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Gusachenko ON, Woodford L, Balbirnie-Cumming K, Evans DJ. First come, first served: superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition. THE ISME JOURNAL 2021; 15:3704-3713. [PMID: 34193965 PMCID: PMC8630095 DOI: 10.1038/s41396-021-01043-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Deformed wing virus (DWV) is the most important globally distributed pathogen of honey bees and, when vectored by the ectoparasite Varroa destructor, is associated with high levels of colony losses. Divergent DWV types may differ in their pathogenicity and are reported to exhibit superinfection exclusion upon sequential infections, an inevitability in a Varroa-infested colony. We used a reverse genetic approach to investigate competition and interactions between genetically distinct or related virus strains, analysing viral load over time, tissue distribution with reporter gene-expressing viruses and recombination between virus variants. Transient competition occurred irrespective of the order of virus acquisition, indicating no directionality or dominance. Over longer periods, the ability to compete with a pre-existing infection correlated with the genetic divergence of the inoculae. Genetic recombination was observed throughout the DWV genome with recombinants accounting for ~2% of the population as determined by deep sequencing. We propose that superinfection exclusion, if it occurs at all, is a consequence of a cross-reactive RNAi response to the viruses involved, explaining the lack of dominance of one virus type over another. A better understanding of the consequences of dual- and superinfection will inform development of cross-protective honey bee vaccines and landscape-scale DWV transmission and evolution.
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Affiliation(s)
- Olesya N. Gusachenko
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - Luke Woodford
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - Katharin Balbirnie-Cumming
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
| | - David J. Evans
- grid.11914.3c0000 0001 0721 1626Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, UK
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2
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Brown DM, Zhang Y, Scheuermann RH. Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses. Microorganisms 2020; 8:microorganisms8121856. [PMID: 33255654 PMCID: PMC7759938 DOI: 10.3390/microorganisms8121856] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) are positive-sense RNA viruses, with over 50,000 nucleotide sequences publicly available. While most human infections are typically associated with mild respiratory symptoms, several different EV types have also been associated with severe human disease, especially acute flaccid paralysis (AFP), particularly with endemic members of the EV-B species and two pandemic types—EV-A71 and EV-D68—that appear to be responsible for recent widespread outbreaks. Here we review the recent literature on the prevalence, characteristics, and circulation dynamics of different enterovirus types and combine this with an analysis of the sequence coverage of different EV types in public databases (e.g., the Virus Pathogen Resource). This evaluation reveals temporal and geographic differences in EV circulation and sequence distribution, highlighting recent EV outbreaks and revealing gaps in sequence coverage. Phylogenetic analysis of the EV genus shows the relatedness of different EV types. Recombination analysis of the EV-A species provides evidence for recombination as a mechanism of genomic diversification. The absence of broadly protective vaccines and effective antivirals makes human enteroviruses important pathogens of public health concern.
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Affiliation(s)
- David M Brown
- Department of Synthetic Biology, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- La Jolla Institute for Immunology, La Jolla, CA 92065, USA
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3
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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Kempf BJ, Watkins CL, Peersen OB, Barton DJ. Picornavirus RNA Recombination Counteracts Error Catastrophe. J Virol 2019; 93:e00652-19. [PMID: 31068422 PMCID: PMC6600191 DOI: 10.1128/jvi.00652-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/24/2023] Open
Abstract
Template-dependent RNA replication mechanisms render picornaviruses susceptible to error catastrophe, an overwhelming accumulation of mutations incompatible with viability. Viral RNA recombination, in theory, provides a mechanism for viruses to counteract error catastrophe. We tested this theory by exploiting well-defined mutations in the poliovirus RNA-dependent RNA polymerase (RDRP), namely, a G64S mutation and an L420A mutation. Our data reveal two distinct mechanisms by which picornaviral RDRPs influence error catastrophe: fidelity of RNA synthesis and RNA recombination. A G64S mutation increased the fidelity of the viral polymerase and rendered the virus resistant to ribavirin-induced error catastrophe, but only when RNA recombination was at wild-type levels. An L420A mutation in the viral polymerase inhibited RNA recombination and exacerbated ribavirin-induced error catastrophe. Furthermore, when RNA recombination was substantially reduced by an L420A mutation, a high-fidelity G64S polymerase failed to make the virus resistant to ribavirin. These data indicate that viral RNA recombination is required for poliovirus to evade ribavirin-induced error catastrophe. The conserved nature of L420 within RDRPs suggests that RNA recombination is a common mechanism for picornaviruses to counteract and avoid error catastrophe.IMPORTANCE Positive-strand RNA viruses produce vast amounts of progeny in very short periods of time via template-dependent RNA replication mechanisms. Template-dependent RNA replication, while efficient, can be disadvantageous due to error-prone viral polymerases. The accumulation of mutations in viral RNA genomes leads to error catastrophe. In this study, we substantiate long-held theories regarding the advantages and disadvantages of asexual and sexual replication strategies among RNA viruses. In particular, we show that picornavirus RNA recombination counteracts the negative consequences of asexual template-dependent RNA replication mechanisms, namely, error catastrophe.
