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Bhat T, Cao A, Yin J. Virus-like Particles: Measures and Biological Functions. Viruses 2022; 14:383. [PMID: 35215979 PMCID: PMC8877645 DOI: 10.3390/v14020383] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
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Affiliation(s)
| | | | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA; (T.B.); (A.C.)
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2
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Yang Y, Lyu T, Zhou R, He X, Ye K, Xie Q, Zhu L, Chen T, Shen C, Wu Q, Zhang B, Zhao W. The Antiviral and Antitumor Effects of Defective Interfering Particles/Genomes and Their Mechanisms. Front Microbiol 2019; 10:1852. [PMID: 31447826 PMCID: PMC6696905 DOI: 10.3389/fmicb.2019.01852] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Defective interfering particles (DIPs), derived naturally from viral particles, are not able to replicate on their own. Several studies indicate that DIPs exert antiviral effects via multiple mechanisms. DIPs are able to activate immune responses and suppress virus replication cycles, such as competing for viral replication products, impeding the packaging, release and invasion of viruses. Other studies show that DIPs can be used as a vaccine against viral infection. Moreover, DIPs/DI genomes display antitumor effects by inducing tumor cell apoptosis and promoting dendritic cell maturation. With genetic modified techniques, it is possible to improve its safety against both viruses and tumors. In this review, a comprehensive discussion on the effects exerted by DIPs is provided. We further highlight the clinical significance of DIPs and propose that DIPs can open up a new platform for antiviral and antitumor therapies.
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Affiliation(s)
- Yicheng Yang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.,The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Taibiao Lyu
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Runing Zhou
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Xiaoen He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Kaiyan Ye
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Qian Xie
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Zhu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Tingting Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Chu Shen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qinghua Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Bao Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
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3
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Abstract
Defective viral genomes (DVGs) are generated during viral replication and are unable to carry out a full replication cycle unless coinfected with a full-length virus. DVGs are produced by many viruses, and their presence correlates with alterations in infection outcomes. Historically, DVGs were studied for their ability to interfere with standard virus replication as well as for their association with viral persistence. More recently, a critical role for DVGs in inducing the innate immune response during infection was appreciated. Here we review the role of DVGs of RNA viruses in shaping outcomes of experimental as well as natural infections and explore the mechanisms by which DVGs impact infection outcome.
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Affiliation(s)
- Emmanuelle Genoyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - Carolina B López
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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4
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Chao L, Elena SF. Nonlinear trade-offs allow the cooperation game to evolve from Prisoner's Dilemma to Snowdrift. Proc Biol Sci 2017; 284:20170228. [PMID: 28490625 PMCID: PMC5443946 DOI: 10.1098/rspb.2017.0228] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/10/2017] [Indexed: 01/21/2023] Open
Abstract
The existence of cooperation, or the production of public goods, is an evolutionary problem. Cooperation is not favoured because the Prisoner's Dilemma (PD) game drives cooperators to extinction. We have re-analysed this problem by using RNA viruses to motivate a model for the evolution of cooperation. Gene products are the public goods and group size is the number of virions co-infecting the same host cell. Our results show that if the trade-off between replication and production of gene products is linear, PD is observed. However, if the trade-off is nonlinear, the viruses evolve into separate lineages of ultra-defectors and ultra-cooperators as group size is increased. The nonlinearity was justified by the existence of real viral ultra-defectors, known as defective interfering particles, which gain a nonlinear advantage by being smaller. The evolution of ultra-defectors and ultra-cooperators creates the Snowdrift game, which promotes high-level production of public goods.
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Affiliation(s)
- Lin Chao
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- Instituto de Biología Integrativa y de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Catedrático Agustín Escardino 9, 46182 Paterna, Valencia, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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5
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Membranous replication factories induced by plus-strand RNA viruses. Viruses 2014; 6:2826-57. [PMID: 25054883 PMCID: PMC4113795 DOI: 10.3390/v6072826] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/02/2014] [Accepted: 06/24/2014] [Indexed: 12/13/2022] Open
Abstract
In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments.
