101
|
Detection of a novel astrovirus in brain tissue of mink suffering from shaking mink syndrome by use of viral metagenomics. J Clin Microbiol 2010; 48:4392-6. [PMID: 20926705 DOI: 10.1128/jcm.01040-10] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In 2000, farmed mink kits in Denmark were affected by a neurological disorder. The characteristic clinical signs included shaking, staggering gait, and ataxia. The disease, given the name shaking mink syndrome, was reproduced by the inoculation of brain homogenate from affected mink kits into healthy ones. However, the etiology remained unknown despite intensive efforts. In this study, random amplification and large-scale sequencing were used, and an astrovirus was detected in the brain tissue of three experimentally infected mink kits. This virus also was found in the brain of three mink kits naturally displaying the disease but not in the six healthy animals investigated. The complete coding region of the detected astrovirus was sequenced and compared to those of both a mink astrovirus associated with preweaning diarrhea and to a recently discovered human astrovirus associated with a case of encephalitis in a boy with x-linked agammaglobulinemia. The identities were 80.4 and 52.3%, respectively, showing that the virus described in this study was more similar to the preweaning diarrhea mink astrovirus. For the nonstructural coding regions the sequence identity was around 90% compared to that of the astrovirus, which is associated with preweaning diarrhea in mink. The region coding for the structural protein was more diverse, showing only 67% sequence identity. This finding is of interest not only because the detected virus may be the etiological agent of the shaking mink syndrome but also because this is one of the first descriptions of an astrovirus found in the central nervous system of animals.
Collapse
|
102
|
Lee JI, Lee GC, Oh YH, Lee YK, Kim MY, Lee CH. Molecular characterization of partial-open reading frames 1a and 2 of the human astroviruses in South Korea. Virol J 2010; 7:221. [PMID: 20831802 PMCID: PMC2944169 DOI: 10.1186/1743-422x-7-221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 09/10/2010] [Indexed: 01/23/2023] Open
Abstract
Human astroviruses (HAstVs) are among the major causes of gastroenteritis in South Korea. In this study, the partial regions of the open reading frame (ORF) 1a and ORF2 genes of HAstVs from gastroenteritis patients in nine hospitals were sequenced, and the molecular characterization of the viruses was revealed. 89 partial nucleotide sequences of ORF1a and 88 partial nucleotide sequences of ORF2 were amplified from 120 stool specimens. Phylogenetic analysis showed that most of the nucleotide sequences of ORF1a and ORF2 were grouped with HAstV type 1 but had evolutionary genetic distance compared with the reference sequences, such as the HAstV-1 prototype, Dresden strain, and Oxford strain. According to the phylogenetic analysis, some nucleotide sequences including SE0506041, SE0506043, and SE0506058, showed the discrepancy of the genotypes, but there was no proof of recombination among the HAstV types. In conclusion, this study showed that the dominant HAstV isolated from the Seoul metropolitan area in 2004-2005 was HAstV type 1, and that Korean HAstV-1 had the genetic distance in evolution compared with the reference sequences of HAstVs. Lots of nucleotide sequences of the ORF1a and ORF2 genes of HAstV will be useful for studying for the control and prevention of HAstV gastroenteritis in South Korea.
Collapse
Affiliation(s)
- Jae In Lee
- Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | | | | | | | | | | |
Collapse
|
103
|
Pinto RM, Abad FX, Gajardo R, Bosch A. Detection of infectious astroviruses in water. Appl Environ Microbiol 2010; 62:1811-3. [PMID: 16535324 PMCID: PMC1388862 DOI: 10.1128/aem.62.5.1811-1813.1996] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method based on the infection of CaCo-2 cells and molecular hybridization with a specific cDNA probe has been developed for the detection of infectious astroviruses in environmental samples. By this procedure wild-type astroviruses have been detected in water from an area where a concurrent gastroenteritis outbreak was reported.
Collapse
|
104
|
Jang SY, Jeong WH, Kim MS, Lee YM, Lee JI, Lee GC, Paik SY, Koh GP, Kim JM, Lee CH. Detection of replicating negative-sense RNAs in CaCo-2 cells infected with human astrovirus. Arch Virol 2010; 155:1383-9. [PMID: 20544235 DOI: 10.1007/s00705-010-0718-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Accepted: 05/31/2010] [Indexed: 10/19/2022]
Abstract
Human astrovirus (HAstV) is the second most important cause of viral diarrhea and acute gastroenteritis in infants under five. However, determination of the infectivity of clinical isolates is difficult, and the replication cycle of HAstV is not yet fully understood. In this study, it was attempted to detect negative-sense (-)RNAs generated during the replication of RNA viruses. We used clinical isolates of HAstV to infect CaCo-2 cells. Reverse transcription using only a sense primer followed by PCR using both sense and antisense primers showed that (-)RNAs were first detected in CaCo-2 cells between 9 and 12 h postinfection (p.i.). However, these (-)RNAs were not detected when cells were treated with the protein synthesis inhibitor cycloheximide during HAstV infection. Next, RT with only an antisense primer followed by PCR was performed to detect (+)RNA of HAstVs after production of (-)RNAs during replication. RT-PCR results using the antisense primer revealed that the amount of (+)RNA began to increase starting 9 h p.i., indicating an accumulation of the newly synthesized (+)RNA genome. Cycloheximide was observed to abrogate the increase of newly made (+)RNA during HAstV infection. In conclusion, the use of sense or antisense primers during the RT reaction together with cycloheximide enabled us to quantitatively detect (-)RNAs, and this proved to be an useful tool in understanding the replication cycle of HAstV.
Collapse
Affiliation(s)
- So Young Jang
- Department of Microbiology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, South Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
105
|
Banos-Lara MDR, Méndez E. Role of individual caspases induced by astrovirus on the processing of its structural protein and its release from the cell through a non-lytic mechanism. Virology 2010; 401:322-32. [PMID: 20347468 DOI: 10.1016/j.virol.2010.02.028] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/13/2009] [Accepted: 02/23/2010] [Indexed: 11/20/2022]
Abstract
Caspases (Casp) activity has been associated with the intracellular proteolytic processing of the structural protein to yield the mature capsid formed by VP70 and with the cell release of human astrovirus (HAstV). This work describes the role of individual Casp on these events. The activity of initiator (-8, -9) and executioner (-3/7) Casp was clearly detected at 12h post-infection. All these proteases were able to cleave VP90 in an in vitro assay, but this processing was blocked in cells transfected with siRNA against Casp-3, -9, but not against Casp-8. In contrast, virus release, observed in the absence of cell lysis, was more drastically affected by either silencing Casp-3 or in the presence of the inhibitor Ac-DEVD-CHO. Cleavage of VP90 to yield VP70 was mapped at motif TYVD(657). These data indicate that the processing of VP90 and the release of HAstV from the cell are two Casp-related, but apparently independent, events.
Collapse
Affiliation(s)
- Ma del Rocío Banos-Lara
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, México
| | | |
Collapse
|
106
|
Guo L, Gonzalez R, Wang W, Li Y, Paranhos-Baccalà G, Vernet G, Wang J. Complete genome sequence of human astrovirus genotype 6. Virol J 2010; 7:29. [PMID: 20137100 PMCID: PMC2829535 DOI: 10.1186/1743-422x-7-29] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/08/2010] [Indexed: 11/30/2022] Open
Abstract
Background Human astroviruses (HAstVs) are one of the important causes of acute gastroenteritis in children. Currently, eight HAstV genotypes have been identified and all but two (HAstV-6 and HAstV-7) have been fully sequenced. We here sequenced and analyzed the complete genome of a HAstV-6 strain (192-BJ07), which was identified in Beijing, China. Results The genome of 192-BJ07 consists of 6745 nucleotides. The 192-BJ07 strain displays a 77.2-78.0% nucleotide sequence identity with other HAstV genotypes and exhibits amino acid sequence identities of 86.5-87.4%, 94.2-95.1%, and 65.5-74.8% in the ORF1a, ORF1b, and ORF2 regions, respectively. Homological analysis of ORF2 shows that 192-BJ07 is 96.3% identical to the documented HAstV-6 strain. Further, phylogenetic analysis indicates that different genomic regions are likely undergoing different evolutionary and selective pressures. No recombination event was observed in HAstV-6 in this study. Conclusion The completely sequenced and characterized genome of HAstV-6 (192-BJ07) provides further insight into the genetics of astroviruses and aids in the surveillance and control of HAstV gastroenteritis.
