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What are the limits of the packaging capacity for genomic RNA in the cores of rotaviruses and of other members of the Reoviridae? Virus Res 2020; 276:197822. [DOI: 10.1016/j.virusres.2019.197822] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022]
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Chen Q, Zhang L, Chen H, Xie L, Wei T. Nonstructural protein Pns4 of rice dwarf virus is essential for viral infection in its insect vector. Virol J 2015; 12:211. [PMID: 26646953 PMCID: PMC4673743 DOI: 10.1186/s12985-015-0438-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/25/2015] [Indexed: 01/04/2023] Open
Abstract
Background Rice dwarf virus (RDV), a plant reovirus, is mainly transmitted by the green rice leafhopper, Nephotettix cincticeps, in a persistent-propagative manner. Plant reoviruses are thought to replicate and assemble within cytoplasmic structures called viroplasms. Nonstructural protein Pns4 of RDV, a phosphoprotein, is localized around the viroplasm matrix and forms minitubules in insect vector cells. However, the functional role of Pns4 minitubules during viral infection in insect vector is still unknown yet. Methods RNA interference (RNAi) system targeting Pns4 gene of RDV was conducted. Double-stranded RNA (dsRNA) specific for Pns4 gene was synthesized in vitro, and introduced into cultured leafhopper cells by transfection or into insect body by microinjection. The effects of the knockdown of Pns4 expression due to RNAi induced by synthesized dsRNA from Pns4 gene on viral replication and spread in cultured cells and insect vector were analyzed using immunofluorescence, western blotting or RT-PCR assays. Results In cultured leafhopper cells, the knockdown of Pns4 expression due to RNAi induced by synthesized dsRNA from Pns4 gene strongly inhibited the formation of minitubules, preventing the accumulation of viroplasms and efficient viral infection in insect vector cells. RNAi induced by microinjection of dsRNA from Pns4 gene significantly reduced the viruliferous rate of N. cincticeps. Furthermore, it also strongly inhibited the formation of minitubules and viroplasms, preventing efficient viral spread from the initially infected site in the filter chamber of intact insect vector. Conclusions Pns4 of RDV is essential for viral infection and replication in insect vector. It may directly participate in the functional role of viroplasm for viral replication and assembly of progeny virions during viral infection in leafhopper vector.
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Affiliation(s)
- Qian Chen
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, PR China.
| | - Linghua Zhang
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, PR China.
| | - Hongyan Chen
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, PR China.
| | - Lianhui Xie
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, PR China.
| | - Taiyun Wei
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, PR China.
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Eusebio-Cope A, Suzuki N. Mycoreovirus genome rearrangements associated with RNA silencing deficiency. Nucleic Acids Res 2015; 43:3802-13. [PMID: 25800742 PMCID: PMC4402544 DOI: 10.1093/nar/gkv239] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 03/06/2015] [Indexed: 01/31/2023] Open
Abstract
Mycoreovirus 1 (MyRV1) has 11 double-stranded RNA genome segments (S1 to S11) and confers hypovirulence to the chestnut blight fungus, Cryphonectria parasitica. MyRV1 genome rearrangements are frequently generated by a multifunctional protein, p29, encoded by a positive-strand RNA virus, Cryphonectria hypovirus 1. One of its functional roles is RNA silencing suppression. Here, we explored a possible link between MyRV1 genome rearrangements and the host RNA silencing pathway using wild-type (WT) and mutant strains of both MyRV1 and the host fungus. Host strains included deletion mutants of RNA silencing components such as dicer-like (dcl) and argonaute-like (agl) genes, while virus strains included an S4 internal deletion mutant MyRV1/S4ss. Consequently, intragenic rearrangements with nearly complete duplication of the three largest segments, i.e. S1, S2 and S3, were observed even more frequently in the RNA silencing-deficient strains Δdcl2 and Δagl2 infected with MyRV1/S4ss, but not with any other viral/host strain combinations. An interesting difference was noted between genome rearrangement events in the two host strains, i.e. generation of the rearrangement required prolonged culture for Δagl2 in comparison with Δdcl2. These results suggest a role for RNA silencing that suppresses genome rearrangements of a dsRNA virus.
