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Xu L, Bie M, Li J, Zhou H, Hu T, Carr MJ, Lu L, Shi W. Isolation and characterization of a novel rodent hepevirus in long-tailed dwarf hamsters ( Cricetulus longicaudatus) in China. J Gen Virol 2024; 105. [PMID: 38767609 DOI: 10.1099/jgv.0.001989] [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] [Indexed: 05/22/2024] Open
Abstract
Hepeviruses have been identified in a broad range of animal hosts, including mammals, birds, and fish. In this study, rodents (n=91) from seven different species and ten pikas (Ochotona curzoniae) were collected in Qinghai Province, China. Using transcriptomic sequencing and confirmatory molecular testing, hepeviruses were detected in 27 of 45 (60 %) long-tailed dwarf hamsters (Cricetulus longicaudatus) and were undetected in other rodents and pika. The complete genome sequences from 14 representative strains were subsequently obtained, and phylogenetic analyses suggested that they represent a novel species within the genus Rocahepevirus, which we tentatively designated as Cl-2018QH. The virus was successfully isolated in human hepatoma (Huh-7) and murine fibroblast (17 Cl-1) cell lines, though both exhibited limited replication as assayed by detection of negative-sense RNA intermediates. A129 immunodeficient mice were inoculated with Cl-2018QH and the virus was consistently detected in multiple organs, despite relatively low viral loads. In summary, this study has described a novel rodent hepevirus, which enhances our knowledge of the genetic diversity of rodent hepeviruses and highlights its potential for cross-species transmission.
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Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan 250117, PR China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Mengyu Bie
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan 250117, PR China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Hong Zhou
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, PR China
| | - Michael J Carr
- National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, D04 E1W1, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Weifeng Shi
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
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Unravelling the tripartite interactions among Hepatitis E virus RNA, miR-140 and hnRNP K: Running title: Interactions between HEV-RNA, miR-140 and hnRNP K. J Mol Biol 2023; 435:168050. [PMID: 36933825 DOI: 10.1016/j.jmb.2023.168050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
In the present investigation, we have identified the functional significance of the highly conserved miR-140 binding site on the Hepatitis E Virus (HEV) genome. Multiple sequence alignment of the viral genome sequences along with RNA folding prediction indicated that the putative miR-140 binding site has significant conservation for sequence and secondary RNA structure among HEV genotypes. Site-directed mutagenesis and reporter assays indicated that an intact sequence of the miR-140 binding site is essential for HEV translation. Provision of mutant miR-140 oligos carrying same mutation as on mutant HEV successfully rescued mutant HEV replication. In vitro cell-based assays with modified oligos proved that host factor-miR-140 is a critical requirement for HEV replication. Biotinylated RNA pulldown and RNA immunoprecipitation assays proved that the predicted secondary RNA structure of the miR-140 binding site allows the recruitment of hnRNP K, which is a key protein of the HEV replication complex. We predicted the model from the obtained results that the miR-140 binding site can serve as a platform for recruitment of hnRNP K and other proteins of HEV replication complex only in the presence of miR-140.
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Barnard TR, Wang AB, Sagan SM. A highly sensitive strand-specific multiplex RT-qPCR assay for quantitation of Zika virus replication. J Virol Methods 2022; 307:114556. [PMID: 35654259 DOI: 10.1016/j.jviromet.2022.114556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is widely used to quantify viral RNA genomes for diagnostics and research, yet conventional RT-qPCR protocols are unable to accurately distinguish between the different viral RNA species that exist during infection. Here we show that false-priming and self-priming occur during reverse transcription with several published Zika virus (ZIKV) primer sets. We developed a RT-qPCR assay using tagged primers and thermostable reverse transcriptase, which greatly reduced the occurrence of nonspecific cDNA products. Furthermore, we optimized the assay for use in multiplex qPCR which allows for simultaneous quantitative detection of positive-strand and negative-strand ZIKV RNA along with an internal control from both human and mosquito cells. Importantly, this assay is sensitive enough to study early stages of virus infection in vitro. Strikingly, using this assay, we detected ZIKV negative-strand RNA as early as 3 h post-infection in mammalian cell culture, at a time point prior to the onset of positive-strand RNA synthesis. Overall, the strand-specific RT-qPCR assay developed herein is a valuable tool to quantify ZIKV RNA and to study viral replication dynamics during infection. The application of these findings has the potential to increase accuracy of RNA detection methods for a variety of viral pathogens.
