1
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Godwe C, Vidal N, Muwonga J, Butel C, Serrano L, Edidi S, Ahuka-Mundeke S, Koro Koro F, Etoa X, Tongo M, Peeters M, Ayouba A. Structural Features and Genetic Diversity in Gag Gene of Rare HIV-1 Subtypes from the Democratic Republic of Congo. AIDS Res Hum Retroviruses 2024; 40:181-187. [PMID: 37335033 DOI: 10.1089/aid.2022.0154] [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: 06/21/2023] Open
Abstract
Type-1 HIV (HIV-1) group M (HIV-1M) genetic diversity is highest in the Congo Basin where the epidemic ignited a century ago. HIV-1M has diversified into multiple subtypes, sub-subtypes, and circulating and unique recombinant forms (CRFs/URFs). An unanswered question is why some rare subtypes never reached epidemic levels despite their age. Several studies identified the role of HIV-1M accessory genes nef and vpu in virus adaptation to human hosts and subsequent spread. Other reports also pointed out the pivotal role of gag in transmissibility, virulence, and replication capacity. In this study we characterized the HIV-1 gag gene of 148 samples collected in different localities of the Democratic Republic of the Congo (DRC) between 1997 and 2013. We used nested polymerase chain reaction (PCR) to amplify the whole gag gene. PCR products were sequenced either by Sanger method or by next generation sequencing on Illumina MiSeq or iSeq100 platforms. Generated sequences were used for subsequent analyses using different bioinformatic tools. Phylogenetic analysis of the generated sequences revealed a high genetic diversity with up to 22 different subtypes, sub-subtypes, CRFs. Up to 15% (22/148) URFs were identified, in addition to rare subtypes such as H, J, and K. At least two amino acid motifs present in the gag gene have been shown to modulate HIV-1 replication, budding, and fitness: the P(T/S)AP and the LYPXnL motifs. Structural analysis revealed the presence of P(T/S)AP in all the 148 sequences with the majority (136/148) bearing the PTAP. Three samples presented a duplication of this motif. The LYPXnL motif was identified in 38 of 148 sequences. There was no clear link between the frequency of these motifs and HIV-1M subtypes. In summary, we confirmed a high genetic diversity of HIV-1M in the DRC. We observed the presence of amino acid motifs important for viral replication and budding even in some rare HIV-1 subtypes. Their impact on viral fitness needs be further evaluated by in vitro studies.
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Affiliation(s)
- Célestin Godwe
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Nicole Vidal
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Jérémie Muwonga
- National AIDS Control Program, Kinshasa, Democratic Republic of the Congo
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Laetitia Serrano
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Samuel Edidi
- National AIDS Control Program, Kinshasa, Democratic Republic of the Congo
| | - Steve Ahuka-Mundeke
- Department of Virology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Service de Microbiologie, Département de Biologie Médicale, Cliniques Universitaires de Kinshasa, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Francioli Koro Koro
- Department of Biochemistry, Faculty of Sciences, University of Douala, Douala, Cameroon
| | - Xavier Etoa
- Department of Microbiology, Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marcel Tongo
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
| | - Martine Peeters
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
| | - Ahidjo Ayouba
- Laboratoire de Virologie-Cremer, Institut de Recherches Médicales et d'Études des Plantes Médicinales (IMPM), Yaoundé, Cameroon
- TransVIHMI, Université de Montpellier, IRD, INSERM, Montpellier, France
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2
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Liu J, Mao Y, Li Q, Qiu Z, Li J, Li X, Liang W, Xu M, Li A, Cai X, Wu W, Chen H, Yan R, Li J, Gu W, Li H. Efficient Gene Transfer to Kidney Using a Lentiviral Vector Pseudotyped with Zika Virus Envelope Glycoprotein. Hum Gene Ther 2022; 33:1269-1278. [PMID: 35904396 DOI: 10.1089/hum.2022.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gene therapy's entrance into clinical settings has made it an ever more attractive field of study for various diseases. However, relatively little progress has been made in targeting kidney diseases due to poor gene delivery efficiency in renal cells. The development of novel gene therapy vectors for medical intervention to treat kidney diseases is needed. In this study, we designed and produced a pseudotyped lentiviral vector with envelope glycoproteins of Zika virus (ZIKV), and evaluated its potential use in viral vector entry, neutralization assay, and gene delivery especially in the renal context. The lentiviral vector, simplified as ZIKV-E, is pseudotyped with Env/G-TC representing the transmembrane (TM) and cytoplasmic (CY) domains of Env replaced with the TM and CY domains of the glycoprotein (G) of the vesicular stomatitis virus. In vivo results show that ZIKV-E induced efficient transduction in tubular epithelial cells in mouse kidneys, demonstrating >100-fold higher expression of exogenous green fluorescent protein gene compared with that achieved by vesicular stomatitis virus G (VSV-G) protein pseudotyped lentiviral vector. The results also showed that the vector ZIKV-E transduced cells in a pH-independent manner and the transduction was inhibited by anti-ZIKV Env domain III antibodies. Results also show that ZIKV-E can be used as a surrogate for studies of ZIKV entry mechanisms and neutralization antibody assay. In all, this study successfully demonstrated a novel pseudotyped lentiviral vector ZIKV-E for inducing high transduction efficiency in renal tubular epithelial cells that could serve as a foundation for gene therapy for the treatment of inherited renal diseases in humans.