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Affiliation(s)
- Ana Eusebio-Cope
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
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Afrad MH, Matthijnssens J, Afroz SF, Rudra P, Nahar L, Rahman R, Hossain ME, Rahman SR, Azim T, Rahman M. Differences in lineage replacement dynamics of G1 and G2 rotavirus strains versus G9 strain over a period of 22 years in Bangladesh. INFECTION GENETICS AND EVOLUTION 2014; 28:214-22. [PMID: 25305473 DOI: 10.1016/j.meegid.2014.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/27/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
Group A rotaviruses (RVAs) have been a major cause of severe gastroenteritis in Bangladesh, mainly in children below the age of five. At the icddr,b, RVA strains collection and characterization dates back for more than 20 years. This sample collection was used to study the molecular evolution of the VP7 gene of G1, G2 and G9 RVA strains, which have been circulating in Bangladesh for most of this study period. The evolutionary rates (95% HPD) for G1, G2 and G9 were calculated to be 0.93×10(-3) (0.68-1.18), 1.45×10(-3) (1.12-1.78) and 1.07×10(-3) (0.78-1.39), respectively, which is in line with previous data for the RVA VP7 outer capsid protein, which is under strong negative selective pressure. Bayesian analyses revealed that for the G1 and G2 genotypes, one or multiple lineages co-circulated for one or a few seasons, frequently followed by replacement with genetically different lineages. This can be explained by the existence of a large variety of G1 and G2 RVA lineages and the rapid dissemination of different lineages across the globe. In contrast, circulating G9 lineages were rather closely related to each other across the study period and they were usually derived from variants circulating in the previous season(s). This is consistent with the fact that G9 RVAs have circulated in the human population for less than 20 years, and therefore their genetic diversity is much smaller, not resulting in the replacement of circulating G9 strains by highly divergent G9 lineages from abroad. Such different evolutionary dynamics for different RVA genotypes may alter their response to the selective pressure that might be exerted by the introduction of RVA vaccines and therefore a continued close monitoring is warranted.
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Affiliation(s)
- Mokibul Hassan Afrad
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh.
| | - Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
| | - Syeda Farhana Afroz
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Pranab Rudra
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Lutfun Nahar
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Rajibur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Mohammad Enayet Hossain
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | | | - Tasnim Azim
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease and Research, Bangladesh (icddr,b), Bangladesh
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Generation of genetically stable recombinant rotaviruses containing novel genome rearrangements and heterologous sequences by reverse genetics. J Virol 2013; 87:6211-20. [PMID: 23536662 DOI: 10.1128/jvi.00413-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The rotavirus (RV) genome consists of 11 segments of double-stranded RNA (dsRNA). Typically, each segment contains 5' and 3' untranslated regions (UTRs) that flank an open reading frame (ORF) encoding a single protein. RV variants with segments of atypical size owing to sequence rearrangements have been described. In many cases, the rearrangement originates from a partial head-to-tail sequence duplication that initiates after the stop codon of the ORF, leaving the protein product of the segment unaffected. To probe the limits of the RV genome to accommodate additional genetic sequence, we used reverse genetics to insert duplications (analogous to synthetic rearrangements) and heterologous sequences into the 3' UTR of the segment encoding NSP2 (gene 8). The approach allowed the recovery of recombinant RVs that contained sequence duplications (up to 200 bp) and heterologous sequences, including those for FLAG, the hepatitis C virus E2 epitope, and the internal ribosome entry site of cricket paralysis virus. The recombinant RVs grew to high titer (>10(7) PFU/ml) and remained genetically stable during serial passage. Despite their longer 3' UTRs, rearranged RNAs of recombinant RVs expressed wild-type levels of protein in vivo. Competitive growth experiments indicated that, unlike RV segments with naturally occurring sequence duplications, genetically engineered segments were less efficiently packaged into progeny viruses. Thus, features of naturally occurring rearranged segments, other than their increased length, contribute to their enhanced packaging phenotype. Our results define strategies for developing recombinant RVs as expression vectors, potentially leading to next-generation RV vaccines that induce protection against other infectious agents.
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Diversity and adaptation of human respiratory syncytial virus genotypes circulating in two distinct communities: public hospital and day care center. Viruses 2012. [PMID: 23202489 PMCID: PMC3509657 DOI: 10.3390/v4112432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
HRSV is one of the most important pathogens causing acute respiratory tract diseases as bronchiolitis and pneumonia among infants. HRSV was isolated from two distinct communities, a public day care center and a public hospital in São José do Rio Preto - SP, Brazil. We obtained partial sequences from G gene that were used on phylogenetic and selection pressure analysis. HRSV accounted for 29% of respiratory infections in hospitalized children and 7.7% in day care center children. On phylogenetic analysis of 60 HRSV strains, 48 (80%) clustered within or adjacent to the GA1 genotype; GA5, NA1, NA2, BA-IV and SAB1 were also observed. SJRP GA1 strains presented variations among deduced amino acids composition and lost the potential O-glycosilation site at amino acid position 295, nevertheless this resulted in an insertion of two potential O-glycosilation sites at positions 296 and 297. Furthermore, a potential O-glycosilation site insertion, at position 293, was only observed for hospital strains. Using SLAC and MEME methods, only amino acid 274 was identified to be under positive selection. This is the first report on HRSV circulation and genotypes classification derived from a day care center community in Brazil.