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Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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5
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Woodman A, Lee KM, Janissen R, Gong YN, Dekker NH, Shih SR, Cameron CE. Predicting Intraserotypic Recombination in Enterovirus 71. J Virol 2019; 93:e02057-18. [PMID: 30487277 PMCID: PMC6364027 DOI: 10.1128/jvi.02057-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses are well known for their ability to cause neurological damage and paralysis. The model enterovirus is poliovirus (PV), the causative agent of poliomyelitis, a condition characterized by acute flaccid paralysis. A related virus, enterovirus 71 (EV-A71), causes similar clinical outcomes in recurrent outbreaks throughout Asia. Retrospective phylogenetic analysis has shown that recombination between circulating strains of EV-A71 produces the outbreak-associated strains which exhibit increased virulence and/or transmissibility. While studies on the mechanism(s) of recombination in PV are ongoing in several laboratories, little is known about factors that influence recombination in EV-A71. We have developed a cell-based assay to study recombination of EV-A71 based upon previously reported assays for poliovirus recombination. Our results show that (i) EV-A71 strain type and RNA sequence diversity impacts recombination frequency in a predictable manner that mimics the observations found in nature; (ii) recombination is primarily a replicative process mediated by the RNA-dependent RNA polymerase; (iii) a mutation shown to reduce recombination in PV (L420A) similarly reduces EV-A71 recombination, suggesting conservation in mechanism(s); and (iv) sequencing of intraserotypic recombinant genomes indicates that template switching occurs by a mechanism that may require some sequence homology at the recombination junction and that the triggers for template switching may be sequence independent. The development of this recombination assay will permit further investigation on the interplay between replication, recombination and disease.IMPORTANCE Recombination is a mechanism that contributes to genetic diversity. We describe the first assay to study EV-A71 recombination. Results from this assay mimic what is observed in nature and can be used by others to predict future recombination events within the enterovirus species A group. In addition, our results highlight the central role played by the viral RNA-dependent RNA polymerase (RdRp) in the recombination process. Further, our results show that changes to a conserved residue in the RdRp from different species groups have a similar impact on viable recombinant virus yields, which is indicative of conservation in mechanism.
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Affiliation(s)
- Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research 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
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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6
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Garcia-Ruiz H, Diaz A, Ahlquist P. Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments. Viruses 2018; 10:v10030131. [PMID: 29543718 PMCID: PMC5869524 DOI: 10.3390/v10030131] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/27/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV) replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules) to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
| | - Arturo Diaz
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Howard Hughes Medical Institute and Morgridge Institute for Research, University of Wisconsin-Madison, MadisonWI 53706, USA.
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7
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Erickson AK, Jesudhasan PR, Mayer MJ, Narbad A, Winter SE, Pfeiffer JK. Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination. Cell Host Microbe 2018; 23:77-88.e5. [PMID: 29290575 PMCID: PMC5764776 DOI: 10.1016/j.chom.2017.11.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/25/2017] [Accepted: 11/15/2017] [Indexed: 01/12/2023]
Abstract
RNA viruses exist in genetically diverse populations due to high levels of mutations, many of which reduce viral fitness. Interestingly, intestinal bacteria can promote infection of several mammalian enteric RNA viruses, but the mechanisms and consequences are unclear. We screened a panel of 41 bacterial strains as a platform to determine how different bacteria impact infection of poliovirus, a model enteric virus. Most bacterial strains, including those extracted from cecal contents of mice, bound poliovirus, with each bacterium binding multiple virions. Certain bacterial strains increased viral co-infection of mammalian cells even at a low virus-to-host cell ratio. Bacteria-mediated viral co-infection correlated with bacterial adherence to cells. Importantly, bacterial strains that induced viral co-infection facilitated genetic recombination between two different viruses, thereby removing deleterious mutations and restoring viral fitness. Thus, bacteria-virus interactions may increase viral fitness through viral recombination at initial sites of infection, potentially limiting abortive infections.
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Affiliation(s)
- Andrea K Erickson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Palmy R Jesudhasan
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Melinda J Mayer
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Arjan Narbad
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UA, UK
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA
| | - Julie K Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9048, USA.
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8
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Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication. J Virol 2016; 90:6864-6883. [PMID: 27194768 PMCID: PMC4944275 DOI: 10.1128/jvi.00469-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/11/2016] [Indexed: 11/20/2022] Open
Abstract
The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. IMPORTANCE Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within replication complexes, and understanding this process can facilitate the development of novel therapeutic strategies. Many of the nonstructural proteins involved in replication possess multiple functions in the viral life cycle, some of which can be supplied to the replication complex from a separate genome (i.e., in trans) while others must originate from the template (i.e., in cis). Here, we present an analysis of cis and trans activities of the RNA-dependent RNA polymerase 3D. We demonstrate a novel cis-acting role of 3D in replication. Our data suggest that this role is distinct from its enzymatic functions and requires interaction with the viral genome. Our data further the understanding of genome replication of this important pathogen.
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9
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Woodman A, Arnold JJ, Cameron CE, Evans DJ. Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination. Nucleic Acids Res 2016; 44:6883-95. [PMID: 27317698 PMCID: PMC5001610 DOI: 10.1093/nar/gkw567] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 11/13/2022] Open
Abstract
Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3′ non-coding region we have further developed a cell-based assay (the 3′CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process.
