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Zhou X, Hou X, Xiao G, Liu B, Jia H, Wei J, Mi X, Guo Q, Wei Y, Zhai SL. Emergence of a Novel G4P[6] Porcine Rotavirus with Unique Sequence Duplication in NSP5 Gene in China. Animals (Basel) 2024; 14:1790. [PMID: 38929409 PMCID: PMC11200575 DOI: 10.3390/ani14121790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Rotavirus is a major causative agent of diarrhoea in children, infants, and young animals around the world. The associated zoonotic risk necessitates the serious consideration of the complete genetic information of rotavirus. A segmented genome makes rotavirus prone to rearrangement and the formation of a new viral strain. Monitoring the molecular epidemiology of rotavirus is essential for its prevention and control. The quantitative RT-PCR targeting the NSP5 gene was used to detect rotavirus group A (RVA) in pig faecal samples, and two pairs of universal primers and protocols were used for amplifying the G and P genotype. The genotyping and phylogenetic analysis of 11 genes were performed by RT-PCR and a basic bioinformatics method. A unique G4P[6] rotavirus strain, designated S2CF (RVA/Pig-tc/CHN/S2CF/2023/G4P[6]), was identified in one faecal sample from a piglet with severe diarrhoea in Guangdong, China. Whole genome sequencing and analysis suggested that the 11 segments of the S2CF strain showed a unique Wa-like genotype constellation and a typical porcine RVA genomic configuration of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. Notably, 4 of the 11 gene segments (VP4, VP6, VP2, and NSP5) clustered consistently with human-like RVAs, suggesting independent human-to-porcine interspecies transmission. Moreover, a unique 344-nt duplicated sequence was identified for the first time in the untranslated region of NSP5. This study further reveals the genetic diversity and potential inter-species transmission of porcine rotavirus.
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Affiliation(s)
- Xia Zhou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Xueyan Hou
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Guifa Xiao
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Bo Liu
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Handuo Jia
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
| | - Jie Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Xiaoyun Mi
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Qingyong Guo
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China;
| | - Yurong Wei
- Xinjiang Key Laboratory of Animal Infectious Diseases, Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi 830013, China; (J.W.); (X.M.)
| | - Shao-Lun Zhai
- Guangdong Provincial Key Laboratory of Livestock Disease Prevention, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Guangzhou 510640, China; (X.Z.); (X.H.); (G.X.); (B.L.); (H.J.)
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Wei J, Radcliffe S, Pirrone A, Lu M, Li Y, Cassaday J, Newhard W, Heidecker GJ, Rose II WA, He X, Freed D, Citron M, Espeseth A, Wang D. A Novel Rotavirus Reverse Genetics Platform Supports Flexible Insertion of Exogenous Genes and Enables Rapid Development of a High-Throughput Neutralization Assay. Viruses 2023; 15:2034. [PMID: 37896813 PMCID: PMC10611407 DOI: 10.3390/v15102034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Despite the success of rotavirus vaccines, rotaviruses remain one of the leading causes of diarrheal diseases, resulting in significant childhood morbidity and mortality, especially in low- and middle-income countries. The reverse genetics system enables the manipulation of the rotavirus genome and opens the possibility of using rotavirus as an expression vector for heterologous proteins, such as vaccine antigens and therapeutic payloads. Here, we demonstrate that three positions in rotavirus genome-the C terminus of NSP1, NSP3 and NSP5-can tolerate the insertion of reporter genes. By using rotavirus expressing GFP, we develop a high-throughput neutralization assay and reveal the pre-existing immunity against rotavirus in humans and other animal species. Our work shows the plasticity of the rotavirus genome and establishes a high-throughput assay for interrogating humoral immune responses, benefiting the design of next-generation rotavirus vaccines and the development of rotavirus-based expression platforms.