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Affiliation(s)
- Jun Liu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Institute of Dermatology and Venereology, Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yingying Mao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Qingqing Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China.,Clinical Laboratory, Foshan Women and Children Hospital, Foshan, China
| | - Zhenzhen Qiu
- Guangzhou Bioneeds Biotechnology Co., Ltd, Guangzhou, China
| | - Jingjing Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xiaoxin Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wenhan Liang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Mingyu Xu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Andrew Li
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Xiangsheng Cai
- Center for Medical Experiments, University of Chinese Academy of Science-Shenzhen Hospital, Shenzhen, China; and
| | - Wangsheng Wu
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Huangyao Chen
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Renhe Yan
- Guangzhou Bioneeds Biotechnology Co., Ltd, Guangzhou, China
| | - Jinlong Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Weiwang Gu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Hongwei Li
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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3
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Haji Abdolvahab M, Venselaar H, Fazeli A, Arab SS, Behmanesh M. Point Mutation Approach to Reduce Antigenicity of Interferon Beta. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09938-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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4
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Methods in isolation and characterization of bovine monocytes and macrophages. Methods 2020; 186:22-41. [PMID: 32622986 DOI: 10.1016/j.ymeth.2020.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/28/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
Monocytes and macrophages belong to the mononuclear phagocyte system and play important roles in both physiological and pathological processes. The cells belonging to the monocyte/macrophage system are structurally and functionally heterogeneous. Several subsets of monocytes have been previously identified in mammalian blood, generating different subpopulations of macrophages in tissues. Although their distribution and phenotype are similar to their human counterpart, bovine monocytes and macrophages feature differences in both functions and purification procedures. The specific roles that monocytes and macrophages fulfil in several important diseases of bovine species, including among the others tuberculosis and paratuberculosis, brucellosis or the disease related to peripartum, remain still partially elusive. The purpose of this review is to discuss the current knowledge of bovine monocytes and macrophages. We will describe methods for their purification and characterization of their major functions, including chemotaxis, phagocytosis and killing, oxidative burst, apoptosis and necrosis. An overview of the flow cytometry and morphological procedures, including cytology, histology and immunohistochemistry, that are currently utilized to describe monocyte and macrophage main populations and functions is presented as well.
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5
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Williams GD, Gokhale NS, Snider DL, Horner SM. The mRNA Cap 2'- O-Methyltransferase CMTR1 Regulates the Expression of Certain Interferon-Stimulated Genes. mSphere 2020; 5:e00202-20. [PMID: 32404510 PMCID: PMC7227766 DOI: 10.1128/msphere.00202-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/29/2020] [Indexed: 02/06/2023] Open
Abstract
Type I interferons (IFN) initiate an antiviral state through a signal transduction cascade that leads to the induction of hundreds of IFN-stimulated genes (ISGs) to restrict viral infection. Recently, RNA modifications on both host and viral RNAs have been described as regulators of infection. However, the impact of host mRNA cap modifications on the IFN response and how this regulates viral infection are unknown. Here, we reveal that CMTR1, an ISG that catalyzes 2'-O-methylation of the first transcribed nucleotide in cellular mRNA (Cap 1), promotes the protein expression of specific ISGs that contribute to the antiviral response. Depletion of CMTR1 reduces the IFN-induced protein levels of ISG15, MX1, and IFITM1, without affecting their transcript abundance. However, CMTR1 depletion does not significantly affect the IFN-induced protein or transcript abundance of IFIT1 and IFIT3. Importantly, knockdown of IFIT1, which acts with IFIT3 to inhibit the translation of RNAs lacking Cap 1 2'-O-methylation, restores protein expression of ISG15, MX1, and IFITM1 in cells depleted of CMTR1. Finally, we found that CMTR1 plays a role in restricting RNA virus replication, likely by ensuring the expression of specific antiviral ISGs. Taken together, these data reveal that CMTR1 is required to establish an antiviral state by ensuring the protein expression of a subset of ISGs during the type I IFN response.IMPORTANCE Induction of an efficient type I IFN response is important to control viral infection. We show that the host 2'-O-methyltransferase CMTR1 facilitates the protein expression of ISGs in human cells by preventing IFIT1 from inhibiting the translation of those mRNAs lacking cap 2'-O-methylation. Thus, CMTR1 promotes the IFN-mediated antiviral response.