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Affiliation(s)
- Andrew Woodman
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - Jamie J Arnold
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - Craig E Cameron
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - David J Evans
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews KY16 9ST, UK
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Cassemiro KMSM, Burlandy FM, da Silva EE. Rare natural type 3/type 2 intertypic capsid recombinant vaccine-related poliovirus isolated from a case of acute flaccid paralysis in Brazil, 2015. J Gen Virol 2016; 97:1545-1550. [PMID: 27082658 DOI: 10.1099/jgv.0.000484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A natural type 3/type 2 intertypic capsid recombinant vaccine-related poliovirus was isolated from an acute flaccid paralytic case in Brazil. Genome sequencing revealed the uncommon location of the crossover site in the VP1 coding region (nucleotides 3251-3258 of Sabin 3 genome). The Sabin 2 donor sequence replaced the last 118 nt of VP1, resulting in the substitution of the complete antigenic site IIIa by PV2-specific amino acids. The low overall number of nucleotide substitutions in P1 region indicated that the predicted replication time of the isolate was about 8-9 weeks. Two of the principal determinants of attenuation in Sabin 3 genomes were mutated (U472C and C2493U), but the temperature-sensitive phenotype of the isolate was preserved. Our results support the theory that there exists a PV3/PV2 recombination hotspot site in the tail region of the VP1 capsid protein and that the recombination may occur soon after oral poliovirus vaccine administration.
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Affiliation(s)
- Klécia M S M Cassemiro
- Enterovirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fernanda M Burlandy
- Enterovirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Edson E da Silva
- Enterovirus Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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11
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Recombination among human non-polio enteroviruses: implications for epidemiology and evolution. Virus Genes 2014; 50:177-88. [PMID: 25537948 DOI: 10.1007/s11262-014-1152-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Abstract
Human enteroviruses (EV) belong to the Picornaviridae family and are among the most common viruses infecting humans. They consist of up to 100 immunologically and genetically distinct types: polioviruses, coxsackieviruses A and B, echoviruses, and the more recently characterized 43 EV types. Frequent recombinations and mutations in enteroviruses have been recognized as the main mechanisms for the observed high rate of evolution, thus enabling them to rapidly respond and adapt to new environmental challenges. The first signs of genetic exchanges between enteroviruses came from polioviruses many years ago, and since then recombination has been recognized, along with mutations, as the main cause for reversion of vaccine strains to neurovirulence. More recently, non-polio enteroviruses became the focus of many studies, where recombination was recognized as a frequent event and was correlated with the appearance of new enterovirus lineages and types. The accumulation of multiple inter- and intra-typic recombination events could also explain the series of successive emergences and disappearances of specific enterovirus types that could in turn explain the epidemic profile of circulation of several types. This review focuses on recombination among human non-polio enteroviruses from all four species (EV-A, EV-B, EV-C, and EV-D) and discusses the recombination effects on enterovirus epidemiology and evolution.
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12
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Lowry K, Woodman A, Cook J, Evans DJ. Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length 'imprecise' intermediates. PLoS Pathog 2014; 10:e1004191. [PMID: 24945141 PMCID: PMC4055744 DOI: 10.1371/journal.ppat.1004191] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 05/02/2014] [Indexed: 01/29/2023] Open
Abstract
Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of ‘evolution by duplication’ in the positive-strand RNA viruses. The rapid evolution of most positive-sense RNA viruses enables them to escape immune surveillance and adapt to new hosts. Genetic variation arises due to their error-prone RNA polymerases and by recombination of viral genomes in co-infected cells. We have developed a novel approach to analyse the poorly understood mechanism of recombination using a poliovirus model system. We characterised the initial viable recombinants and demonstrate the majority are longer than genome length due to an imprecise crossover event that duplicates part of the genome. These viruses are unfit, but rapidly lose the duplicated material and regain full fitness upon serial passage, a process we term resolution. We show this is a replicative recombination process by modifying the fidelity of the viral polymerase, or replication complex coalescence, using methods that have no influence on a previously reported, less efficient, non-replicative recombination mechanism. We conclude that recombination is a biphasic process involving separate generation and resolution events. These new insights into an important evolutionary mechanism have implications for our understanding of virus evolution through partial genome duplication, they suggest ways in which recombination might be modified and provides an approach that may be exploited to analyse recombination in other RNA viruses.
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Affiliation(s)
- Kym Lowry
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Andrew Woodman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jonathan Cook
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David J. Evans
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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13
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Galli A, Bukh J. Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus. Trends Microbiol 2014; 22:354-64. [DOI: 10.1016/j.tim.2014.02.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 12/17/2022]
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14
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Rhinoviruses. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7120790 DOI: 10.1007/978-1-4899-7448-8_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Inoue T, Tsai B. How viruses use the endoplasmic reticulum for entry, replication, and assembly. Cold Spring Harb Perspect Biol 2013; 5:a013250. [PMID: 23284050 DOI: 10.1101/cshperspect.a013250] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To cause infection, a virus enters a host cell, replicates, and assembles, with the resulting new viral progeny typically released into the extracellular environment to initiate a new infection round. Virus entry, replication, and assembly are dynamic and coordinated processes that require precise interactions with host components, often within and surrounding a defined subcellular compartment. Accumulating evidence pinpoints the endoplasmic reticulum (ER) as a crucial organelle supporting viral entry, replication, and assembly. This review focuses on the molecular mechanism by which different viruses co-opt the ER to accomplish these crucial infection steps. Certain bacterial toxins also hijack the ER for entry. An interdisciplinary approach, using rigorous biochemical and cell biological assays coupled with advanced microscopy strategies, will push to the next level our understanding of the virus-ER interaction during infection.