Collapse
Affiliation(s)
- Li Guo
- Dr, Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing 100730, PR China
| | | | | | | | | | | | | |
Collapse
|
107
|
Firth AE, Atkins JF. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning. Virol J 2010; 7:17. [PMID: 20100346 PMCID: PMC2832772 DOI: 10.1186/1743-422x-7-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 01/25/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However, annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. RESULTS Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively).
Collapse
Affiliation(s)
- Andrew E Firth
- BioSciences Institute, University College Cork, Cork, Ireland.
| | | |
Collapse
|
108
|
Liu Y, Wimmer E, Paul AV. Cis-acting RNA elements in human and animal plus-strand RNA viruses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:495-517. [PMID: 19781674 PMCID: PMC2783963 DOI: 10.1016/j.bbagrm.2009.09.007] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 09/09/2009] [Accepted: 09/13/2009] [Indexed: 02/08/2023]
Abstract
The RNA genomes of plus-strand RNA viruses have the ability to form secondary and higher-order structures that contribute to their stability and to their participation in inter- and intramolecular interactions. Those structures that are functionally important are called cis-acting RNA elements because their functions cannot be complemented in trans. They can be involved not only in RNA/RNA interactions but also in binding of viral and cellular proteins during the complex processes of translation, RNA replication and encapsidation. Most viral cis-acting RNA elements are located in the highly structured 5'- and 3'-nontranslated regions of the genomes but sometimes they also extend into the adjacent coding sequences. In addition, some cis-acting RNA elements are embedded within the coding sequences far away from the genomic ends. Although the functional importance of many of these structures has been confirmed by genetic and biochemical analyses, their precise roles are not yet fully understood. In this review we have summarized what is known about cis-acting RNA elements in nine families of human and animal plus-strand RNA viruses with an emphasis on the most thoroughly characterized virus families, the Picornaviridae and Flaviviridae.
Collapse
Affiliation(s)
- Ying Liu
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11790, USA
| | | | | |
Collapse
|
109
|
Al-Mutairy B, Walter JE, Pothen A, Mitchell DK. Genome prediction of putative genome-linked viral protein (VPg) of astroviruses. Virus Genes 2009; 31:21-30. [PMID: 15965605 DOI: 10.1007/s11262-004-2196-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Accepted: 12/22/2004] [Indexed: 10/25/2022]
Abstract
Positive-sense single-stranded RNA (+ssRNA) viruses replicate by uncoating the RNA genome for translation to provide viral proteins essential for genome replication and the production of new viral particles. The viral proteins are synthesized from a polyprotein precursor, which is cleaved nascently. The synthesized proteins include viral RNA-dependent RNA polymerase (RdRP), viral genome-linked protein (VPg), and a helicase. VPg is covalently attached to the genomic form of +ssRNA viruses. Helicases and NTPase unwind the RNA before replication. VPg and helicases have been identified in +ssRNA families, however, the presence of VPg and helicase in the Astroviridae, another +ssRNA family, has not been fully elucidated. Computational tools were utilized to provide sequence analysis evidence for the presence and genomic location of astrovirus VPg and helicase. HMMER program v2.1.1 was used to build Hidden Markov Model (HMM) profile for calicivirus VPg to search for conserved motifs in the astrovirus genome. We performed phylogenetic analysis of two genomic regions of astroviruses and caliciviruses (encoding the RdRP and VPg). We identified a putative VPg coding region in astrovirus. This region was located in open reading frame 1a (ORF1 a) and included sites with high sequence similarity to the VPg coding regions of Caliciviridae, Piconaviridae, and Potyviridae. A region encoding a putative astrovirus helicase identified conserved motifs only with pestivirus helicase sequences. Sequence analysis and comparison to other +ssRNA viruses supports the presence of VPg in the Astroviridae. Further laboratory analysis will be necessary to confirm these findings.
Collapse
Affiliation(s)
- Badr Al-Mutairy
- Computer Science Department, Old Dominion University, Norfolk, Virginia 23529-0162, USA
| | | | | | | |
Collapse
|
110
|
Cai G, Myers K, Hillman BI, Fry WE. A novel virus of the late blight pathogen, Phytophthora infestans, with two RNA segments and a supergroup 1 RNA-dependent RNA polymerase. Virology 2009; 392:52-61. [DOI: 10.1016/j.virol.2009.06.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/10/2009] [Accepted: 06/24/2009] [Indexed: 10/20/2022]
|
111
|
Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J Virol 2009; 83:10836-9. [PMID: 19706703 DOI: 10.1128/jvi.00998-09] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The etiology of a large proportion of gastrointestinal illness is unknown. In this study, random Sanger sequencing and pyrosequencing approaches were used to analyze fecal specimens from a gastroenteritis outbreak of unknown etiology in a child care center. Multiple sequences with limited identity to known astroviruses were identified. Assembly of the sequences and subsequent reverse transcription-PCR (RT-PCR) and rapid amplification of cDNA ends generated a complete genome of 6,586 nucleotides. Phylogenetic analysis demonstrated that this virus, named astrovirus VA1 (AstV-VA1), is highly divergent from all previously described astroviruses. Based on RT-PCR, specimens from multiple patients in this outbreak were unequivocally positive for Ast-VA1.
Collapse
|
112
|
Fu Y, Pan M, Wang X, Xu Y, Xie X, Knowles NJ, Yang H, Zhang D. Complete sequence of a duck astrovirus associated with fatal hepatitis in ducklings. J Gen Virol 2009; 90:1104-1108. [PMID: 19264607 DOI: 10.1099/vir.0.008599-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Duck astroviruses (DAstVs) are known to cause duck viral hepatitis; however, little is known regarding their molecular biology. Here, we report the complete sequence of a DAstV associated with a recent outbreak of fatal hepatitis in ducklings in China. Sequence analyses indicated that the genome of DAstV possessed a typical astrovirus organization and also exhibited two unique features. The polyadenylated genome comprised 7722 nt, which is the largest among astroviruses sequenced to date. The ORF2 of DAstV was not in the same reading frame as either ORF1a or ORF1b, which was distinct from all other astroviruses. Sequence comparisons and phylogenetic analyses revealed that DAstV was more closely related to turkey astrovirus (TAstV) type 2, TAstV-3 and TAstV/MN/01 (a possible new TAstV serotype) than to TAstV-1 or other astroviruses. These findings suggest that astroviruses may transmit across ducks and turkeys.
Collapse
Affiliation(s)
- Yu Fu
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Meng Pan
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Xiaoyan Wang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Yongliang Xu
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Xiaoyu Xie
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Nick J Knowles
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Hanchun Yang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Dabing Zhang
- Key Laboratory of Zoonosis of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
113
|
YOKOI H, KITAHASHI T. Astrovirus RNA Detection Using Real-Time Reverse Transcription-Polymerase Chain Reaction. ACTA ACUST UNITED AC 2009; 83:120-6. [DOI: 10.11150/kansenshogakuzasshi.83.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
114
|
Koonin EV, Wolf YI, Nagasaki K, Dolja VV. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 2008; 6:925-39. [PMID: 18997823 DOI: 10.1038/nrmicro2030] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA
| | | | | | | |
Collapse
|
115
|
Pantin-Jackwood MJ, Spackman E, Day JM. Pathogenesis of type 2 turkey astroviruses with variant capsid genes in 2-day-old specific pathogen free poults. Avian Pathol 2008; 37:193-201. [PMID: 18393099 DOI: 10.1080/03079450801932200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The pathogenicity of three different type 2 turkey astroviruses (TAstV-2) was studied in specific pathogen free turkeys. These viruses differ based on sequence analysis of the capsid gene. Poults were inoculated at 2 days of age and examined during 14 days for clinical signs and virus shedding. All inoculated poults presented signs of enteric disease including diarrhoea and growth depression. Virus presence and shedding was detected by real-time reverse transcriptase-polymerase chain reaction from intestinal contents and cloacal swabs collected at 3, 7 and 14 days post-inoculation. Viraemia was also confirmed by this method. Common lesions observed at necropsy were dehydration; distended intestines filled with watery contents and undigested feed, and dilated caeca with foamy contents. Microscopic lesions present in the intestines consisted of mild crypt hyperplasia, villous atrophy and lymphocytic infiltration, and were most common in the jejunum. Presence of the viruses was demonstrated by immunohistochemistry and by in situ hybridization in both villi and crypt enterocytes in the jejunum and, less frequently, the duodenum, ileum and caeca. Mild lesions consisting mainly of lymphocytic infiltration were also observed in other organs including the pancreas, liver, spleen and kidneys. Mild to moderate bursal atrophy occurred in all TAstV-2-infected poults examined; however, no specific viral staining was observed in this organ or any other tissues examined apart from the intestines. In conclusion, TAstV-2 viruses with variant capsids produce a similar enteric disease in young turkeys and may also affect the immune system of the birds by causing bursal lymphoid depletion.