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Affiliation(s)
- Trisha R Barnard
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B Wang
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M Sagan
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada; Department of Biochemistry, McGill University, Montreal, QC, Canada.
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Ravn Warncke S, Rohde Knudsen C. Detection methods targeting the positive- and negative-sense RNA transcripts from plus-stranded RNA viruses. APMIS 2021; 130:284-292. [PMID: 34939239 PMCID: PMC9306919 DOI: 10.1111/apm.13202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/16/2021] [Indexed: 11/27/2022]
Abstract
The largest group of viruses in the Baltimore classification system comprises viruses with a positive-sense, single-stranded RNA genome. Once the viral genome is released into the cytoplasm of a specific host cell following virus entry, it functions directly as a mRNA and the virus-encoded proteins that are essential for genome replication, are produced by the translation apparatus of the host cell. The positive-sense genome is replicated in two stages, initially the positive strand is copied to make a negative-sense RNA, which then functions as the template for transcription of many new positive-sense genomes. Virus infections can be detected at different stages throughout the infection cycle for diagnostic and scientific purposes. Here, the advantages and disadvantages of some of the relevant methods for genome detection will be briefly reviewed with special emphasis on techniques allowing strand-specific RNA detection. Furthermore, tools of the future are considered.
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Affiliation(s)
- Signe Ravn Warncke
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
| | - Charlotte Rohde Knudsen
- Department of Molecular Biology & Genetics, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000, Aarhus C, Denmark
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Sayed IM, Abd Elhameed ZA, Abd El-Kareem DM, Abdel-Malek MAY, Ali ME, Ibrahim MA, Sayed AAR, Khalaf KAB, Abdel-Wahid L, El-Mokhtar MA. Hepatitis E Virus Persistence and/or Replication in the Peripheral Blood Mononuclear Cells of Acute HEV-Infected Patients. Front Microbiol 2021; 12:696680. [PMID: 34335528 PMCID: PMC8322848 DOI: 10.3389/fmicb.2021.696680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) causes about 14 million infections with 300,000 deaths and 5,200 stillbirths worldwide annually. Extrahepatic manifestations are reported with HEV infections, such as renal, neurological, and hematological disorders. Recently, we reported that stool-derived HEV-1 replicates efficiently in human monocytes and macrophages in vitro. However, another study reports the presence of viral RNA but no evidence of replication in the PBMCs of acute hepatitis E (AHE) patients. Therefore, the replication of HEV in PBMCs during AHE infection is not completely understood. METHODS PBMCs were isolated from AHE patients (n = 17) enrolled in Assiut University Hospitals, Egypt. The viral load, positive (+) and negative (-) HEV RNA strands and viral protein were assessed. The gene expression profile of PBMCs from AHE patients was assessed. In addition, the level of cytokines was measured in the plasma of the patients. RESULTS HEV RNA was detected in the PBMCs of AHE patients. The median HEV load in the PBMCs was 1.34 × 103 IU/ml. A negative HEV RNA strand and HEV open reading frame 2 protein were recorded in 4/17 (23.5%) of the PBMCs. Upregulation of inflammatory transcripts and increased plasma cytokines were recorded in the AHE patients compared with healthy individuals with significantly elevated transcripts and plasma cytokines in the AHE with detectable (+) and (-) RNA strands compared with the AHE with the detectable (+) RNA strand only. There was no significant difference in terms of age, sex, and liver function tests between AHE patients with detectable (+) and (-) RNA strands in the PBMCs and AHE patients with the (+) RNA strand only. CONCLUSION Our study shows evidence for in vivo HEV persistence and replication in the PBMCs of AHE patients. The replication of HEV in the PBMCs was associated with an enhanced immune response, which could affect the pathogenesis of HEV.
