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Isolation and Identification of Two Clinical Strains of the Novel Genotype Enterovirus E5 in China. Microbiol Spectr 2022; 10:e0266221. [PMID: 35652637 PMCID: PMC9241952 DOI: 10.1128/spectrum.02662-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Most enterovirus (EV) infections are subclinical but, occasionally, can cause severe and potentially fatal diseases in humans and animals. Currently, EVs are divided into 12 types (A to L) based on phylogenetic analysis and on their natural hosts. Bovine enterovirus (BEV) is an essential member of the enterovirus belonging to the types E and F that attacks cattle as its natural host and causes clinical disorders in the digestive, respiratory, and reproductive tracts. In 2020, several dairy farms in China experienced cow mortality with acute clinical signs, including fever, and diarrhea. In these cases, GX20-1 and JS20-1 virus strains were isolated and sequenced. Cellular adaptation of these two strains showed efficient replications on Madin-Darby bovine kidney (MDBK) cells and produced a significant cytopathogenic effect (CPE). However, on baby hamster kidney (BHK-21) and Vero cells, viral replication was inefficient and did not produce CPE. As noted in comparative genomics analysis, these two strains showed distant evolutionary relationships with the well-known E1 to E4 and F1 to F4 subtypes of BEV and high sequence identities with the candidate type Enterovirus E5, a novel genotype recently identified based on the genomic data of three strains, including the GX20-1 and JS20-1 strains. This study provides the first evidence of a novel genotype bovine enterovirus infection in Chinese cattle herds, a potential threat to the cattle industry in China. IMPORTANCE Bovine enterovirus (BEV) is a cattle-infecting pathogen. This study is the first report of natural infection of a novel genotype of enterovirus in herds of cattle in China. The homology of the novel enterovirus is far different from the structural protein of other enteroviruses and has different cellular adaptations. This study provides a reference for the biological characteristics and prevalence of the novel enterovirus in Chinese cattle populations.
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Mahmud B, Horn CM, Tapprich WE. Structure of the 5' Untranslated Region of Enteroviral Genomic RNA. J Virol 2019; 93:e01288-19. [PMID: 31534036 PMCID: PMC6854513 DOI: 10.1128/jvi.01288-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Enteroviral RNA genomes share a long, highly structured 5' untranslated region (5' UTR) containing a type I internal ribosome entry site (IRES). The 5' UTR is composed of stably folded RNA domains connected by unstructured RNA regions. Proper folding and functioning of the 5' UTR underlies the efficiency of viral replication and also determines viral virulence. We have characterized the structure of 5' UTR genomic RNA from coxsackievirus B3 using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical probes in solution. Our results revealed novel structural features, including realignment of major domains, newly identified long-range interactions, and an intrinsically disordered connecting region. Together, these newly identified features contribute to a model for enteroviral 5' UTRs with type I IRES elements that links structure to function during the hierarchical processes directed by genomic RNA during viral infection.IMPORTANCE Enterovirus infections are responsible for human diseases, including myocarditis, pancreatitis, acute flaccid paralysis, and poliomyelitis. The virulence of these viruses depends on efficient recognition of the RNA genome by a large family of host proteins and protein synthesis factors, which in turn relies on the three-dimensional folding of the first 750 nucleotides of the molecule. Structural information about this region of the genome, called the 5' untranslated region (5' UTR), is needed to assist in the process of vaccine and antiviral development. This work presents a model for the structure of the enteroviral 5' UTR. The model includes an RNA element called an intrinsically disordered RNA region (IDRR). Intrinsically disordered proteins (IDPs) are well known, but correlates in RNA have not been proposed. The proposed IDRR is a 20-nucleotide region, long known for its functional importance, where structural flexibility helps explain recognition by factors controlling multiple functional states.
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Affiliation(s)
- Bejan Mahmud
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Christopher M Horn
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - William E Tapprich
- Biology Department, University of Nebraska at Omaha, Omaha, Nebraska, USA
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Kumari S, Saikumar G, Desingu PA, Das T, Singh R. Immunohistochemical detection of naturally occurring porcine Sapelovirus infection in Indian pigs. J Immunoassay Immunochem 2019; 40:676-684. [PMID: 31603022 DOI: 10.1080/15321819.2019.1675695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We investigated immunohistochemical detection of porcine Sapelovirus (PSV) in naturally infected pigs of different ages. Forty-nine fecal samples, intestinal contents and other tissue samples from dead pigs were screened in previous study using reverse transcription polymerase chain reaction (RT-PCR) for PSV infection. Eight animals were positive for PSV based on RT-PCR examination. Gross lesions were recorded mainly in the large and small intestines. Microscopic examination of intestines showed severe enteritis. Tissue sections of all organs from PSV positive animals were immunostained using hyperimmune serum raised in rats against PSV that had been grown in a BHK-21 cell line. Staining of PSV was found only in the large and small intestines.
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Affiliation(s)
- Swati Kumari
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - G Saikumar
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - P A Desingu
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - T Das
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
| | - Rahul Singh
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Bareilly, India
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KUMARI SWATI, RAY PK, SINGH RAHUL, SAIKUMAR G. Pathogenicity of porcine sapelovirus infection in mice. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i2.87322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Porcine Sapelovirus (PSV) is a RNA virus belonging to a new genus Sapelovirus of family Picornaviridae. PSV has been isolated from India in 2016. In the present study, mice experiment was conducted to detect the ability of PSV to infect mice and its ability to induce pathological lesions. The intestinal and extra intestinal spread of the PSV virus in three week-old Swiss albino mice inoculated with PSV virus quantified by probe based real time PCR are described. Herein, three groups were made with 10 mice per group (both sex). The first group was infected through oral route (8×106, TCID50, 240 μl/mice) while the second through intra-peritoneal route (8×106, TCID50, 240 μl/mice) and the third group was inoculated with PBS of neutral pH orally and intra-peritoneal route. Seven mice (each from oral and intraperitoneal route and three from control group were sacrificed at 5th, 7th, 9th, 12th, 15th, 17th, 21st day post infection (DPI). Indian strain was able to replicate in mice organs up to 15 DPI in oral route and 9 DPI in intraperitoneal route. By real-time reverse transcription (RT) PCR, PSV was detected in most of the organs but with highest viral load in the small intestine and large intestine than extra-intestinal organs in the orally infected mice. In addition, this Indian strain is enteropathogenic but could spread to the bloodstream from the gut and disseminate to extra-intestinal organs. These results will contribute to our understanding of PSV pathogenesis.
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Kumari S, Ray PK, Singh R, Desingu PA, Sharma GT, Saikumar G. Development of a Taqman-based real-time PCR assay for detection of porcine sapelovirus infection in pigs. Anim Biotechnol 2018; 31:264-267. [PMID: 30583714 DOI: 10.1080/10495398.2018.1549561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The objective of the present study was to develop a rapid, simple, specific and sensitive Taqman-based real-time PCR assay for porcine sapelovirus (PSV) detection. Specific primers and probe were designed from the five untranslated regions (UTRs) of the viral genome. The detection limit of the real-time PCR was 102 copies. The specificity of the Taqman real-time PCR assay was evaluated using other animal viruses and nuclease free water as a negative control. Strong fluorescent signals were obtained only in the detection of PSV real-time PCR and conventional RT-PCR were preformed simultaneously on 90 faecal samples. Based on conventional RT-PCR study 17.7% (16/90) of the faecal samples were positive for PSV. Whereas 21 of 90 samples (23.3%) were positive by real-time RT-PCR. The results showed that real-time PCR was more sensitive than the conventional RT-PCR assay. In conclusion, the Taqman real-time PCR assay for detection of PSV developed, herein, is sensitive, specific, and reliable. This assay will be useful for clinical diagnosis, epidemiological, and pathogenesis studies.