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6
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Maeda A, Maeda J, Takagi H, Kurane I. Detection of small RNAs containing the 5'- and the 3'-end sequences of viral genome during West Nile virus replication. Virology 2007; 371:130-8. [PMID: 17963811 DOI: 10.1016/j.virol.2007.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 07/31/2007] [Accepted: 09/18/2007] [Indexed: 10/22/2022]
Abstract
In the first step of flavivirus replication, the 5'-end of viral genomic RNA is thought to interact with the 3'-end of the genomic RNA at the complimentary sequences (CSs) located at both ends of the genomic RNA. However, there is little evidence of direct interaction between the two ends of the viral genomic RNA in virus-replicating cells. Herein, we show that viral small negative-strand RNA species, composed of two ends corresponding to the upstream of the 5'-end CS and the downstream of the 3'-end CS of viral genomic RNA, were synthesized during viral replication. We hypothesized that the viral small negative-sense RNAs were synthesized during viral negative-sense RNA synthesis through the template-jumping of viral RNA-dependent RNA polymerase from the 3'-end to the 5'-end of viral genomic RNA used as a template. Our present results strongly indicate that the two ends of viral genomic RNA associate with each other during viral replication.
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Affiliation(s)
- Akihiko Maeda
- Department of Prion Diseases, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan.
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7
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Vinayagamoorthy T, Mulatz K, Drebot M, Hodkinson R. Molecular typing of West Nile Virus, Dengue, and St. Louis encephalitis using multiplex sequencing. J Mol Diagn 2005; 7:152-9. [PMID: 15858138 PMCID: PMC1867533 DOI: 10.1016/s1525-1578(10)60541-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2004] [Indexed: 11/16/2022] Open
Abstract
We report the development of an assay to simultaneously identify three of the clinically important flaviviruses (West Nile Virus, Dengue, and St. Louis encephalitis). This assay is based on the nucleotide sequence variations within a 266-bp region of the non-structural protein 5. Further, based on the nucleotide variations in the same region of the non-structural protein 5, four of the present Dengue serotypes were identified. To identify some of the subtypes of WNV we have developed a second assay using multiplex sequencing technology. The format of the result of this assay is an electropherogram of two genomic segments of the WNV genome: a 48-nucleotide sequence from the anchored core protein C and a 45-nucleotide sequence coding for the non-structural proteins (proteinase and putative helicase genes).
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8
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Urosevic N, Shellam GR. Host genetic resistance to Japanese encephalitis group viruses. Curr Top Microbiol Immunol 2002; 267:153-70. [PMID: 12082988 DOI: 10.1007/978-3-642-59403-8_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
MESH Headings
- Animals
- Animals, Wild/genetics
- Animals, Wild/immunology
- Chromosome Mapping
- Cloning, Molecular
- Defective Viruses/immunology
- Encephalitis Viruses, Japanese/classification
- Encephalitis Viruses, Japanese/immunology
- Encephalitis Viruses, Japanese/physiology
- Encephalitis, Arbovirus/genetics
- Encephalitis, Arbovirus/immunology
- Flavivirus Infections/genetics
- Flavivirus Infections/immunology
- Humans
- Immunity, Innate/genetics
- Mice
- Mice, Congenic
- Virus Replication
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Affiliation(s)
- N Urosevic
- Department of Microbiology, University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands 6907, Australia
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9
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Abstract
Almost all viruses produce replication-defective mutants that have complex effects on the growth and evolution of the virus in culture. These effects can be explained qualitatively by a simple mathematical model. However, the model shows that the quantitative effects of these mutants are intrinsically unpredictable.