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Affiliation(s)
- Ibrahim M. Sayed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA, United States
| | | | - Doaa M. Abd El-Kareem
- Department of Clinical Pathology, Faculty of Medicine Assiut University, Assiut, Egypt
| | | | - Mohamed E. Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Maggie A. Ibrahim
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | - Khaled Abo bakr Khalaf
- Department of Tropical Medicine and Gastroenterology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Lobna Abdel-Wahid
- Gastroenterology and Hepatology Unit, Department of Internal Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed A. El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, Sphinx University, Assiut, Egypt
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Ngamdee T, Yin LS, Vongpunsawad S, Poovorawan Y, Surareungchai W, Lertanantawong B. Target Induced-DNA strand displacement reaction using gold nanoparticle labeling for hepatitis E virus detection. Anal Chim Acta 2020; 1134:10-17. [PMID: 33059855 DOI: 10.1016/j.aca.2020.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
DNA strand displacement is an attractive, enzyme-free target hybridization strategy for nano-biosensing. The target DNA induces a strand displacement reaction by replacing the pre-hybridized strand that is labeled with gold nanoparticles (AuNPs). Thus, the amount of displaced-AuNP-labeled strand is proportional to the amount of target DNA in the sample. The use of a magnetogenosensing technique to isolate the target DNA allows for a simple, one-pot detection approach, which minimizes possible carry-over contamination and pipetting errors. We sought a proof-of-concept for this technology in its ability to detect DNA-equivalent of hepatitis E virus (HEV), which causes acute viral hepatitis for which rapid and simple diagnostic methods remain limited. Signal detection was done via visual observation, spectrophotometry, and electrochemistry. The sensor demonstrated good sensitivity with detection limits of 10 pM (visual), 10 pM (spectrophotometry) and 1 fM (electrochemical). This sensor also exhibited high specificity for real target amplicons and could discriminate between perfect and mismatched sequences. Lyophilized biosensor reagents stored at 4 °C, 25 °C, and outdoor ambient temperature, were stable for up to 90, 50, and 40 days, respectively. The integration of magnetic separation and target DNA-induced strand displacement reaction in a dry reagent form makes the sensing platform easy-to-use and suitable for field settings.
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Affiliation(s)
- Tatchanun Ngamdee
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Lee Su Yin
- Faculty of Applied Sciences, AIMST University, Bedong, Kedah, 08100, Malaysia
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Werasak Surareungchai
- Department of Biotechnology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand; Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand
| | - Benchaporn Lertanantawong
- Nanoscience and Nanotechnology Program, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10140, Thailand; Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand.
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A strand-specific real-time quantitative RT-PCR assay for distinguishing the genomic and antigenomic RNAs of Rift Valley fever phlebovirus. J Virol Methods 2019; 272:113701. [PMID: 31315022 DOI: 10.1016/j.jviromet.2019.113701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/13/2019] [Indexed: 11/21/2022]
Abstract
Rift Valley Fever phlebovirus (RVFV), genus Phlebovirus, family Phenuiviridae, order Bunyavirales, has a single-stranded, negative-sense RNA genome, consisting of L, M and S segments. Here, we report the establishment of a strand-specific, quantitative reverse transcription (RT)-PCR assay system that can selectively distinguish between the genomic and antigenomic RNAs of each of the three viral RNA segments produced in RVFV-infected cells. To circumvent the obstacle of primer-independent cDNA synthesis during RT, we used a tagged, strand-specific RT primer, carrying a non-viral 'tag' sequence at the 5' end, which ensured the strand-specificity through the selective amplification of only the tagged cDNA in the real-time PCR assay. We used this assay system to examine the kinetics of intracellular accumulation of genomic and antigenomic viral RNAs in mammalian cells infected with the MP-12 strain of RVFV. The genomic RNA copy numbers, for all three viral RNA segments, were higher than that of their corresponding antigenomic RNAs throughout the time-course of infection, with a notable exception, wherein the M segment genomic and antigenomic RNAs exhibited similar copy numbers at specific times post-infection. Overall, this assay system could be a useful tool to gain an insight into the mechanisms of RNA replication and packaging in RVFV.