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Affiliation(s)
- Jiajie Wei
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Scott Radcliffe
- Department of Quantitative Biosciences, Merck & Co., Inc., West Point, PA 19486, USA; (S.R.); (W.A.R.II)
| | - Amanda Pirrone
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Meiqing Lu
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Yuan Li
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Jason Cassaday
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - William Newhard
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Gwendolyn J. Heidecker
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - William A. Rose II
- Department of Quantitative Biosciences, Merck & Co., Inc., West Point, PA 19486, USA; (S.R.); (W.A.R.II)
| | - Xi He
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Daniel Freed
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Michael Citron
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Amy Espeseth
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
| | - Dai Wang
- Department of Infectious Diseases and Vaccines, Merck & Co., Inc., West Point, PA 19486, USA; (A.P.); (M.L.); (Y.L.); (J.C.); (W.N.); (G.J.H.); (X.H.); (D.F.); (M.C.); (A.E.); (D.W.)
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Omatola CA, Olaniran AO. Genetic heterogeneity of group A rotaviruses: a review of the evolutionary dynamics and implication on vaccination. Expert Rev Anti Infect Ther 2022; 20:1587-1602. [PMID: 36285575 DOI: 10.1080/14787210.2022.2139239] [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: 01/12/2023]
Abstract
INTRODUCTION Human rotavirus remains a major etiology of acute gastroenteritis among under 5-year children worldwide despite the availability of oral vaccines. The genetic instability of rotavirus and the ability to form different combinations from the different G- and P-types reshapes the antigenic landscape of emerging strains which often display limited or no antigen identities with the vaccine strain. As evidence also suggests, the selection of the antigenically distinct novel or rare strains and their successful spread in the human population has raised concerns regarding undermining the effectiveness of vaccination programs. AREAS COVERED We review aspects related to current knowledge about genetic and antigenic heterogeneity of rotavirus, the mechanism of genetic diversity and evolution, and the implication of genetic change on vaccination. EXPERT OPINION Genetic changes in the segmented genome of rotavirus can alter the antigenic landscape on the virion capsid and further promote viral fitness in a fully vaccinated population. Against this background, the potential risk of the appearance of new rotavirus strains over the long term would be better predicted by a continued and increased close monitoring of the variants across the globe to identify any change associated with disease dynamics.
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Affiliation(s)
- Cornelius A Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Ademola O Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban, Republic of South Africa
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4
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Papa G, Venditti L, Braga L, Schneider E, Giacca M, Petris G, Burrone OR. CRISPR-Csy4-Mediated Editing of Rotavirus Double-Stranded RNA Genome. Cell Rep 2021; 32:108205. [PMID: 32997981 PMCID: PMC7523552 DOI: 10.1016/j.celrep.2020.108205] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/14/2020] [Accepted: 09/04/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR-nucleases have been widely applied for editing cellular and viral genomes, but nuclease-mediated genome editing of double-stranded RNA (dsRNA) viruses has not yet been reported. Here, by engineering CRISPR-Csy4 nuclease to localize to rotavirus viral factories, we achieve the nuclease-mediated genome editing of rotavirus, an important human and livestock pathogen with a multisegmented dsRNA genome. Rotavirus replication intermediates cleaved by Csy4 is edited through the formation of precise deletions in the targeted genome segments in a single replication cycle. Using CRISPR-Csy4-mediated editing of rotavirus genome, we label the products of rotavirus secondary transcription made by newly assembled viral particles during rotavirus replication, demonstrating that this step largely contributes to the overall production of viral proteins. We anticipate that the nuclease-mediated cleavage of dsRNA virus genomes will promote an advanced level of understanding of viral replication and host-pathogen interactions, also offering opportunities to develop therapeutics.
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Affiliation(s)
- Guido Papa
- Molecular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.
| | - Luca Venditti
- Molecular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Luca Braga
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy; British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King's College London, London, UK
| | - Edoardo Schneider
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy; British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King's College London, London, UK
| | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy; British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine & Sciences, King's College London, London, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Oscar R Burrone
- Molecular Immunology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy.
