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Journal articles on the topic 'Capsid coding region'

Author: Grafiati
Published: 6 September 2023
Last updated: 19 July 2025

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1

Chinsangaram, Jarasvech, Clayton Beard, Peter W. Mason, Marla K. Zellner, Gordon Ward, and Marvin J. Grubman. "Antibody Response in Mice Inoculated with DNA Expressing Foot-and-Mouth Disease Virus Capsid Proteins." Journal of Virology 72, no. 5 (1998): 4454–57. http://dx.doi.org/10.1128/jvi.72.5.4454-4457.1998.

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ABSTRACT Candidate foot-and-mouth disease (FMD) DNA vaccines designed to produce viral capsids lacking infectious viral nucleic acid were evaluated. Plasmid DNAs containing a portion of the FMDV genome coding for the capsid precursor protein (P1-2A) and wild-type or mutant viral proteinase 3C (plasmids P12X3C or P12X3C-mut, respectively) were constructed. Cell-free translation reactions programmed with pP12X3C (wild-type 3C) and pP12X3C-mut produced a capsid precursor, but only the reactions programmed with the plasmid encoding the functional proteinase resulted in P1-2A processing and capsid
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2

Jia, Xi-Yu, Marc Van Eden, Marc G. Busch, Ellie Ehrenfeld, and Donald F. Summers. "trans-Encapsidation of a Poliovirus Replicon by Different Picornavirus Capsid Proteins." Journal of Virology 72, no. 10 (1998): 7972–77. http://dx.doi.org/10.1128/jvi.72.10.7972-7977.1998.

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ABSTRACT A trans-encapsidation assay was established to study the specificity of picornavirus RNA encapsidation. A poliovirus replicon with the luciferase gene replacing the capsid protein-coding region was coexpressed in transfected HeLa cells with capsid proteins from homologous or heterologous virus. Successfultrans-encapsidation resulted in assembly and production of virions whose replication, upon subsequent infection of HeLa cells, was accompanied by expression of luciferase activity. The amount of luciferase activity was proportional to the amount oftrans-encapsidated virus produced fro
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3

Bouslama, Lamjed, Dorsaf Nasri, Lionel Chollet, et al. "Natural Recombination Event within the Capsid Genomic Region Leading to a Chimeric Strain of Human Enterovirus B." Journal of Virology 81, no. 17 (2007): 8944–52. http://dx.doi.org/10.1128/jvi.00180-07.

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ABSTRACT Recombination between two strains is a known phenomenon for enteroviruses replicating within a single cell. We describe a recombinant strain recovered from human stools, typed as coxsackievirus B4 (CV-B4) and CV-B3 after partial sequencing of the VP1 and VP2 coding regions, respectively. The strain was neutralized by a polyclonal CV-B3-specific antiserum but not by a CV-B4-specific antiserum. The nucleotide sequence analysis of the whole structural genomic region showed the occurrence of a recombination event at position 1950 within the VP3 capsid gene, in a region coding for the 2b a
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4

Déjardin, Jérôme, Guillaume Bompard-Maréchal, Muriel Audit, Thomas J. Hope, Marc Sitbon, and Marylène Mougel. "A Novel Subgenomic Murine Leukemia Virus RNA Transcript Results from Alternative Splicing." Journal of Virology 74, no. 8 (2000): 3709–14. http://dx.doi.org/10.1128/jvi.74.8.3709-3714.2000.

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ABSTRACT Here we show the existence of a novel subgenomic 4.4-kb RNA in cells infected with the prototypic replication-competent Friend or Moloney murine leukemia viruses (MuLV). This RNA derives by splicing from an alternative donor site (SD′) within the capsid-coding region to the canonical envelope splice acceptor site. The position and the sequence of SD′ was highly conserved among mammalian type C and D oncoviruses. Point mutations used to inactivate SD′ without changing the capsid-coding ability affected viral RNA splicing and reduced viral replication in infected cells.
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5

Sasaki, Jun, and Nobuhiko Nakashima. "Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro." Journal of Virology 73, no. 2 (1999): 1219–26. http://dx.doi.org/10.1128/jvi.73.2.1219-1226.1999.

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ABSTRACT AUG-unrelated translation initiation was found in an insect picorna-like virus, Plautia stali intestine virus (PSIV). The positive-strand RNA genome of the virus contains two nonoverlapping open reading frames (ORFs). The capsid protein gene is located in the 3′-proximal ORF and lacks an AUG initiation codon. We examined the translation mechanism and the initiation codon of the capsid protein gene by using various dicistronic and monocistronic RNAs in vitro. The capsid protein gene was translated cap independently in the presence of the upstream cistron, indicating that the gene is tr
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6

Dahourou, George, Sophie Guillot, Olivier Le Gall, and Radu Crainic. "Genetic recombination in wild-type poliovirus." Journal of General Virology 83, no. 12 (2002): 3103–10. http://dx.doi.org/10.1099/0022-1317-83-12-3103.

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Poliovirus isolates were screened for recombinants by combined analysis of two distant polymorphic segments of the poliovirus genome (one in the capsid and the other in the polymerase-coding region). Using a restriction fragment length polymorphism (RFLP) assay, a high number of recombinant genomes was found among vaccine-derived strains excreted by poliovirus vaccine vaccinees or vaccine-associated paralytic poliomyelitis cases. Some of these subjects carried a wild-type poliovirus (non-vaccine-specific) nucleotide sequence in the 3′ part of the genome. Using a similar approach, a collection
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7

Harvala, Heli, Hannu Kalimo, Leif Dahllund, et al. "Mapping of tissue tropism determinants in coxsackievirus genomes." Journal of General Virology 83, no. 7 (2002): 1697–706. http://dx.doi.org/10.1099/0022-1317-83-7-1697.