Collapse
Affiliation(s)
- Mary J Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agricultural Research Service, US Department of Agriculture, Athens, GA 30605, USA.
| | | | | |
Collapse
|
116
|
Finkbeiner SR, Kirkwood CD, Wang D. Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea. Virol J 2008; 5:117. [PMID: 18854035 PMCID: PMC2576171 DOI: 10.1186/1743-422x-5-117] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 10/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Astroviruses infect a variety of mammals and birds and are causative agents of diarrhea in humans and other animal hosts. We have previously described the identification of several sequence fragments with limited sequence identity to known astroviruses in a stool specimen obtained from a child with acute diarrhea, suggesting that a novel virus was present. RESULTS In this study, the complete genome of this novel virus isolate was sequenced and analyzed. The overall genome organization of this virus paralleled that of known astroviruses, with 3 open reading frames identified. Phylogenetic analysis of the ORFs indicated that this virus is highly divergent from all previously described animal and human astroviruses. Molecular features that are highly conserved in human serotypes 1-8, such as a 3'NTR stem-loop structure and conserved nucleotide motifs present in the 5'NTR and ORF1b/2 junction, were either absent or only partially conserved in this novel virus. CONCLUSION Based on the analyses described herein, we propose that this newly discovered virus represents a novel species in the family Astroviridae. It has tentatively been named Astrovirus MLB1.
Collapse
Affiliation(s)
- Stacy R Finkbeiner
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, St, Louis, MO, USA.
| | | | | |
Collapse
|
117
|
Abstract
Bats are increasingly recognized to harbor a wide range of viruses, and in most instances these viruses appear to establish long-term persistence in these animals. They are the reservoir of a number of human zoonotic diseases including Nipah, Ebola, and severe acute respiratory syndrome. We report the identification of novel groups of astroviruses in apparently healthy insectivorous bats found in Hong Kong, in particular, bats belonging to the genera Miniopterus and Myotis. Astroviruses are important causes of diarrhea in many animal species, including humans. Many of the bat astroviruses form distinct phylogenetic clusters in the genus Mamastrovirus within the family Astroviridae. Virus detection rates of 36% to 100% and 50% to 70% were found in Miniopterus magnater and Miniopterus pusillus bats, respectively, captured within a single bat habitat during four consecutive visits spanning 1 year. There was high genetic diversity of viruses in bats found within this single habitat. Some bat astroviruses may be phylogenetically related to human astroviruses, and further studies with a wider range of bat species in different geographic locations are warranted. These findings are likely to provide new insights into the ecology and evolution of astroviruses and reinforce the role of bats as a reservoir of viruses with potential to pose a zoonotic threat to human health.
Collapse
|
118
|
Abstract
Human astroviruses are nonenveloped, positive-sense single-strand RNA viruses associated with self-limiting diarrhea. Although they are recognized as a leading cause of disease in young children, the cellular factors involved in astrovirus replication are not well defined. The extracellular signal-regulated kinase (ERK) pathway has been shown to regulate many viral infections, but its role during astrovirus infection is unknown. In this report, we show that astrovirus activates ERK1/2 early in infection independently of replication. Inhibition of ERK activation with U0126, a specific ERK inhibitor, significantly reduced viral production. Investigations into the mechanism of ERK1/2 regulation revealed that all steps of the viral life cycle, including early and late protein expression as well as subgenomic and genomic RNA transcription, were diminished during U0126 treatment of monolayers. These data support a role for ERK1/2 in a postattachment step, although the precise mechanism remains under investigation.
Collapse
|
119
|
Krishna NK, Cunnion KM. Human Astrovirus Coat Protein: A Novel C1 Inhibitor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008. [DOI: 10.1007/978-0-387-78952-1_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
120
|
Gabbay YB, Leite JPG, Oliveira DS, Nakamura LS, Nunes MRT, Mascarenhas JDP, Heinemann MB, Linhares AC. Molecular epidemiology of astrovirus type 1 in Belém, Brazil, as an agent of infantile gastroenteritis, over a period of 18 years (1982–2000): Identification of two possible new lineages. Virus Res 2007; 129:166-74. [PMID: 17714822 DOI: 10.1016/j.virusres.2007.07.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/12/2007] [Indexed: 12/16/2022]
Abstract
Human astroviruses (HAstV) are worldwide recognized as important viral enteropathogens during childhood. This study aims to determine the incidence, genetic diversity and intertype variability of HAstV-1 in children less than 5 years of age enrolled in several studies conducted in Belém/Pará, and São Luís/Maranhão, Brazil, from December 1982 to May 2000. Using EIA and RT-PCR, an overall positivity of 6.1% (155/2.534) was achieved, of these, 140 were positive by RT-PCR. The analysis of a 348bp ORF2 fragment revealed that HAstV-1 was the predominant genotype (85/140, 60.7%) throughout the 18 years of study. Phylogenetic analysis was performed for 81 of these strains, and 76 (93.8%) were genetically classified as HAstV-1a. The remainder of strains (n=5) were assigned to possible new lineages, 1e and 1f. Four of these five strains were detected in 1983 and 1984, and the lineage 1a circulated during 10 consecutive years (1990/2000). Genome sequence variation was found among the HAstV-1 strains involving all lineages, but only five nucleotide changes translated into aminoacid changes over this period, suggesting that HAstV-1 was very stable. The data obtained in this study should be useful for further studies at molecular level, including improvement of disease surveillance based on molecular diagnostic tools, and vaccine development.
Collapse
Affiliation(s)
- Yvone B Gabbay
- Virology Section, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Rodovia BR 316, Km 07, S/N, Levilândia 67030-000, Ananindeua, PA, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
121
|
Human astrovirus coat protein inhibits serum complement activation via C1, the first component of the classical pathway. J Virol 2007; 82:817-27. [PMID: 17959658 DOI: 10.1128/jvi.01847-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human astroviruses (HAstVs) belong to a family of nonenveloped, icosahedral RNA viruses that cause noninflammatory gastroenteritis, predominantly in infants. Eight HAstV serotypes have been identified, with a worldwide distribution. While the HAstVs represent a significant public health concern, very little is known about the pathogenesis of and host immune response to these viruses. Here we demonstrate that HAstV type 1 (HAstV-1) virions, specifically the viral coat protein (CP), suppress the complement system, a fundamental component of the innate immune response in vertebrates. HAstV-1 virions and purified CP both suppress hemolytic complement activity. Hemolytic assays utilizing sera depleted of individual complement factors as well as adding back purified factors demonstrated that HAstV CP suppresses classical pathway activation at the first component, C1. HAstV-1 CP bound the A chain of C1q and inhibited serum complement activation, resulting in decreased C4b, iC3b, and terminal C5b-9 formation. Inhibition of complement activation was also demonstrated for HAstV serotypes 2 to 4, suggesting that this phenomenon is a general feature of these human pathogens. Since complement is a major contributor to the initiation and amplification of inflammation, the observed CP-mediated inhibition of complement activity may contribute to the lack of inflammation associated with astrovirus-induced gastroenteritis. Although diverse mechanisms of inhibition of complement activation have been described for many enveloped animal viruses, this is the first report of a nonenveloped icosahedral virus CP inhibiting classical pathway activation at C1.
Collapse
|
122
|
Méndez E, Aguirre-Crespo G, Zavala G, Arias CF. Association of the astrovirus structural protein VP90 with membranes plays a role in virus morphogenesis. J Virol 2007; 81:10649-58. [PMID: 17652389 PMCID: PMC2045458 DOI: 10.1128/jvi.00785-07] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VP90, the capsid polyprotein precursor of human astrovirus Yuc8, is assembled into viral particles, and its processing at the carboxy terminus by cellular caspases, to yield VP70, has been correlated with the cell release of the virus. Here, we characterized the effect of the VP90-VP70 processing on the properties of these proteins, as well as on their intracellular distribution. VP90 was found in membrane-enriched fractions (mVP90), as well as in fractions enriched in cytosolic proteins (cVP90), while VP70 was found exclusively in the latter fractions. Upon trypsin activation, infectivity was detected in all VP90-containing fractions, confirming that both mVP90 and cVP90 are able to assemble into particles; however, the two forms of VP90 showed differential sensitivities to trypsin, especially at their carboxy termini, which in the case of mVP90 was shown to remain membrane associated after protease digestion. Structural protein oligomers were detected in purified VP70-containing viruses, as well as in membrane-enriched fractions, but they were less evident in cytosolic fractions. Ultrastructural studies of infected cells revealed different types of viral particles, some of which appeared to be associated with membranes. By immunoelectron microscopy, structural proteins were shown to form virus particles in clusters and to associate with the edges of vesicles induced during infection, which also appear to contain subviral particles inside. Nonstructural proteins and viral RNA colocalized with mVP90, but not with cVP90, suggesting that mVP90 might represent the form of the protein that is initially assembled into particles, at the sites where the virus genome is being replicated.