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Tanaka T, Eusebio-Cope A, Sun L, Suzuki N. Mycoreovirus genome alterations: similarities to and differences from rearrangements reported for other reoviruses. Front Microbiol 2012; 3:186. [PMID: 22675320 PMCID: PMC3365852 DOI: 10.3389/fmicb.2012.00186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/04/2012] [Indexed: 11/13/2022] Open
Abstract
The family Reoviridae is one of the largest virus families with genomes composed of 9-12 double-stranded RNA segments. It includes members infecting organisms from protists to humans. It is well known that reovirus genomes are prone to various types of genome alterations including intragenic rearrangement and reassortment under laboratory and natural conditions. Recently distinct genetic alterations were reported for members of the genus Mycoreovirus, Mycoreovirus 1 (MyRV1), and MyRV3 with 11 (S1-S11) and 12 genome segments (S1-S12), respectively. While MyRV3 S8 is lost during subculturing of infected host fungal strains, MyRV1 rearrangements undergo alterations spontaneously and inducibly. The inducible MyRV1 rearrangements are different from any other previous examples of reovirus rearrangements in their dependence on an unrelated virus factor, a multifunctional protein, p29, encoded by a distinct virus Cryphonectria parasitica hypovirus 1 (CHV1). A total of 5 MyRV1 variants with genome rearranged segments (S1-S3, S6 and S10) are generated in the background of a single viral strain in the presence of CHV1 p29 supplied either transgenically or by coinfection. MyRV1 S4 and S10 are rearranged, albeit very infrequently, in a CHV1 p29 independent fashion. A variant of MyRV1 with substantial deletions in both S4 and S10, generated through a combined reassortment and rearrangement approach, shows comparable replication levels to the wild-type MyRV1. In vivo and in vitro interactions of CHV1 p29 and MyRV1 VP9 are implicated in the induction of MyRV1 rearrangements. However, the mechanism underlying p29-mediated rearrangements remains largely unknown. MyRV1 S4 rearrangements spontaneously occurred independently of CHV1 p29. In the absence of reverse genetics systems for mycoreoviruses, molecular and biological characterization of these MyRV1 and MyRV3 variants contribute to functional analyses of the protein products encoded by those rearranged segments.
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Affiliation(s)
- Toru Tanaka
- Agrivirology Laboratory, Institute of Plant Science and Bioresources, Okayama University Kurashiki, Okayama, Japan
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Eshaghi A, Duvvuri VR, Lai R, Nadarajah JT, Li A, Patel SN, Low DE, Gubbay JB. Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication. PLoS One 2012; 7:e32807. [PMID: 22470426 PMCID: PMC3314658 DOI: 10.1371/journal.pone.0032807] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/06/2012] [Indexed: 12/02/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the main cause of acute lower respiratory infections in children under 2 years of age and causes repeated infections throughout life. We investigated the genetic variability of RSV-A circulating in Ontario during 2010–2011 winter season by sequencing and phylogenetic analysis of the G glycoprotein gene. Among the 201 consecutive RSV isolates studied, RSV-A (55.7%) was more commonly observed than RSV-B (42.3%). 59.8% and 90.1% of RSV-A infections were among children ≤12 months and ≤5 years old, respectively. On phylogenetic analysis of the second hypervariable region of the 112 RSV-A strains, 110 (98.2%) clustered within or adjacent to the NA1 genotype; two isolates were GA5 genotype. Eleven (10%) NA1-related isolates clustered together phylogenetically as a novel RSV-A genotype, named ON1, containing a 72 nucleotide duplication in the C-terminal region of the attachment (G) glycoprotein. The predicted polypeptide is lengthened by 24 amino acids and includes a23 amino acid duplication. Using RNA secondary structural software, a possible mechanism of duplication occurrence was derived. The 23 amino acid ON1 G gene duplication results in a repeat of 7 potential O-glycosylation sites including three O-linked sugar acceptors at residues 270, 275, and 283. Using Phylogenetic Analysis by Maximum Likelihood analysis, a total of 19 positively selected sites were observed among Ontario NA1 isolates; six were found to be codons which reverted to the previous state observed in the prototype RSV-A2 strain. The tendency of codon regression in the G-ectodomain may infer a decreased avidity of antibody to the current circulating strains. Further work is needed to document and further understand the emergence, virulence, pathogenicity and transmissibility of this novel RSV-A genotype with a72 nucleotide G gene duplication.