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Wang L, Cappelle K, Santos D, Vanden Broeck J, Smagghe G, Swevers L. Short-term persistence precedes pathogenic infection: Infection kinetics of cricket paralysis virus in silkworm-derived Bm5 cells. JOURNAL OF INSECT PHYSIOLOGY 2019; 115:1-11. [PMID: 30905610 DOI: 10.1016/j.jinsphys.2019.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/16/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
Next generation sequencing has revealed the widespread occurrence of persistent virus infections in insects but little is known regarding to what extent persistent infections can affect cellular physiology and how they might contribute to the development of disease. In contrast to the pathogenic infections occurring in Drosophila S2 cells, it was observed that Cricket Paralysis virus (CrPV; Dicistroviridae) causes persistent infections in 9 lepidopteran and 2 coleopteran cell lines. The status of the persistent infection was subsequently investigated in more detail using silkworm-derived Bm5 cells, where the infection eventually becomes pathogenic after 3-4 weeks. The short-term persistence period in Bm5 cells is characterized by low levels of viral replication and virion production as well as by the production of viral siRNAs. However, during this period cellular physiology also becomes altered since the cells become susceptible to infection by the nodavirus Flock House virus (FHV). Pathogenicity and widespread mortality at 4 weeks is preceded by a large increase in virion production and the transcriptional activation of immune-related genes encoding RNAi factors and transcription factors in the Toll, Imd and Jak-STAT pathways. During the infection of Bm5 cells, the infective properties of CrPV are not altered, indicating changes in the physiology of the host cells during the transition from short-term persistence to pathogenicity. The in vitro system of Bm5 cells persistently infected with CrPV can therefore be presented as an easily accessible model to study the nature of persistent virus infections and the processes that trigger the transition to pathogenicity, for instance through the application of different "omics" approaches (transcriptomics, proteomics, metabolomics). The different factors that can cause the transition from persistence to pathogenicity in the Bm5-CrPV infection model are discussed.
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Affiliation(s)
- Luoluo Wang
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Kaat Cappelle
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Dulce Santos
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Leuven, Belgium.
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece.
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Novel Synthesis and Phenotypic Analysis of Mutant Clouds for Hepatitis E Virus Genotype 1. J Virol 2018; 92:JVI.01932-17. [PMID: 29167341 DOI: 10.1128/jvi.01932-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
Many RNA viruses exist as an ensemble of genetically diverse, replicating populations known as a mutant cloud. The genetic diversity (cloud size) and composition of this mutant cloud may influence several important phenotypic features of the virus, including its replication capacity. We applied a straightforward, bacterium-free approach using error-prone PCR coupled with reverse genetics to generate infectious mutant RNA clouds with various levels of genetic diversity from a genotype 1 strain of hepatitis E virus (HEV). Cloning and sequencing of a genomic fragment encompassing 70% of open reading frame 1 (ORF1) or of the full genome from variants in the resultant clouds showed the occurrence of nucleotide mutations at a frequency on the order of 10-3 per nucleotide copied and the existence of marked genetic diversity, with a high normalized Shannon entropy value. The mutant clouds showed transient replication in cell culture, while wild-type HEV did not. Cross-sectional data from these cell cultures supported the existence of differential effects of clouds of various sizes and compositions on phenotypic characteristics, such as the replication level of (+)-RNA progeny, the amounts of double-stranded RNA (a surrogate for the rate of viral replication) and ORF1 protein, and the expression of interferon-stimulated genes. Since mutant cloud size and composition influenced the viral phenotypic properties, a better understanding of this relationship may help to provide further insights into virus evolution and prediction of emerging viral diseases.IMPORTANCE Several biological or practical limitations currently prevent the study of phenotypic behavior of a mutant cloud in vitro We developed a simple and rapid method for synthesizing mutant clouds of hepatitis E virus (HEV), a single-stranded (+)-RNA [ss(+) RNA] virus, with various and controllable levels of genetic diversity, which could then be used in a cell culture system to study the effects of cloud size and composition on viral phenotype. In a cross-sectional analysis, we demonstrated that a particular mutant cloud which had an extremely high genetic diversity had a replication rate exceeding that of wild-type HEV. This method should thus provide a useful model for understanding the phenotypic behavior of ss(+) RNA viruses.