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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6
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Abstract
Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS IRD University of Montpellier), Centre National de la Recherche Scientifique (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| | - Mark P Zwart
- Netherlands Institute of Ecology (NIOO-KNAW), Postbus 50, 6700 AB, Wageningen, The Netherlands
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Borodavka A, Desselberger U, Patton JT. Genome packaging in multi-segmented dsRNA viruses: distinct mechanisms with similar outcomes. Curr Opin Virol 2018; 33:106-112. [PMID: 30145433 PMCID: PMC6289821 DOI: 10.1016/j.coviro.2018.08.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/20/2022]
Abstract
Segmented double-stranded (ds)RNA viruses share remarkable similarities in their replication strategy and capsid structure. During virus replication, positive-sense single-stranded (+)RNAs are packaged into procapsids, where they serve as templates for dsRNA synthesis, forming progeny particles containing a complete equimolar set of genome segments. How the +RNAs are recognized and stoichiometrically packaged remains uncertain. Whereas bacteriophages of the Cystoviridae family rely on specific RNA-protein interactions to select appropriate +RNAs for packaging, viruses of the Reoviridae instead rely on specific inter-molecular interactions between +RNAs that guide multi-segmented genome assembly. While these families use distinct mechanisms to direct +RNA packaging, both yield progeny particles with a complete set of genomic dsRNAs.
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Affiliation(s)
- Alexander Borodavka
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ulrich Desselberger
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John T Patton
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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Zafari E, Soleimanjahi H, Mohammadi A, Teimoori A, Mahravani H. Molecular and biological characterization of the human-bovine rotavirus-based reassortant rotavirus. Microb Pathog 2018; 121:65-69. [PMID: 29753872 DOI: 10.1016/j.micpath.2018.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022]
Abstract
Rotaviruses (RV) are the leading cause of acute infantile gastroenteritis, associated with elevated mortality in low-income countries. Morbidity and mortality, length and rates of hospitalization due to RV gastroenteritis are dropping. Improving the quality of newborns life is an ongoing challenge for health-care providers. In this study, homemade reassortant human-bovine rotavirus was developed and biological activity and molecular characterization of candidate vaccine were evaluated for the vaccine stability. Virus titration and purification of reassortant rotavirus strains were evaluated by plaque assays, electropherotyping. The genetic stability after first, third and sixth passage was by sequencing. Due to WHO recommendation, developingment of national capacity for vaccine production in appropriate quantities and at affordable prices is the cornerstone of developing global vaccination policies. Such studies are critical to producing national vaccines and modeling herd protection.
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Affiliation(s)
- Ehsan Zafari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ashraf Mohammadi
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Ali Teimoori
- Department of Virology, Ahwaz Joundishpor University of Medical Sciences, Ahvaz, IR Iran
| | - Homayon Mahravani
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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Rotavirus genotypes in children with gastroenteritis in Erzurum: first detection of G12P[6] and G12P[8] genotypes in Turkey. GASTROENTEROLOGY REVIEW 2016; 12:122-127. [PMID: 28702101 PMCID: PMC5497125 DOI: 10.5114/pg.2016.59423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/24/2015] [Indexed: 02/06/2023]
Abstract
Introduction Rotavirus is one of the leading pathogens which cause acute gastroenteritis in children and is responsible for a substantial proportion of childhood deaths worldwide. Aim To determine the group A rotavirus (RVA) prevalence and genotypes of circulating RVA strains in 0–5-year-old children with complaints of vomiting and diarrhoea in Eastern Anatolia in Turkey. Material and methods RNA extracted from stool specimens of 329 children aged 0–5 years with acute diarrhoea was subjected to reverse transcription polymerase reaction (RT-PCR) and multiplex-nested PCR. The genotypes were identified based on the expected size of the amplicon, which was amplified with a genotype-specific primer. Results Out of 329 stool samples analyzed, 109 (33.1%) were positive for RVA. G1P[8] was the dominant genotype combination (42.2%), followed by G9P[8] (21.1%) and G12P[6] (11.0%). Mixed infections were identified in 5 cases: G3,9 in 2 cases, G1,9 in 1 case, P[4,8] in 1 case, and P[6,8] in 1 case. The P genotype could not be typed in two patients. Conclusions In the study, we detected six different rotavirus G genotypes, 3 different P genotypes, 11 different G-P combinations and 5 different mixed genotypes combinations. G1, G9, G12 and P[8] were found to be the predominant genotypes. G12P[6] and G12P[8] genotypes, showing an increase as new rotavirus genotypes in the world, are reported for the first time for our regions. We determined the dominant genotypes, mixed genotypes and unconventional genotypes of rotavirus in our region.