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Affiliation(s)
- AliReza Eshaghi
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
| | - Venkata R. Duvvuri
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rachel Lai
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
| | | | - Aimin Li
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
| | - Samir N. Patel
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
| | - Donald E. Low
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Jonathan B. Gubbay
- Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada
- Mount Sinai Hospital, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
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9
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Arnold MM, Brownback CS, Taraporewala ZF, Patton JT. Rotavirus variant replicates efficiently although encoding an aberrant NSP3 that fails to induce nuclear localization of poly(A)-binding protein. J Gen Virol 2012; 93:1483-1494. [PMID: 22442114 DOI: 10.1099/vir.0.041830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rotavirus (RV) non-structural protein NSP3 forms a dimer that has binding domains for the translation initiation factor eIF4G and for a conserved 3'-terminal sequence of viral mRNAs. Through these activities, NSP3 has been proposed to promote viral mRNA translation by directing circularization of viral polysomes. In addition, by disrupting interactions between eIF4G and the poly(A)-binding protein (PABP), NSP3 has been suggested to inhibit translation of host polyadenylated mRNAs and to stimulate relocalization of PABP from the cytoplasm to the nucleus. Herein, we report the isolation and characterization of SA11-4Fg7re, an SA11-4F RV derivative that contains a large sequence duplication initiating within the genome segment (gene 7) encoding NSP3. Our analysis showed that mutant NSP3 (NSP3m) encoded by SA11-4Fg7re is almost twice the size of the wild-type protein and retains the capacity to dimerize. However, in comparison to wild-type NSP3, NSP3m has a decreased capacity to interact with eIF4G and to suppress the translation of polyadenylated mRNAs. In addition, NSP3m fails to induce the nuclear accumulation of PABP in infected cells. Despite the defective activities of NSP3m, the levels of viral protein and progeny virus produced in SA11-4Fg7re- and SA11-4F-infected cells were indistinguishable. Collectively, these data are consistent with a role for NSP3 in suppressing host protein synthesis through antagonism of PABP activity, but also suggest that NSP3 functions may have little or no impact on the efficiency of virus replication in widely used RV-permissive cell lines.
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Affiliation(s)
- Michelle M Arnold
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - Catie Small Brownback
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - Zenobia F Taraporewala
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
| | - John T Patton
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive MSC 8026, Room 6314, Bethesda, MD 20892-8026, USA
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Anthony SJ, Darpel KE, Belaganahalli MN, Maan N, Nomikou K, Sutton G, Attoui H, Maan S, Mertens PPC. RNA segment 9 exists as a duplex concatemer in an Australian strain of epizootic haemorrhagic disease virus (EHDV): Genetic analysis and evidence for the presence of concatemers as a normal feature of orbivirus replication. Virology 2011; 420:164-71. [PMID: 21968198 DOI: 10.1016/j.virol.2011.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/11/2011] [Accepted: 09/12/2011] [Indexed: 11/26/2022]
Abstract
This paper reports a concatemeric RNA in a strain of epizootic haemorrhagic disease virus (EHDV) serotype 5. Sequencing showed that the concatemeric RNA contains two identical full-length copies of genome segment 9, arranged in series, which has apparently replaced the monomeric form of the segment. In vitro translation demonstrated that the concatemeric RNA can act as a viable template for VP6 translation, but that no double-sized protein is produced. Studies were also performed to assess whether mutations might be easily introduced into the second copy (which might indicate some potential evolutionary significance of a concatemeric RNA segment), however multiple (n=40) passages generated no changes in the sequence of either the upstream or downstream segments. Further, we present results that demonstrate the presence of concatemers or partial gene duplications in multiple segments of different orbiviruses (in tissue culture and purified virus), suggesting their generation is likely to be a normal feature of orbivirus replication.
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Affiliation(s)
- S J Anthony
- Vector-borne Disease Program, Institute for Animal Health, Ash Road, Pirbright, Surrey, GU24 0NF, UK.
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11
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Ghosh S, Kobayashi N. Whole-genomic analysis of rotavirus strains: current status and future prospects. Future Microbiol 2011; 6:1049-65. [DOI: 10.2217/fmb.11.90] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal–human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.
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Affiliation(s)
- Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, S 1, W 17, Chuo-Ku, Sapporo, Hokkaido 060-8556, Japan
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Donker NC, Boniface K, Kirkwood CD. Phylogenetic analysis of rotavirus A NSP2 gene sequences and evidence of intragenic recombination. INFECTION GENETICS AND EVOLUTION 2011; 11:1602-7. [PMID: 21689784 DOI: 10.1016/j.meegid.2011.05.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 05/19/2011] [Accepted: 05/27/2011] [Indexed: 11/17/2022]
Abstract
The rotavirus non-structural protein NSP2 is one of the earliest and most abundant viral proteins produced during infection. This protein has multiple essential roles in the replication cycle involving RNA binding, viroplasm formation, helicase and can hydrolyse the γ-phosphate of RNA and NTPs acting as an RTPase and NTPase. In studying sequences from rotavirus strains isolated in Australia between 1984 and 2009, the NSP2 gene was seen to be highly conserved and clustered with defined NSP2 genotypes N1 and N2 according to the full genome based rotavirus classification system. Phylogenetic analysis indicated that NSP2 gene sequences isolated from Australian rotavirus strains formed four distinct lineages. Temporal variation was observed in several clusters during the 26 year period, with lineage D identified throughout the entire study period and lineage A only detected since 1999. Phylogenetic analysis and dendrograms identified NSP2 genes that exhibited reassortment between different virus VP7 genotypes, as well as a sequence from a human strain that grouped closely with the NSP2 genes of bovine rotavirus strains. This study also identified a sequence that fell between lineages and exhibited evidence of recombination, the first time that intergenic recombination has been detected in a NSP2 gene sequence. This study increases the understanding of the evolution mechanisms of NSP2 in view of improved vaccine design.