Collapse
Affiliation(s)
- Ernesto Méndez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Colonia Miraval, Cuernavaca, Morelos 62250, Mexico.
| | | | | | | |
Collapse
|
123
|
van Hemert FJ, Lukashov VV, Berkhout B. Different rates of (non-)synonymous mutations in astrovirus genes; correlation with gene function. Virol J 2007; 4:25. [PMID: 17343744 PMCID: PMC1828050 DOI: 10.1186/1743-422x-4-25] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 03/07/2007] [Indexed: 11/30/2022] Open
Abstract
Background Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species. Results We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species. Conclusion Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a) more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase)). Integrin recognition may play a key role in astrovirus to target cell attachment.
Collapse
Affiliation(s)
- Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Vladimir V Lukashov
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| |
Collapse
|
124
|
Pantin-Jackwood MJ, Spackman E, Woolcock PR. Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: implications for diagnostics. Avian Dis 2006; 50:397-404. [PMID: 17039840 DOI: 10.1637/7512-020606r.1] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Avian astroviruses were detected by reverse transcriptase and polymerase chain reaction in intestinal contents collected from commercial chickens and turkeys from throughout the United States from 2003 through 2005. Astroviruses were detected in birds from both healthy and poorly performing flocks with or without enteric disease. Phylogenetic analysis was performed with sequence data from the polymerase (ORF-1b) genes of 41 turkey-origin astroviruses and 23 chicken-origin astroviruses. All currently available avian astrovirus sequence data and selected mammalian astrovirus sequence data were included in the analysis. Four groups of avian astroviruses were observed by phylogenetic analysis: turkey astrovirus type 1 (TAstV-1)-like viruses, turkey astrovirus type 2 (TAstV-2)-like viruses, both detected in turkeys; avian nephritis virus (ANV)-like viruses, detected in both chickens and turkeys; and a novel group of chicken-origin astroviruses (CAstV). Among these four groups, amino acid identity was between 50.1% and 73.8%, and was a maximum of 49.4% for all avian isolates when compared with the mammalian astroviruses. There were multiple phylogenetic subgroups within the TAstV-2, ANV, and CAstV groups based on 9% nucleotide sequence divergence. Phylogenetic analysis revealed no clear assortment by geographic region or isolation date. Furthermore, no correlation was observed between the detection of a particular astrovirus and the presence of enteric disease or poor performance. Based on these data, a revision of the present taxonomic classification for avian astroviruses within the genus Avastrovirus is warranted.
Collapse
Affiliation(s)
- Mary J Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 934 College Station Rd., Athens, Georgia 30605, USA
| | | | | |
Collapse
|
125
|
Bhattacharya R, Sahoo GC, Nayak MK, Ghosh S, Dutta P, Bhattacharya MK, Mitra U, Gangopadhyay D, Dutta S, Niyogi SK, Saha DR, Naik TN, Bhattacharya SK, Krishnan T. Molecular epidemiology of human astrovirus infections in Kolkata, India. INFECTION GENETICS AND EVOLUTION 2006; 6:425-35. [PMID: 16546454 DOI: 10.1016/j.meegid.2006.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 02/13/2006] [Indexed: 11/21/2022]
Abstract
UNLABELLED The study is aimed to determine the seasonal distribution and clinical characteristics of astroviruses associated with acute watery diarrhoea among children in Kolkata and characterize them at the molecular level. METHOD OF STUDY Faecal specimens of acute watery diarrhoea cases (n=857) and non-diarrhoeic samples (n=211) from the hospitals and a nearby field community were screened with IDEIA Astrovirus detection kit; astrovirus co-infections with rotavirus and/or picobirnavirus were detected by RNA-PAGE and silver staining. Further RT-PCR was carried out using specific primers, viz. Mon340 (+) and Mon348 (-) targeting a highly conserved domain of ORF1a (289 bp) of human astroviruses. RESULTS Astrovirus infection was detected in 50 cases (50/857); astroviruses were detected mostly in children aged 6-12 months (50%); all non-diarrhoeic samples (n=211) were negative for astrovirus. In 52% of astrovirus positive cases, the virus was detected as the sole agent; mixed infections were also detected with other diarrhoeic pathogens such as rotavirus (32%), picobirnavirus (2%), rotavirus and picobirnavirus (2%), picobirnavirus and Enterotoxigenic E. coli (ETEC) (2%), rotavirus and ETEC (2%), rotavirus and Enteroaggregative E. coli (EAEC) (2%), Enteropathogenic E. coli (EPEC) (2%), Shigella flexneri type 3a (2%) and Ascaris (2%). RT-PCR and sequencing of amplicons of astroviruses from Kolkata, with specific primers targeted to the conserved domain of ORF1a (289 bp) of the astrovirus genome, showed maximum homology to the astrovirus strain ("5-158") from Seoul (98%). RESULTS AND CONCLUSIONS Clinical characteristics of the diarrhoeic children in Kolkata indicated that astrovirus infections were detected throughout the year and were associated with varying degree of dehydration and acute watery diarrhoea. In-depth molecular epidemiological surveillance of astroviruses in Kolkata is essential for better understanding of their overall genetic nature.
Collapse
Affiliation(s)
- Rittwika Bhattacharya
- Division of Virology, National Institute of Cholera and Enteric Diseases, P 33 CIT Road, Scheme XM, Beliaghata, Kolkata (Calcutta) 700010, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
126
|
Pantin-Jackwood MJ, Spackman E, Woolcock PR. Phylogenetic analysis of Turkey astroviruses reveals evidence of recombination. Virus Genes 2006; 32:187-92. [PMID: 16604451 PMCID: PMC7089065 DOI: 10.1007/s11262-005-6875-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 08/13/2005] [Indexed: 12/04/2022]
Abstract
Sequence data was obtained from the capsid (ORF-2) and the polymerase (ORF-lb) genes of 23 turkey astrovirus (TAstV) isolates collected from commercial turkey flocks around the United States between 2003 and 2004. A high level of genetic variation was observed among the isolates, particularly in the capsid gene, where nucleotide sequence identity among them was as low as 69%. Isolates collected on the same farm, on the same day, but from different houses could have as little as 72% identity between their capsid gene sequences when compared. Phylogenetic analysis of the capsid gene revealed no clear assortment by geographic region or isolation date. The polymerase gene was more conserved with between 86 and 99% nucleotide identity and did assort in a geographic manner. Based on differing topologies of the capsid and polymerase gene phylogenetic trees, TAstV appears to undergo recombination.
Collapse
Affiliation(s)
- Mary J. Pantin-Jackwood
- Southeast Poultry Research Laboratory, Agriculture Research Service, US Department of Agriculture, 934 College Station Rd., Athens, GA 30605 USA
| | - Erica Spackman
- Southeast Poultry Research Laboratory, Agriculture Research Service, US Department of Agriculture, 934 College Station Rd., Athens, GA 30605 USA
| | - Peter R. Woolcock
- California Animal Health and Food Safety Laboratory System, University of California Davis, Davis, California 39616 USA
| |
Collapse
|
127
|
Royuela E, Negredo A, Sánchez-Fauquier A. Development of a one step real-time RT-PCR method for sensitive detection of human astrovirus. J Virol Methods 2006; 133:14-9. [PMID: 16321452 DOI: 10.1016/j.jviromet.2005.10.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 09/14/2005] [Accepted: 10/03/2005] [Indexed: 11/16/2022]
Abstract
Human astrovirus (HAstV) has been recognized as the second most common cause of diarrhoea among children under 5 years old. To date, the true incidence of HAstV was underestimated when using enzyme immunoabsorbent assays (EIAs) and conventional reverse transcription (RT)-polymerase chain reaction (PCR) methods. The sensitivity of detection of EIA is insufficient and, although RT-PCR is more sensitive than EIA, the time required is a limitation for astrovirus detection. The aim of the study was to develop a real-time RT-PCR method in order to increase the sensitivity, to quantify the viral load and to minimize the time required for HAstV detection. The real-time RT-PCR reported here requires only one rapid step to obtain a high sensitivity (0.0052 infectious units (IU) (0.0026 IU/microl)) in all human astrovirus detected. The real-time RT-PCR detected IUs down to a 10(-6) dilution with an improvement in the detection limit of factor 10(4), whereas the conventional RT-PCR detected down to IUs 10(-2) dilution. This process is able to reduce the time of the assay and avoids the risk of contamination. The method described below has been validated with a panel of 100 clinical samples and the results obtained confirmed the high specificity of the assay; consequently, the application of this assay for molecular diagnosis is feasible as a versatile tool for ascertaining the true implication of HAstV in acute viral gastroenteritis.