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Alavi M, Karimi N, Safaei M. Application of Various Types of Liposomes in Drug Delivery Systems. Adv Pharm Bull 2017; 7:3-9. [PMID: 28507932 PMCID: PMC5426731 DOI: 10.15171/apb.2017.002] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/17/2017] [Accepted: 02/22/2017] [Indexed: 11/23/2022] Open
Abstract
Liposomes, due to their various forms, require further exploration. These structures can deliver both hydrophilic and hydrophobic drugs for cancer, antibacterial, antifungal, immunomodulation, diagnostics, ophtalmica, vaccines, enzymes and genetic elements. Preparation of liposomes results in different properties for these systems. In addition, based on preparation methods, liposomes types can be unilamellar, multilamellar and giant unilamellar; however, there are many factors and difficulties that affect the development of liposome drug delivery structure. In the present review, we discuss some problems that impact drug delivery by liposomes. In addition, we discuss a new generation of liposomes, which is utilized for decreasing the limitation of the conventional liposomes.
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Affiliation(s)
- Mehran Alavi
- Department of nanobiotecnology, 67149 Baghabrisham, Razi University, Kermanshah, Iran
| | - Naser Karimi
- Department of nanobiotecnology, 67149 Baghabrisham, Razi University, Kermanshah, Iran
| | - Mohsen Safaei
- Department of nanobiotecnology, 67149 Baghabrisham, Razi University, Kermanshah, Iran
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Alcid EA, Tsukiyama T. Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. Nat Struct Mol Biol 2016; 23:450-5. [PMID: 27018804 PMCID: PMC4856548 DOI: 10.1038/nsmb.3192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 02/16/2016] [Indexed: 01/25/2023]
Abstract
Antisense long noncoding RNAs (ASlncRNAs) have been implicated in regulating gene expression in response to physiological cues. However, little is known about the evolutionary dynamics of ASlncRNA and what underlies the evolution of their expression. Here, using budding yeast Saccharomyces spp. and Naumovozyma castellii as models, we show that ASlncRNA repertoires have expanded since the loss of RNA interference (RNAi), in terms of their expression levels, their lengths and their degree of overlap with coding genes. Furthermore, we show that RNAi is inhibitory to ASlncRNA transcriptomes and that increased expression of ASlncRNAs in the presence of RNAi is deleterious to N. castellii, which has retained RNAi. Together, our results suggest that the loss of RNAi had substantial effects on the genome-wide increase in expression of ASlncRNAs during the evolution of budding yeasts.