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Affiliation(s)
- Nicole C Donker
- Enteric Virus Group, Murdoch Childrens Research Institute, Royal Childrens Hospital, Parkville, Victoria 3052, Australia.
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13
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Troupin C, Schnuriger A, Duponchel S, Deback C, Schnepf N, Dehee A, Garbarg-Chenon A. Rotavirus rearranged genomic RNA segments are preferentially packaged into viruses despite not conferring selective growth advantage to viruses. PLoS One 2011; 6:e20080. [PMID: 21611152 PMCID: PMC3096661 DOI: 10.1371/journal.pone.0020080] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 04/21/2011] [Indexed: 12/02/2022] Open
Abstract
The rotavirus (RV) genome consists of 11 double-stranded RNA segments. Sometimes, partial sequence duplication of an RNA segment leads to a rearranged RNA segment. To specify the impact of rearrangement, the replication efficiencies of human RV with rearranged segments 7, 11 or both were compared to these of the homologous human wild-type RV (wt-RV) and of the bovine wt-RV strain RF. As judged by viral growth curves, rotaviruses with a rearranged genome (r-RV) had no selective growth advantage over the homologous wt-RV. In contrast, r-RV were selected over wt-RV during competitive experiments (i.e mixed infections between r-RV and wt-RV followed by serial passages in cell culture). Moreover, when competitive experiments were performed between a human r-RV and the bovine wt-RV strain RF, which had a clear growth advantage, rearranged segments 7, 11 or both always segregated in viral progenies even when performing mixed infections at an MOI ratio of 1 r-RV to 100 wt-RV. Lastly, bovine reassortant viruses that had inherited a rearranged segment 7 from human r-RV were generated. Although substitution of wt by rearranged segment 7 did not result in any growth advantage, the rearranged segment was selected in the viral progenies resulting from mixed infections by bovine reassortant r-RV and wt-RV, even for an MOI ratio of 1 r-RV to 107 wt-RV. Lack of selective growth advantage of r-RV over wt-RV in cell culture suggests a mechanism of preferential packaging of the rearranged segments over their standard counterparts in the viral progeny.
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Affiliation(s)
- Cécile Troupin
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
| | - Aurélie Schnuriger
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
- ERL U1057/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Laboratoire de Virologie, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Sarah Duponchel
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
- ERL U1057/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Claire Deback
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
| | - Nathalie Schnepf
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
| | - Axelle Dehee
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
- Laboratoire de Virologie, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Antoine Garbarg-Chenon
- Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie - Paris 6, Paris, France
- ERL U1057/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Laboratoire de Virologie, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France
- * E-mail:
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14
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Mlera L, Jere KC, van Dijk AA, O'Neill HG. Determination of the whole-genome consensus sequence of the prototype DS-1 rotavirus using sequence-independent genome amplification and 454® pyrosequencing. J Virol Methods 2011; 175:266-71. [PMID: 21600242 DOI: 10.1016/j.jviromet.2011.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 04/20/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
Abstract
The prototype DS-1 rotavirus strain, is characterised by a short electropherotype and G2P[4] serotype specificity. Following sequence-independent genome amplification and 454(®) pyrosequencing of genomic cDNA, differences between the newly determined consensus sequence and GenBank sequences were observed in 10 of the 11 genome segments. Only the consensus sequence of genome segment 1 was identical to sequences deposited in GenBank. A novel isoleucine at position 397 in a hydrophobic region of VP4 is described. An additional 7 N-terminal amino acids was found in NSP1. For genome segment 10 the first 34 and last 30 nucleotides of the 5' and 3'-terminal ends, respectively, were identified. Genome segment 11 was found to be 821 bp long, which is 148 bp longer than the full length genome segment 11 sequence reported previously. This paper reports the first complete consensus genome sequence for the tissue culture adapted DS-1 strain free from cloning bias and the limitations of Sanger sequencing. Sequence differences in previous publications reporting on DS-1 rotavirus genome segment sequencing, were identified and discussed.