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Affiliation(s)
- Graham D Williams
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Daltry L Snider
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
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6
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Rius-Rocabert S, Presa JL, Esteban-Rubio S, Ayuso-Sacido A, Nistal-Villan E. A Digital Method to Quantify Type I Interferon. J Interferon Cytokine Res 2019; 39:711-719. [PMID: 31268382 DOI: 10.1089/jir.2019.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interferon (IFN), the first ever-described cytokine, has a potent activity against viruses. Soon since its discovery, quantification of IFN has been an important issue. Most of the traditional methods to measure IFN biological activity rely on indirect methods that quantify dyes retained by IFN-protected cells against a lytic virus, or by techniques that indirectly quantify viral replication by measuring the expression level of viral-encoded reporter proteins such as the green fluorescent protein (GFP). In both cases, the IFN units are determined by the quantification of an effective dose 50, defined as the IFN dose that prevents 50% cell death of 50% reduction of the maximal amount of GFP intensity. In this study we propose the use of an alternative approach to measure IFN activity by calculating the minimal IFN dose 50 as the amount of IFN able to completely protect 50% of the cells from infection measured by the total absence of virus-dependent GFP signal in a cell culture plate. This sensitive approach could be used to easily quantify the Z value to determine IFN bioassay robustness. We believe that this approximation could be interesting to be considered by the IFN community.
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Affiliation(s)
- Sergio Rius-Rocabert
- Microbiology Section, Dpto. CC, Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad CEU San Pablo, CEU Universities, Boadilla del Monte, Madrid, Spain.,CEMBIO (Centre for Metabolomics and Bioanalysis), Facultad de Farmacia, Universidad CEU San Pablo, CEU Universities, Boadilla del Monte, Madrid, Spain.,Instituto de Medicina Molecular Aplicada (IMMA), Universidad CEU San Pablo, Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
| | | | - Susana Esteban-Rubio
- Facultad de Medicina, Universidad CEU San Pablo, CEU Universities, Boadilla del Monte, Madrid, Spain
| | - Angel Ayuso-Sacido
- Facultad de Medicina, Universidad CEU San Pablo, CEU Universities, Boadilla del Monte, Madrid, Spain.,Fundación de Investigación HM Hospitales, HM Hospitales, Madrid, Spain.,Instituto de Investigación Sanitaria HM Hospitales, Madrid, Spain
| | - Estanislao Nistal-Villan
- Microbiology Section, Dpto. CC, Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad CEU San Pablo, CEU Universities, Boadilla del Monte, Madrid, Spain.,Instituto de Medicina Molecular Aplicada (IMMA), Universidad CEU San Pablo, Pablo-CEU, CEU Universities, Boadilla del Monte, Madrid, Spain
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7
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Panda D, Gjinaj E, Bachu M, Squire E, Novatt H, Ozato K, Rabin RL. IRF1 Maintains Optimal Constitutive Expression of Antiviral Genes and Regulates the Early Antiviral Response. Front Immunol 2019; 10:1019. [PMID: 31156620 PMCID: PMC6529937 DOI: 10.3389/fimmu.2019.01019] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
Viral defense at mucosal sites depends on interferons (IFN) and IFN stimulated genes (ISGs), either of which may be constitutively expressed to maintain an “antiviral state” (AVS). However, the mechanisms that govern the AVS are poorly defined. Using a BEAS-2B respiratory epithelial cell line deficient in IRF1, we demonstrate higher susceptibility to infection with vesicular stomatitis virus (VSV) and influenza virus. IRF1-mediated restriction of VSV is IFN-independent, as blockade of types I and III IFNs and JAK-STAT signaling before infection did not affect VSV infection of either parent or IRF1 KO cells. Transcriptome analysis revealed that IRF1 regulates constitutive expression of ~300 genes, including antiviral ISGs: OAS2, BST2, and RNASEL and knockdown of any of these IRF1-dependent genes increased VSV infection. Additionally, IRF1 enhances rapid expression of IFNβ and IFNλ after stimulation with poly I:C and also regulates ISG expression. Mechanistically, IRF1 enhances recruitment of BRD4 to promotor-enhancer regions of ISGs for rapid expression and maintains levels of histone H3K4me1 for optimal constitutive expression. Finally, IRF1 also regulates constitutive expression of TLR2 and TLR3 and promotes signaling through these pattern recognition receptors (PRR). These data reveal multiple roles for IRF1 toward effective anti-viral responses by maintaining IFN-independent constitutive expression of anti-viral ISGs and supporting early IFN-dependent responses to PRR stimulation.