Collapse
Affiliation(s)
- Enrique Royuela
- Servicio de Virología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctr. Majadahonda-Pozuelo km 2, 28220 Majadahonda, Madrid, Spain
| | | | | |
Collapse
|
128
|
Smits SL, Snijder EJ, de Groot RJ. Characterization of a torovirus main proteinase. J Virol 2006; 80:4157-67. [PMID: 16571831 PMCID: PMC1440467 DOI: 10.1128/jvi.80.8.4157-4167.2006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 02/02/2006] [Indexed: 11/20/2022] Open
Abstract
Viruses of the order Nidovirales encode huge replicase polyproteins. These are processed primarily by the chymotrypsin-like main proteinases (M(pro)s). So far, M(pro)s have been studied only for corona-, arteri-, and roniviruses. Here, we report the characterization of the M(pro) of toroviruses, the fourth main Nidovirus branch. Comparative sequence analysis of polyprotein 1a of equine torovirus (EToV) strain Berne, identified a serine proteinase domain, flanked by hydrophobic regions. Heterologous expression of this domain resulted in autoprocessing at flanking cleavage sites. N-terminal sequence analysis of cleavage products tentatively identified FxxQ downward arrow(S, A) as the substrate consensus sequence. EToV M(pro) combines several traits of its closest relatives. It has a predicted three-domain structure, with two catalytic beta-barrel domains and an additional C-terminal domain of unknown function. With respect to substrate specificity, the EToV M(pro) resembles its coronavirus homologue in its preference for P1-Gln, but its substrate-binding subsite, S1, more closely resembles that of arteri- and ronivirus M(pro)s, which prefer P1-Glu. Surprisingly, in contrast to the M(pro)s of corona- and roniviruses, but like that of arterivirus, the torovirus M(pro) uses serine instead of cysteine as its principal nucleophile. Under the premise that the M(pro)s of corona- and toroviruses are more closely related to each other than to those of arteri- and roniviruses, the transition from serine- to cysteine-based proteolytic catalysis (or vice versa) must have happened more than once in the course of nidovirus evolution. In this respect, it is of interest that a mutant EToV M(pro) with a Ser165-->Cys substitution retained partial enzymatic activity.
Collapse
Affiliation(s)
- Saskia L Smits
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | | | | |
Collapse
|
129
|
Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ. Nidovirales: evolving the largest RNA virus genome. Virus Res 2006; 117:17-37. [PMID: 16503362 PMCID: PMC7114179 DOI: 10.1016/j.virusres.2006.01.017] [Citation(s) in RCA: 640] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Revised: 01/13/2006] [Accepted: 01/18/2006] [Indexed: 11/19/2022]
Abstract
This review focuses on the monophyletic group of animal RNA viruses united in the order Nidovirales. The order includes the distantly related coronaviruses, toroviruses, and roniviruses, which possess the largest known RNA genomes (from 26 to 32 kb) and will therefore be called ‘large’ nidoviruses in this review. They are compared with their arterivirus cousins, which also belong to the Nidovirales despite having a much smaller genome (13–16 kb). Common and unique features that have been identified for either large or all nidoviruses are outlined. These include the nidovirus genetic plan and genome diversity, the composition of the replicase machinery and virus particles, virus-specific accessory genes, the mechanisms of RNA and protein synthesis, and the origin and evolution of nidoviruses with small and large genomes. Nidoviruses employ single-stranded, polycistronic RNA genomes of positive polarity that direct the synthesis of the subunits of the replicative complex, including the RNA-dependent RNA polymerase and helicase. Replicase gene expression is under the principal control of a ribosomal frameshifting signal and a chymotrypsin-like protease, which is assisted by one or more papain-like proteases. A nested set of subgenomic RNAs is synthesized to express the 3′-proximal ORFs that encode most conserved structural proteins and, in some large nidoviruses, also diverse accessory proteins that may promote virus adaptation to specific hosts. The replicase machinery includes a set of RNA-processing enzymes some of which are unique for either all or large nidoviruses. The acquisition of these enzymes may have improved the low fidelity of RNA replication to allow genome expansion and give rise to the ancestors of small and, subsequently, large nidoviruses.
Collapse
Affiliation(s)
- Alexander E Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
| | | | | | | |
Collapse
|
130
|
Silva PA, Cardoso DDP, Schreier E. Molecular characterization of human astroviruses isolated in Brazil, including the complete sequences of astrovirus genotypes 4 and 5. Arch Virol 2006; 151:1405-17. [PMID: 16421636 DOI: 10.1007/s00705-005-0704-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 11/25/2005] [Indexed: 10/25/2022]
Abstract
Human astroviruses (HAstV) are recognized as an important cause of gastroenteritis in young children worldwide. This study describes the molecular characteristics of astroviruses isolated in Brazil, using RT-PCR and molecular sequencing of segments of all three viral ORFs. Genetic analysis of a 348-nucleotide segment from ORF 2 demonstrated that the Brazilian isolates belong to HAstV genotypes 1 to 5 and 8. ORF 1b sequences displayed a high degree of nucleotide identity even between different genotypes, which disfavours HAstV genotyping in this region. ORF 1a sequence analysis classified all Brazilian samples as genogroup A. The complete sequences of HAstV genotype 4 (putative serotype 4) and genotype 5 (putative serotype 5) were determined for the first time.
Collapse
Affiliation(s)
- P A Silva
- Laboratory of Virology, Institute of Pathology and Public Health, Federal University of Goiás, Goiânia, Brazil
| | | | | |
Collapse
|
131
|
Molecular Virology of Enteric Viruses (with Emphasis on Caliciviruses). VIRUSES IN FOODS 2006:43-100. [PMCID: PMC7120911 DOI: 10.1007/0-387-29251-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
|
132
|
Gabbay YB, Luz CRNED, Costa IV, Cavalcante-Pepino EL, Sousa MS, Oliveira KK, Wanzeller ALM, Mascarenhas JDP, Leite JPG, Linhares AC. Prevalence and genetic diversity of astroviruses in children with and without diarrhea in São Luís, Maranhão, Brazil. Mem Inst Oswaldo Cruz 2005; 100:709-14. [PMID: 16410955 DOI: 10.1590/s0074-02762005000700004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human astroviruses (HAstV) have been increasingly identified as important etiological agents of acute gastroenteritis in children up to five years old. The aim of this study was to determine the prevalence and genotype diversity of HAstV in children with symptomatic and asymptomatic infections in São Luís, Maranhão, Brazil. From June 1997 to July 1999 a total of 183 fecal samples 84 from symptomatic and 99 from asymptomatic children were tested by enzyme immunoassay for HAstV. Prevalence rates were found to be 11 and 3% for symptomatic and asymptomatic children, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) was carried out in 46 specimens (26 symptomatic and 20 asymptomatic) including the 12 samples that were positive by enzyme immunoassay (EIA). The overall positivity yielded by both methods was 8% (15/184); of these, 11% (9/84) for symptomatic and 5% (5/99) for those without symptoms or signs. Sequence analysis of amplicons revealed that HAstV-1 genotype was the most prevalent, accounting for 60% of isolates. Genotypes 2, 3, 4, and 5 were also detected, as one single isolate (10%) for each type. Variations in the sequences were observed when Brazilian isolates were compared to prototype strains identified in the United Kingdom. No seasonal pattern of occurrence was observed during these two years of study, and peak detection rate was observed in children aged between 3 and 6 months in the symptomatic group, and between 18 and 24 months in the controls.
Collapse
Affiliation(s)
- Yvone B Gabbay
- Seção de Virologia, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, 67030-000 Ananindeua, PA, Brazil.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
133
|
Abstract
Coat proteins of non-enveloped, icosahedral viruses must perform a variety of functions during their life cycle such as assembly of the coat protein subunits into a closed shell, specific encapsidation of the viral nucleic acid, maturation of the capsid, interaction with host receptors, and disassembly to deliver the genetic information into the newly infected cell. A thorough understanding of the multiple capsid properties at the molecular level is required in order to identify potential targets for antiviral therapy and the prevention of viral disease. The system we have chosen for study is the astrovirus, a family of icosahedral, single-stranded RNA viruses that cause disease in mammals and birds. Very little is known about what regions of the coat protein contribute to the diverse capsid functions. This review will present novel structural predictions for the coat protein sequence of different astrovirus family members. Based on these predictions, we hypothesize that the assembly and RNA packaging functions of the astrovirus coat protein constitutes an individual domain distinct from the determinants required for receptor binding and internalization. Information derived from these structural predictions will serve as an important tool in designing experiments to understand astrovirus biology.