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Abstract
Rotavirus, a member of the family Reoviridae, was identified as the leading etiological agent of severe gastroenteritis in infants and young children in 1973. The rotavirus genome is composed of 11 gene segments of double-stranded (ds)RNA. During the last 40 years, a large amount of basic research on rotavirus structure, genome, antigen, replication, pathogenesis, epidemiology, immune responses, and evolution has been accumulated. This article reviews the fundamental aspects of rotavirology including recent important achievements in research.
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11
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Boyce M, McCrae MA, Boyce P, Kim JT. Inter-segment complementarity in orbiviruses: a driver for co-ordinated genome packaging in the Reoviridae? J Gen Virol 2016; 97:1145-1157. [PMID: 26763979 DOI: 10.1099/jgv.0.000400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The process by which eukaryotic viruses with segmented genomes select a complete set of genome segments for packaging into progeny virus particles is not understood. In this study a model based on the association of genome segments through specific RNA-RNA interactions driven by base pairing was formalized and tested in the Orbivirus genus of the Reoviridae family. A strategy combining screening of the genomic sequences for inter-segment complementarity with direct functional testing of inter-segment RNA-RNA interactions using reverse genetics is described in the type species of the Orbivirus genus, Bluetongue virus (BTV). Two examples, involving four of the ten BTV genomic segments, of specific inter-segment interaction motifs whose maintenance is essential for the generation of infectious virus, were identified. Equivalent inter-segment complementarities were found between the identified regions of the orthologous genome segments of all orbiviruses, including phylogenetically distant species. Specific interaction of the participating RNA segments was confirmed in vitro using electrophoretic mobility shift assays, with the interactions inhibited using oligonucleotides complementary to the interaction motif of one of the interacting partners, and also through mutagenesis of the motifs. In each example, the base pairing rather than the absolute sequence was critical to the formation of a functional inter-segment interaction, with mutations only being tolerated in rescued virus if compensating changes were made in the interacting partner to restore uninterrupted base pairing. The absolute sequence of the complementarity motifs varied between species, indicating that this newly identified phenomenon may contribute to the observed lack of reassortment between Orbivirus species.
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Affiliation(s)
- Mark Boyce
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK
| | | | - Paul Boyce
- Mott MacDonald, Mott MacDonald House, 8-10 Sydenham Road, Croydon, CR0 2EE
| | - Jan T Kim
- The Pirbright Institute, Pirbright, Woking GU24 0NF, UK
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12
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Boyce M, McCrae MA. Rapid mapping of functional cis-acting RNA elements by recovery of virus from a degenerate RNA population: application to genome segment 10 of bluetongue virus. J Gen Virol 2015; 96:3072-3082. [PMID: 26248463 DOI: 10.1099/jgv.0.000259] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The regulatory elements which control the processes of virus replication and gene expression in the Orbivirus genus are uncharacterized in terms of both their locations within genome segments and their specific functions. The reverse genetics system for the type species, Bluetongue virus, has been used in combination with RNA secondary structure prediction to identify and map the positions of cis-acting regions within genome segment 10. Through the simultaneous introduction of variability at multiple nucleotide positions in the rescue RNA population, the functional contribution of these positions was used to map regions containing cis-acting elements essential for virus viability. Nucleotides that were individually lethal when varied mapped within a region of predicted secondary structure involving base pairing between the 5' and 3' ends of the transcript. An extended region of predicted perfect base pairing located within the 3' untranslated region of the genome segment was also found to be required for virus viability. In contrast to the identification of individually lethal mutations, gross alteration of the composition of this predicted stem region was possible, providing the base-pairing potential between the two strands was maintained, identifying a structural feature predicted to be conserved throughout the Orbivirus genus. The approach of identifying cis-acting sequences through sequencing the recovered virus following the rescue of a degenerate RNA population is broadly applicable to viruses where reverse genetics is available.