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Affiliation(s)
- Eric A Alcid
- Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Toshio Tsukiyama
- Divison of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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12
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Chatterjee SN, Devhare PB, Pingle SY, Paingankar MS, Arankalle VA, Lole KS. Hepatitis E virus (HEV)-1 harbouring HEV-4 non-structural protein (ORF1) replicates in transfected porcine kidney cells. J Gen Virol 2016; 97:1829-1840. [PMID: 27072797 DOI: 10.1099/jgv.0.000478] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Hepatitis E virus (HEV) is a causative agent of acute hepatitis and a major public health problem in India. There are four mammalian HEV genotypes worldwide. In India, genotype 1 (HEV-1) is restricted to humans whereas genotype 4 (HEV-4) circulates in pigs. Studies from our laboratory have shown that HEV-4 (swine) virus can establish experimental infection in rhesus monkeys; however, HEV-1 (human) virus cannot infect pigs. Viral and/or cellular factors responsible for this host specificity are not yet known. We developed 12 different genotype 1-4 chimeric full genome clones with pSK-HEV2 as the backbone and by replacing structural (ORF2 and ORF3), non-structural (ORF1) and non-coding regions (NCR) with corresponding segments from the HEV-4 clone. S10-3 (human hepatoma) and PK-15 (pig kidney) cells were transfected with transcripts generated from the above clones to test their replication competence. Transfected cells were monitored for successful virus replication by detecting replicative intermediate RNA and capsid protein (immunofluorescence assay). All the chimeric constructs were able to replicate in S10-3 cells. However, only two chimeric clones, HEV-1 (HEV-4 5'NCR-ORF1) and HEV-1 (HEV-4 ORF1), containing 5'NCR-ORF1 and ORF1 regions from the HEV-4 clone, respectively, were able to replicate in PK-15 cells. We demonstrate for the first time the crucial role of ORF1 polyprotein in crossing the species barrier at the cellular level. These results indicate the importance of interactions between ORF1 protein domains and host cell specific factors during HEV replication and the critical role of cellular factors as post-entry barrier/s in virus establishment.
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Affiliation(s)
- Subhashis N Chatterjee
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
| | - Pradip B Devhare
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
| | - Shweta Y Pingle
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
| | - Mandar S Paingankar
- Molecular Biology Research Laboratory, Department of Zoology Savitribai Phule Pune University, Pune 411007, India
| | - Vidya A Arankalle
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
| | - Kavita S Lole
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune 411021, India
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Identification and characterization of cellular proteins interacting with Hepatitis E virus untranslated regions. Virus Res 2015; 208:98-109. [DOI: 10.1016/j.virusres.2015.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 02/06/2023]
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14
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Carrillo-Tripp J, Bonning BC, Miller WA. Challenges associated with research on RNA viruses of insects. CURRENT OPINION IN INSECT SCIENCE 2015; 8:62-68. [PMID: 32846681 DOI: 10.1016/j.cois.2014.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 11/14/2014] [Indexed: 06/11/2023]
Abstract
Dicistroviridae and Iflaviridae (part of the group formerly identified as picorna-like viruses) are rapidly growing families within the order Picornavirales. Work on these emerging groups of arthropod viruses offers a unique and exciting opportunity for virologist, but this task comes with particular challenges. The lack of cell culture systems and infectious clones has imposed limitations on the advancement of study of these viruses. Here we discuss the goals and challenges regarding the establishment of controlled systems as well as some issues associated with insect RNA virology at the organismal level. These concerns apply to RNA viruses affecting other organisms for which basic research tools are limited. A list of pitfalls associated with RNA virus research along with recommendations is provided.
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Affiliation(s)
- Jimena Carrillo-Tripp
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, United States.
| | - Bryony C Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, United States
| | - W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, United States
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Analysis of helicase domain mutations in the hepatitis E virus derived from patients with fulminant hepatic failure: effects on enzymatic activities and virus replication. Virus Res 2014; 184:103-10. [PMID: 24630891 PMCID: PMC7172619 DOI: 10.1016/j.virusres.2014.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/19/2014] [Accepted: 02/19/2014] [Indexed: 12/30/2022]
Abstract
Effect of fulminant hepatic failure (FHF) associated mutations on helicase activities and virus replication were checked. All the FHF mutants showed comparable unwinding activities with the wild type protein despite the differences in ATPase activities. All the FHF mutant replicons showed marginal decrease in virus replication compared to the wild type replicon suggesting alternate function/s of the helicase protein. Walker A motif and Walker B motif in the helicase domain are indispensable for HEV replication.