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Affiliation(s)
- Swati Kumari
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - P K Ray
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Rahul Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - P A Desingu
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - G Taru Sharma
- Division of Physiology and Climatology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - G Saikumar
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
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Kumari S, Singh R, Saikumar G. Epidemiological study of porcine sapelovirus infection in pigs at Bareilly area of Uttar Pradesh, India. BIOL RHYTHM RES 2018. [DOI: 10.1080/09291016.2018.1557838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Swati Kumari
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, India
| | - Rahul Singh
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, India
| | - G. Saikumar
- Division of Pathology, ICAR- Indian Veterinary Research Institute, Bareilly, India
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Goto Y, Yaegashi G, Kumagai Y, Ogasawara F, Goto M, Mase M. Detection of avian encephalomyelitis virus in chickens in Japan using RT-PCR. J Vet Med Sci 2018; 81:103-106. [PMID: 30464075 PMCID: PMC6361656 DOI: 10.1292/jvms.18-0550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A reverse transcription-polymerase chain reaction (RT-PCR) method was developed for broadly detecting the avian encephalomyelitis virus (AEV). The new primers were based on conserved
sequences of the 5’-untranslated region of AEV, because the virus was not detected using previous reported RT-PCR. By applying this method to the chicken samples with suspected AEV infection
in Japan, we successfully obtained PCR products of the predicted size from all samples, and we confirmed the presence of AEV via sequence analysis.
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Affiliation(s)
- Yusuke Goto
- Iwate Prefecture Central Livestock Hygiene Service Center, 390-5 Sunakomi, Takizawa, Iwate 020-0605, Japan
| | - Gakuji Yaegashi
- Iwate Prefecture Central Livestock Hygiene Service Center, 390-5 Sunakomi, Takizawa, Iwate 020-0605, Japan
| | - Yoshihiro Kumagai
- Iwate Prefecture Central Livestock Hygiene Service Center, 390-5 Sunakomi, Takizawa, Iwate 020-0605, Japan
| | - Fusae Ogasawara
- Iwate Prefecture Central Livestock Hygiene Service Center, 390-5 Sunakomi, Takizawa, Iwate 020-0605, Japan
| | - Makiko Goto
- Iwate Prefecture Central Livestock Hygiene Service Center, 390-5 Sunakomi, Takizawa, Iwate 020-0605, Japan
| | - Masaji Mase
- National Institute of Animal Health, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan
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A novel enterovirus species identified from severe diarrheal goats. PLoS One 2017; 12:e0174600. [PMID: 28376123 PMCID: PMC5380325 DOI: 10.1371/journal.pone.0174600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/07/2017] [Indexed: 11/23/2022] Open
Abstract
Backgrounds The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown. Methods Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China. Results CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5’-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8–51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses. Conclusions CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the current understanding of enteroviruses.
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Tsuchiaka S, Rahpaya SS, Otomaru K, Aoki H, Kishimoto M, Naoi Y, Omatsu T, Sano K, Okazaki-Terashima S, Katayama Y, Oba M, Nagai M, Mizutani T. Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein. BMC Microbiol 2017; 17:18. [PMID: 28095784 PMCID: PMC5240211 DOI: 10.1186/s12866-016-0923-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/28/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Bovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5' untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted. RESULTS The complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5'UTR, open reading frame encoding a single polyprotein, and 3'UTR. The results of secondary RNA structure analysis showed that in the 5'UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region. CONCLUSIONS We identified novel BEV possessing highly divergent aa sequences in the VP1 coding region in Japan. According to species definition, we proposed naming this strain as "Enterovirus K", which is a novel species within genus Enterovirus. Further genomic studies are needed to understand the pathogenicity of BEVs.
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Affiliation(s)
- Shinobu Tsuchiaka
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Sayed Samim Rahpaya
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Konosuke Otomaru
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Tsutomu Omatsu
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Sachiko Okazaki-Terashima
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan.,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan
| | - Makoto Nagai
- Faculty of Bioresources and Environmental Sciences, Ishikawa prefectural University, 1-308, Suematsu, Nonoichi-shi, Ishikawa, 921-8836, Japan
| | - Tetsuya Mizutani
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagito, Gifu-shi, Gifu, 501-1193, Japan. .,Research and Education Center for Prevention of Global Infectious Disease of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo, 183-8509, Japan.
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Isolation and characterization of a new enterovirus F in yak feces in the Qinghai-Tibetan Plateau. Arch Virol 2016; 162:523-527. [DOI: 10.1007/s00705-016-3119-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
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Kosoltanapiwat N, Yindee M, Chavez IF, Leaungwutiwong P, Adisakwattana P, Singhasivanon P, Thawornkuno C, Thippornchai N, Rungruengkitkun A, Soontorn J, Pearsiriwuttipong S. Genetic variations in regions of bovine and bovine-like enteroviral 5'UTR from cattle, Indian bison and goat feces. Virol J 2016; 13:13. [PMID: 26811239 PMCID: PMC4727389 DOI: 10.1186/s12985-016-0468-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 01/17/2016] [Indexed: 11/16/2022] Open
Abstract
Background Bovine enteroviruses (BEV) are members of the genus Enterovirus in the family Picornaviridae. They are predominantly isolated from cattle feces, but also are detected in feces of other animals, including goats and deer. These viruses are found in apparently healthy animals, as well as in animals with clinical signs and several studies reported recently suggest a potential role of BEV in causing disease in animals. In this study, we surveyed the presence of BEV in domestic and wild animals in Thailand, and assessed their genetic variability. Methods Viral RNA was extracted from fecal samples of cattle, domestic goats, Indian bison (gaurs), and deer. The 5’ untranslated region (5’UTR) was amplified by nested reverse transcription-polymerase chain reaction (RT-PCR) with primers specific to BEV 5’UTR. PCR products were sequenced and analyzed phylogenetically using the neighbor-joining algorithm to observe genetic variations in regions of the bovine and bovine-like enteroviral 5’UTR found in this study. Results BEV and BEV-like sequences were detected in the fecal samples of cattle (40/60, 67 %), gaurs (3/30, 10 %), and goats (11/46, 24 %). Phylogenetic analyses of the partial 5’UTR sequences indicated that different BEV variants (both EV-E and EV-F species) co-circulated in the domestic cattle, whereas the sequences from gaurs and goats clustered according to the animal species, suggesting that these viruses are host species-specific. Conclusions Varieties of BEV and BEV-like 5’UTR sequences were detected in fecal samples from both domestic and wild animals. To our knowledge, this is the first report of the genetic variability of BEV in Thailand.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Marnoch Yindee
- Faculty of Veterinary Science, Mahidol University, Bangkok, Thailand.
| | - Irwin Fernandez Chavez
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pratap Singhasivanon
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Narin Thippornchai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Juthamas Soontorn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Sasipan Pearsiriwuttipong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Souii A, Ben M'hadheb-Gharbi M, Gharbi J. Role of RNA structure motifs in IRES-dependent translation initiation of the coxsackievirus B3: new insights for developing live-attenuated strains for vaccines and gene therapy. Mol Biotechnol 2014; 55:179-202. [PMID: 23881360 DOI: 10.1007/s12033-013-9674-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Internal ribosome entry site (IRES) elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, the mechanism of IRES-mediated translation initiation is still poorly understood. Translation initiation of the coxsackievirus B3 (CVB3), a causative agent of viral myocarditis, has been shown to be mediated by a highly ordered structure of the 5' untranslated region (5'UTR), which harbors an IRES. Taking into account that efficient initiation of mRNA translation depends on temporally and spatially orchestrated sequence of RNA-protein and RNA-RNA interactions, and that, at present, little is known about these interactions, we aimed to describe recent advances in our understanding of molecular structures and biochemical functions of the translation initiation process. Thus, this review will explore the IRES elements as important RNA structures and the significance of these structures in providing an alternative mechanism of translation initiation of the CVB3 RNA. Since translation initiation is the first intracellular step during the CVB3 infection cycle, the IRES region provides an ideal target for antiviral therapies. Interestingly, the 5' and 3'UTRs represent promising candidates for the study of CVB3 cardiovirulence and provide new insights for developing live-attenuated vaccines.
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Affiliation(s)
- Amira Souii
- Institut Supérieur de Biotechnologie de Monastir-Université de Monastir, Avenue Tahar Hadded, BP 74, 5000, Monastir, Tunisia
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Zhu L, Xing Z, Gai X, Li S, San Z, Wang X. Identification of a novel enterovirus E isolates HY12 from cattle with severe respiratory and enteric diseases. PLoS One 2014; 9:e97730. [PMID: 24830424 PMCID: PMC4022658 DOI: 10.1371/journal.pone.0097730] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 03/31/2014] [Indexed: 12/04/2022] Open
Abstract
In this study, a virus strain designated as HY12 was isolated from cattle with a disease of high morbidity and mortality in Jilin province. Biological and physiochemical properties showed that HY12 isolates is cytopathic with an extremely high infectivity. HY12 is resistant to treatment of organic solvent and acid, and unstable at 60°C for 1 h. Electron microscopy observation revealed the virus is an approximately 22–28 nm in diameter. The complete genome sequence of HY12 consists of 7416 nucleotides, with a typical picornavirus genome organization including a 5′-untranslated region (UTR), a large single ORF encoding a polyprotein of 2176 amino acids, and a 3′-UTR. Phylogenetic analysis clustered HY12 isolates to a new serotype/genotype within the clade of enterovirus E (formerly BEV-A). Alignment analysis revealed a unique insertion of 2 amino acid residues (NF) at the C-terminal of VP1 protein between aa 825 and 826, and several rare mutations in VP1 and VP4 of HY12 isolates in relation to known bovine enterovirus (BEV) strains. This is the first report of an enterovirus E in China, which is potentially associated with an outbreak in cattle with severe respiratory and enteric diseases.