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Affiliation(s)
- Takamasa Inoue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48103, USA
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16
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Reiter J, Pérez-Vilaró G, Scheller N, Mina LB, Díez J, Meyerhans A. Hepatitis C virus RNA recombination in cell culture. J Hepatol 2011; 55:777-83. [PMID: 21334392 DOI: 10.1016/j.jhep.2010.12.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 12/14/2010] [Accepted: 12/20/2010] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The Hepatitis C virus (HCV) exhibits large genetic diversity, both on a global scale and at the level of the infected individual. A major underlying mechanism of the observed sequence differences is error-prone virus replication by the viral RNA polymerase NS5B. In addition, based on phylogenetic comparisons of patient-derived HCV sequences, there is evidence of HCV recombination. However, to date little is known about the frequency by which recombination events occur in HCV and under what conditions recombination may become important in HCV evolution. We, therefore, aimed to set up an experimental model system that would allow us to analyze and to characterize recombination events during HCV replication. METHODS A neomycin-selectable, HCV replicon-based recombination detection system was established. HCV replicons were mutated within either the neomycin-phosphotransferase gene or the NS5B polymerase. Upon co-transfection of hepatic cells lines, recombination between the mutated sites is necessary to restore the selectable phenotype. RESULTS Recombinants were readily detected with frequencies correlating to the distance between the mutations. The recombinant frequency normalized to a crossover range of one nucleotide was around 4 × 10(-8). CONCLUSIONS An experimental system to select for HCV recombinants in cell culture was successfully established. It allowed deriving first estimates of recombinant frequencies. Based on these, recombination in HCV seems rare. However, due to the rapid virus turnover and the large number of HCV-infected liver cells in vivo, it is expected that recombination will be of biological importance when strong selection pressures are operative.
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Affiliation(s)
- Jochen Reiter
- Department of Virology, Saarland University, D-66421 Hamburg, Germany
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17
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Pliaka V, Filliponi M, Kyriakopoulou Z, Ruether I, Tsakogiannis D, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Retrospective molecular and phenotypic analysis of poliovirus vaccine strains isolated in Greece. Clin Microbiol Infect 2011; 17:1554-62. [DOI: 10.1111/j.1469-0691.2011.03470.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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den Boon JA, Ahlquist P. Organelle-like membrane compartmentalization of positive-strand RNA virus replication factories. Annu Rev Microbiol 2010; 64:241-56. [PMID: 20825348 DOI: 10.1146/annurev.micro.112408.134012] [Citation(s) in RCA: 329] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Positive-strand RNA virus genome replication is invariably associated with extensively rearranged intracellular membranes. Recent biochemical and electron microscopy analyses, including three-dimensional electron microscope tomographic imaging, have fundamentally advanced our understanding of the ultrastructure and function of organelle-like RNA replication factories. Notably, for a range of positive-strand RNA viruses embodying many major differences, independent studies have revealed multiple common principles. These principles include that RNA replication often occurs inside numerous virus-induced vesicles invaginated or otherwise elaborated from a continuous, often endoplasmic reticulum-derived membrane network. Where analyzed, each such vesicle typically contains only one or a few genome replication intermediates in conjunction with many copies of viral nonstructural proteins. In addition, these genome replication compartments often are closely associated with sites of virion assembly and budding. Our understanding of these complexes is growing, providing substantial new insights into the organization, coordination, and potential control of crucial processes in virus replication.
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Affiliation(s)
- Johan A den Boon
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
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19
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Pliaka V, Achilleos C, Kyriakopoulou Z, Tsakogiannis D, Ruether IGA, Gartzonica C, Levidiotou-Stefanou S, Markoulatos P. Determination of antigenic properties of vaccine derived poliovirus strains. Vaccine 2010; 29:26-33. [DOI: 10.1016/j.vaccine.2010.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/29/2010] [Accepted: 10/10/2010] [Indexed: 10/18/2022]
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20
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Making of viral replication organelles by remodeling interior membranes. Viruses 2010; 2:2436-42. [PMID: 21994625 PMCID: PMC3185585 DOI: 10.3390/v2112436] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 10/29/2010] [Accepted: 11/01/2010] [Indexed: 12/31/2022] Open
Abstract
Positive-stranded RNA (+RNA) viruses exploit host cell machinery by subverting host proteins and membranes and altering cellular pathways during infection. To achieve robust replication, some +RNA viruses, such as poliovirus (PV), build special intracellular compartments, called viral replication organelles. A recent work from the Altan-Bonnett laboratory [1] gave new insights into the formation of poliovirus replication organelles, which are unique subcellular structures containing many individual replication complexes as a result of dynamic cellular membrane remodeling.
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21
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Abstract
Many viruses that replicate in the cytoplasm compartmentalize their genome replication and transcription in organelle-like structures that enhance replication efficiency and protection from host defenses. In particular, recent studies with diverse positive-strand RNA viruses have further elucidated the ultrastructure of membrane-bound RNA replication complexes and how these complexes function in close coordination with virion assembly and budding. The structure, function, and assembly of some positive-strand RNA virus replication complexes have parallels and potential evolutionary links with the replicative cores of double-strand RNA virus and retrovirus virions and more general similarities with the replication factories of cytoplasmic DNA viruses.