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Affiliation(s)
- Debasis Panda
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Erisa Gjinaj
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Mahesh Bachu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Erica Squire
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Hilary Novatt
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
| | - Keiko Ozato
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Ronald L Rabin
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States
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8
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Torelli F, Zander S, Ellerbrok H, Kochs G, Ulrich RG, Klotz C, Seeber F. Recombinant IFN-γ from the bank vole Myodes glareolus: a novel tool for research on rodent reservoirs of zoonotic pathogens. Sci Rep 2018; 8:2797. [PMID: 29434310 PMCID: PMC5809609 DOI: 10.1038/s41598-018-21143-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/25/2018] [Indexed: 12/28/2022] Open
Abstract
Rodent species like Myodes glareolus and Microtus spp. are natural reservoirs for many zoonotic pathogens causing human diseases and are gaining increasing interest in the field of eco-immunology as candidate animal models. Despite their importance the lack of immunological reagents has hampered research in these animal species. Here we report the recombinant production and functional characterization of IFN-γ, a central mediator of host’s innate and adaptive immune responses, from the bank vole M. glareolus. Soluble dimeric recMgIFN-γ was purified in high yield from Escherichia coli. Its activity on M. glareolus and Microtus arvalis kidney cell lines was assessed by immunofluorescent detection of nuclear translocation and phosphorylation of the transcription factor STAT1. RecMgIFN-γ also induced expression of an IFN-γ-regulated innate immunity gene. Inhibition of vesicular stomatitis virus replication in vole cells upon recMgIFN-γ treatment provided further evidence of its biological activity. Finally, we established a recMgIFN-γ-responsive bank vole reporter cell line that allows the sensitive titration of the cytokine activity via a bioluminescence reporter assay. Taken together, we report valuable tools for future investigations on the immune response against zoonotic pathogens in their natural animal hosts, which might foster the development of novel animal models.
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Affiliation(s)
- Francesca Torelli
- Department of Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institut, Berlin, Germany
| | - Steffen Zander
- Department of Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institut, Berlin, Germany
| | - Heinz Ellerbrok
- Center for Biological Threats and Special Pathogens, Highly Pathogenic Viruses, Robert Koch-Institut, Berlin, Germany
| | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Christian Klotz
- Department of Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institut, Berlin, Germany
| | - Frank Seeber
- Department of Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institut, Berlin, Germany.