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Affiliation(s)
- C R Bangham
- Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
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10
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Sangster MY, Heliams DB, MacKenzie JS, Shellam GR. Genetic studies of flavivirus resistance in inbred strains derived from wild mice: evidence for a new resistance allele at the flavivirus resistance locus (Flv). J Virol 1993; 67:340-7. [PMID: 8380081 PMCID: PMC237368 DOI: 10.1128/jvi.67.1.340-347.1993] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Studies of genetic resistance to flavivirus infection in laboratory mice have led to the development of a single model in which resistance is conferred by an autosomal dominant gene designated Flvr. Because of evidence suggesting that wild mice carry virus resistance genes which are not present in laboratory mice, we compared flavivirus resistance in the inbred strains CASA/Rk, CAST/Ei, and MOLD/Rk, which are derived directly from wild mice, and the congenic strains C3H/RV (Flvr/Flvr) and C3H/HeJ (Flvs/Flvs). Resistance to the Murray Valley encephalitis virus strain OR2 and the 17D vaccine strain of yellow fever virus was assessed by determining the lethality of intracerebral infection and by measuring virus replication in the brain. The resistance of the CASA/Rk and CAST/Ei strains resembled the resistance of C3H/RV mice, whereas the resistance of the MOLD/Rk strain was intermediate between those of C3H/RV and C3H/HeJ mice. Genetic analyses showed that resistance in both the CASA/Rk and MOLD/Rk strains is conferred by single autosomal dominant alleles at the Flv locus. Our data indicate that flavivirus resistance in the CASA/Rk strain is due to a gene which is similar or identical to Flvr, whereas resistance in the MOLD/Rk strain is due to a previously undescribed gene which we designate Flvmr to indicate minor resistance to flavivirus infection. Since genetic resistance to flaviviruses is rare in laboratory mice, the CASA/Rk and MOLD/Rk strains will be valuable for further investigation of this phenomenon.
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Affiliation(s)
- M Y Sangster
- Department of Microbiology, University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands
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11
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Roux L, Simon AE, Holland JJ. Effects of defective interfering viruses on virus replication and pathogenesis in vitro and in vivo. Adv Virus Res 1991; 40:181-211. [PMID: 1957718 PMCID: PMC7131706 DOI: 10.1016/s0065-3527(08)60279-1] [Citation(s) in RCA: 181] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DI viruses and defective viruses generally are widespread in nature. Laboratory studies show that they can sometimes exert powerful disease-modulating effects (either attenuation or intensification of symptoms). Their role in nature remains largely unexplored, despite recent suggestive evidence for their importance in a number of systems.
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Affiliation(s)
- L Roux
- Département de Microbiologie, CMU, Geneva, Switzerland
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12
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Giachetti C, Holland JJ. Altered replicase specificity is responsible for resistance to defective interfering particle interference of an Sdi- mutant of vesicular stomatitis virus. J Virol 1988; 62:3614-21. [PMID: 2843664 PMCID: PMC253502 DOI: 10.1128/jvi.62.10.3614-3621.1988] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The in vitro resistance of an Sdi- mutant of vesicular stomatitis virus to interference by wild-type defective interfering (DI) particles was expressed quantitatively in a cell-free replication system derived from mutant-infected cells. Added wild-type DI particle templates were replicated very poorly by extracts of Sdi- mutant-infected cells. However, the addition of purified viral polymerase (a complex of L and NS proteins) from wild-type vesicular stomatitis virus allowed efficient replication of wild-type DI particle genomes in these cell extracts. Added wild-type NS protein alone did not complement DI particle genome replication in these cell extracts, but it did complement a defect in the in vitro transcriptional activity of Sdi- mutant virus. These results clearly implicate the vesicular stomatitis virus polymerase complex in the inability of Sdi- mutants to replicate DI particles and in the quantitative escape from DI particle interference in evolving virus populations.
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Affiliation(s)
- C Giachetti
- Center for Molecular Genetics, University of California, San Diego, La Jolla 92093
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13
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DePolo NJ, Giachetti C, Holland JJ. Continuing coevolution of virus and defective interfering particles and of viral genome sequences during undiluted passages: virus mutants exhibiting nearly complete resistance to formerly dominant defective interfering particles. J Virol 1987; 61:454-64. [PMID: 3027375 PMCID: PMC253969 DOI: 10.1128/jvi.61.2.454-464.1987] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We quantitatively analyzed the interference interactions between defective interfering (DI) particles and mutants of cloned vesicular stomatitis virus passaged undiluted hundreds of times in BHK-21 cells. DI particles which predominated at different times in these serial passages always interfered most strongly (and very efficiently) with virus isolated a number of passages before the isolation of the DI particles. Virus isolated at the same passage level as the predominant DI particles usually exhibited severalfold resistance to these DI particles. Virus mutants (Sdi- mutants) isolated during subsequent passages always showed increasing resistance to these DI particles, followed by decreasing resistance as new DI particles arose to predominate and exert their own selective pressures on the virus mutant population. It appears that such coevolution of virus and DI particle populations proceeds indefinitely through multiple cycles of selection of virus mutants resistant to a certain DI particle (or DI particle class), followed by mutants resistant to a newly predominant DI particle, etc. At the peak of resistance, virus mutants were isolated which were essentially completely resistant to a particular DI particle; i.e., they were several hundred thousand-fold resistant, and they formed plaques of normal size and numbers in the presence of extremely high multiplicities of the DI particle. However, they were sensitive to interference by other DI particles. Recurring population interactions of this kind can promote rapid virus evolution. Complete sequencing of the N (nucleocapsid) and NS (polymerase associated) genes of numerous Sdi- mutants collected at passage intervals showed very few changes in the NS protein, but the N gene gradually accumulated a series of stable nucleotide and amino acid substitutions, some of which correlated with extensive changes in the Sdi- phenotype. Likewise, the 5' termini (and their complementary plus-strand 3' termini) continued to accumulate extensive base substitutions which were strikingly confined to the first 47 nucleotides. We also observed addition and deletion mutations in noncoding regions of the viral genome at a level suggesting that they probably occur at a high frequency throughout the genome, but usually with lethal or debilitating consequences when they occur in coding regions.