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Genomic regions responsible for the different tissue tropisms of coxsackievirus A9 (CAV9) and coxsackievirus B3 (CBV3) in newborn mice were investigated using recombinant viruses. Infectious cDNA clones of CAV9, a virus known to infect striated muscle, and CBV3, affecting the central nervous system, pancreas, liver, brown fat and striated muscle, were used to generate chimeric viruses. In situ hybridization analysis of different tissues from mice infected with the recombinant viruses, constructed by exchanging the 5′ non-coding region (5′NCR), structural and non-structural genes, demonstrated
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8

Savolainen, Carita, Pia Laine, Mick N. Mulders, and Tapani Hovi. "Sequence analysis of human rhinoviruses in the RNA-dependent RNA polymerase coding region reveals large within-species variation." Journal of General Virology 85, no. 8 (2004): 2271–77. http://dx.doi.org/10.1099/vir.0.79897-0.

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Human rhinoviruses (HRVs; family Picornaviridae), the most frequent causative agents of respiratory infections, comprise more than 100 distinct serotypes. According to previous phylogenetic analysis of the VP4/VP2-coding sequences, all but one of the HRV prototype strains distribute between the two established species, Human rhinovirus A (HRV-A) and Human rhinovirus B (HRV-B). Here, partial sequences of the RNA-dependent RNA polymerase (3D polymerase)-coding gene of 48 HRV prototype strains and 12 field isolates were analysed. The designated division of the HRV strains into the species HRV-A a
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9

Shibuya, Norihiro, Takashi Nishiyama, Yasushi Kanamori, Hitoshi Saito, and Nobuhiko Nakashima. "Conditional Rather than Absolute Requirements of the Capsid Coding Sequence for Initiation of Methionine-Independent Translation in Plautia stali Intestine Virus." Journal of Virology 77, no. 22 (2003): 12002–10. http://dx.doi.org/10.1128/jvi.77.22.12002-12010.2003.

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ABSTRACT The positive-stranded RNA genome of Plautia stali intestine virus (PSIV) has an internal ribosome entry site (IRES) in an intergenic region (IGR). The IGR-IRES of PSIV initiates translation of the capsid protein by using CAA, the codon for glutamine. It was previously reported (J. Sasaki and N. Nakashima, J. Virol. 73:1219-1226, 1999) that IGR-IRES extended by several nucleotides into the capsid open reading frame (ORF). Despite the fact that the secondary structure model of the IGR-IRES is highly conserved, we were unable to find structural similarities in the 5′ region of the capsid
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10

Audit, Muriel, Jérôme Déjardin, Barbara Hohl, et al. "Introduction of a cis-Acting Mutation in the Capsid-Coding Gene of Moloney Murine Leukemia Virus Extends Its Leukemogenic Properties." Journal of Virology 73, no. 12 (1999): 10472–79. http://dx.doi.org/10.1128/jvi.73.12.10472-10479.1999.

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ABSTRACT Inoculation of newborn mice with the retrovirus Moloney murine leukemia virus (MuLV) results in the exclusive development of T lymphomas with gross thymic enlargement. The T-cell leukemogenic property of Moloney MuLV has been mapped to the U3 enhancer region of the viral promoter. However, we now describe a mutant Moloney MuLV which can induce the rapid development of a uniquely broad panel of leukemic cell types. This mutant Moloney MuLV with synonymous differences (MSD1) was obtained by introduction of nucleotide substitutions at positions 1598, 1599, and 1601 in the capsid gene whi
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11

Martín, Javier, Elena Samoilovich, Glynis Dunn, et al. "Isolation of an Intertypic Poliovirus Capsid Recombinant from a Child with Vaccine-Associated Paralytic Poliomyelitis." Journal of Virology 76, no. 21 (2002): 10921–28. http://dx.doi.org/10.1128/jvi.76.21.10921-10928.2002.

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ABSTRACT The isolation of a capsid intertypic poliovirus recombinant from a child with vaccine-associated paralytic poliomyelitis is described. Virus 31043 had a Sabin-derived type 3-type 2-type 1 recombinant genome with a 5′-end crossover point within the capsid coding region. The result was a poliovirus chimera containing the entire coding sequence for antigenic site 3a derived from the Sabin type 2 strain. The recombinant virus showed altered antigenic properties but did not acquire type 2 antigenic characteristics. The significance of the presence in nature of such poliovirus chimeras and
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12

Yong, Xin Ee, V. Raghuvamsi Palur, Ganesh S. Anand, Thorsten Wohland, and Kamal K. Sharma. "Dengue virus 2 capsid protein chaperones the strand displacement of 5′-3′ cyclization sequences." Nucleic Acids Research 49, no. 10 (2021): 5832–44. http://dx.doi.org/10.1093/nar/gkab379.