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Affiliation(s)
- M Boyce
- The Pirbright Institute, Woking GU24 0NF, UK
| | - M A McCrae
- The Pirbright Institute, Woking GU24 0NF, UK
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Duponchel S, Troupin C, Vu LT, Schnuriger A, Trugnan G, Garbarg-Chenon A. Transfection of exogenous rotavirus rearranged RNA segments in cells infected with a WT rotavirus results in subsequent gene rearrangements. J Gen Virol 2014; 95:2089-2098. [PMID: 24906979 DOI: 10.1099/vir.0.065573-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Group A rotaviruses, members of the family Reoviridae, are a major cause of infantile acute gastroenteritis. The rotavirus genome consists of 11 dsRNA segments. In some cases, an RNA segment is replaced by a rearranged RNA segment, which is derived from its standard counterpart by partial sequence duplication. It has been shown that some rearranged segments are preferentially encapsidated into viral progenies after serial passages in cell culture. Based on this characteristic, a reverse genetics system was used previously to introduce exogenous segment 7 rearrangements into an infectious rotavirus. This study extends this reverse genetics system to RNA segments 5 and 11. Transfection of exogenous rotavirus rearranged RNA segment 5 or 11 into cells infected with a WT helper rotavirus (bovine strain RF) resulted in subsequent gene rearrangements in the viral progeny. Whilst recombinant viruses were rescued with an exogenous rearranged segment 11, the exogenous segment was modified by a secondary rearrangement. The occurrence of spontaneous rearrangements of WT or exogenous segments is a major hindrance to the use of this reverse genetics approach.
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Affiliation(s)
- Sarah Duponchel
- ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Cécile Troupin
- ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Lan Trang Vu
- ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Aurélie Schnuriger
- Laboratoire de Virologie, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France.,ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Germain Trugnan
- ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
| | - Antoine Garbarg-Chenon
- Laboratoire de Virologie, Hôpital Armand Trousseau, Assistance Publique - Hôpitaux de Paris, Paris, France.,ERL U1157/UMR 7203, Institut National de la Santé et de la Recherche Médicale, Paris, France.,Micro-Organismes, Molécules Bioactives et Physiopathologie Intestinale, Université Pierre et Marie Curie, Paris 6, Paris, France
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Engineering recombinant reoviruses with tandem repeats and a tetravirus 2A-like element for exogenous polypeptide expression. Proc Natl Acad Sci U S A 2013; 110:E1867-76. [PMID: 23630248 DOI: 10.1073/pnas.1220107110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We tested a strategy for engineering recombinant mammalian reoviruses (rMRVs) to express exogenous polypeptides. One important feature is that these rMRVs are designed to propagate autonomously and can therefore be tested in animals as potential vaccine vectors. The strategy has been applied so far to three of the 10 MRV genome segments: S3, M1, and L1. To engineer the modified segments, a 5' or 3' region of the essential, long ORF in each was duplicated, and then exogenous sequences were inserted between the repeats. The inner repeat and exogenous insert were positioned in frame with the native protein-encoding sequences but were separated from them by an in-frame "2A-like" sequence element that specifies a cotranslational "stop/continue" event releasing the exogenous polypeptide from the essential MRV protein. This design preserves a terminal region of the MRV genome segment with essential activities in RNA packaging, assortment, replication, transcription, and/or translation and alters the encoded MRV protein to a limited degree. Recovery of rMRVs with longer inserts was made more efficient by wobble-mutagenizing both the inner repeat and the exogenous insert, which possibly helped via respective reductions in homologous recombination and RNA structure. Immunogenicity of a 300-aa portion of the simian immunodeficiency virus Gag protein expressed in mice by an L1-modified rMRV was confirmed by detection of Gag-specific T-cell responses. The engineering strategy was further used for mapping the minimal 5'-terminal region essential to MRV genome segment S3.