Fulminant hepatic failure (FHF) is the severe form of hepatitis E virus infection. Virus sequence analyses from severe cases have shown presence of unique and highly conserved mutations in the helicase domain of genotype 1, 3 and 4 viruses. We evaluated role of two amino acid replacements (L1110F) and (V1120I); found to be frequent in genotype 1 FHF-E viruses from India. Three mutant helicase proteins (two with single point mutations and one with dual mutations) were expressed in Escherichia coli and evaluated for their ATPase and RNA unwinding activities. Both L1110F and V1120I helicase mutants showed marginal decrease in ATPase activity, while L1110F/V1120I dual mutant showed normal ATPase activity. All three mutants proteins showed RNA unwinding activities comparable to wild type protein. Corresponding mutations were made in the helicase domain of HEV RLuc replicon and replication efficiencies were tested in the S10-3 (Huh 7) cells. The mutant replicon V1120I showed lower replication as compared to L1110F and L1110F/V1120I mutants. However, all three replicon mutants showed lower replication efficiencies as compared to the wild type replicon. Walker A and Walker B motif mutant HEV replicons were unable to replicate indicating essential role of the virus encoded helicase domain during HEV replication. FHF-E associated helicase mutations resulted in only marginal decrease in the virus replication suggesting alternate function/s of the helicase protein. Mutations in the helicase domain of FHF-E viruses may be responsible for changing virus or host-virus protein–protein interactions, causing alterations in the host responses, eventually leading to more severe disease manifestations.
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Devhare PB, Chatterjee SN, Arankalle VA, Lole KS. Analysis of antiviral response in human epithelial cells infected with hepatitis E virus. PLoS One 2013; 8:e63793. [PMID: 23671700 PMCID: PMC3650073 DOI: 10.1371/journal.pone.0063793] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Hepatitis E virus (HEV) is a major cause of enterically transmitted acute hepatitis in developing nations and occurs in sporadic and epidemic forms. The disease may become severe with high mortality (20%) among pregnant women. Due to lack of efficient cell culture system and small animal model, early molecular events of HEV infection are not yet known. In the present study, human lung epithelial cells, A549, were infected with HEV to monitor expression levels of genes/proteins in antiviral pathways. Both live and UV inactivated virus elicited robust induction of inflammatory cytokines/chemokines such as IL-6, IL-8, TNF-α, and RANTES within 12 h of infection. Cells exposed to soluble capsid protein showed no induction suggesting the capsid structure and not the protein being detected as the pathogen pattern by cells. A delayed up-regulation of type I interferon genes only by the live virus at 48 h post HEV infection indicated the need of virus replication. However, absence of secreted interferons till 96 h suggested possible involvement of post-transcriptional regulation of type I IFN expression. HEV infected cells showed activation of both NF-κB and IRF3 transcription factors when seen at protein levels; however, reporter gene assays showed predominant expression via NF-κB promoter as compared to IRF3 promoter. Knockdown experiments done using siRNAs showed involvement of MyD88 and TRIF adaptors in generating antiviral response thus indicating role of TLR2, TLR4 and TLR3 in sensing viral molecules. MAVS knockdown surprisingly enhanced only proinflammatory cytokines and not type I IFNs. This suggested that HEV not only down-regulates RIG-I helicase like receptor mediated IFN induction but also employs MAVS in curtailing host inflammatory response. Our findings uncover an early cellular response in HEV infection and associated molecular mechanisms suggesting the potential role of inflammatory response triggered by HEV infection in host immune response and pathogenesis.
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Affiliation(s)
- Pradip B. Devhare
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
| | - Subhashis N. Chatterjee
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
| | - Vidya A. Arankalle
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
| | - Kavita S. Lole
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
- * E-mail:
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