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22
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Dedepsidis E, Kyriakopoulou Z, Pliaka V, Markoulatos P. Correlation between recombination junctions and RNA secondary structure elements in poliovirus Sabin strains. Virus Genes 2010; 41:181-91. [PMID: 20640496 PMCID: PMC7089419 DOI: 10.1007/s11262-010-0512-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 06/28/2010] [Indexed: 11/25/2022]
Abstract
In order to test the hypothesis that RNA structural elements promote the distribution of certain types of recombination junctions in each one of the 2C and 3D poliovirus genomic regions (Sabin 3/Sabin 2 or Sabin 1 in 2C and Sabin 2/Sabin 1 or Sabin 3 in 3D), we searched in 2C and 3D regions of reference Sabin strains for high probability RNA structural elements that could promote recombination. Recombination junctions that were identified in clinical strains of this study, as well as in clinical strains of previous studies, were superimposed on RNA secondary structure models of 2C and 3D genomic regions. Furthermore, we created an in vitro model, based on double infection of cell-culture with two poliovirus strains, for the production and identification of recombinant Sabin strains in 2C and 3D regions. Our intention was to compare the results that refer to the correlation of recombination junctions and RNA secondary structures in 2C and 3D regions of clinical strains, with the respective results of the in vitro model. Most of the recombination junctions of the clinical strains were correlated with RNA secondary structure elements, which were identical between recombining Sabin strains, and also presented high predictive value. In consensus were, the respective results originated from the in vitro model. We propose that the distribution of specific types of recombination junctions in certain regions of Sabin strains is not fortuitous and is correlated with RNA secondary structure elements identical to both recombination partners. Furthermore, results of this study highlight an important role for the stem region of the RNA structure elements in promoting recombination.
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Affiliation(s)
- Evaggelos Dedepsidis
- Department of Biochemistry and Biotechnology, Microbiology–Virology Laboratory, University of Thessaly, 26 Ploutonos and Aiolou Str., Larisa, 41221 Greece
| | - Zaharoula Kyriakopoulou
- Department of Biochemistry and Biotechnology, Microbiology–Virology Laboratory, University of Thessaly, 26 Ploutonos and Aiolou Str., Larisa, 41221 Greece
| | - Vaia Pliaka
- Department of Biochemistry and Biotechnology, Microbiology–Virology Laboratory, University of Thessaly, 26 Ploutonos and Aiolou Str., Larisa, 41221 Greece
| | - Panayotis Markoulatos
- Department of Biochemistry and Biotechnology, Microbiology–Virology Laboratory, University of Thessaly, 26 Ploutonos and Aiolou Str., Larisa, 41221 Greece
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23
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Cameron CE, Oh HS, Moustafa IM. Expanding knowledge of P3 proteins in the poliovirus lifecycle. Future Microbiol 2010; 5:867-81. [PMID: 20521933 PMCID: PMC2904470 DOI: 10.2217/fmb.10.40] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Poliovirus is the most extensively studied member of the order Picornavirales, which contains numerous medical, veterinary and agricultural pathogens. The picornavirus genome encodes a single polyprotein that is divided into three regions: P1, P2 and P3. P3 proteins are known to participate more directly in genome replication, for example by containing the viral RNA-dependent RNA polymerase (RdRp or 3Dpol), among several other proteins and enzymes. We will review recent data that provide new insight into the structure, function and mechanism of P3 proteins and their complexes, which are required for initiation of genome replication. Replication of poliovirus genomes occurs within macromolecular complexes, containing viral RNA, viral proteins and host-cell membranes, collectively referred to as replication complexes. P2 proteins clearly contribute to interactions with the host cell that are required for virus multiplication, including formation of replication complexes. We will discuss recent data that suggest a role for P3 proteins in formation of replication complexes. Among the least understood steps of the poliovirus lifecycle is encapsidation of genomic RNA. We will also describe data that suggest a role for P3 proteins in this step.
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Affiliation(s)
- Craig E Cameron
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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24
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Pliaka V, Dedepsidis E, Kyriakopoulou Z, Mpirli K, Tsakogiannis D, Pratti A, Levidiotou-Stefanou S, Markoulatos P. A new RT-PCR assay for the identification of the predominant recombination types in 2C and 3D genomic regions of vaccine-derived poliovirus strains. Mol Cell Probes 2009; 24:115-23. [PMID: 19948215 DOI: 10.1016/j.mcp.2009.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 11/10/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
In the post-eradication era of wild polioviruses, the only remaining sources of poliovirus infection worldwide would be the vaccine-derived polioviruses (VDPVs). As the preponderance of countries certified to be polio-free has switched from OPV (oral poliovirus vaccine) to IPV (inactivated poliovirus vaccine), importation of recombinant evolved derivatives of vaccinal strains would have serious implication for public health. To test the robustness of the proposed RT-PCR screening analysis, eleven recombinant vaccine-derived polioviruses that were characterized previously by sequencing by our group, in addition to three recently identified recombinant environmental isolates were assayed. Although the most definitive characterization of VDPVs is by genomic sequencing, in this study we describe a new, inexpensive and broadly applicable RT-PCR assay for the identification of the predominant recombination types S3/Sx in 2C and S2/Sx in 3D genomic regions respectively of VDPVs, that can be readily implemented in laboratories lacking sequencing facilities as a first approach for the early detection of vaccine-derived poliovirus (VDPVs).