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Affiliation(s)
- Lisai Zhu
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zeli Xing
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xiaochun Gai
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Sujing Li
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhihao San
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xinping Wang
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
- * E-mail:
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14
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Novel marker for recombination in the 3'-untranslated region of members of the species Human enterovirus A. Arch Virol 2012. [PMID: 23178966 DOI: 10.1007/s00705-012-1533-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human enterovirus A (HEV-A) is a species in the genus Enterovirus. Viruses belonging to this species are often responsible for hand, foot and mouth disease and associated acute neurological disease. Studies of the 3' untranslated region (UTR) of human enterovirus 71 (HEV71) revealed a possible role in virus replication. We compared the 3'-UTRs of all members of HEV-A and confirmed the presence of a secondary structure comprising three stem-loop domains (SLDs). SLD-Z is situated closest to the stop codon and has been shown previously to affect plaque morphology. The prototype strains of coxsackieviruses A4 (CVA4), CVA14, and CVA16 carried the longer group I SLD-Z, whilst other CVAs and HEV71 carried the shorter group II SLD-Z. We demonstrate the importance of SLD-Z as a marker for the emergence of newer strains of HEV71 and CVA16 through inter-typic recombination and propose that SLD-Z is a novel evolutionary marker for recombination in HEV-A.
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15
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The survey of porcine teschoviruses in field samples in China with a universal rapid probe real-time RT-PCR assay. Trop Anim Health Prod 2012; 45:1057-61. [DOI: 10.1007/s11250-012-0312-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2012] [Indexed: 11/28/2022]
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16
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Boros Á, Pankovics P, Knowles NJ, Reuter G. Natural interspecies recombinant bovine/porcine enterovirus in sheep. J Gen Virol 2012; 93:1941-1951. [DOI: 10.1099/vir.0.041335-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the genus Enterovirus (family Picornaviridae) are believed to be common and widespread among humans and different animal species, although only a few enteroviruses have been identified from animal sources. Intraspecies recombination among human enteroviruses is a well-known phenomenon, but only a few interspecies examples have been reported and, to our current knowledge, none of these have involved non-primate enteroviruses. In this study, we report the detection and complete genome characterization (using RT-PCR and long-range PCR) of a natural interspecies recombinant bovine/porcine enterovirus (ovine enterovirus type 1; OEV-1) in seven (44 %) of 16 faecal samples from 3-week-old domestic sheep (Ovis aries) collected in two consecutive years. Phylogenetic analysis of the complete coding region revealed that OEV-1 (ovine/TB4-OEV/2009/HUN; GenBank accession no. JQ277724) was a novel member of the species Porcine enterovirus B (PEV-B), implying the endemic presence of PEV-B viruses among sheep. However, the 5′ UTR of OEV-1 showed a high degree of sequence and structural identity to bovine enteroviruses. The presumed recombination breakpoint was mapped to the end of the 5′ UTR at nucleotide position 814 using sequence and SimPlot analyses. The interspecies-recombinant nature of OEV-1 suggests a closer relationship among bovine and porcine enteroviruses, enabling the exchange of at least some modular genetic elements that may evolve independently.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, H-7623, Szabadság út 7, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, H-7623, Szabadság út 7, Pécs, Hungary
| | - Nick J. Knowles
- Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, H-7623, Szabadság út 7, Pécs, Hungary
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17
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Lan YC, Lin TH, Tsai JD, Yang YC, Peng CT, Shih MC, Lin YJ, Lin CW. Molecular epidemiology of the 2005 enterovirus 71 outbreak in central Taiwan. ACTA ACUST UNITED AC 2011; 43:354-9. [PMID: 21231813 DOI: 10.3109/00365548.2010.545995] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Since 1998, Taiwan has experienced annual outbreaks of enterovirus 71 (EV71) nationwide. The area around Taichung City experienced a particularly large outbreak in 2005, after which EV71 disappeared for 2 y before re-emerging in 2008. Here we present the clinical, genotypic, and epidemiological baseline data for the 2005 Taichung outbreak. METHODS Throat swab, stool and cerebrospinal fluid samples were collected and stored in viral transport medium. Samples were tested by reverse-transcriptase polymerase chain reaction and viral culture. Epidemiological, laboratory, and clinical data were extracted from medical record reviews. A total of 27 virus isolates were selected for phylogenetic analysis. RESULTS Confirmed phylogenetic results of the viruses were separated into 5 groups. The 5'-UTR regions served as a focus for investigating genetic relationships among the 27 EV71 isolates, all of which belonged to a distinct clade in the C4 genotype. Most of the strains belonged to 5 observed epidemic groups. CONCLUSION In conclusion, the 2005 outbreak in central Taiwan was caused by divergent EV71 strains belonging to the C4 genotype.
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Affiliation(s)
- Yu-Ching Lan
- Department of Health Risk Management, China Medical University, Taichung City, Taiwan
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18
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Gaglia MM, Glaunsinger BA. Viruses and the cellular RNA decay machinery. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:47-59. [PMID: 21956906 PMCID: PMC7169783 DOI: 10.1002/wrna.3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ability to control cellular and viral gene expression, either globally or selectively, is central to a successful viral infection, and it is also crucial for the host to respond and eradicate pathogens. In eukaryotes, regulation of message stability contributes significantly to the control of gene expression and plays a prominent role in the normal physiology of a cell as well as in its response to environmental and pathogenic stresses. Not surprisingly, emerging evidence indicates that there are significant interactions between the eukaryotic RNA turnover machinery and a wide variety of viruses. Interestingly, in many cases viruses have evolved mechanisms not only to evade eradication by these pathways, but also to manipulate them for enhanced viral replication and gene expression. Given our incomplete understanding of how many of these pathways are normally regulated, viruses should be powerful tools to help deconstruct the complex networks and events governing eukaryotic RNA stability. Copyright © 2010 John Wiley & Sons, Ltd. This article is categorized under:
RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Disease
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Affiliation(s)
- Marta Maria Gaglia
- Department of Plant and Microbiology, University of California, Berkeley, CA 94720‐3102, USA
| | - Britt A. Glaunsinger
- Department of Plant and Microbiology, University of California, Berkeley, CA 94720‐3102, USA
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19
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Wu TY, Hsieh CC, Hong JJ, Chen CY, Tsai YS. IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico. BMC Bioinformatics 2009; 10:160. [PMID: 19473520 PMCID: PMC2698906 DOI: 10.1186/1471-2105-10-160] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 05/27/2009] [Indexed: 12/21/2022] Open
Abstract
Background Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements. Results We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters. Conclusion IRSS is freely available at this website . In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.
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Affiliation(s)
- Tzong-Yuan Wu
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan.
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20
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Zell R, Ihle Y, Effenberger M, Seitz S, Wutzler P, Görlach M. Interaction of poly(rC)-binding protein 2 domains KH1 and KH3 with coxsackievirus RNA. Biochem Biophys Res Commun 2008; 377:500-503. [PMID: 18929541 DOI: 10.1016/j.bbrc.2008.09.156] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 09/30/2008] [Indexed: 11/19/2022]
Abstract
Recombinant hnRNP K-homology (KH) domains 1 and 3 of the poly(rC)-binding protein (PCBP) 2 were purified and assayed for interaction with coxsackievirus B3 RNA in electrophoretic mobility shift assays using in vitro transcribed RNAs which represent signal structures of the 5'-nontranslated region. KH domains 1 and 3 interact with the extended cloverleaf RNA and domain IV RNA of the internal ribosome entry site (IRES). KH1 but not KH3 interacts with subdomain IV/C RNA, whereas KH3 interacts with subdomain IV/B. All in vitro results are consistent with yeast three-hybrid experiments performed in parallel. The data demonstrate interaction of isolated PCBP2 KH1 and KH3 domains to four distinct target sites within the 5'-nontranslated region of the CVB3 genomic RNA.