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Abstract By virtue of its chaperone activity, the capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements. However, the role of DENV2C during the interaction of RNA elements involved in stabilizing the 5′-3′ panhandle structure of DENV RNA is still unclear. Therefore, we determined how DENV2C affects structural functionality of the capsid-coding region hairpin element (cHP) during annealing and strand displacement of the 9-nt cyclization sequence (5CS) and its complementary 3CS. cHP has two distinct functions: a role in translation start codon selection
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13

Brown, Betty, M. Steven Oberste, Kaija Maher, and Mark A. Pallansch. "Complete Genomic Sequencing Shows that Polioviruses and Members of Human Enterovirus Species C Are Closely Related in the Noncapsid Coding Region." Journal of Virology 77, no. 16 (2003): 8973–84. http://dx.doi.org/10.1128/jvi.77.16.8973-8984.2003.

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ABSTRACT The 65 human enterovirus serotypes are currently classified into five species: Poliovirus (3 serotypes), Human enterovirus A (HEV-A) (12 serotypes), HEV-B (37 serotypes), HEV-C (11 serotypes), and HEV-D (2 serotypes). Coxsackie A virus (CAV) serotypes 1, 11, 13, 15, 17, 18, 19, 20, 21, 22, and 24 constitute HEV-C. We have determined the complete genome sequences for the remaining nine HEV-C serotypes and compared them with the complete sequences of CAV21, CAV24, and the polioviruses. The viruses were most diverse in the capsid region (4 to 36% amino acid difference). A high degree of
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14

Blomqvist, Soile, Carita Savolainen-Kopra, Anja Paananen, Tapani Hovi, and Merja Roivainen. "Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses." Journal of General Virology 90, no. 6 (2009): 1371–81. http://dx.doi.org/10.1099/vir.0.008508-0.

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Human rhinoviruses (HRVs), which are the most frequent causative agents of acute upper respiratory tract infections, are abundant worldwide. We have identified HRV strains in environmental specimens collected in Finland, Latvia and Slovakia during the surveillance of polio- and other enteroviruses. These acid-sensitive HRV strains were isolated under conditions optimized for growth of most of the enteroviruses, i.e. in stationary human rhabdomyosarcoma cells incubated at 36 °C. Phylogenetic analysis of the sequences derived from the partial 5′ non-coding region and the capsid region coding for
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15

McInerney, Gerald M., Andrew M. Q. King, Natalie Ross-Smith, and Graham J. Belsham. "Replication-competent foot-and-mouth disease virus RNAs lacking capsid coding sequences." Microbiology 81, no. 7 (2000): 1699–702. http://dx.doi.org/10.1099/0022-1317-81-7-1699.

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RNA transcripts were prepared from plasmids encoding an infectious cDNA of foot-and-mouth disease virus (FMDV) or derivatives in which the leader (Lab and Lb) and capsid protein coding sequences were deleted or replaced by sequences encoding chloramphenicol acetyltransferase (CAT). The transcripts were electroporated into BHK cells and the expression of CAT and the FMDV 3C protease was monitored. Detection of CAT and 3C was dependent on the ability of the transcript to replicate. All of the Lb coding sequence and 94% of P1 (the capsid protein precursor) coding sequence could be deleted without
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16

Santti, Juhana, Timo Hyypiä, Leena Kinnunen, and Mika Salminen. "Evidence of Recombination among Enteroviruses." Journal of Virology 73, no. 10 (1999): 8741–49. http://dx.doi.org/10.1128/jvi.73.10.8741-8749.1999.

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ABSTRACT Human enteroviruses consist of more than 60 serotypes, reflecting a wide range of evolutionary divergence. They have been genetically classified into four clusters on the basis of sequence homology in the coding region of the single-stranded RNA genome. To explore further the genetic relationships between human enteroviruses and to characterize the evolutionary mechanisms responsible for variation, previously sequenced genomes were subjected to detailed comparison. Bootstrap and genetic similarity analyses were used to systematically scan the alignments of complete genomic sequences.
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17

López-Bueno, Alberto, Noelia Valle, Jesús M. Gallego, Joel Pérez, and José M. Almendral. "Enhanced Cytoplasmic Sequestration of the Nuclear Export Receptor CRM1 by NS2 Mutations Developed in the Host Regulates Parvovirus Fitness." Journal of Virology 78, no. 19 (2004): 10674–84. http://dx.doi.org/10.1128/jvi.78.19.10674-10684.2004.

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ABSTRACT To investigate whether a DNA virus can evade passive immunotherapy with a polyclonal antiserum, we analyzed the protection of a neutralizing capsid antiserum against a lethal infection of the immunosuppressive strain of the parvovirus minute virus of mice (MVMi) in 42 immunodeficient mice over a period of 200 days. A few mice were effectively protected, but most developed a delayed lethal leukopenic syndrome during the treatment or weeks afterwards. Unexpectedly, viruses isolated from treated but also from control leukopenic mice showed no amino acid changes throughout the entire caps
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18

Clyde, Karen, and Eva Harris. "RNA Secondary Structure in the Coding Region of Dengue Virus Type 2 Directs Translation Start Codon Selection and Is Required for Viral Replication." Journal of Virology 80, no. 5 (2006): 2170–82. http://dx.doi.org/10.1128/jvi.80.5.2170-2182.2006.