Collapse
Affiliation(s)
- Neel K Krishna
- Department of Pediatrics and the Center for Pediatric Research, Norfolk, VA 23510, USA.
| |
Collapse
|
134
|
Guix S, Caballero S, Bosch A, Pintó RM. Human astrovirus C-terminal nsP1a protein is involved in RNA replication. Virology 2005; 333:124-31. [PMID: 15708598 DOI: 10.1016/j.virol.2004.12.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2004] [Revised: 10/07/2004] [Accepted: 12/20/2004] [Indexed: 11/23/2022]
Abstract
Human astrovirus nonstructural C-terminal nsP1a protein, which contains a hypervariable region (HVR) and colocalizes with the endoplasmic reticulum and viral RNA, has been suggested to be involved in the RNA replication process. Four viruses differing only in their C-terminal nsP1a protein, corresponding to HVR-derived genotypes IV, V, VI, and XII, were all able to replicate in CaCo-2 cells but displayed differences in their RNA replication and growth properties. Two overall patterns of replication were observed: types IV and V on one side, and types VI and XII on the other. The main detected differences were on the levels of antigenomic and subgenomic RNAs, being the latter significantly higher in types IV and V. Accordingly, quantification of viral RNA load in feces from children with gastroenteritis showed that HVR-derived genotypes IV and V occur in significantly higher numbers. In consequence, it may be concluded that the variability of the C-terminal nsP1a gene affects the virus replication phenotype.
Collapse
Affiliation(s)
- Susana Guix
- Department of Microbiology, Enteric Virus Laboratory, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | | | | | | |
Collapse
|
135
|
Guix S, Caballero S, Bosch A, Pintó RM. C-terminal nsP1a protein of human astrovirus colocalizes with the endoplasmic reticulum and viral RNA. J Virol 2004; 78:13627-36. [PMID: 15564473 PMCID: PMC533902 DOI: 10.1128/jvi.78.24.13627-13636.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Computational and biological approaches were undertaken to characterize the role of the human astrovirus nonstructural protein nsP1a/4, located at the C-terminal fragment of nsP1a. Computer analysis reveals sequence similarities to other nonstructural viral proteins involved in RNA replication and/or transcription and allows the identification of a glutamine- and proline-rich region, the prediction of many phosphorylation and O-glycosylation sites, and the occurrence of a KKXX-like endoplasmic reticulum retention signal. Immunoprecipitation analysis with an antibody against a synthetic peptide of the nsP1a/4 sequence detected polyprotein precursors of 160, 75, and 38 to 40 kDa as well as five smaller proteins in the range of 21 to 27 kDa. Immunofluorescence labeling showed that the nsP1a/4 protein is accumulated at the perinuclear region, in association with the endoplasmic reticulum and the viral RNA. These results suggest the involvement of nsP1a/4 protein in the RNA replication process in endoplasmic reticulum-derived intracellular membranes.
Collapse
Affiliation(s)
- Susana Guix
- Enteric Virus Laboratory, Department of Microbiology, University of Barcelona, Avda Diagonal 645, 08028 Barcelona, Spain
| | | | | | | |
Collapse
|
136
|
Brierley I, Vidakovic M. V, 2.Ribosomal frameshifting in astroviruses. ACTA ACUST UNITED AC 2004; 9:587-606. [PMID: 32287603 PMCID: PMC7133818 DOI: 10.1016/s0168-7069(03)09035-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This chapter reviews ribosomal frameshifting with an emphasis on the frameshifting process in astroviruses. Frameshifting is a potential antiviral target. It is possible that the replication cycle of any virus that uses this process could be disrupted by modulation of frameshift efficiencies, but a better understanding of the occurrence and the molecular basis of frameshifting will be required before it can be considered a genuine target. To date, there are no confirmed examples of frameshift signals from conventional eukaryotic cellular genes, although computer-assisted database searches have identified a number of candidates. The frameshift allows the required ratio of viral proteins to be produced, but it may also serve to downregulate levels of viral replicases that may be toxic in high amounts.
Collapse
Affiliation(s)
- Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 l QP, U.K
| | - Marijana Vidakovic
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 l QP, U.K
| |
Collapse
|
137
|
Méndez E, Salas-Ocampo E, Arias CF. Caspases mediate processing of the capsid precursor and cell release of human astroviruses. J Virol 2004; 78:8601-8. [PMID: 15280469 PMCID: PMC479052 DOI: 10.1128/jvi.78.16.8601-8608.2004] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work we have shown that astrovirus infection induces apoptosis of Caco-2 cells, since fragmentation of cellular DNA, cleavage of cellular proteins which are substrate of activated caspases, and a change in the mitochondrial transmembrane potential occur upon virus infection. The human astrovirus Yuc8 polyprotein capsid precursor VP90 is initially processed to yield VP70, and we have shown that this processing is trypsin independent and occurs intracellularly through four cleavages at its carboxy-terminal region. We further showed that VP90-VP70 processing is mediated by caspases, since it was blocked by the pancaspase inhibitor benzyloxycarbonyl-Val-Ala-Asp fluoromethylketone (z-VAD-fmk), and it was promoted by the apoptosis inducer TNF-related apoptosis-inducing ligand (TRAIL). Although the cell-associated virus produced in the presence of these compounds was not affected, the release of infectious virus to the cell supernatant was drastically reduced in the presence of z-VAD-fmk and increased by TRAIL, indicating that VP90-VP70 cleavage is important for the virus particles to be released from the cell. This is the first report that describes the induction and utilization of caspase activity by a virus to promote processing of the capsid precursor and dissemination of the viral particles.
Collapse
Affiliation(s)
- Ernesto Méndez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado Postal 510-3, Colonia Miraval, Cuernavaca, Morelos 62250, Mexico.
| | | | | |
Collapse
|
138
|
Guix S, Bosch A, Ribes E, Dora Martínez L, Pintó RM. Apoptosis in astrovirus-infected CaCo-2 cells. Virology 2004; 319:249-61. [PMID: 14980485 PMCID: PMC7127648 DOI: 10.1016/j.virol.2003.10.036] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2003] [Revised: 10/20/2003] [Accepted: 10/23/2003] [Indexed: 02/08/2023]
Abstract
Cell death processes during human astrovirus replication in CaCo-2 cells and their underlying mechanisms were investigated. Morphological and biochemical alterations typical of apoptosis were analyzed in infected cells using a combination of techniques, including DAPI staining, the sub-G0/G1 technique and the TUNEL assay. The onset of apoptosis was directly proportional to the virus multiplicity of infection. Transient expression experiments showed a direct link between astrovirus ORF1a encoded proteins and apoptosis induction. A computer analysis of the astrovirus genome revealed the presence of a death domain in the nonstructural protein p38 of unknown function, encoded in ORF1a. Apoptosis inhibition experiments suggested the involvement of caspase 8 in the apoptotic response, and led to a reduction in the infectivity of the virus progeny released to the supernatant. We conclude that apoptotic death of host cells seems necessary for efficient human astrovirus replication and particle maturation.
Collapse
Affiliation(s)
- Susana Guix
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Spain
- Corresponding author. Department of Microbiology, School of Biology, University of Barcelona, Avda Diagonal 645, 08028 Barcelona, Spain. Fax: +34-93-4034629.
| | - Enric Ribes
- Enteric Virus Group, Department of Cell Biology, University of Barcelona, Spain
| | - L. Dora Martínez
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Spain
| | - Rosa M. Pintó
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Spain
| |
Collapse
|
139
|
Méndez-Toss M, Griffin DD, Calva J, Contreras JF, Puerto FI, Mota F, Guiscafré H, Cedillo R, Muñoz O, Herrera I, López S, Arias CF. Prevalence and genetic diversity of human astroviruses in Mexican children with symptomatic and asymptomatic infections. J Clin Microbiol 2004; 42:151-7. [PMID: 14715746 PMCID: PMC321733 DOI: 10.1128/jcm.42.1.151-157.2004] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalence and type diversity of human astroviruses (HAstV) in children with symptomatic and asymptomatic infections were determined in five localities of Mexico. HAstV were detected in 4.6 (24 of 522) and 2.6% (11 of 428) of children with and without diarrhea, respectively. Genotyping of the detected strains showed that at least seven (types 1 to 4 and 6 to 8) of the eight known HAstV types circulated in Mexico between October 1994 and March 1995. HAstV types 1 and 3 were the most prevalent in children with diarrhea, although they were not found in all localities studied. HAstV type 8 was found in Mexico City, Monterrey, and Mérida; in the last it was as prevalent (40%) as type 1 viruses, indicating that this astrovirus type is more common than previously recognized. A correlation between the HAstV infecting type and the presence or absence of diarrheic symptoms was not observed. Enteric adenoviruses were also studied, and they were found to be present in 2.3 (12 of 522) and 1.4% (6 of 428) of symptomatic and asymptomatic children, respectively.