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Affiliation(s)
- Roland Zell
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany.
| | - Yvonne Ihle
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Madlen Effenberger
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Simone Seitz
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Peter Wutzler
- Institute for Virology and Antiviral Therapy, Friedrich Schiller University, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Matthias Görlach
- Biomolecular NMR Spectroscopy, Leibniz Institute for Age Research, Fritz Lipmann Institute, Beutenbergstr. 11, D-07745 Jena, Germany
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21
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Spear A, Sharma N, Flanegan JB. Protein-RNA tethering: the role of poly(C) binding protein 2 in poliovirus RNA replication. Virology 2008; 374:280-91. [PMID: 18252259 DOI: 10.1016/j.virol.2007.12.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 09/20/2007] [Accepted: 12/28/2007] [Indexed: 10/22/2022]
Abstract
The exploitation of cellular functions and host proteins is an essential part of viral replication. The study of this interplay has provided significant insight into host cell processes in addition to advancing the understanding of the viral life-cycle. Poliovirus utilizes a multifunctional cellular protein, poly(C) binding protein 2 (PCBP2), for RNA stability, translation and RNA replication. In its cellular capacity, PCBP2 is involved in many functions, including transcriptional activation, mRNA stability and translational silencing. Using a novel protein-RNA tethering system, we establish PCBP2 as an essential co-factor in the initiation of poliovirus negative-strand synthesis. Furthermore, we identified the conserved KH domains in PCBP2 that are required for the initiation of poliovirus negative-strand synthesis, and showed that this required neither direct RNA binding or dimerization of PCBP2. This study demonstrates the novel application of a protein-RNA tethering system for the molecular characterization of cellular protein involvement in viral RNA replication.
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Affiliation(s)
- Allyn Spear
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, USA
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22
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Poly(rC)-binding protein 2 interacts with the oligo(rC) tract of coxsackievirus B3. Biochem Biophys Res Commun 2008; 366:917-21. [DOI: 10.1016/j.bbrc.2007.12.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 12/04/2007] [Indexed: 11/23/2022]
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23
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Oberste MS, Maher K, Pallansch MA. Complete genome sequences for nine simian enteroviruses. J Gen Virol 2008; 88:3360-3372. [PMID: 18024906 DOI: 10.1099/vir.0.83124-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
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 enteroviruses. Phylogenetic and pairwise sequence relationships for the P1 region paralleled those of VP1 alone, and confirmed that SV4/A-2 plaque virus, SV6 and N125/N203 represent unique genetic clusters that probably correspond to three new species. However, sequence relationships in the P2 and P3 regions were quite different. In 2C, SV19, SV43 and SV46 remain clustered with the human viruses of HEV-A, but BaEV, SV6 and N125/N203 cluster together; in 3CD, SA5 (HEV-B) also joined this cluster. The 3'-non-translated region (NTR) sequences are highly conserved within each of the four human enterovirus species, but the 3'-NTRs of the simian enteroviruses are distinct from those of all human enteroviruses and generally distinct from one another. These results suggest that host species may have a significant influence on the evolution of enterovirus non-capsid sequences.
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Affiliation(s)
- M Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kaija Maher
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Mark A Pallansch
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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24
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Sandager MM, Nugent JL, Schulz WL, Messner RP, Tam PE. Interactions between multiple genetic determinants in the 5' UTR and VP1 capsid control pathogenesis of chronic post-viral myopathy caused by coxsackievirus B1. Virology 2007; 372:35-47. [PMID: 18029287 DOI: 10.1016/j.virol.2007.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 08/20/2007] [Accepted: 10/19/2007] [Indexed: 11/29/2022]
Abstract
Mice infected with coxsackievirus B1 Tucson (CVB1(T)) develop chronic, post-viral myopathy (PVM) with clinical manifestations of hind limb muscle weakness and myositis. The objective of the current study was to establish the genetic basis of myopathogenicity in CVB1(T). Using a reverse genetics approach, full attenuation of PVM could only be achieved by simultaneously mutating four sites located at C706U in the 5' untranslated region (5' UTR) and at Y87F, V136A, and T276A in the VP1 capsid. Engineering these four myopathic determinants into an amyopathic CVB1(T) variant restored the ability to cause PVM. Moreover, these same four determinants controlled PVM expression in a second strain of mice, indicating that the underlying mechanism is operational in mice of different genetic backgrounds. Modeling studies predict that C706U alters both local and long range pairing in the 5' UTR, and that VP1 determinants are located on the capsid surface. However, these differences did not affect viral titers, temperature stability, pH stability, or the antibody response to virus. These studies demonstrate that PVM develops from a complex interplay between viral determinants in the 5' UTR and VP1 capsid and have uncovered intriguing similarities between genetic determinants that cause PVM and those involved in pathogenesis of other enteroviruses.
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Affiliation(s)
- Maribeth M Sandager
- Department of Medicine, Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN 55455, USA.
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25
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Bailey JM, Tapprich WE. Structure of the 5' nontranslated region of the coxsackievirus b3 genome: Chemical modification and comparative sequence analysis. J Virol 2006; 81:650-68. [PMID: 17079314 PMCID: PMC1797431 DOI: 10.1128/jvi.01327-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coxsackievirus B3 (CVB3) is a picornavirus which causes myocarditis and pancreatitis and may play a role in type I diabetes. The viral genome is a single 7,400-nucleotide polyadenylated RNA encoding 11 proteins in a single open reading frame. The 5' end of the viral genome contains a highly structured nontranslated region (5'NTR) which folds to form an internal ribosome entry site (IRES) as well as structures responsible for genome replication, both of which are critical for virulence. A structural model of the CVB3 5'NTR, generated primarily by comparative sequence analysis and energy minimization, shows seven domains (I to VII). While this model provides a preliminary basis for structural analysis, the model lacks comprehensive experimental validation. Here we provide experimental evidence from chemical modification analysis to determine the structure of the CVB3 5'NTR. Chemical probing results show that the theoretical model for the CVB3 5'NTR is largely, but not completely, supported experimentally. In combination with our chemical probing data, we have used the RNASTRUCTURE algorithm and sequence comparison of 105 enterovirus sequences to provide evidence for novel secondary and tertiary interactions. A comprehensive examination of secondary structure is discussed, along with new evidence for tertiary interactions. These include a loop E motif in domain III and a long-range pairing interaction that links domain II to domain V. The results of our work provide mechanistic insight into key functional elements in the cloverleaf and IRES, thereby establishing a base of structural information from which to interpret experiments with CVB3 and other picornaviruses.
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Affiliation(s)
- Jennifer M Bailey
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St, Omaha, NE 68182, USA
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26
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Zell R, Krumbholz A, Dauber M, Hoey E, Wutzler P. Molecular-based reclassification of the bovine enteroviruses. J Gen Virol 2006; 87:375-385. [PMID: 16432025 DOI: 10.1099/vir.0.81298-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bovine enteroviruses are currently classified into two serotypes within the species Bovine enterovirus (BEV). Comparison of the sequences of six American and eleven German BEV isolates with published BEV sequences revealed the necessity to revise the taxonomy of these viruses. Molecular data indicate that the bovine enteroviruses are composed of two clusters (designated BEV-A and -B) each with two and three geno-/serotypes, respectively. Whereas low amino acid identity of the capsid proteins 1C (VP3) and 1D (VP1) is the main criterion for the discrimination of geno-/serotypes, the BEV clusters, presumably representing species, differ in sequence identity of all viral proteins. In addition, characteristic lengths of (i) the capsid proteins 1B, 1C and 1D, (ii) the 2C protein, and (iii) the 3'-non-translated region are observed. The BEVs can be distinguished from the other enteroviruses by sequence identity and unique features of the 5'-non-translated region, i.e. a conserved second cloverleaf and characteristic RNA structures of the internal ribosome entry site. Phylogenetically, the closest relatives of the bovine enteroviruses are the porcine enteroviruses. Incongruent phylogenies of the 5'-non-translated region, the capsid proteins and the 3D polymerase indicate frequent intraserotypic and interserotypic recombination within the non-capsid and the capsid region of the BEV genome.