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9
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Chen W, Wen Z, Zhang J, Li C, Huang K, Bu Z. Establishing a safe, rapid, convenient and low-cost antiviral assay of interferon bioactivity based on recombinant VSV expressing GFP. J Virol Methods 2018; 252:1-7. [DOI: 10.1016/j.jviromet.2017.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/13/2017] [Accepted: 08/14/2017] [Indexed: 10/19/2022]
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10
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Kim BJ, Cho SW, Jeon YJ, An S, Jo A, Lim JH, Kim DY, Won TB, Han DH, Rhee CS, Kim HJ. Intranasal delivery of Duox2 DNA using cationic polymer can prevent acute influenza A viral infection in vivo lung. Appl Microbiol Biotechnol 2017; 102:105-115. [DOI: 10.1007/s00253-017-8512-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/25/2017] [Accepted: 09/09/2017] [Indexed: 12/14/2022]
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11
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Cook BWM, Ranadheera C, Nikiforuk AM, Cutts TA, Kobasa D, Court DA, Theriault SS. Limited Effects of Type I Interferons on Kyasanur Forest Disease Virus in Cell Culture. PLoS Negl Trop Dis 2016; 10:e0004871. [PMID: 27479197 PMCID: PMC4968803 DOI: 10.1371/journal.pntd.0004871] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/30/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The tick-borne flavivirus, Kyasanur Forest disease virus (KFDV) causes seasonal infections and periodic outbreaks in south-west India. The current vaccine offers poor protection with reported issues of coverage and immunogenicity. Since there are no approved prophylactic therapeutics for KFDV, type I IFN-α/β subtypes were assessed for antiviral potency against KFDV in cell culture. METHODOLOGY/PRINCIPAL FINDINGS The continued passage of KFDV-infected cells with re-administered IFN-α2a treatment did not eliminate KFDV and had little effect on infectious particle production whereas the IFN-sensitive, green fluorescent protein-expressing vesicular stomatitis virus (VSV-GFP) infection was controlled. Further evaluation of the other IFN-α/β subtypes versus KFDV infection indicated that single treatments of either IFN-αWA and IFN-αΚ appeared to be more effective than IFN-α2a at reducing KFDV titres. Concentration-dependent analysis of these IFN-α/β subtypes revealed that regardless of subtype, low concentrations of IFN were able to limit cytopathic effects (CPE), while significantly higher concentrations were needed for inhibition of virion release. Furthermore, expression of the KFDV NS5 in cell culture before IFN addition enabled VSV-GFP to overcome the effects of IFN-α/β signalling, producing a robust infection. CONCLUSIONS/SIGNIFICANCE Treatment of cell culture with IFN does not appear to be suitable for KFDV eradication and the assay used for such studies should be carefully considered. Further, it appears that the NS5 protein is sufficient to permit KFDV to bypass the antiviral properties of IFN. We suggest that other prophylactic therapeutics should be evaluated in place of IFN for treatment of individuals with KFDV disease.
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Affiliation(s)
- Bradley W. M. Cook
- Applied Biosafety Research Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health and National Microbiology Laboratory at the J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada
| | - Charlene Ranadheera
- High Containment Respiratory Viruses Group, Special Pathogens Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Aidan M. Nikiforuk
- Applied Biosafety Research Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health and National Microbiology Laboratory at the J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada
| | - Todd A. Cutts
- Applied Biosafety Research Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health and National Microbiology Laboratory at the J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- High Containment Respiratory Viruses Group, Special Pathogens Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada
| | - Deborah A. Court
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada
| | - Steven S. Theriault
- Applied Biosafety Research Program, National Microbiology Laboratory at the Canadian Science Centre for Human and Animal Health and National Microbiology Laboratory at the J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Microbiology, The University of Manitoba, Winnipeg, Manitoba, Canada
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12
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Voigt EA, Swick A, Yin J. Rapid induction and persistence of paracrine-induced cellular antiviral states arrest viral infection spread in A549 cells. Virology 2016; 496:59-66. [PMID: 27254596 DOI: 10.1016/j.virol.2016.05.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/20/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
Abstract
The virus/host interaction is a complex interplay between pro- and anti-viral factors that ultimately determines the spread or halt of virus infections in tissues. This interplay develops over multiple rounds of infection. The purpose of this study was to determine how cellular-level processes combine to impact the spatial spread of infection. We measured the kinetics of virus replication (VSV), antiviral paracrine signal upregulation and secretion, spatial spread of virus and paracrine antiviral signaling, and inhibition of virus production in antiviral-exposed A549 human lung epithelial cells. We found that initially infected cells released antiviral signals 4-to-7h following production of virus. However, the subsequent rapid dissemination of signal and fast induction of a robust and persistent antiviral state ultimately led to a suppression of infection spread. This work shows how cellular responses to infection and activation of antiviral responses can integrate to ultimately control infection spread across host cell populations.