Collapse
Affiliation(s)
- Martha Méndez-Toss
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
140
|
Yan H, Yagyu F, Okitsu S, Nishio O, Ushijima H. Detection of norovirus (GI, GII), Sapovirus and astrovirus in fecal samples using reverse transcription single-round multiplex PCR. J Virol Methods 2003; 114:37-44. [PMID: 14599677 DOI: 10.1016/j.jviromet.2003.08.009] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A reverse transcription (RT) single-round multiplex polymerase chain reaction (smPCR) assay was developed to detect simultaneously Norovirus genogroup I and II, Sapovirus and astrovirus. A total of 377 diarrhea stool samples (screened for rotavirus- and adenorivus-negative) from four regions in Japan during July 2000 to June 2001 were examined by RT-smPCR. The positive rate was 16.4% (62 out of 377 stool samples). Norovirus, Sapovirus and astrovirus were detected in 42, 16, 4 of 60 positive samples, respectively. Coinfection was not found in these samples. Infections occurred mainly in November, December and January. The key elements of the RT-smPCR are (i) the cDNA synthesis with the Superscript RTII and random primer at 42 degrees C for 1 h, at 99 degrees C for 5 min, and (ii) single-round multiplex PCR by using Taq polymerase mixed together with a mixture of four different primer pairs (G1-SKF/G1-SKR for Norovirus genogroup I, COG2F/G2-SKR for Norovirus genogroup II, SLV5317/SLV5749 for Sapovirus, PreCAP1/82b for astrovirus). All of the four primer pairs amplify the capsid region of target viral genome, produce four size-specific amplicons of 330, 387, 434, 719 bp for Norovirus genogroup I and II, Sapovirus and astrovirus, respectively. This assay provides a more rapid and efficient way to detect these viruses from fecal samples in a single test, and also offers the potential for their molecular detection in food and environmental samples.
Collapse
Affiliation(s)
- Hainian Yan
- Department of Developmental Medical Sciences, Graduate School of Medicine, Institute of International Health, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | | | | | | |
Collapse
|
141
|
Mittelholzer C, Hedlund KO, Englund L, Dietz HH, Svensson L. Molecular characterization of a novel astrovirus associated with disease in mink. J Gen Virol 2003; 84:3087-3094. [PMID: 14573813 DOI: 10.1099/vir.0.19267-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-weaning diarrhoea is a well-known problem in mink farming in Europe, causing morbidity that varies between farms, regions and season. Different causalities for the disease have been proposed, but only most recently has a novel astrovirus been identified as an important risk factor. In this report, the molecular characterization, origin and evolution of this novel astrovirus of mink are discussed. The polyadenylated, positive-stranded RNA genome was sequenced and found to contain 6610 nt, organized into three ORFs and two short UTRs. A ribosomal frameshift sequence links the 5' two ORFs, containing sequence motifs for a serine protease (ORF1a) and an RNA-dependent RNA polymerase (ORF1b). The structural proteins are encoded by ORF2 and, presumably, are expressed as a polyprotein precursor to be cleaved into the mature capsid proteins. These results indicate that mink astrovirus (MiAstV) has all of the features typical of members of the Astroviridae. Phylogenetic analyses revealed that MiAstV is distantly related to established astroviruses, showing less than 67 % similarity at the nucleotide level with its closest relative, ovine astrovirus, and even lower identities at the predicted amino acid level. Nevertheless, sequence analysis of MiAstV isolates from geographically distinct Swedish and Danish farms showed much less diversity. This suggests either the spread in the mink population of a virus that has evolved a long time ago or the recent introduction of an ancient virus into a new host species.
Collapse
Affiliation(s)
- Christian Mittelholzer
- Department of Virology, Swedish Institute for Infectious Disease Control, S-171 82 Solna, Sweden
| | - Kjell-Olof Hedlund
- Department of Molecular Epidemiology and Biotechnology, Swedish Institute for Infectious Disease Control, S-171 82 Solna, Sweden
| | - Lena Englund
- Department of Small Animals, National Veterinary Institute, S-751 89 Uppsala, Sweden
| | - Hans-Henrik Dietz
- Department of Poultry, Fish and Fur Animals, Danish Veterinary Institute, DK-8200 Århus, Denmark
| | - Lennart Svensson
- Department of Virology, Swedish Institute for Infectious Disease Control, S-171 82 Solna, Sweden
| |
Collapse
|
142
|
Méndez E, Salas-Ocampo MPE, Munguía ME, Arias CF. Protein products of the open reading frames encoding nonstructural proteins of human astrovirus serotype 8. J Virol 2003; 77:11378-84. [PMID: 14557623 PMCID: PMC229263 DOI: 10.1128/jvi.77.21.11378-11384.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2003] [Accepted: 08/04/2003] [Indexed: 11/20/2022] Open
Abstract
Human astroviruses have a positive-strand RNA genome, which contains three open reading frames (ORF1a, ORF1b, and ORF2). The genomic RNA is translated into two nonstructural polyproteins, nsp1a and nsp1ab, that contain sequences derived from ORF1a and from both ORF1a and ORF1b, respectively. Proteins nsp1a and nsp1ab are thought to be proteolytically processed to yield the viral proteins implicated in the replication of the virus genome; however, the intermediate and final products of this processing have been poorly characterized. To identify the cleavage products of the nonstructural polyproteins of a human astrovirus serotype 8 strain, antisera to selected recombinant proteins were produced and were used to analyze the viral proteins synthesized in astrovirus-infected Caco-2 cells and in cells transfected with recombinant plasmids expressing the ORF1a and ORF1b polyproteins. Pulse-chase experiments identified proteins of approximately 145, 88, 85, and 75 kDa as cleavage intermediates during the polyprotein processing. In addition, these experiments and kinetic analysis of the synthesis of the viral proteins identified polypeptides of 57, 20, and 19 kDa, as well as two products of around 27 kDa, as final cleavage products, with the 57-kDa polypeptide most probably being the virus RNA polymerase and the two approximately 27-kDa products being the viral protease. Based on the differential reactivities of the astrovirus proteins with the various antisera used, the individual polypeptides detected were mapped to the virus ORF1a and ORF1b regions.
Collapse
Affiliation(s)
- Ernesto Méndez
- Departamento de Genética y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Miraval, Cuernavaca, Morelos 62250, Mexico.
| | | | | | | |
Collapse
|
143
|
Dalton RM, Pastrana EP, Sánchez-Fauquier A. Vaccinia virus recombinant expressing an 87-kilodalton polyprotein that is sufficient to form astrovirus-like particles. J Virol 2003; 77:9094-8. [PMID: 12885927 PMCID: PMC167206 DOI: 10.1128/jvi.77.16.9094-9098.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human astrovirus is an important cause of acute gastroenteritis. We have generated, for the first time, a vaccinia virus recombinant expressing the astrovirus 87-kDa structural polyprotein. The results demonstrate that this expression results in the formation of virus-like particles in the absence of other astrovirus proteins and genomic RNA. The purified trypsin-activated virus-like particles strongly resemble the complete astrovirus particles.
Collapse
Affiliation(s)
- Rosa M Dalton
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | | | | |
Collapse
|
144
|
Tai JH, Ewert MS, Belliot G, Glass RI, Monroe SS. Development of a rapid method using nucleic acid sequence-based amplification for the detection of astrovirus. J Virol Methods 2003; 110:119-27. [PMID: 12798238 DOI: 10.1016/s0166-0934(03)00108-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have developed a rapid method to detect astrovirus in fecal specimens utilizing nucleic acid sequence-based amplification (NASBA) and several detection methodologies, including a sandwich hybridization assay based on DNA-tagged liposomes (liposome-strip detection assay). RNA was extracted from 65 stool specimens that were positive for astrovirus by enzyme immunoassay and was amplified by both NASBA and reverse transcriptase PCR (RT-PCR). Also extracted and amplified were 19 specimens containing rotavirus, 20 specimens containing norovirus, five specimens containing adenovirus, 15 water negative control specimens, and eight specimens containing astrovirus reference strains. NASBA products were detected by electrochemiluminescence detection (ECL) and by liposome-strip detection; RT-PCR products were detected by ethidium bromide staining following gel electrophoresis and by liquid hybridization assay (LHA). There was no significant difference in the detection rates of NASBA- and RT-PCR-based assays, with one exception in which the NASBA/ECL assay detected astrovirus in eight specimens that tested negative by the RT-PCR/LHA assay. These results suggest that these NASBA-based detection methods have detection rates that are as good as or better than those of RT-PCR-based methods. Both NASBA and liposome-strip detection may be useful for field studies and environmental testing because these methods are rapid and do not require specialized equipment.