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Affiliation(s)
- Roland Zell
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Andi Krumbholz
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Malte Dauber
- Institute for Virus Diagnostics, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Boddenblick 5a, 17493 Insel Riems, Germany
| | - Elizabeth Hoey
- School of Biology & Biochemistry, Medical Biology Centre, The Queen's University of Belfast, UK
| | - Peter Wutzler
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, 07745 Jena, Germany
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27
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Brown DM, Cornell CT, Tran GP, Nguyen JHC, Semler BL. An authentic 3' noncoding region is necessary for efficient poliovirus replication. J Virol 2005; 79:11962-73. [PMID: 16140772 PMCID: PMC1212627 DOI: 10.1128/jvi.79.18.11962-11973.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Picornavirus RNA replication involves the specific synthesis of negative-strand intermediates followed by an accumulation of positive-strand viral RNA in the presence of a multitude of cellular mRNAs. Previously, in an effort to identify cis-acting elements required for initiation of negative-strand RNA synthesis, we deleted the entire 3' noncoding regions from human rhinovirus and poliovirus genomic RNAs. These deletion mutation transcripts displayed a severe delay in RNA accumulation following transfection of HeLa cells. Interestingly, in subsequent infection of HeLa cells, the deletion-mutant poliovirus displayed only a moderate deficiency in RNA synthesis. These data suggested that the delay in the production of cytopathic effects after transfection may have been due to an RNA replication defect overcome by the accumulation of a compensatory mutation(s) generated during initial rounds of RNA synthesis. In this study, we have sequenced the entire genome of the deletion-mutant virus and found only two nucleotide changes from the parental clone. Transfection analysis of these sequence variants revealed that the sequence changes did not provide compensatory functions for the 3' noncoding region deletion mutation replication defect. Further examination of the deletion mutant phenotype revealed that the severe replication defect following RNA transfection is due, in part, to nonviral terminal sequences present in the in vitro-derived deletion mutation transcripts. Our data suggest that poliovirus RNA harboring a complete 3' noncoding region deletion mutation is infectious (not merely quasi-infectious).
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Affiliation(s)
- David M Brown
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
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28
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Jiménez-Clavero MA, Escribano-Romero E, Mansilla C, Gómez N, Córdoba L, Roblas N, Ponz F, Ley V, Sáiz JC. Survey of bovine enterovirus in biological and environmental samples by a highly sensitive real-time reverse transcription-PCR. Appl Environ Microbiol 2005; 71:3536-43. [PMID: 16000759 PMCID: PMC1168977 DOI: 10.1128/aem.71.7.3536-3543.2005] [Citation(s) in RCA: 69] [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
Animal enteroviruses shed in the feces of infected animals are likely environmental contaminants and thus can be used as indicators of animal fecal pollution. Previous work has demonstrated that bovine enterovirus (BEV) present in bovine feces contaminates waters adjacent to cattle herds and that BEV-like sequences are also present in shellfish and in deer feces from the same geographical area. However, little information is available about the prevalence, molecular epidemiology, and genomic sequence variation of BEV field isolates. Here we describe an optimized highly sensitive real-time reverse transcription-PCR method to detect BEV RNA in biological and environmental samples. A combination of the amplification procedure with a previously described filtration step with electropositive filters allowed us to detect up to 12 BEV RNA molecules per ml of water. The feasibility of using the method to detect BEV in surface waters at a high risk of fecal pollution was confirmed after analysis of water samples obtained from different sources. The method was also used to study the prevalence of BEV in different cattle herds around Spain, and the results revealed that 78% (78 of 100) of the fecal samples were BEV positive. BEV-like sequences were also detected in feces from sheep, goats, and horses. Nucleotide sequence analyses showed that BEV isolates are quite heterogeneous and suggested the presence of species-specific BEV-like variants. Detection of BEV-like sequences may help in the differentiation and characterization of animal sources of contamination.
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Affiliation(s)
- Miguel Angel Jiménez-Clavero
- Environmental Virology, Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. A Coruña Km 7.5, 28040 Madrid, Spain
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29
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Ihle Y, Ohlenschläger O, Häfner S, Duchardt E, Zacharias M, Seitz S, Zell R, Ramachandran R, Görlach M. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA. Nucleic Acids Res 2005; 33:2003-11. [PMID: 15814817 PMCID: PMC1074726 DOI: 10.1093/nar/gki501] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Revised: 03/07/2005] [Accepted: 03/21/2005] [Indexed: 11/24/2022] Open
Abstract
The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3C(pro)), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 A (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel 'pseudo base pair' without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence.
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Affiliation(s)
- Yvonne Ihle
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Oliver Ohlenschläger
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Sabine Häfner
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Elke Duchardt
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
| | - Martin Zacharias
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
| | - Simone Seitz
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Roland Zell
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Ramadurai Ramachandran
- Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V.Beutenbergstraße 11, D-07745 Jena, Germany
- Institut für Organische Chemie, Johann-Wolfgang-Goethe-UniversitätMarie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
- International University Bremen, School of Engineering and ScienceCampus Ring 1, D-28759 Bremen, Germany
- Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-UniversitätWinzerlaer Straße 10, D-07745 Jena, Germany
| | - Matthias Görlach
- To whom correspondence should be addressed. Tel: +49 3641 656220; Fax: +49 3641 656225;
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Sharma N, O'Donnell BJ, Flanegan JB. 3'-Terminal sequence in poliovirus negative-strand templates is the primary cis-acting element required for VPgpUpU-primed positive-strand initiation. J Virol 2005; 79:3565-77. [PMID: 15731251 PMCID: PMC1075688 DOI: 10.1128/jvi.79.6.3565-3577.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The 5' cloverleaf in poliovirus RNA has a direct role in regulating the stability, translation, and replication of viral RNA. In this study, we investigated the role of stem a in the 5' cloverleaf in regulating the stability and replication of poliovirus RNA in HeLa S10 translation-replication reactions. Our results showed that disrupting the duplex structure of stem a destabilized viral RNA and inhibited efficient negative-strand synthesis. Surprisingly, the duplex structure of stem a was not required for positive-strand synthesis. In contrast, altering the primary sequence at the 5'-terminal end of stem a had little or no effect on negative-strand synthesis but dramatically reduced positive-strand initiation and the formation of infectious virus. The inhibition of positive-strand synthesis observed in these reactions was most likely a consequence of nucleotide alterations in the conserved sequence at the 3' ends of negative-strand RNA templates. Previous studies suggested that VPgpUpU synthesized on the cre(2C) hairpin was required for positive-strand synthesis. Therefore, these results are consistent with a model in which preformed VPgpUpU serves as the primer for positive-strand initiation on the 3'AAUUUUGUC5' sequence at the 3' ends of negative-strand templates. Our results suggest that this sequence is the primary cis-acting element that is required for efficient VPgpUpU-primed positive-strand initiation.
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Affiliation(s)
- Nidhi Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610-0245, USA
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31
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Park K, Lee K, Lee J, Yeo S, Lee S, Cheon DS, Choi W, Ahn J, Kim S, Jee Y. Acute hemorrhagic conjunctivitis epidemic caused by coxsackievirus A24 variants in Korea during 2002-2003. J Med Virol 2005; 78:91-7. [PMID: 16299722 DOI: 10.1002/jmv.20508] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A variant of coxsackievirus A24 (CA24v) is one of the agents causing acute hemorrhagic conjunctivitis. There was an epidemic of acute hemorrhagic conjunctivitis caused by CA24v in Korea from 2002 to 2003. Seventy-one strains of CA24v were isolated from 159 conjunctival specimens (45%). Most of the patients were school children under the age of 20. The epidemic began in the first week of August in 2002, and spread extensively, with a peak in the third week of September. CA24v strains were also isolated from conjunctival specimens in 2003. Reverse transcription polymerase chain reaction (RT-PCR) was performed and sequencing of the 340 bp fragment of the VP1 region of the viruses. Sequencing data were multiple-aligned using CLUSTAL W (version 1.81). Phylogenetic trees were plotted using TreeView (version 1.6.6). Homologies ranged from 97.7%-100%, depending on geographical regions: from 99.4%-100% in 2002 and 98.4%-100% in 2003. A phylogenetic tree based on the nucleotide sequence homologies formed clusters depending on years rather than on geographical regions. Identities (98%-100%) were found among the Korean CA24v strains, and there was 85%-90% homology between these and the prototype strain.