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Affiliation(s)
- V Pliaka
- University of Thessaly, School of Health Sciences, Department of Biochemistry & Biotechnology, Ploutonos 26 & Aiolou, Larissa, Greece
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25
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Site of human rhinovirus RNA uncoating revealed by fluorescent in situ hybridization. J Virol 2009; 83:3770-7. [PMID: 19158243 DOI: 10.1128/jvi.00265-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
By using fluorescent in situ hybridization (FISH), we visualized viral RNA of human rhinovirus type 2 (HRV2) during its entry into HeLa cells. RNA uncoating of HRV2 is entirely dependent on low endosomal pH (< or =5.6). When internalized into cells treated with bafilomycin, which results in neutralization of the endosomal pH, no FISH signal was recorded, whereas in the absence of the drug, fluorescent dots were seen. Therefore, FISH detects the genomic viral RNA only upon its release from the capsid. Free viral RNA was first seen at 10 min postinfection (p.i.) in the perinuclear area of the cell, which is indicative of RNA release in/from late endosomal compartments. Pulse-chase experiments and observation of HRV2 RNA and capsid proteins via microscopy, Western blotting, and reverse transcription-PCR revealed that the RNA signal persisted whereas the protein signal disappeared. This demonstrates transport of capsids to lysosomes and degradation. In contrast, viral RNA that had already been transferred into the cytoplasm escaped lysosomal breakdown as indicated by a persistent FISH signal. Taken together, our results demonstrate by direct means RNA arrival in the cytosol within 10 min p.i. Based on persistence of the FISH signal and productive infection in the presence of the microtubule-depolymerizing drug nocodazole, we localized this process to endosomal carrier vesicles/late endosomes.
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26
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Garcia-Ruiz H, Ahlquist P. Inducible yeast system for Viral RNA recombination reveals requirement for an RNA replication signal on both parental RNAs. J Virol 2006; 80:8316-28. [PMID: 16912283 PMCID: PMC1563876 DOI: 10.1128/jvi.01790-05] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
To facilitate RNA recombination studies, we tested whether Saccharomyces cerevisiae, which supports brome mosaic virus (BMV) replication, also supports BMV RNA recombination. Yeast strains expressing BMV RNA replication proteins 1a and 2a(pol) were engineered to transiently coexpress two independently inducible, overlapping, nonreplicating derivatives of BMV genomic RNA3. B3Delta3' lacked the coat protein gene and negative-strand RNA promoter. B3Delta5' lacked the positive-strand RNA promoter and had the coat gene replaced by the selectable URA3 gene. After 12 to 72 h of induction, B3Delta3' and B3Delta5' transcription was repressed and Ura(+) yeast cells were selected. All Ura(+) cells contained recombinant RNA3 replicons expressing URA3. Most replicons arose by intermolecular homologous recombination between B3Delta3' and B3Delta5'. Such recombinants were isolated only when 1a and 2a(pol) were expressed and after transient transcription of both B3Delta3' and B3Delta5', showing that recombination occurred at the RNA, not DNA, level. A minority of URA3-expressing replicons were derived from B3Delta5', independently of B3Delta3', by 5' truncation and modification, generating novel positive-strand promoters and demonstrating that BMV can give rise to subgenomic RNA replicons. Intermolecular B3Delta3'-B3Delta5' recombination occurred only when both parental RNAs bore a functional, cis-acting template recognition and recruitment element targeting viral RNAs to replication complexes. The results imply that recombination occurred in RNA replication complexes to which parental RNAs were independently recruited. Moreover, the ability to obtain intermolecular recombinants at precisely measurable, reproducible frequencies, to control genetic background and induction conditions, and other features of this system will facilitate further studies of virus and host functions in RNA recombination.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Institute for Molecular Virology and Department of Plant Pathology, University of Wisconsin--Madison, 53706 USA
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27
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Bolanaki E, Kottaridi C, Markoulatos P, Margaritis L, Katsorchis T. Evolution of 2B and 2C genomic parts of species B Coxsackie viruses. Phylogenetic study and comparison with other regions. Virus Genes 2006; 32:249-59. [PMID: 16732477 DOI: 10.1007/s11262-005-6909-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Accepted: 08/25/2005] [Indexed: 11/24/2022]
Abstract
Modern molecular approaches on the genome of enteroviruses' circulating strains have established new data about the mechanism and significance of its evolution. In the present study, 46 enteroviruses isolates, belonging to HEV-B species and exhibiting distinct origin in geographical or chronological terms, were investigated concerning their primary structure and phylogeny. Two regions of the aforementioned strains genome, which have not been thoroughly investigated (2B and 5' extreme of 2C) were amplified and sequenced for the first time. Phylogenetic and nucleotide analysis of the isolates' fragments, along with representative prototype sequences, demonstrate that the classification scheme of monophyly and accordance with the genotype, which characterizes VP1 region, is seriously disturbed. Moreover, the phylogenetic trees constructed from adjacent regions of the genome appear radically incongruent suggesting that the parameters that affect these portions are different or act in a different extent. Our study results an additional step in the study of enteroviruses evolution and inheritance, by investigating unstudied regions of newly sequenced strains and revealing that the primary structure and phylogeny of them is different not only comparably to the structural genome but also from one to another.