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ABSTRACT Dengue virus is a positive-strand RNA virus and a member of the genus Flavivirus, which includes West Nile, yellow fever, and tick-borne encephalitis viruses. Flavivirus genomes are translated as a single polyprotein that is subsequently cleaved into 10 proteins, the first of which is the viral capsid (C) protein. Dengue virus type 2 (DENV2) and other mosquito-borne flaviviruses initiate translation of C from a start codon in a suboptimal context and have multiple in-frame AUGs downstream. Here, we show that an RNA hairpin structure in the capsid coding region (cHP) directs translatio
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19

Arita, Minetaro, David R. Kilpatrick, Tomofumi Nakamura, et al. "Development of an Efficient Entire-Capsid-Coding-Region Amplification Method for Direct Detection of Poliovirus from Stool Extracts." Journal of Clinical Microbiology 53, no. 1 (2014): 73–78. http://dx.doi.org/10.1128/jcm.02384-14.

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Laboratory diagnosis has played a critical role in the Global Polio Eradication Initiative since 1988, by isolating and identifying poliovirus (PV) from stool specimens by using cell culture as a highly sensitive system to detect PV. In the present study, we aimed to develop a molecular method to detect PV directly from stool extracts, with a high efficiency comparable to that of cell culture. We developed a method to efficiently amplify the entire capsid coding region of human enteroviruses (EVs) including PV. cDNAs of the entire capsid coding region (3.9 kb) were obtained from as few as 50 c
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20

Honkimaa, Anni, Bryn Kimura, Amir-Babak Sioofy-Khojine, et al. "Genetic Adaptation of Coxsackievirus B1 during Persistent Infection in Pancreatic Cells." Microorganisms 8, no. 11 (2020): 1790. http://dx.doi.org/10.3390/microorganisms8111790.

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Coxsackie B (CVB) viruses have been associated with type 1 diabetes. We have recently observed that CVB1 was linked to the initiation of the autoimmune process leading to type 1 diabetes in Finnish children. Viral persistency in the pancreas is currently considered as one possible mechanism. In the current study persistent infection was established in pancreatic ductal and beta cell lines (PANC-1 and 1.1B4) using four different CVB1 strains, including the prototype strain and three clinical isolates. We sequenced 5′ untranslated region (UTR) and regions coding for structural and non-structural
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21

Haldeman-Cahill, Ruth, José-Antonio Daròs, and James C. Carrington. "Secondary Structures in the Capsid Protein Coding Sequence and 3′ Nontranslated Region Involved in Amplification of the Tobacco Etch Virus Genome." Journal of Virology 72, no. 5 (1998): 4072–79. http://dx.doi.org/10.1128/jvi.72.5.4072-4079.1998.

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ABSTRACT The 3′-terminal 350 nucleotides of the tobacco etch potyvirus (TEV) genome span the end of the capsid protein (CP)-coding sequence and the 3′ nontranslated region (NTR). The CP-coding sequence within this region contains a 105-nucleotide cis-active element required for genome replication (S. Mahajan, V. V. Dolja, and J. C. Carrington, J. Virol. 70:4370–4379, 1996). To investigate the sequence and secondary structure requirements within the CP cis-active region and the 3′ NTR, a systematic linker-scanning mutagenesis analysis was done. Forty-six mutations, each with two to six nucleoti
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22

Mueller, Steffen, Dimitris Papamichail, J. Robert Coleman, Steven Skiena, and Eckard Wimmer. "Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity." Journal of Virology 80, no. 19 (2006): 9687–96. http://dx.doi.org/10.1128/jvi.00738-06.

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ABSTRACT Exploring the utility of de novo gene synthesis with the aim of designing stably attenuated polioviruses (PV), we followed two strategies to construct PV variants containing synthetic replacements of the capsid coding sequences either by deoptimizing synonymous codon usage (PV-AB) or by maximizing synonymous codon position changes of the existing wild-type (wt) poliovirus codons (PV-SD). Despite 934 nucleotide changes in the capsid coding region, PV-SD RNA produced virus with wild-type characteristics. In contrast, no viable virus was recovered from PV-AB RNA carrying 680 silent mutat
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23

Martín, Javier, Kofi Odoom, Gráinne Tuite, et al. "Long-Term Excretion of Vaccine-Derived Poliovirus by a Healthy Child." Journal of Virology 78, no. 24 (2004): 13839–47. http://dx.doi.org/10.1128/jvi.78.24.13839-13847.2004.

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ABSTRACT A child was found to be excreting type 1 vaccine-derived poliovirus (VDPV) with a 1.1% sequence drift from Sabin type 1 vaccine strain in the VP1 coding region 6 months after he was immunized with oral live polio vaccine. Seventeen type 1 poliovirus isolates were recovered from stools taken from this child during the following 4 months. Contrary to expectation, the child was not deficient in humoral immunity and showed high levels of serum neutralization against poliovirus. Selected virus isolates were characterized in terms of their antigenic properties, virulence in transgenic mice,
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24

Sokolowski, Marcus, Wei Tan, Marianne Jellne, and Stefan Schwartz. "mRNA Instability Elements in the Human Papillomavirus Type 16 L2 Coding Region." Journal of Virology 72, no. 2 (1998): 1504–15. http://dx.doi.org/10.1128/jvi.72.2.1504-1515.1998.