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Affiliation(s)
- Kwisung Park
- Division of Enteric and Hepatitis Viruses, Department of Virology, National Institute of Health, Korea Center for Disease Control and Prevention, Seoul, Korea
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Goens SD, Botero S, Zemla A, Zhou CE, Perdue ML. Bovine enterovirus 2: complete genomic sequence and molecular modelling of a reference strain and a wild-type isolate from endemically infected US cattle. J Gen Virol 2004; 85:3195-3203. [PMID: 15483232 DOI: 10.1099/vir.0.80159-0] [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] [Indexed: 02/04/2023] Open
Abstract
Bovine enteroviruses are members of the family Picornaviridae, genus Enterovirus. Whilst little is known about their pathogenic potential, they are apparently endemic in some cattle and cattle environments. Only one of the two current serotypes has been sequenced completely. In this report, the entire genome sequences of bovine enterovirus 2 (BEV-2) strain PS87 and a recent isolate from an endemically infected herd in Maryland, USA (Wye3A) are presented. The recent isolate clearly segregated phylogenetically with sequences representing the BEV-2 serotype, as did other isolates from the endemic herd. The Wye3A isolate shared 82 % nucleotide sequence identity with the PS87 strain and 68 % identity with a BEV-1 strain (VG5-27). Comparison of BEV-2 and BEV-1 deduced protein sequences revealed 72-73 % identity and showed that most differences were single amino acid changes or single deletions, with the exception of the VP1 protein, where both BEV-2 sequences were 7 aa shorter than that of BEV-1. Homology modelling of the capsid proteins of BEV-2 against protein database entries for picornaviruses indicated six significant differences among bovine enteroviruses and other members of the family Picornaviridae. Five of these were on the 'rim' of the proposed enterovirus receptor-binding site or 'canyon' (VP1) and one was near the base of the canyon (VP3). Two of these regions varied enough to distinguish BEV-2 from BEV-1 strains. This is the first report and analysis of full-length sequences for BEV-2. Continued analysis of these wild-type strains should yield useful information for genotyping enteroviruses and modelling enterovirus capsid structure.
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Affiliation(s)
- S D Goens
- Environmental Microbial Safety Laboratory, Animal and Natural Resources Institute, Beltsville Agriculture Research Center, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Building 173, BARC-East, Beltsville, MD 20705, USA
| | - S Botero
- Environmental Microbial Safety Laboratory, Animal and Natural Resources Institute, Beltsville Agriculture Research Center, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Building 173, BARC-East, Beltsville, MD 20705, USA
| | - A Zemla
- Bioinformatics, Chemical and Biological National Security Program, Computing Applications and Research Department, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - C Ecale Zhou
- Bioinformatics, Chemical and Biological National Security Program, Computing Applications and Research Department, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA
| | - M L Perdue
- Environmental Microbial Safety Laboratory, Animal and Natural Resources Institute, Beltsville Agriculture Research Center, Agricultural Research Service, United States Department of Agriculture, 10300 Baltimore Avenue, Building 173, BARC-East, Beltsville, MD 20705, USA
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Ohlenschläger O, Wöhnert J, Bucci E, Seitz S, Häfner S, Ramachandran R, Zell R, Görlach M. The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C. Structure 2004; 12:237-48. [PMID: 14962384 DOI: 10.1016/j.str.2004.01.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Revised: 10/24/2003] [Accepted: 10/24/2003] [Indexed: 11/25/2022]
Abstract
Stemloop D (SLD) of the 5' cloverleaf RNA is the cognate ligand of the coxsackievirus B3 (CVB3) 3C proteinase (3Cpro). Both are indispensable components of the viral replication initiation complex. SLD is a structurally autonomous subunit of the 5' cloverleaf. The SLD structure was solved by NMR spectroscopy to an rms deviation of 0.66 A (all heavy atoms). SLD contains a novel triple pyrimidine mismatch motif with a central Watson-Crick type C:U pair. SLD is capped by an apical uCACGg tetraloop adopting a structure highly similar to stable cUNCGg tetraloops. Binding of CVB3 3Cpro induces changes in NMR spectra for nucleotides adjacent to the triple pyrimidine mismatch and of the tetraloop implying them as sites of specific SLD:3Cpro interaction. The binding of 3Cpro to SLD requires the integrity of those structural elements, strongly suggesting that 3Cpro recognizes a structural motif instead of a specific sequence.
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Affiliation(s)
- Oliver Ohlenschläger
- Institut für Molekulare Biotechnologie eV, Bentenbergstr 100813, D-07745 Jena, Germany
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Palmquist JM, Munir S, Taku A, Kapur V, Goyal SM. Detection of porcine teschovirus and enterovirus type II by reverse transcription-polymerase chain reaction. J Vet Diagn Invest 2002; 14:476-80. [PMID: 12423029 DOI: 10.1177/104063870201400605] [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: 11/16/2022] Open
Abstract
Porcine enteroviruses (PEVs) have been recognized as the causative agents of various clinical manifestations such as fertility disorders, neurological defects, and dermal lesions in pigs. Currently, the diagnosis of PEV infection is carried out by virus isolation, which although useful, is labor- and time-intensive. The present investigation describes the development of a reverse transcription-polymerase chain reaction (RT-PCR) assay for the rapid and sensitive detection of PEVs of cytopathic effect groups I (now known as porcine teschoviruses [PTVs]) and II. The assay described not only detects the PTVs and CPE group II of PEVs but also allows them to be differentiated on the basis of the size of the amplification product, using the same set of oligonucleotide primers. The availability of specific and sensitive molecular diagnostic tools such as the RT-PCR assay described herein should facilitate efficient diagnosis of PTV and CPE group II infections in pigs.
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Affiliation(s)
- Joseph M Palmquist
- Department of Veterinary Diagnostic Medicine, College of Veterinary Medicine, University of Minnesota, St Paul 55108, USA
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35
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Merkle I, van Ooij MJM, van Kuppeveld FJM, Glaudemans DHRF, Galama JMD, Henke A, Zell R, Melchers WJG. Biological significance of a human enterovirus B-specific RNA element in the 3' nontranslated region. J Virol 2002; 76:9900-9. [PMID: 12208967 PMCID: PMC136489 DOI: 10.1128/jvi.76.19.9900-9909.2002] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2002] [Accepted: 06/24/2002] [Indexed: 11/20/2022] Open
Abstract
The secondary structures predicted for the enteroviral 3' nontranslated region (3'NTR) all seem to indicate a conformation consisting of two (X and Y) hairpin structures. The higher-order RNA structure of the 3'NTR appears to exist as an intramolecular kissing interaction between the loops of these two hairpin structures. The enterovirus B-like subgroup possesses an additional stem-loop structure, domain Z, which is not present in the poliovirus-like enteroviruses. It has been suggested that the Z domain originated from a burst of short sequence repetitions (E. V. Pilipenko, S. V. Maslova, A. N. Sinyakov, and V. I. Agol, Nucleic Acids Res. 20:1739-1745, 1992). However, no functional features have yet been ascribed to this enterovirus B-like-specific RNA element in the 3'NTR. In this study, we tested the functional characteristics and biological significance of domain Z. A mutant of the cardiovirulent coxsackievirus group B3 strain Nancy which completely lacked the Z domain and which therefore acquired enterovirus C-like secondary structures exhibited a wild-type growth phenotype, as determined by single-cycle growth analysis with BGM cells. This result proves that the Z domain is virtually dispensable for viral growth in tissue cultures. Partial distortion of the Z domain structure resulted in a disabled virus with reduced growth kinetics, probably due to alternative conformations of the overall structure of the domain. Infection of mice showed that the recombinant coxsackievirus group B3 mutant which completely lacked the Z domain was less virulent. Pancreatic tissues from mice infected with wild-type virus and recombinant virus were equally affected. However, the heart tissue from mice infected with the recombinant virus showed only slight signs of myocarditis. These results suggest that the enterovirus B-like-specific Z domain plays a role in coxsackievirus-induced pathogenesis.
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Affiliation(s)
- Ingrid Merkle
- Institute of Virology, Friedrich Schiller University, D-07745 Jena, Germany
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36
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Abstract
Surface waters frequently have been contaminated with human enteric viruses, and it is likely that animal enteric viruses have contaminated surface waters also. Bovine enteroviruses (BEV), found in cattle worldwide, usually cause asymptomatic infections and are excreted in the feces of infected animals in large numbers. In this study, the prevalence and genotype of BEV in a closed herd of cattle were evaluated and compared with BEV found in animals in the immediate environment and in environmental specimens. BEV was found in feces from 76% of cattle, 38% of white-tailed deer, and one of three Canada geese sharing the same pastures, as well as the water obtained from animal watering tanks, from the pasture, from streams running from the pasture to an adjacent river, and from the river, which emptied into the Chesapeake Bay. Furthermore, BEV was found in oysters collected from that river downstream from the farm. These findings suggest that BEV could be used as an indicator of fecal pollution originating from animals (cattle and/or deer). Partial sequence analysis of the viral genomes indicates that different viral variants coexist in the same area. The possibility of identifying the viral strains found in the animals and in the contaminated areas by sequencing the RNA genome, could provide a tool to find the origin of the contamination and should be useful for epidemiological and viral molecular evolution studies.
