beneficial coinfection increases the relative fitness of rare variants through negative frequency dependence, and maintains diversity. We further find that coexisting variants sometimes reach unequal frequencies, depending on the extent to which different variants benefit from coinfection, and the ratio of variants which leads to the most productive infected cells. These factors could help drive the evolution of defective interfering particles, and help to explain why the different segments of multipartite viruses persist at different equilibrium frequencies.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ernesto A Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València, València, Spain
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, UK
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19
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Goya S, Valinotto LE, Tittarelli E, Rojo GL, Nabaes Jodar MS, Greninger AL, Zaiat JJ, Marti MA, Mistchenko AS, Viegas M. An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates. PLoS One 2018; 13:e0199714. [PMID: 29940028 PMCID: PMC6016902 DOI: 10.1371/journal.pone.0199714] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/12/2018] [Indexed: 11/25/2022] Open
Abstract
Over the last decade, the number of viral genome sequences deposited in available databases has grown exponentially. However, sequencing methodology vary widely and many published works have relied on viral enrichment by viral culture or nucleic acid amplification with specific primers rather than through unbiased techniques such as metagenomics. The genome of RNA viruses is highly variable and these enrichment methodologies may be difficult to achieve or may bias the results. In order to obtain genomic sequences of human respiratory syncytial virus (HRSV) from positive nasopharyngeal aspirates diverse methodologies were evaluated and compared. A total of 29 nearly complete and complete viral genomes were obtained. The best performance was achieved with a DNase I treatment to the RNA directly extracted from the nasopharyngeal aspirate (NPA), sequence-independent single-primer amplification (SISPA) and library preparation performed with Nextera XT DNA Library Prep Kit with manual normalization. An average of 633,789 and 1,674,845 filtered reads per library were obtained with MiSeq and NextSeq 500 platforms, respectively. The higher output of NextSeq 500 was accompanied by the increasing of duplicated reads percentage generated during SISPA (from an average of 1.5% duplicated viral reads in MiSeq to an average of 74% in NextSeq 500). HRSV genome recovery was not affected by the presence or absence of duplicated reads but the computational demand during the analysis was increased. Considering that only samples with viral load ≥ E+06 copies/ml NPA were tested, no correlation between sample viral loads and number of total filtered reads was observed, nor with the mapped viral reads. The HRSV genomes showed a mean coverage of 98.46% with the best methodology. In addition, genomes of human metapneumovirus (HMPV), human rhinovirus (HRV) and human parainfluenza virus types 1–3 (HPIV1-3) were also obtained with the selected optimal methodology.
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Affiliation(s)
- Stephanie Goya
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura E. Valinotto
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Estefania Tittarelli
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Gabriel L. Rojo
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
| | - Mercedes S. Nabaes Jodar
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Ministerio de Salud de la Ciudad de Buenos Aires, Buenos Aires, Argentina
| | - Alexander L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jonathan J. Zaiat
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
- Argentine Bioinformatic Platform (BIA), Buenos Aires, Argentina
| | - Marcelo A. Marti
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
- Argentine Bioinformatic Platform (BIA), Buenos Aires, Argentina
| | - Alicia S. Mistchenko
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Comisión de Investigaciones Científicas (CIC), Buenos Aires, Argentina
| | - Mariana Viegas
- Ricardo Gutiérrez Children’s Hospital, Ciudad Autónoma Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
- * E-mail:
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