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15
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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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Genetics and reverse genetics of rotavirus. Curr Opin Virol 2012; 2:399-407. [PMID: 22749758 DOI: 10.1016/j.coviro.2012.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 06/08/2012] [Accepted: 06/08/2012] [Indexed: 11/23/2022]
Abstract
Rotavirus is a member of the family Reoviridae, which have genomes consisting of 10-12 double-stranded RNA segments. The functions of proteins encoded by each segment of the rotavirus genome have been studied extensively by several methods including reassortants, temperature-sensitive mutants, isolates with rearranged RNA segments, RNAi analysis, and other procedures. However, as found for most RNA viruses, the technique of reverse genetics is required for precise genotype/phenotype correlation, for the analysis of the role of specific mutation in replication process and pathogenesis, and for the development of vectors and vaccines. In 2006, we presented the first description of a reverse genetics system for rotavirus, although a helper virus and a selection system are required. Since then, two other approaches have been reported for rotavirus reverse genetics, both requiring the presence of a helper virus. A tractable, helper virus-free reverse genetics system for rotavirus has not been developed so far, in contrast to the recent developments of plasmid only-based reverse genetics systems for other members of the Reoviridae.
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Trask SD, Boehme KW, Dermody TS, Patton JT. Comparative analysis of Reoviridae reverse genetics methods. Methods 2012; 59:199-206. [PMID: 22687622 DOI: 10.1016/j.ymeth.2012.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/16/2012] [Accepted: 05/31/2012] [Indexed: 01/08/2023] Open
Abstract
Effective methods to engineer the segmented, double-stranded RNA genomes of Reoviridae viruses have only recently been developed. Mammalian orthoreoviruses (MRV) and bluetongue virus (BTV) can be recovered from entirely recombinant reagents, significantly improving the capacity to study the replication, pathogenesis, and transmission of these viruses. Conversely, rotaviruses (RVs), which are the major etiological agent of severe gastroenteritis in infants and children, have thus far only been modified using single-segment replacement methods. Reoviridae reverse genetics techniques universally rely on site-specific initiation of transcription by T7 RNA polymerase to generate the authentic 5' end of recombinant RNA segments, but they vary in how the RNAs are introduced into cells: recombinant BTV is recovered by transfection of in vitro transcribed RNAs, whereas recombinant MRV and RV RNAs are transcribed intracellularly from transfected plasmid cDNAs. Additionally, several parameters have been identified in each system that are essential for recombinant virus recovery. Generating recombinant BTV requires the use of 5' capped RNAs and is enhanced by multiple rounds of RNA transfection, suggesting that translation of viral proteins is likely the rate-limiting step. For RV, the efficiency of recovery is almost entirely dependent on the strength of the selection mechanism used to isolate the single-segment recombinant RV from the unmodified helper virus. The reverse genetics methods for BTV and RV are presented and compared to the previously described MRV methods. Analysis and comparison of each method suggest several key lines of research that might lead to a reverse genetics system for RV, analogous to those used for MRV and BTV.
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Affiliation(s)
- Shane D Trask
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 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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