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Affiliation(s)
- Emily A Voigt
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Adam Swick
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - John Yin
- Systems Biology Theme, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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13
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Van den Hoecke S, Verhelst J, Saelens X. Illumina MiSeq sequencing disfavours a sequence motif in the GFP reporter gene. Sci Rep 2016; 6:26314. [PMID: 27193250 PMCID: PMC4872057 DOI: 10.1038/srep26314] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/03/2016] [Indexed: 01/14/2023] Open
Abstract
Green fluorescent protein (GFP) is one of the most used reporter genes. We have used next-generation sequencing (NGS) to analyse the genetic diversity of a recombinant influenza A virus that expresses GFP and found a remarkable coverage dip in the GFP coding sequence. This coverage dip was present when virus-derived RT-PCR product or the parental plasmid DNA was used as starting material for NGS and regardless of whether Nextera XT transposase or Covaris shearing was used for DNA fragmentation. Therefore, the sequence coverage dip in the GFP coding sequence was not the result of emerging GFP mutant viruses or a bias introduced by Nextera XT fragmentation. Instead, we found that the Illumina MiSeq sequencing method disfavours the 'CCCGCC' motif in the GFP coding sequence.
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Affiliation(s)
- Silvie Van den Hoecke
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Judith Verhelst
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
| | - Xavier Saelens
- Medical Biotechnology Center, VIB, Ghent, B-9052, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9052, Belgium
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14
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Li C, Li H, Chen Y, Chen Y, Wang S, Weng SP, Xu X, He J. Activation of Vago by interferon regulatory factor (IRF) suggests an interferon system-like antiviral mechanism in shrimp. Sci Rep 2015; 5:15078. [PMID: 26459861 PMCID: PMC4602278 DOI: 10.1038/srep15078] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/07/2015] [Indexed: 12/27/2022] Open
Abstract
There is a debate on whether invertebrates possess an antiviral immunity similar to the interferon (IFN) system of vertebrates. The Vago gene from arthropods encodes a viral-activated secreted peptide that restricts virus infection through activating the JAK-STAT pathway and is considered to be a cytokine functionally similar to IFN. In this study, the first crustacean IFN regulatory factor (IRF)-like gene was identified in Pacific white shrimp, Litopenaeus vannamei. The L. vannamei IRF showed similar protein nature to mammalian IRFs and could be activated during virus infection. As a transcriptional regulatory factor, L. vannamei IRF could activate the IFN-stimulated response element (ISRE)-containing promoter to regulate the expression of mammalian type I IFNs and initiate an antiviral state in mammalian cells. More importantly, IRF could bind the 5′-untranslated region of L. vannamei Vago4 gene and activate its transcription, suggesting that shrimp Vago may be induced in a similar manner to that of IFNs and supporting the opinion that Vago might function as an IFN-like molecule in invertebrates. These suggested that shrimp might possess an IRF-Vago-JAK/STAT regulatory axis, which is similar to the IRF-IFN-JAK/STAT axis of vertebrates, indicating that invertebrates might possess an IFN system-like antiviral mechanism.
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Affiliation(s)
- Chaozheng Li
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Haoyang Li
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Yixiao Chen
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Yonggui Chen
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,School of Marine Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Sheng Wang
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Shao-Ping Weng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,Institute of Aquatic Economic Animals and Guangdong Provice Key Laboratory for Aquatic Economic Animals, Sun Yat-sen University, Guangzhou, P.R. China.,School of Marine Sciences, Sun Yat-sen University, Guangzhou, P.R. China.,South China Sea Resource Exploitation and Protection Collaborative Innovation Center (SCS-REPIC), Guangzhou, P.R. China
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15
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Cloning and expression of mink (Neovison vison) interferon-γ gene and development of an antiviral assay. Res Vet Sci 2015; 101:93-8. [PMID: 26267097 DOI: 10.1016/j.rvsc.2015.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 03/18/2015] [Accepted: 06/21/2015] [Indexed: 11/22/2022]
Abstract
Minks (Neovison vison) farming is under a threat of a variety of viral infections with increasingly growing number of breeding in Northeastern and Western China. While interferon is effective in controlling viral infection, IFN among different species rarely share high homology enough to provide cross protective effect on inhibition of virus replication. We cloned, sequenced, phlogenetically analyzed and expressed the miIFN-γ gene in prokaryotic and eukaryotic cells. The anti-vesicular stomatitis virus (VSV) activity of miIFN-γ protein was tested in MDCK cells using in vitro cytopathic inhibition assay. The recombinant miIFN-γ could inhibit VSV replication in MDCK cells, which was confirmed by that pre-incubation of rabbit anti-miIFN-γ antibodies with miIFN-γ abrogated the miIFN-γ protective effect. Our findings implicated that the miIFN-γ gene may be a potential counter measure against viral infection in the mink farming.