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Affiliation(s)
- Victoria Ley
- Animal Waste Pathogen Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA.
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37
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Witwer C, Rauscher S, Hofacker IL, Stadler PF. Conserved RNA secondary structures in Picornaviridae genomes. Nucleic Acids Res 2001; 29:5079-89. [PMID: 11812840 PMCID: PMC97546 DOI: 10.1093/nar/29.24.5079] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The family Picornaviridae contains important pathogens including, for example, hepatitis A virus and foot-and-mouth disease virus. The genome of these viruses is a single messenger-active (+)-RNA of 7200-8500 nt. Besides coding for the viral proteins, it also contains functionally important RNA secondary structures, among them an internal ribosomal entry site (IRES) region towards the 5'-end. This contribution provides a comprehensive computational survey of the complete genomic RNAs and a detailed comparative analysis of the conserved structural elements in seven of the currently nine genera in the family PICORNAVIRIDAE: Compared with previous studies we find: (i) that only smaller sections of the IRES region than previously reported are conserved at single base-pair resolution and (ii) that there is a number of significant structural elements in the coding region. Furthermore, we identify potential cis-acting replication elements in four genera where this feature has not been reported so far.
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Affiliation(s)
- C Witwer
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, A-1090 Wien, Austria
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38
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Barton DJ, O’Donnell BJ, Flanegan JB. 5' cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J 2001; 20:1439-48. [PMID: 11250909 PMCID: PMC145522 DOI: 10.1093/emboj/20.6.1439] [Citation(s) in RCA: 220] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A cloverleaf structure at the 5' terminus of poliovirus RNA binds viral and cellular proteins. To examine the role of the cloverleaf in poliovirus replication, we determined how cloverleaf mutations affected the stability, translation and replication of poliovirus RNA in HeLa S10 translation-replication reactions. Mutations within the cloverleaf destabilized viral RNA in these reactions. Adding a 5' 7-methyl guanosine cap fully restored the stability of the mutant RNAs and had no effect on their translation. These results indicate that the 5' cloverleaf normally protects uncapped poliovirus RNA from rapid degradation by cellular nucleases. Preinitiation RNA replication complexes formed with the capped mutant RNAs were used to measure negative-strand synthesis. Although the mutant RNAs were stable and functional mRNAs, they were not active templates for negative-strand RNA synthesis. Therefore, the 5' cloverleaf is a multifunctional cis-acting replication element required for the initiation of negative-strand RNA synthesis. We propose a replication model in which the 5' and 3' ends of viral RNA interact to form a circular ribonucleoprotein complex that regulates the stability, translation and replication of poliovirus RNA.
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Affiliation(s)
- David J. Barton
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610-0245, USA Present address: Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, USA Corresponding author e-mail:
| | - Brian J. O’Donnell
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610-0245, USA Present address: Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, USA Corresponding author e-mail:
| | - James B. Flanegan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610-0245, USA Present address: Department of Microbiology, University of Colorado Health Sciences Center, Denver, CO 80262, USA Corresponding author e-mail:
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Abstract
The genetic diversity of porcine teschoviruses (PTVs; previously named porcine enterovirus 1) and most serotypes of porcine enteroviruses (PEVs) was studied. Following the determination of the major portion of the genomic sequence of PTV reference strain Talfan, the nucleotide and derived amino acid sequences of the RNA-dependent RNA polymerase (RdRp) region, the capsid VP2 region and the 3' non-translated region (3'-NTR) were compared among PTVs and PEVs and with other picornaviruses. The sequences were obtained by RT-PCR and 3'-RACE with primers based on the sequences of Talfan and available PEV strains. Phylogenetic analysis of RdRp/VP2 and analysis of the predicted RNA secondary structure of the 3'-NTR indicated that PEVs should be reclassified genetically into at least three groups, one that should be assigned to PTVs and two PEV subspecies represented by strain PEV-8 V13 and strain PEV-9 UKG410/73.
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Affiliation(s)
- Yoshihiro Kaku
- Department of Virology, National Institute of Animal Health, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-0856, Japan1
| | - Akinori Sarai
- Tsukuba Life Science Center, The Institute of Physical & Chemical Research (RIKEN), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan2
| | - Yosuke Murakami
- Department of Virology, National Institute of Animal Health, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-0856, Japan1
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40
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Zell R, Krumbholz A, Henke A, Birch-Hirschfeld E, Stelzner A, Doherty M, Hoey E, Dauber M, Prager D, Wurm R. Detection of porcine enteroviruses by nRT-PCR: differentiation of CPE groups I-III with specific primer sets. J Virol Methods 2000; 88:205-18. [PMID: 10960708 DOI: 10.1016/s0166-0934(00)00189-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Porcine enteroviruses (PEV) comprising at least 13 serotypes grouped into three species are described as causative agents of neurological disorders, fertility disorders, and dermal lesions of swine. Despite their well-documented acid stability, enteric infection route, and similarity of clinical symptoms, most of the porcine enterovirus (PEV) serotypes are set apart from the genus Enterovirus of the Picornaviridae. Hence, PCR procedures used commonly to detect enteroviruses are not applicable to epizootic relevant PEV serotypes. A nested RT-PCR protocol is described now suited to detect all known porcine enterovirus serotypes using three sets of primer pairs. These primer pairs were designed to amplify either highly conserved sequences of the 5'-nontranslated region (5'-NTR) or the polymerase gene region of the relevant virus species. All 13 acknowledged serotypes of three PEV species and several field isolates of clinical specimens were detectable. The specificity of the PCR procedure is supported by the observation that RT-PCR-positive field isolates coincide with serological PEV classification. PEV PCR is more rapid and less laborious than the time-consuming virus isolation by tissue culture techniques over several passages and serotyping. Because other viruses such as classical swine fever virus, pseudorabies virus, porcine parvovirus, swine vesicular disease virus, and foot-and-mouth disease virus may cause diseases with similar clinical symptoms, PCR detection of all PEVs closes a diagnostic gap and offers the opportunity to use comprehensive PCR procedures for the diagnosis of all relevant viruses causing such symptoms.
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Affiliation(s)
- R Zell
- Institut für Virologie, Klinikum der Friedrich-Schiller-Universität, Winzerlaer Str. 10, 07745 Jena, Germany.
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41
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Henke A, Launhardt H, Klement K, Stelzner A, Zell R, Munder T. Apoptosis in coxsackievirus B3-caused diseases: interaction between the capsid protein VP2 and the proapoptotic protein siva. J Virol 2000; 74:4284-90. [PMID: 10756043 PMCID: PMC111945 DOI: 10.1128/jvi.74.9.4284-4290.2000] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coxsackievirus B3 (CVB3) is a common factor in human myocarditis. Apoptotic events are present in CVB3-induced disease, but it is unclear how CVB3 is involved in apoptosis and which viral proteins may induce the apoptotic pathway. In this report we demonstrate that the human and murine proapoptotic protein Siva specifically interact with the CVB3 capsid protein VP2. Furthermore, the transcription of Siva is strongly induced in tissue of CVB3-infected mice and is present in the same area which is positively stained for apoptosis, CD27, and CD70. It has been proposed that Siva is involved in the CD27/CD70-transduced apoptosis. Therefore, we suggest a molecular mechanism through which apoptotic events contributes to CVB3-caused pathogenesis.
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Affiliation(s)
- A Henke
- Institute of Virology, Medical Center, Friedrich Schiller University Jena, Germany.
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42
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Bellmunt A, May G, Zell R, Pring-Akerblom P, Verhagen W, Heim A. Evolution of poliovirus type I during 5.5 years of prolonged enteral replication in an immunodeficient patient. Virology 1999; 265:178-84. [PMID: 10600590 DOI: 10.1006/viro.1999.0003] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Poliovirus type 1 was isolated from an immunodeficient patient 4 days after onset of paresis (IS1) and after 5.5 years of prolonged enteral virus replication (IS2). Antigenic characterization revealed that IS1 was Sabin 1-like, whereas IS2 reacted like poliovirus 1 Mahoney. Complete genomic sequencing demonstrated the phylogenetic relationship (94.9% identity) of IS1 and IS2, which differed from the most closely related Sabin 1 by 5.4 and 8.3%, respectively. Both isolates had revertant-like mutations at nucleotides 480 and 6203. Deduced amino acid sequences indicated significant changes between IS1 and IS2 at the neutralizing antigenic site 1. Prolonged enteral replication, evolution, and shedding of poliovirus by immunodeficient patients should be considered in the poliovirus eradication strategy.