Collapse
Affiliation(s)
- Jennifer H Tai
- Viral Gastroenteritis Section, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS G04, Atlanta, GA 30333, USA
| | | | | | | | | |
Collapse
|
145
|
Brierley I, Pennell S. Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:233-48. [PMID: 12762025 DOI: 10.1101/sqb.2001.66.233] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- I Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | | |
Collapse
|
146
|
Choi J, Xu Z, Ou JH. Triple decoding of hepatitis C virus RNA by programmed translational frameshifting. Mol Cell Biol 2003; 23:1489-97. [PMID: 12588970 PMCID: PMC151691 DOI: 10.1128/mcb.23.5.1489-1497.2003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2002] [Revised: 08/21/2002] [Accepted: 11/27/2002] [Indexed: 11/20/2022] Open
Abstract
Ribosomes can be programmed to shift from one reading frame to another during translation. Hepatitis C virus (HCV) uses such a mechanism to produce F protein from the -2/+1 reading frame. We now report that the HCV frameshift signal can mediate the synthesis of the core protein of the zero frame, the F protein of the -2/+1 frame, and a 1.5-kDa protein of the -1/+2 frame. This triple decoding function does not require sequences flanking the frameshift signal and is apparently independent of membranes and the synthesis of the HCV polyprotein. Two consensus -1 frameshift sequences in the HCV type 1 frameshift signal facilitate ribosomal frameshifts into both overlapping reading frames. A sequence which is located immediately downstream of the frameshift signal and has the potential to form a double stem-loop structure can significantly enhance translational frameshifting in the presence of the peptidyl-transferase inhibitor puromycin. Based on these results, a model is proposed to explain the triple decoding activities of the HCV ribosomal frameshift signal.
Collapse
Affiliation(s)
- Jinah Choi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | | | | |
Collapse
|
147
|
Jonassen CM, Jonassen T TØ, Sveen TM, Grinde B. Complete genomic sequences of astroviruses from sheep and turkey: comparison with related viruses. Virus Res 2003; 91:195-201. [PMID: 12573498 DOI: 10.1016/s0168-1702(02)00269-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The genomes of astroviruses infecting sheep and turkey were sequenced. Detailed analyses of these sequences were performed, including comparison with the other complete astrovirus sequences available as well as with other RNA virus sequences, with focus on the non-structural proteins and RNA sequences. Earlier postulated functional astrovirus RNA motifs and protein domains could in most cases be recognised in the sheep and turkey astrovirus sequences. In addition, analyses of the available astrovirus sequences revealed: two protein regions with the potential for forming coiled coils, differences in the postulated transmembrane region, a similarity between the putative astrovirus nuclear localisation signal and calicivirus genome-linked proteins, and a stretch of a highly conserved RNA sequence with a possible role in the astrovirus capsid gene expression. The present analyses contribute to the deciphering of pertinent functions of the astrovirus genomes.
Collapse
Affiliation(s)
- Christine M Jonassen
- Division of Infectious Disease Control, Norwegian Institute of Public Health, PO Box 4404 Nydalen, NO-0403, Oslo, Norway
| | | | | | | |
Collapse
|
148
|
Schnagl RD, Belfrage K, Farrington R, Hutchinson K, Lewis V, Erlich J, Morey F. Incidence of human astrovirus in central Australia (1995 to 1998) and comparison of deduced serotypes detected from 1981 to 1998. J Clin Microbiol 2002; 40:4114-20. [PMID: 12409383 PMCID: PMC139637 DOI: 10.1128/jcm.40.11.4114-4120.2002] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2002] [Revised: 07/12/2002] [Accepted: 08/19/2002] [Indexed: 11/20/2022] Open
Abstract
The incidence of astrovirus infection was determined among infants and young children admitted to Alice Springs Hospital (central Australia) with gastroenteritis from 1995 to 1998. Astrovirus was detected by reverse transcription-PCR in 33 of 495 stool samples, and this represented 4.3% of a total of 774 stool samples tested for astrovirus, rotavirus, and Norwalk-like viruses. Astrovirus incidence was substantially lower than that of rotavirus but higher than that of Norwalk-like viruses both overall and in each of the 4 years individually. Over the period from 1981 to 1998, including the period from 1981 to 1994 during which astrovirus was identified only by electron microscopy, astrovirus serotypes (deduced from genotypes) 1, 2, 3, and 4 were identified. Deduced serotypes 1, 3, and 4 all appeared regularly over this 18-year period. Also over this period, nucleotide variation (in some cases substantial) in a section of the capsid protein precursor region of the virus genome was evident among strains of all four of the deduced central Australian serotypes. Consequent amino acid changes were, however, only evident among deduced serotype 3 strains. Geographic variation at both the genome and the resultant amino acid levels was evident among strains of all four of the deduced central Australian serotypes and their respective prototypes isolated in the United Kingdom.
Collapse
Affiliation(s)
- Roger D Schnagl
- Department of Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | | | | | | | | | | | | |
Collapse
|
149
|
Méndez E, Fernández-Luna T, López S, Méndez-Toss M, Arias CF. Proteolytic processing of a serotype 8 human astrovirus ORF2 polyprotein. J Virol 2002; 76:7996-8002. [PMID: 12134004 PMCID: PMC155114 DOI: 10.1128/jvi.76.16.7996-8002.2002] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2002] [Accepted: 05/07/2002] [Indexed: 01/18/2023] Open
Abstract
Astroviruses require the proteolytic cleavage of the capsid protein to infect the host cell. Here we describe the processing pathway of the primary translation product of the structural polyprotein (ORF2) encoded by a human astrovirus serotype 8 (strain Yuc8). The primary translation product of ORF2 is of approximately 90 kDa, which is subsequently cleaved to yield a 70-kDa protein (VP70) which is assembled into the viral particles. Limited trypsin treatment of purified particles containing VP70 results in the generation of polypeptides VP41 and VP28, which are then further processed to proteins of 38.5, 35, and 34 kDa and 27, 26, and 25 kDa, respectively. VP34, VP27 and VP25 are the predominant proteins in fully cleaved virions, which correlate with the highest level of infectivity. Processing of the VP41 protein to yield VP38.5 to VP34 polypeptides occurred at its carboxy terminus, as suggested by immunoblot analysis using hyperimmune sera to different regions of the ORF2, while processing of VP28 to generate VP27 and VP25 occurred at its carboxy and amino terminus, respectively, as determined by immunoblot, as well as by N-terminal sequencing of those products. Based on these data, the processing pathway for the 90-kDa primary product of astrovirus Yuc8 ORF2 is presented.
Collapse
Affiliation(s)
- Ernesto Méndez
- Departamento de Genética y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Colonia Miraval, Cuernavaca, Morelos 62250, Mexico.
| | | | | | | | | |
Collapse
|
150
|
Cunliffe NA, Dove W, Gondwe JS, Thindwa BDM, Greensill J, Holmes JL, Bresee JS, Monroe SS, Glass RI, Broadhead RL, Molyneux ME, Hart CA. Detection and characterisation of human astroviruses in children with acute gastroenteritis in Blantyre, Malawi. J Med Virol 2002; 67:563-6. [PMID: 12116005 DOI: 10.1002/jmv.10139] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In a 2-year hospital-based study of paediatric gastroenteritis in Blantyre, Malawi, astroviruses were detected by enzyme immunoassay in 15 (1.9%) of 786 inpatients and in 9 (2.3%) of 400 outpatients. Greater disease severity was noted in children coinfected with human immunodeficiency virus (HIV). Six human astrovirus (HAstV) genotypes were identified, including HAstV-1 (25%), HAstV-2 (21%), HAstV-3 (25%), HAstV-4 (13%), HAstV-5 (4%), and HAstV-8 (13%). Although astroviruses are not major causes of gastroenteritis among children admitted to hospital in Blantyre, concomitant HIV infection appears to be a risk factor for increased severity of disease.
Collapse
Affiliation(s)
- Nigel A Cunliffe
- Wellcome Trust Research Laboratories, Universities of Malawi and Liverpool, College of Medicine, Blantyre, Malawi.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|