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Affiliation(s)
- Eugenia Bolanaki
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimioupolis, Athens, Greece.
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28
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Paximadi E, Karakasiliotis I, Mamuris Z, Stathopoulos C, Krikelis V, Markoulatos P. Genomic analysis of recombinant sabin clinical isolates. Virus Genes 2006; 32:203-10. [PMID: 16604453 DOI: 10.1007/s11262-005-6877-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 08/14/2005] [Indexed: 11/26/2022]
Abstract
Recombination in Poliovirus vaccine strains is a very frequent phenomenon. In this report 23 polio/Sabin strains isolated from healthy vaccinees or from VAPP patients after OPV administration, were investigated in order to identify recombination sites from 2C to 3D regions of the poliovirus genome. RT-PCR, followed by Restriction Fragment Length Polymorphism (RFLP) screening analysis were applied in four distant genomic regions (5' UTR, VP1, 2C and 3C-3D) in order to detect any putative recombinant. The detected recombinants were sequenced from 2C to the end of the genome (3' UTR) and the exact recombination sites were determined with computational analysis. Five of the 23 isolated strains were recombinant in one genomic region, two of them in 2C, isolates EP16:S3/S2, EP23:S3/S1, two in 3D isolates EP6:S2/S1, EP12:S2/S1 and one in 3A isolate EP9:S2/Sl. Point mutations were found in strains EP3, EP6, EP9 and EP12. Recombination specific types and sites re-occurrence along with point mutations are discussed concerning the polioviruses evolution.
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Affiliation(s)
- Eleni Paximadi
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Ploutonos, Larissa, Greece
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29
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Mackenzie J. Wrapping things up about virus RNA replication. TRAFFIC (COPENHAGEN, DENMARK) 2006. [PMID: 16190978 DOI: 10.1111/j.1600-08 54.2005.00339.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
All single-stranded 'positive-sense' RNA viruses that infect mammalian, insect or plant cells rearrange internal cellular membranes to provide an environment facilitating virus replication. A striking feature of these unique membrane structures is the induction of 70-100 nm vesicles (either free within the cytoplasm, associated with other induced vesicles or bound within a surrounding membrane) harbouring the viral replication complex (RC). Although similar in appearance, the cellular composition of these vesicles appears to vary for different viruses, implying different organelle origins for the intracellular sites of viral RNA replication. Genetic analysis has revealed that induction of these membrane structures can be attributed to a particular viral gene product, usually a non-structural protein. This review will highlight our current knowledge of the formation and composition of virus RCs and describe some of the similarities and differences in RNA-membrane interactions observed between the virus families Flaviviridae and Picornaviridae.
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Affiliation(s)
- Jason Mackenzie
- School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia.
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30
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Abstract
All single-stranded 'positive-sense' RNA viruses that infect mammalian, insect or plant cells rearrange internal cellular membranes to provide an environment facilitating virus replication. A striking feature of these unique membrane structures is the induction of 70-100 nm vesicles (either free within the cytoplasm, associated with other induced vesicles or bound within a surrounding membrane) harbouring the viral replication complex (RC). Although similar in appearance, the cellular composition of these vesicles appears to vary for different viruses, implying different organelle origins for the intracellular sites of viral RNA replication. Genetic analysis has revealed that induction of these membrane structures can be attributed to a particular viral gene product, usually a non-structural protein. This review will highlight our current knowledge of the formation and composition of virus RCs and describe some of the similarities and differences in RNA-membrane interactions observed between the virus families Flaviviridae and Picornaviridae.
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Affiliation(s)
- Jason Mackenzie
- School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia.
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31
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Egger D, Bienz K. Intracellular location and translocation of silent and active poliovirus replication complexes. J Gen Virol 2005; 86:707-718. [PMID: 15722531 DOI: 10.1099/vir.0.80442-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Replication of poliovirus (PV) genomic RNA in HeLa cells has previously been found to start at distinct sites at the nuclear periphery. In the present study, the earliest steps in the virus replication cycle, i.e. the appearance and intracellular translocation of viral protein and negative-strand RNA prior to positive-strand RNA synthesis, were followed. During translation, positive-strand RNA and newly synthesized viral protein presented as a dispersed endoplasmic reticulum (ER)-like pattern. Concomitant with translation, individual PV vesicle clusters emerged at the ER and formed nascent replication complexes, which contained newly synthesized negative-strand RNA. The complexes rapidly moved centripetally, in a microtubule-dependent way, to the perinuclear area to engage in positive-strand viral RNA synthesis. Replication complexes made transcriptionally silent with guanidine/HCl followed the anterograde membrane pathway to the Golgi complex within the microtubule-organizing centre (MTOC), whereas replication complexes active in positive-strand RNA synthesis were retained at the nuclear periphery. If the silent replication complexes that had accumulated at the MTOC were released from the guanidine block, transcription was not readily resumed. Rather, positive-strand RNA was redistributed back to the ER to start, after a lag phase, translation, followed by negative- and positive-strand RNA synthesis in replication complexes migrating to the nuclear periphery. As some of the findings appear to be in contrast to events reported in cell-free guanidine-synchronized translation/transcription systems, implications for the comparison of in vitro systems with the living cell are discussed.