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ABSTRACT Human papillomavirus capsid proteins L1 and L2 are detected only in terminally differentiated cells, indicating that expression of the L1 and L2 genes is blocked in dividing cells. The results presented here establish that the human papillomavirus type 16 L2 coding region contains cis-acting inhibitory sequences. When placed downstream of a reporter gene, the human papillomavirus type 16 L2 sequence reduced both mRNA and protein levels in an orientation-dependent manner. Deletion analysis revealed that the L2 sequence contains two cis-acting inhibitory RNA regions. We identified an in
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25

Fasina, Olufemi O., Yanming Dong, and David J. Pintel. "NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing." Journal of Virology 90, no. 4 (2015): 1718–28. http://dx.doi.org/10.1128/jvi.02618-15.

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ABSTRACTMinute virus of canines (MVC) is an autonomous parvovirus in the genusBocaparvovirus. It has a single promoter that generates a single pre-mRNA processed via alternative splicing and alternative polyadenylation to produce at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another complex site, (pA)p, within the capsid-coding region. During viral infection, the mRNAs must extend through (pA)p and undergo additional splicing of the immediately upstream 3D∕3A intron to access the capsid gene. MVC NP1 is a 22-kDa nuclear
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Burns, Cara C., Ray Campagnoli, Jing Shaw, Annelet Vincent, Jaume Jorba, and Olen Kew. "Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons." Journal of Virology 83, no. 19 (2009): 9957–69. http://dx.doi.org/10.1128/jvi.00508-09.

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ABSTRACT Replicative fitness of poliovirus can be modulated systematically by replacement of preferred capsid region codons with synonymous unpreferred codons. To determine the key genetic contributors to fitness reduction, we introduced different sets of synonymous codons into the capsid coding region of an infectious clone derived from the type 2 prototype strain MEF-1. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased sharply with increased frequencies of the dinucleotides CpG (suppressed in higher eukaryotes and most R
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27

Bøtner, Anette, Naresh K. Kakker, Cyril Barbezange, Stephen Berryman, Terry Jackson, and Graham J. Belsham. "Capsid proteins from field strains of foot-and-mouth disease virus confer a pathogenic phenotype in cattle on an attenuated, cell-culture-adapted virus." Journal of General Virology 92, no. 5 (2011): 1141–51. http://dx.doi.org/10.1099/vir.0.029710-0.

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Chimeric foot-and-mouth disease viruses (FMDVs) have been generated from plasmids containing full-length FMDV cDNAs and characterized. The parental virus cDNA was derived from the cell-culture-adapted O1Kaufbeuren B64 (O1K B64) strain. Chimeric viruses, containing capsid coding sequences derived from the O/UKG/34/2001 or A/Turkey 2/2006 field viruses, were constructed using the backbone from the O1K B64 cDNA, and viable viruses (O1K/O-UKG and O1K/A-Tur, respectively) were successfully rescued in each case. These viruses grew well in primary bovine thyroid cells but grew less efficiently in BHK
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Rao, Qing, Zhen Zhang, Hongchao Jiang, et al. "Comparison of coxsackievirus A12 genome isolated from patients with different symptoms in Yunnan, Southwest China." Future Virology 15, no. 10 (2020): 683–91. http://dx.doi.org/10.2217/fvl-2020-0103.

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Aim: Coxsackievirus A12 (CVA12) mainly causes hand–foot–mouth disease (HFMD) or herpangina (HA). Thus, the genomic characteristics of CVA12 isolates from Southwest China, especially the discrepancy between CVA12-HFMD and CVA12-HA were analyzed. Patients & methods: The full-length genome sequences of CVA12-HFMD and CVA12-HA were obtained and phylogenetic, nucleotide mutation, amino acid substitution and recombinant analyses were performed. Results: All CVA12 were closest to the Netherlands (2013) and have possibly recombined in the capsid coding region (P1) with other HEV-A. In the coding r
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29

Garlapati, Srinivas, and Ching C. Wang. "Structural Elements in the 5′-Untranslated Region of Giardiavirus Transcript Essential for Internal Ribosome Entry Site-Mediated Translation Initiation." Eukaryotic Cell 4, no. 4 (2005): 742–54. http://dx.doi.org/10.1128/ec.4.4.742-754.2005.

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ABSTRACT Translation of uncapped giardiavirus (GLV) mRNA in Giardia lamblia requires the presence of a 5′-untranslated region (5′-UTR) and a viral capsid coding region. We used dicistronic viral constructs to show that the downstream 253 nucleotides (nt) of the 5′-UTR plus the initial 264-nt capsid coding region constitute an internal ribosome entry site (IRES). Predicted secondary structures in the 253-nt 5′-UTR include stem-loops U3, U4a, U4b, U4c, and U5. Chemical and enzymatic probing analysis confirmed the presence of all predicted stem-loops except U4a. Disruption of stem-loop structures
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30

Jamal, Syed M., Giancarlo Ferrari, Safia Ahmed, Preben Normann, Stephen Curry, and Graham J. Belsham. "Evolutionary analysis of serotype A foot-and-mouth disease viruses circulating in Pakistan and Afghanistan during 2002–2009." Journal of General Virology 92, no. 12 (2011): 2849–64. http://dx.doi.org/10.1099/vir.0.035626-0.