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16
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Voigt EA, Yin J. Kinetic Differences and Synergistic Antiviral Effects Between Type I and Type III Interferon Signaling Indicate Pathway Independence. J Interferon Cytokine Res 2015; 35:734-47. [PMID: 25938799 DOI: 10.1089/jir.2015.0008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The spread of acute respiratory viral infections is controlled by type I and III interferon (IFN) signaling. While the mechanisms of type I IFN signaling have been studied in detail, features that distinguish type III IFN signaling remain poorly understood. Type III IFNs play an essential role in limiting infections of intestinal and respiratory epithelial surfaces; however, type III IFNs have been shown to activate similar genes to type I IFNs, raising the question of how these IFNs differ and their signals interact. We measured the kinetics of type I and III IFN activation, functional stability, and downstream antiviral responses on A549 human lung epithelial cells. Similar kinetics were found for transcriptional upregulation and secretion of type I and III IFNs in response to infection by an RNA virus, peaking at 12 h postinfection, and both protein types had similar stabilities with functional half-lives extending beyond 2 days. Both IFNs activated potent cellular antiviral responses; however, responses to type III IFNs were delayed by 2-6 h relative to type I IFN responses. Combined treatments with type I and III IFNs produced enhanced antiviral effects, and quantitative analysis of these data with a Bliss interaction model provides evidence for independence of type I and III IFN downstream signaling pathways. This novel synergistic interaction has therapeutic implications for treatment of respiratory virus infections.
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Affiliation(s)
- Emily A Voigt
- 1 Department of Chemical and Biological Engineering, University of Wisconsin-Madison , Madison, Wisconsin.,2 Systems Biology Theme, Wisconsin Institute for Discovery , Madison, Wisconsin
| | - John Yin
- 1 Department of Chemical and Biological Engineering, University of Wisconsin-Madison , Madison, Wisconsin.,2 Systems Biology Theme, Wisconsin Institute for Discovery , Madison, Wisconsin
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17
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Pesko K, Voigt EA, Swick A, Morley VJ, Timm C, Yin J, Turner PE. Genome rearrangement affects RNA virus adaptability on prostate cancer cells. Front Genet 2015; 6:121. [PMID: 25883601 PMCID: PMC4381649 DOI: 10.3389/fgene.2015.00121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/13/2015] [Indexed: 11/13/2022] Open
Abstract
Gene order is often highly conserved within taxonomic groups, such that organisms with rearranged genomes tend to be less fit than wild type gene orders, and suggesting natural selection favors genome architectures that maximize fitness. But it is unclear whether rearranged genomes hinder adaptability: capacity to evolutionarily improve in a new environment. Negative-sense non-segmented RNA viruses (order Mononegavirales) have specific genome architecture: 3' UTR - core protein genes - envelope protein genes - RNA-dependent RNA-polymerase gene - 5' UTR. To test how genome architecture affects RNA virus evolution, we examined vesicular stomatitis virus (VSV) variants with the nucleocapsid (N) gene moved sequentially downstream in the genome. Because RNA polymerase stuttering in VSV replication causes greater mRNA production in upstream genes, N gene translocation toward the 5' end leads to stepwise decreases in N transcription, viral replication and progeny production, and also impacts the activation of type 1 interferon mediated antiviral responses. We evolved VSV gene-order variants in two prostate cancer cell lines: LNCap cells deficient in innate immune response to viral infection, and PC-3 cells that mount an IFN stimulated anti-viral response to infection. We observed that gene order affects phenotypic adaptability (reproductive growth; viral suppression of immune function), especially on PC-3 cells that strongly select against virus infection. Overall, populations derived from the least-fit ancestor (most-altered N position architecture) adapted fastest, consistent with theory predicting populations with low initial fitness should improve faster in evolutionary time. Also, we observed correlated responses to selection, where viruses improved across both hosts, rather than suffer fitness trade-offs on unselected hosts. Whole genomics revealed multiple mutations in evolved variants, some of which were conserved across selective environments for a given gene order.
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Affiliation(s)
- Kendra Pesko
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
| | - Emily A Voigt
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison Madison, WI, USA
| | - Adam Swick
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison Madison, WI, USA
| | - Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
| | - Collin Timm
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison Madison, WI, USA
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison Madison, WI, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University New Haven, CT, USA
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