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Affiliation(s)
- Luwanika Mlera
- Biochemistry Division, North-West University, Potchefstroom, South Africa
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15
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Rose TL, Miagostovich MP, Leite JPG. Rotavirus A genotype G1P[8]: a novel method to distinguish wild-type strains from the Rotarix® vaccine strain. Mem Inst Oswaldo Cruz 2010; 105:1068-72. [DOI: 10.1590/s0074-02762010000800021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 10/27/2010] [Indexed: 11/21/2022] Open
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16
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Matthijnssens J, Heylen E, Zeller M, Rahman M, Lemey P, Van Ranst M. Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread. Mol Biol Evol 2010; 27:2431-6. [PMID: 20522727 DOI: 10.1093/molbev/msq137] [Citation(s) in RCA: 230] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rotaviruses (RVs) are responsible for more than 600,000 child deaths each year. The worldwide introduction of two life oral vaccines RotaTeq and Rotarix is believed to reduce this number significantly. Before the licensing of both vaccines, two new genotypes, G9 and G12, emerged in the human population and were able to spread across the entire globe in a very short time span. To quantify the VP7 mutation rates of these G9 and G12 genotypes and to estimate their most recent common ancestors, we used a Bayesian Markov chain Monte Carlo framework. Based on 356 sequences for G9 and 140 sequences for G12, we estimated mutation rates (nt substitutions/site/year) of 1.87 × 10(-3) (1.45-2.27 × 10(-3)) for G9 and 1.66 × 10(-3) (1.13-2.32 × 10(-3)) for G12. For both the G9 and G12 strains, one particular (sub) lineage was able to disseminate and cause disease across the world. The most recent common ancestors of these particular lineages were dated back to 1989 (1986-1992) and 1995 (1992-1998) for the G9 and G12 genotypes, respectively. These estimates suggest that a single novel RV (e.g., a vaccine escape mutant) can spread worldwide in little more than a decade. These results re-emphasize the need for thorough and continued RV surveillance in order to detect such potential spreading events at an early stage.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium.
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17
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Eusebio-Cope A, Sun L, Hillman BI, Suzuki N. Mycoreovirus 1 S4-coded protein is dispensable for viral replication but necessary for efficient vertical transmission and normal symptom induction. Virology 2010; 397:399-408. [DOI: 10.1016/j.virol.2009.11.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/11/2009] [Accepted: 11/22/2009] [Indexed: 02/04/2023]
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18
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Bányai K, Matthijnssens J, Szücs G, Forgách P, Erdélyi K, van Ranst M, Lorusso E, Decaro N, Elia G, Martella V. Frequent rearrangement may explain the structural heterogeneity in the 11th genome segment of lapine rotaviruses - short communication. Acta Vet Hung 2009; 57:453-61. [PMID: 19635717 DOI: 10.1556/avet.57.2009.3.11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In rotaviruses, intragenic recombination or gene rearrangement occurs almost exclusively in the genome segments encoding for non-structural proteins. Rearranged RNA originates by mechanisms of partial sequence duplications and deletions or insertions of non-templated nucleotides. Of interest, epidemiological investigations have pointed out an unusual bias to rearrangements in genome segment 11, notably in rotavirus strains of lapine origin, as evidenced by the detection of numerous lapine strains with super-short genomic electropherotype. The sequence of the full-length genome segment 11 of two lapine strains with super-short electropherotype, LRV-4 and 3489/3, was determined and compared with rearranged and normal cognate genome segments of lapine rotaviruses. The rearranged genome segments contained head-to-tail partial duplications at the 3' end of the main ORF encoding NSP5. Unlike the strains Alabama and B4106, intermingled stretches of non-templated sequences were not present in the accessory RNA of LRV-4 and 3489/3, while multiple deletions were mapped, suggesting the lack of functional constraints. Altogether, these findings suggest that independent rearrangement events have given origin to the various lapine strains that have super-short genome pattern.
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Affiliation(s)
| | - Jelle Matthijnssens
- 3 University of Leuven Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research Leuven Belgium
| | - György Szücs
- 2 University of Pécs Department of Medical Microbiology and Immunology, Faculty of Medicine Pécs Hungary
| | - Petra Forgách
- 4 Szent István University Department of Microbiology and Infectious Diseases, Faculty of Veterinary Science Budapest Hungary
| | - Károly Erdélyi
- 5 Central Veterinary Institute Department of Wildlife Diseases and Parasitology Budapest Hungary
| | - Marc van Ranst
- 3 University of Leuven Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research Leuven Belgium
| | - Eleonora Lorusso
- 6 University of Bari Department of Animal Health and Well-Being Bari Italy
| | - Nicola Decaro
- 6 University of Bari Department of Animal Health and Well-Being Bari Italy
| | - Gabriella Elia
- 6 University of Bari Department of Animal Health and Well-Being Bari Italy
| | - Vito Martella
- 6 University of Bari Department of Animal Health and Well-Being Bari Italy
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19
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Sun L, Suzuki N. Intragenic rearrangements of a mycoreovirus induced by the multifunctional protein p29 encoded by the prototypic hypovirus CHV1-EP713. RNA (NEW YORK, N.Y.) 2008; 14:2557-2571. [PMID: 18945807 PMCID: PMC2590959 DOI: 10.1261/rna.1125408] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 09/01/2008] [Indexed: 05/26/2023]
Abstract
Mycoreovirus 1 (MyRV1), a member of the Reoviridae family possessing a genome consisting of 11 dsRNA segments (S1-S11), and the prototype hypovirus (CHV1-EP713) of the Hypoviridae family, which is closely related to the monopartite picorna-like superfamily with a ssRNA genome, infect the chestnut blight fungus and cause virulence attenuation and distinct phenotypic alterations in the host. Here, we present evidence for reproducible induction of intragenic rearrangements of MyRV1 S6 and S10, mediated by the multifunctional protein p29 encoded by CHV1. S6 and S10 underwent an almost full-length ORF duplication (S6L) and an internal deletion of three-fourths of the ORF (S10ss). No significant influence on symptom induction in the fungal host was associated with the S6L rearrangement. In contrast, S10-encoded VP10, while nonessential for MyRV1 replication, was shown to contribute to virulence reduction and reduced growth of aerial mycelia. Furthermore, p29 was found to copurify with MyRV1 genomic RNA and bind to VP9 in vitro and in vivo, suggesting direct interactions of p29 with the MyRV1 replication machinery. This study provides the first example of a viral factor involved in RNA genome rearrangements of a different virus and shows its usefulness as a probe into the mechanism of replication and symptom expression of a heterologous virus.