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Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. Three different serotypes of the virus, namely O, A and Asia-1, are responsible for the outbreaks of this disease in these countries. In the present study, the nucleotide-coding sequences for the VP1 capsid protein (69 samples) or for all four capsid proteins (P1, seven representative samples) of the serotype A FMD viruses circulating in Pakistan and Afghanistan were determined. Phylogenetic analysis of the foot-and-mouth disease virus (FMDV) VP1-coding sequences from these countries collected between 2002 and 2009 revealed t
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de Borba, Luana, Sergio M. Villordo, Nestor G. Iglesias, Claudia V. Filomatori, Leopoldo G. Gebhard, and Andrea V. Gamarnik. "Overlapping Local and Long-Range RNA-RNA Interactions Modulate Dengue Virus Genome Cyclization and Replication." Journal of Virology 89, no. 6 (2015): 3430–37. http://dx.doi.org/10.1128/jvi.02677-14.

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The dengue virus genome is a dynamic molecule that adopts different conformations in the infected cell. Here, using RNA folding predictions, chemical probing analysis, RNA binding assays, and functional studies, we identified newcis-acting elements present in the capsid coding sequence that facilitate cyclization of the viral RNA by hybridization with a sequence involved in a local dumbbell structure at the viral 3′ untranslated region (UTR). The identified interaction differentially enhances viral replication in mosquito and mammalian cells.
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32

Belsham, Graham J. "Influence of the Leader protein coding region of foot-and-mouth disease virus on virus replication." Journal of General Virology 94, no. 7 (2013): 1486–95. http://dx.doi.org/10.1099/vir.0.052126-0.

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The foot-and-mouth disease virus (FMDV) Leader (L) protein is produced in two forms, Lab and Lb, differing only at their amino-termini, due to the use of separate initiation codons, usually 84 nt apart. It has been shown previously, and confirmed here, that precise deletion of the Lab coding sequence is lethal for the virus, whereas loss of the Lb coding sequence results in a virus that is viable in BHK cells. In addition, it is now shown that deletion of the ‘spacer’ region between these two initiation codons can be tolerated. Growth of the virus precisely lacking just the Lb coding sequence
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33

Cumming, Sarah A., Thanaporn Cheun-Im, Stephen G. Milligan, and Sheila V. Graham. "Human papillomavirus type 16 late gene expression is regulated by cellular RNA processing factors in response to epithelial differentiation." Biochemical Society Transactions 36, no. 3 (2008): 522–24. http://dx.doi.org/10.1042/bst0360522.

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HPV16 (human papillomavirus type 16) is a 7.9 kb double-stranded DNA virus that infects anogenital mucosal epithelia. In some rare cases, in women, infection can progress to cervical cancer. HPV16 gene expression is regulated through use of multiple promoters and alternative splicing and polyadenylation. The virus genome can be divided into an early and a late coding region. The late coding region contains the L1 and L2 genes. These encode the virus capsid proteins L1 and L2; protein expression is confined to the upper epithelial layers and is regulated post-transcriptionally in response to ep
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34

Rector, Annabel, Koenraad Van Doorslaer, Mads Bertelsen, et al. "Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers." Journal of General Virology 86, no. 7 (2005): 2029–33. http://dx.doi.org/10.1099/vir.0.80874-0.

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Partial sequences of a novel papillomavirus were amplified from a cutaneous lesion biopsy of a raccoon (Procyon lotor), by using PCR with degenerate papillomavirus-specific primers. The Procyon lotor papillomavirus type 1 (PlPV-1) DNA was amplified with long template PCR in two overlapping fragments, together encompassing the entire genome, and the complete PlPV-1 genomic sequence was determined. The PlPV-1 genome consists of 8170 bp, and contains the typical papillomaviral open reading frames, encoding five early proteins and two late capsid proteins. Besides the classical non-coding region (
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35

Gallinella, G., S. Venturoli, G. Gentilomi, M. Musiani, and M. Zerbini. "Extent of sequence variability in a genomic region coding for capsid proteins of B19 parvovirus." Archives of Virology 140, no. 6 (1995): 1119–25. http://dx.doi.org/10.1007/bf01315420.

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36

Ching, Karen Z., Tatsunori Nakano, Louisa E. Chapman, Austin Demby, and Betty H. Robertson. "Genetic characterization of wild-type genotype VII hepatitis A virus." Journal of General Virology 83, no. 1 (2002): 53–60. http://dx.doi.org/10.1099/0022-1317-83-1-53.

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The complete genome sequence of the only identified genotype VII hepatitis A virus (HAV), strain SLF88, was obtained from PCR amplicons generated by a modified long PCR approach. There was 90% nucleotide identity in the 5′ untranslated region compared to other known HAV sequences. In the remainder of the genome containing the long open reading frame, there was about 85% nucleotide identity to human HAV genotypes IA and IB and 80% identity to simian HAV genotype V. Compared to HAV strain HM-175, the capsid amino acids were highly conserved, with only four homologous amino acid changes, while an
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37

Caro, Valérie, Sophie Guillot, Francis Delpeyroux, and Radu Crainic. "Molecular strategy for ‘serotyping’ of human enteroviruses." Journal of General Virology 82, no. 1 (2001): 79–91. http://dx.doi.org/10.1099/0022-1317-82-1-79.

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To explore further the phylogenetic relationships between human enteroviruses and to develop new diagnostic approaches, we designed a pair of generic primers in order to study a 1452 bp genomic fragment (relative to the poliovirus Mahoney genome), including the 3′ end of the VP1-coding region, the 2A- and 2B-coding regions, and the 5′ moiety of the 2C-coding region. Fifty-nine of the 64 prototype strains and 45 field isolates of various origins, involving 21 serotypes and 6 strains untypeable by standard immunological techniques, were successfully amplified with these primers. By determining t
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38

Lazzari, Elisabetta, Gabriella Rozera, Roberta Gagliardini, et al. "Investigation of Natural Resistance to Fostemsavir and Lenacapavir in Naïve Primary Infections by Ultra-Deep Sequencing of near Full-Length HIV-1 Genomes." Viruses 17, no. 5 (2025): 636. https://doi.org/10.3390/v17050636.