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Affiliation(s)
- A Bellmunt
- Institut für Virologie, Medizinische Hochschule, Hannover, Germany
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Zell R, Sidigi K, Henke A, Schmidt-Brauns J, Hoey E, Martin S, Stelzner A. Functional features of the bovine enterovirus 5'-non-translated region. J Gen Virol 1999; 80 ( Pt 9):2299-2309. [PMID: 10501480 DOI: 10.1099/0022-1317-80-9-2299] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bovine enterovirus (BEV) serotypes exhibit unique features of the non-translated regions (NTRs) which separate them from the other enteroviruses. Their most remarkable property is an additional genome region of 110 nt located between the 5'-cloverleaf and the internal ribosome entry site (IRES). This genome region has the potential to form an additional cloverleaf structure (domain I*) separated from the 5'-cloverleaf (domain I) by a small stem-loop (domain I**). Other characteristics involve the putative IRES domains III and VI. In order to investigate the features of the 5'-NTR, several full-length coxsackievirus B3 (CVB3) cDNA plasmids with hybrid 5'-NTRs were engineered. After exchange of the CVB3 cloverleaf with the BEV1 genome region representing both cloverleafs, a viable virus chimera was generated. Deletion of domain I** within the exchanged region also yielded viable virus albeit with reduced growth capacity. Deletion of sequences encoding either the first or the second BEV cloverleaf resulted in non-infectious constructs. Hybrid plasmids with exchanges of the IRES-encoding sequence or the complete 5'-NTR were non-infectious. Transfection experiments with SP6 transcripts containing 5'-NTRs fused to the luciferase message indicated that IRES-driven translation is enhanced by the presence of the CVB3 cloverleaf and both BEV1 cloverleaf structures, respectively. Deletion of either the first or the second BEV cloverleaf domain reduced but did not abolish enhanced luciferase expression. These results suggest that the substitution of two putative BEV cloverleaf structures for the putative coxsackieviral cloverleaf yields viable virus, while BEV sequences encoding the IRES fail to functionally replace CVB3 IRES-encoding sequences.
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Affiliation(s)
- Roland Zell
- Institut für Virologie, Klinikum der Friedrich-Schiller-Universität, Winzerlaer Str. 10, D-07745 Jena, Germany1
| | - Karim Sidigi
- Institut für Virologie, Klinikum der Friedrich-Schiller-Universität, Winzerlaer Str. 10, D-07745 Jena, Germany1
| | - Andreas Henke
- Institut für Virologie, Klinikum der Friedrich-Schiller-Universität, Winzerlaer Str. 10, D-07745 Jena, Germany1
| | | | - Elizabeth Hoey
- School of Biology and Biochemistry, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK3
| | - Sam Martin
- School of Biology and Biochemistry, The Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, UK3
| | - Axel Stelzner
- Institut für Virologie, Klinikum der Friedrich-Schiller-Universität, Winzerlaer Str. 10, D-07745 Jena, Germany1
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AbuBakar S, Chee HY, Al-Kobaisi MF, Xiaoshan J, Chua KB, Lam SK. Identification of enterovirus 71 isolates from an outbreak of hand, foot and mouth disease (HFMD) with fatal cases of encephalomyelitis in Malaysia. Virus Res 1999; 61:1-9. [PMID: 10426204 DOI: 10.1016/s0168-1702(99)00019-2] [Citation(s) in RCA: 165] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Thirteen enterovirus 71 (EV71) isolates were obtained from both fatal and non-fatal infections of patients seen in Peninsula Malaysia and in Sarawak during an outbreak of hand, foot and mouth disease (HFMD) in Malaysia in 1997, with incidences of fatal brainstem encephalomyelitis. The isolates were identified using immunofluorescence staining, neutralization assays, and partial sequencing of the 5' untranslated regions (UTR). Assessment of the potential genetic relationships of the isolates using the partial 5'UTR sequences suggested clustering of the isolates into at least two main clusters. Isolates from Peninsula Malaysia were found in both clusters whereas Sarawak-derived isolates clustered only in cluster II. Isolates derived from fatal infections, however, occurred in both clusters and no distinctive nucleotide sequences could be attributed to the fatal isolates. Examination of the nucleotide sequences revealed at least 13 nucleotide positions in all the isolates which differ completely from the previously reported EV71 5'UTR sequences. In addition, at least 11 nucleotide position differences within the 5'UTR were noted which differentiated cluster I from cluster II. Predicted secondary RNA structures drawn using the nucleotide sequences also suggested differences between isolates from the two clusters. These findings suggest the presence of at least two potentially virulent EV71 co-circulating in Malaysia during the 1997 HFMD outbreak.
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Affiliation(s)
- S AbuBakar
- Department of Medical Microbiology, University Malaya Medical Center, Kuala Lumpur, Malaysia.
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Oberste MS, Maher K, Kilpatrick DR, Pallansch MA. Molecular evolution of the human enteroviruses: correlation of serotype with VP1 sequence and application to picornavirus classification. J Virol 1999; 73:1941-8. [PMID: 9971773 PMCID: PMC104435 DOI: 10.1128/jvi.73.3.1941-1948.1999] [Citation(s) in RCA: 666] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/1998] [Accepted: 11/30/1998] [Indexed: 11/20/2022] Open
Abstract
Sixty-six human enterovirus serotypes have been identified by serum neutralization, but the molecular determinants of the serotypes are unknown. Since the picornavirus VP1 protein contains a number of neutralization domains, we hypothesized that the VP1 sequence should correspond with neutralization (serotype) and, hence, with phylogenetic lineage. To test this hypothesis and to analyze the phylogenetic relationships among the human enteroviruses, we determined the complete VP1 sequences of the prototype strains of 47 human enterovirus serotypes and 10 antigenic variants. Our sequences, together with those available from GenBank, comprise a database of complete VP1 sequences for all 66 human enterovirus serotypes plus additional strains of seven serotypes. Phylogenetic trees constructed from complete VP1 sequences produced the same four major clusters as published trees based on partial VP2 sequences; in contrast to the VP2 trees, however, in the VP1 trees strains of the same serotype were always monophyletic. In pairwise comparisons of complete VP1 sequences, enteroviruses of the same serotype were clearly distinguished from those of heterologous serotypes, and the limits of intraserotypic divergence appeared to be about 25% nucleotide sequence difference or 12% amino acid sequence difference. Pairwise comparisons suggested that coxsackie A11 and A15 viruses should be classified as strains of the same serotype, as should coxsackie A13 and A18 viruses. Pairwise identity scores also distinguished between enteroviruses of different clusters and enteroviruses from picornaviruses of different genera. The data suggest that VP1 sequence comparisons may be valuable in enterovirus typing and in picornavirus taxonomy by assisting in the genus assignment of unclassified picornaviruses.
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Affiliation(s)
- M S Oberste
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Oberste MS, Maher K, Pallansch MA. Molecular phylogeny of all human enterovirus serotypes based on comparison of sequences at the 5' end of the region encoding VP2. Virus Res 1998; 58:35-43. [PMID: 9879760 DOI: 10.1016/s0168-1702(98)00101-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Sixty-six human enterovirus serotypes have been described using antibody neutralization, with antigenic variants defined within several serotypes. Despite the availability of sequence data for numerous enteroviruses, the molecular basis of serotype is unknown. Previous studies by others have identified four major phylogenetic groups within the human enteroviruses, but there has been no complete database of homologous sequences for all human enterovirus serotypes. We have determined the homologous partial VP2 sequences for the 12 prototype strains for which VP2 sequence was unavailable and for eight well-characterized antigenic variants. Phylogenetic analysis of all prototype strains produced four major groups, consistent with published enterovirus phylogenies. Many antigenic variants, however, failed to cluster with their respective prototype strains, suggesting that this portion of VP2 may be inappropriate for consistent molecular inference of serotype and for detailed study of enterovirus evolution.
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Affiliation(s)
- M S Oberste
- Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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