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Affiliation(s)
- Liying Sun
- Agrivirology Laboratory, Research Institute for Bioresources, Okayama University Kurashiki, Okayama 710-0046, Japan
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20
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Full genomic analysis of human rotavirus strain TB-Chen isolated in China. Virology 2008; 375:361-73. [DOI: 10.1016/j.virol.2008.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2007] [Revised: 12/05/2007] [Accepted: 01/03/2008] [Indexed: 11/19/2022]
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21
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Rearrangements of rotavirus genomic segment 11 are generated during acute infection of immunocompetent children and do not occur at random. J Virol 2008; 82:3689-96. [PMID: 18216096 DOI: 10.1128/jvi.01770-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Group A rotaviruses are the main cause of viral gastroenteritis in infants. The viral genome consists of 11 double-stranded RNA (dsRNA) segments. Dysfunction of the viral RNA polymerase can lead to gene rearrangements, which most often consist of partial sequence duplication of a dsRNA segment. Gene rearrangements have been detected in vivo during chronic infection in immunodeficient children or in vitro during passages at a high multiplicity of infection in cell culture, suggesting that these replication conditions lead to selective advantages favoring the recovery of viruses with rearranged genes. During acute rotavirus infection, the replication level is high, but the occurrence of rearrangement events has never been reported. By the use of a reverse transcription-PCR assay specifically designed to detect small numbers of copies of rearranged forms of segment 11 in a high background of its standard counterpart, we detected 12 rearrangement events among 161 cases (7.5%) of acute rotavirus infection in immunocompetent children. Strikingly, in all but one case, rearrangement took place at the same location within the short direct repeat AUGU sequence. For the unique case with a different rearrangement pattern, the rearrangement occurred within the direct repeat ACAAGUC that was specific for this isolate. In conclusion, we report the occurrence of segment 11 rearrangements during acute rotavirus infection in immunocompetent children. We show that under such conditions of infection, the viral RNA polymerase generates rearrangements which occur not at random but within direct repeats which might constitute hot spots for RNA recombination.
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Attoui H, Sailleau C, Mohd Jaafar F, Belhouchet M, Biagini P, Cantaloube JF, de Micco P, Mertens P, Zientara S. Complete nucleotide sequence of Middelburg virus, isolated from the spleen of a horse with severe clinical disease in Zimbabwe. J Gen Virol 2007; 88:3078-3088. [PMID: 17947533 DOI: 10.1099/vir.0.83076-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of Middelburg virus (MIDV) was determined for strain MIDV-857 from Zimbabwe. The isolation of this virus in 1993 from a horse that died showing severe clinical signs represents the first indication that MIDV can cause severe disease in equids. Full-length cDNA copies of the viral genome were successfully synthesized by an innovative RT-PCR amplification approach using an 'anchor primer' combined with the SMART methodology described previously for the synthesis of full-length cDNA copies from genome segments of dsRNA viruses. The MIDV-857 genome is 11,674 nt, excluding the 5'-terminal cap structure and poly(A) tail (which varies in length from approximately 180 to approximately 220 residues). The organization of the genome is like that of other alphaviruses, including a read-through stop codon between the nsP3 and nsP4 genes. However, phylogenetic analyses of the structural protein amino acid sequences suggested that the MIDV E1 gene was generated by recombination with a Semliki Forest virus-like virus. This hypothesis was supported by bootscanning analysis using a recombination-detection program. The 3' untranslated region of MIDV-857 also contains a 112 nt duplication. This study reports the first full-length sequence of MIDV, which was obtained from a single RT-PCR product.