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Next-generation sequencing (NGS) of near full-length HIV genomes was performed to investigate natural resistance to Fostemsavir (FTR) and Lenacapavir (LEN) at the quasispecies level in nine naïve primary HIV infections harboring different HIV subtypes and recombinant forms. Reconstructed genomes provided a median (IQR) coverage for gag and env of 1710 (750–6063) and 1768 (871–5270), respectively. In the gp120 encoding region, the M426R variant was found with a frequency of 100% in two HIV subtypes B: one of these also showed the A204T variant at 100%. In the more conserved capsid coding region
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Collier, Brian, Daniel Öberg, Xiaomin Zhao, and Stefan Schwartz. "Specific Inactivation of Inhibitory Sequences in the 5′ End of the Human Papillomavirus Type 16 L1 Open Reading Frame Results in Production of High Levels of L1 Protein in Human Epithelial Cells." Journal of Virology 76, no. 6 (2002): 2739–52. http://dx.doi.org/10.1128/jvi.76.6.2739-2752.2002.

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ABSTRACT The expression of human papillomavirus type 16 late genes encoding virus capsid proteins L1 and L2 is restricted to terminally differentiated epithelial cells in the superficial layers of the squamous epithelium. We wish to understand the molecular mechanisms that determine the levels of expression of the human papillomavirus type 16 late genes. We have previously shown that the L1 coding region contains inhibitory sequences. Here we extend previous findings to show that the 5′ end of the L1 gene contains strong inhibitory sequences but that the 3′ end does not. We show that the first
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Tosh, Chakradhar, Divakar Hemadri, and Aniket Sanyal. "Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus." Journal of General Virology 83, no. 10 (2002): 2455–60. http://dx.doi.org/10.1099/0022-1317-83-10-2455.

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41

Lai, Vicky C. H., Weidong Zhong, Angela Skelton, et al. "Generation and Characterization of a Hepatitis C Virus NS3 Protease-Dependent Bovine Viral Diarrhea Virus." Journal of Virology 74, no. 14 (2000): 6339–47. http://dx.doi.org/10.1128/jvi.74.14.6339-6347.2000.

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ABSTRACT Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhea virus (BVDV) genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein (C). This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. To develop an antiviral assay that allows the assessment of anti-hepatitis C virus (HCV) NS3 protease inhibitors, a chimeric BVDV in which the coding region of Npro was replaced by that of an NS4A cofactor-tethered HC
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42

Brunet, Sylvie, Cécile Sigoillot-Claude, Daniel Pialot, and Hervé Poulet. "Multiple Correspondence Analysis on Amino Acid Properties within the Variable Region of the Capsid Protein Shows Differences between Classical and Virulent Systemic Feline Calicivirus Strains." Viruses 11, no. 12 (2019): 1090. http://dx.doi.org/10.3390/v11121090.

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Feline calicivirus (FCV) is a widespread and highly prevalent pathogen of domestic cats, responsible for mild upper respiratory tract disease. Outbreaks of severe virulent systemic disease (VSD) associated with FCV infection have been reported worldwide. VSD FCV strains have a broader tropism and cause a systemic vascular compromise. Despite clear differences in the pathogenesis of VSD and oral respiratory infections, attempts to identify specific molecular markers of VSD strains on the major capsid protein VP1 have failed. Region E of VP1 is responsible for the interaction with the cell recep
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43

Zheng, Huai-Ying, Tomokazu Takasaka, Kazuyuki Noda, et al. "New sequence polymorphisms in the outer loops of the JC polyomavirus major capsid protein (VP1) possibly associated with progressive multifocal leukoencephalopathy." Journal of General Virology 86, no. 7 (2005): 2035–45. http://dx.doi.org/10.1099/vir.0.80863-0.

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JC polyomavirus (JCPyV) causes progressive multifocal leukoencephalopathy (PML) in patients with decreased immune competence. To elucidate genetic changes in JCPyV associated with the pathogenesis of PML, multiple complete JCPyV DNA clones originating from the brains of three PML cases were established and sequenced. Although unique rearranged control regions occurred in all clones, a low level of nucleotide variation was also found in the coding region. In each case, a parental coding sequence was identified, from which variant coding sequences with nucleotide substitutions would have been ge
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44

Khalifeh, Anthony, Simona Kraberger, Daria Dziewulska, Arvind Varsani, and Tomasz Stenzel. "A Pilot Study Investigating the Dynamics of Pigeon Circovirus Recombination in Domesticated Pigeons Housed in a Single Loft." Viruses 13, no. 6 (2021): 964. http://dx.doi.org/10.3390/v13060964.