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Affiliation(s)
- Denise Egger
- Institute for Medical Microbiology, University of Basel, Petersplatz 10, CH-4000 Basel, Switzerland
| | - Kurt Bienz
- Institute for Medical Microbiology, University of Basel, Petersplatz 10, CH-4000 Basel, Switzerland
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32
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Abstract
All plus-strand RNA viruses replicate in association with cytoplasmic membranes of infected cells. The RNA replication complex of many virus families is associated with the endoplasmic reticulum membranes, for example, picorna-, flavi-, arteri-, and bromoviruses. However, endosomes and lysosomes (togaviruses), peroxisomes and chloroplasts (tombusviruses), and mitochondria (nodaviruses) are also used as sites for RNA replication. Studies of individual nonstructural proteins, the virus-specific components of the RNA replicase, have revealed that the replication complexes are associated with the membranes and targeted to the respective organelle by the ns proteins rather than RNA. Many ns proteins have hydrophobic sequences and may transverse the membrane like polytopic integral membrane proteins, whereas others interact with membranes monotopically. Hepatitis C virus ns proteins offer examples of polytopic transmembrane proteins (NS2, NS4B), a “tip-anchored” protein attached to the membrane by an amphipathic α-helix (NS5A) and a “tail-anchored” posttranslationally inserted protein (NS5B). Semliki Forest virus nsP1 is attached to the plasma membrane by a specific binding peptide in the middle of the protein, which forms an amphipathic α-helix. Interaction of nsP1 with membrane lipids is essential for its capping enzyme activities. The other soluble replicase proteins are directed to the endo-lysosomal membranes only as part of the initial polyprotein. Poliovirus ns proteins utilize endoplasmic reticulum membranes from which vesicles are released in COPII coats. However, these vesicles are not directed to the normal secretory pathway, but accumulate in the cytoplasm. In many cases the replicase proteins induce membrane invaginations or vesicles, which function as protective environments for RNA replication.
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Affiliation(s)
- Mark Marsh
- Cell Biology Unit, MRC-LMCB, University College London, Gower Street, London, WC1E 6BT UK
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Abstract
Enteroviruses, members of the Picornaviridae family, comprise a large (over 70 serotypes) group of viruses that are ubiquitous in nature, infect different species and cause a wide range of diseases. Human enteroviruses were recently classified into five species, human enterovirus A-D and poliovirus. Recombination has long been known to be an important property of poliovirus genetics. Recently, several publications demonstrated that recombination is extremely frequent also in non-polio enteroviruses, and allows independent evolution of enterovirus genome fragments even on a microevolutionary scale. Prototype enterovirus strains were shown to have complex phylogenetic relations, and almost all modern enterovirus isolates turned out to be recombinants compared with the prototype strains. Recombination takes place strictly between members of the same species, and usually spares the capsid-encoding genome region. Therefore, it can be concluded that the enterovirus species exist as a worldwide reservoir of genetic material comprising a limited quantity of capsid gene sets defining a finite number of serotypes and a range of non-structural genes that recombine frequently to produce new virus variants. This new model of enterovirus genetics helps to explain the failure of previous attempts to connect serotype and disease profile in non-polio enteroviruses, and seriously questions existing typing approaches that are based solely on the capsid-encoding genome region. It remains to be determined what role recombination plays in the emergence of new enterovirus variants and in the macroevolution of animal enteroviruses and viruses of the picorna-like supergroup.
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Affiliation(s)
- Alexander N Lukashev
- Chumakov Institute of Poliomyelitis and Viral Encephalitides RAMS, Moscow, Russia.
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34
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Oberste MS, Maher K, Pallansch MA. Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven serotypes. J Virol 2004; 78:855-67. [PMID: 14694117 PMCID: PMC368751 DOI: 10.1128/jvi.78.2.855-867.2004] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The species Human enterovirus B (HEV-B) in the family Picornaviridae consists of coxsackievirus A9; coxsackieviruses B1 to B6; echoviruses 1 to 7, 9, 11 to 21, 24 to 27, and 29 to 33; and enteroviruses 69 and 73. We have determined complete genome sequences for the remaining 22 HEV-B serotypes whose sequences were not represented in public databases and analyzed these in conjunction with previously available complete sequences in GenBank. Members of HEV-B were monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5'-nontranslated region (NTR), where they are known to cluster with members of HEV-A. Within HEV-B, phylogenies constructed from the structural (P1) and nonstructural regions of the genome (P2 and P3) are incongruent, suggesting that recombination had occurred. Similarity plots and bootscanning analysis across the complete genome identified multiple sites at which the phylogeny of a given strain's sequence shifted, indicating potential recombination points. These points are distributed in the 5'-NTR and throughout P2 and P3, but no sites with >80% bootstrap support were identified within the capsid. Individual sequence comparisons and phylogenetic analyses suggest that members of HEV-B have recombined with one another on multiple occasions, resulting in a complex mosaic of sequences derived from multiple parental viruses in the nonstructural regions of the genome. We conclude that RNA recombination is a common mechanism for enterovirus evolution and that recombination within the nonstructural regions of the genome (P2 and P3) has been observed only among members of the same species.
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Affiliation(s)
- M Steven Oberste
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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