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Affiliation(s)
- Houssam Attoui
- Department of Arbovirology, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Corinne Sailleau
- Agence Française de Sécurité Sanitaire des Aliments, 22 rue Pierre Curie, 94703 Maisons-Alfort Cedex 07, France
| | - Fauziah Mohd Jaafar
- Department of Arbovirology, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Mourad Belhouchet
- Unité de Virologie Moléculaire, Etablissement Français du Sang Alpes-Méditerranée, 149 Boulevard Baille, 13005 Marseille, France
| | - Philippe Biagini
- Unité de Virologie Moléculaire, Etablissement Français du Sang Alpes-Méditerranée, 149 Boulevard Baille, 13005 Marseille, France
| | - Jean François Cantaloube
- Unité de Virologie Moléculaire, Etablissement Français du Sang Alpes-Méditerranée, 149 Boulevard Baille, 13005 Marseille, France
| | - Philippe de Micco
- Unité de Virologie Moléculaire, Etablissement Français du Sang Alpes-Méditerranée, 149 Boulevard Baille, 13005 Marseille, France
| | - Peter Mertens
- Department of Arbovirology, Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Stephan Zientara
- Agence Française de Sécurité Sanitaire des Aliments, 22 rue Pierre Curie, 94703 Maisons-Alfort Cedex 07, France
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Matthijnssens J, Rahman M, Yang X, Delbeke T, Arijs I, Kabue JP, Muyembe JJT, Van Ranst M. G8 rotavirus strains isolated in the Democratic Republic of Congo belong to the DS-1-like genogroup. J Clin Microbiol 2006; 44:1801-9. [PMID: 16672410 PMCID: PMC1479174 DOI: 10.1128/jcm.44.5.1801-1809.2006] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several G8P[6] and G8P[8] rotavirus strains were isolated from hospitalized patients in the Democratic Republic of Congo in 2003. To investigate their overall genomic relatedness and to determine to which genogroup they belonged, the complete genomes of strains DRC88 (G8P[8]) and DRC86 (G8P[6]) were determined. Genomic comparison of these two African G8 strains revealed that 10 out of their 11 gene segments, except for VP4, were nearly identical (>98.9% identical at the nucleotide level), suggesting that this rare G8P[8] rotavirus strain originated recently from a reassortment between a common G8P[6] strain and a strain with a P[8] specificity. A very close evolutionary relationship between 9 out of the 11 gene segments of DRC88 and DRC86 and rotavirus strains belonging to the DS-1-like (G2P[4]) "genogroup" was found, and several possible reassortment events preceding the occurrence of G8P[8] and G8P[6] human rotaviruses were hypothesized. Since the genes of G2P[4] rotavirus strains are very well adapted to infect humans, the acquirement of a new VP7 (G8) gene, and especially the replacement of P[6] (believed to be of animal origin) by P[8] (most common in human rotaviruses), might make DRC88-like rotaviruses very well equipped to become a predominant human rotavirus strain and an important pathogen on the African continent and the rest of the world. These findings have important implications for rotavirus vaccine development and highlight that typing of new rotavirus strains by merely sequencing their VP7 and VP4 genes provides us with only the tip of the iceberg regarding rotavirus diversity.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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24
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Matthijnssens J, Rahman M, Martella V, Xuelei Y, De Vos S, De Leener K, Ciarlet M, Buonavoglia C, Van Ranst M. Full genomic analysis of human rotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence for interspecies transmission. J Virol 2006; 80:3801-10. [PMID: 16571797 PMCID: PMC1440464 DOI: 10.1128/jvi.80.8.3801-3810.2006] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Belgian rotavirus strain B4106, isolated from a child with gastroenteritis, was previously found to have VP7 (G3), VP4 (P[14]), and NSP4 (A genotype) genes closely related to those of lapine rotaviruses, suggesting a possible lapine origin or natural reassortment of strain B4106. To investigate the origin of this unusual strain, the gene sequences encoding VP1, VP2, VP3, VP6, NSP1, NSP2, NSP3, and NSP5/6 were also determined. To allow comparison to a lapine strain, the 11 double-stranded RNA segments of a European G3P[14] rabbit rotavirus strain 30/96 were also determined. The complete genome similarity between strains B4106 and 30/96 was 93.4% at the nucleotide level and 96.9% at the amino acid level. All 11 genome segments of strain B4106 were closely related to those of lapine rotaviruses and clustered with the lapine strains in phylogenetic analyses. In addition, sequence analyses of the NSP5 gene of strain B4106 revealed that the altered electrophoretic mobility of NSP5, resulting in a super-short pattern, was due to a gene rearrangement (head-to-tail partial duplication, combined with two short insertions and a deletion). Altogether, these findings confirm that a rotavirus strain with an entirely lapine genome complement was able to infect and cause severe disease in a human child.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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