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Pigeon circovirus (PiCV) infects pigeon populations worldwide and has been associated with immunosuppression in younger pigeons. Recombination is a common mechanism of evolution that has previously been shown in various members of the Circoviridae family, including PiCV. In this study, three groups of pigeons acquired from separate lofts were screened for PiCV, and their genome sequence was determined. Following this, they were housed in a single loft for 22 days, during which blood and cloacal swab samples were taken. From these blood and cloacal swabs, PiCV genomes were determined with the a
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45

Chehadeh, Wassim, Sanaa Abdulkader Moalim Ali, and Syeda Mubeen Maimoona. "Molecular characterization of three enteroviral strains isolated in Kuwait from young children with serious conditions." Journal of Infection in Developing Countries 11, no. 08 (2017): 626–39. http://dx.doi.org/10.3855/jidc.9065.

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Introduction: Human enteroviruses are single stranded RNA viruses associated with many serious diseases such as encephalitis and myocarditis. They consist of up to 100 immunologically and genetically distinct types. Three enteroviral isolates, 2104, 3936 and 3988, were previously isolated from patients with neurological disorders or sepsis-like illness. In this study, the molecular characterization of the three isolates was investigated.
 Methodology: A full genome sequencing was performed by Sanger method, followed by phylogenetic and bootscanning analyses. A detailed analysis of genetic
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46

Ali, Hashim, Aleksei Lulla, Alex S. Nicholson, et al. "Attenuation hotspots in neurotropic human astroviruses." PLOS Biology 21, no. 7 (2023): e3001815. http://dx.doi.org/10.1371/journal.pbio.3001815.

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During the last decade, the detection of neurotropic astroviruses has increased dramatically. The MLB genogroup of astroviruses represents a genetically distinct group of zoonotic astroviruses associated with gastroenteritis and severe neurological complications in young children, the immunocompromised, and the elderly. Using different virus evolution approaches, we identified dispensable regions in the 3′ end of the capsid-coding region responsible for attenuation of MLB astroviruses in susceptible cell lines. To create recombinant viruses with identified deletions, MLB reverse genetics (RG)
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47

Oberste, M. Steven, Kaija Maher, and Mark A. Pallansch. "Complete genome sequences for nine simian enteroviruses." Journal of General Virology 88, no. 12 (2007): 3360–72. http://dx.doi.org/10.1099/vir.0.83124-0.

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Analysis of the VP1 capsid-coding sequences of the simian picornaviruses has suggested that baboon enterovirus (BaEV), SV19, SV43 and SV46 belong to the species Human enterovirus A (HEV-A) and SA5 belongs to HEV-B, whereas SV4/A2 plaque virus (two isolates of a single serotype), SV6 and N125/N203 (two isolates of a single serotype) appear to represent new species in the genus. We have further characterized by complete genomic sequencing the genetic relationships among the simian enteroviruses serotypes (BaEV, N125/N203, SA5, SV4/A2 plaque virus, SV6, SV19, SV43 and SV46) and to other enterovir
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48

Queirós, Gonçalo, Lesya Yefimenko, Filomena M. Pereira, and João Piedade. "Genetic Diversity in the Capsid Protein-Coding Region of HIV-1 Circulating in Benguela, Angola: Implications for Primary Resistance to the Novel Capsid Inhibitor Lenacapavir." Viruses 17, no. 5 (2025): 711. https://doi.org/10.3390/v17050711.

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In 2023, the HIV-1 pandemic claimed around 630,000 lives worldwide due to AIDS-related complications. Its burden is significantly heavier in Sub-Saharan Africa, where an increased HIV-1 genetic diversity is common, which increases the risk of resistance to antiretroviral (ARV) drugs. This study aims to update the molecular epidemiology of HIV-1 in Angola, focusing specifically on the gag gene, which is often overlooked, and to assess the potential viability of lenacapavir (LEN)-based ARV therapy in the region. A total of 243 blood samples were collected from ARV-naïve, HIV-infected patients at
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Harvala, Heli, Hannu Kalimo, Jeffrey Bergelson, Glyn Stanway, and Timo Hyypiä. "Tissue tropism of recombinant coxsackieviruses in an adult mouse model." Journal of General Virology 86, no. 7 (2005): 1897–907. http://dx.doi.org/10.1099/vir.0.80603-0.

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Recombinant viruses, constructed by exchanging the 5′ non-coding region (5′NCR), structural and non-structural protein coding sequences were used to investigate determinants responsible for differences between coxsackievirus A9 (CAV9) and coxsackievirus B3 (CBV3) infections in adult mice and two cell lines. Plaque assay titration of recombinant and parental viruses from different tissues from adult BALB/c mice demonstrated that the structural region of CBV3 determined tropism to the liver tissue due to receptor recognition, and the 5′NCR of CBV3 enhanced viral multiplication in the mouse pancr
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50

Kao, J., L. Jia, T. Tian, L. Rubio, and B. W. Falk. "First Report of Cucurbit Yellow Stunting Disorder Virus (Genus Crinivirus) in North America." Plant Disease 84, no. 1 (2000): 101. http://dx.doi.org/10.1094/pdis.2000.84.1.101c.

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In late summer 1999, field- and greenhouse-grown melon plants (Cucumis melo) showing severe stunting and yellowing symptoms were observed near Donna in southern Texas and near the town of Reynosa in northern Mexico. Symptoms were typical of those caused by viruses in the genus Crinivirus, family Closteroviridae. High populations of Bemisia spp. whiteflies were associated with these plantings, with many plants showing heavy infestation. Laboratory analyses showed that melon plants from both locations were infected by the whitefly-transmitted Cucurbit yellow stunting disorder virus (CYSDV). Posi
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