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Brinton MA, Fernandez AV, Dispoto JH. The 3'-nucleotides of flavivirus genomic RNA form a conserved secondary structure. Virology 1986; 153:113-21. [PMID: 3016981 DOI: 10.1016/0042-6822(86)90012-7] [Citation(s) in RCA: 181] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The terminal noncoding regions of viral RNA genomes are presumed to contain signal sequences and sometimes also secondary structures involved in regulating viral RNA synthesis. Such signals would be expected to be highly conserved among related viruses. In order to identify replication signal features for flaviviruses we have compared the 3'-terminal nucleotide sequences of West Nile virus (WNV), Saint Louis encephalitis (SLE) virus, and yellow fever virus (YFV) genome RNAs. The existence of a stable 3'-terminal secondary structure was previously predicted by a cDNA sequence obtained from YFV genome RNA. We have confirmed the existence of this structure by direct RNA sequencing methods. Even though the size and shape of the 3'-terminal secondary structure is highly conserved, sequence conservation is restricted to the loop regions of the secondary structure and to 27 nucleotides immediately adjacent to the 5' side of the structure. The regions of conserved sequence represent likely signals for viral polymerase recognition and binding. However, the preservation of the configuration of the secondary structure by a means other than sequence conservation indicate that this structure is important for the survival of the virus. A WNV mutant, which replicates progeny genome RNA more efficiently than parental WNV, was found to have a 3'-genomic sequence identical to that of its parent virus. The sequence change conferring the phenotype of this mutant is therefore located in another region of the genome.
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Abstract
A specific, saturable receptor for rabies virus was analyzed on cultured cells of neural or non-neural origin. Viral attachment kinetics were enhanced by DEAE-dextran, an effect which in turn enhanced the apparent infectivity of the virus inoculum. Under optimized conditions, the attachment of metabolically labeled ERA strain rabies virus obeyed the laws of mass action, whereby the amount of virus bound to cells varied proportionally with the concentration of cells or virus. Attachment was sensitive to changes of temperature and pH, did not require divalent cations such as Mg2+ or Ca2+, and occurred despite prior treatment of cells with proteolytic or sialic acid-specific enzymes. Saturation of the cell surface with rabies virus could be accomplished with 3 X 10(3) to 15 X 10(3) attached virions per cell. Competition for the rabies receptor occurred with rabies nonpathogenic variant virus, RV194 -2, and vesicular stomatitis virus. Reovirus type 3, another neurotropic virus, failed to inhibit rabies virus binding, and West Nile virus only slightly inhibited rabies virus binding, suggesting independent cellular receptors were recognized by these viruses. Isolated rabies virus glycoprotein failed to compete in an equivalent manner. However, solubilization of BHK-21 cells with octylglucoside yielded a chloroform-methanol-soluble extract which blocked rabies virus attachment. The binding inhibition activity of this extract was resistant to proteases but could be destroyed by phospholipases and neuraminidase, suggesting a phospholipid or glycolipid component at the receptor site. These data provide evidence for a rhabdovirus-common mechanism for cellular attachment to cells in culture.
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