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Brillet K, Janczuk-Richter M, Poon A, Laukart-Bradley J, Ennifar E, Lebars I. Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein. Biochimie 2024; 222:87-100. [PMID: 38408720 DOI: 10.1016/j.biochi.2024.02.005] [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: 11/09/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
The Dengue virus (DENV) is the most significant arthropod-borne viral pathogen in humans with 400 million infections annually. DENV comprises four distinct serotypes (DENV-1 to -4) which complicates vaccine development. Any of the four serotypes can cause clinical illness but with distinctive infection dynamics. Variations in sequences identified within the four genomes induce structural differences in crucial RNA motifs that were suggested to be correlated to the degree of pathogenicity among DENV-1 to -4. In particular, the RNA Stem-loop A (SLA) at the 5'-end of the genome, acts as a key regulator of the viral replication cycle by interacting with the viral NS5 polymerase to initiate the minus-strand viral RNA synthesis and later to methylate and cap the synthesized RNA. The molecular details of this interaction remain not fully described. Here, we report the solution secondary structures of SLA from DENV-1 to -4. Our results highlight that the four SLA exhibit structural and dynamic differences. Secondly, to determine whether SLA RNA contains serotype-specific determinants for the recognition by the viral NS5 protein, we investigated interactions between SLA from DENV -1 to -4 and DENV2 NS5 using combined biophysical approaches. Our results show that NS5 from DENV2 is able to bind SLA from other serotypes, but that other viral or host factors may be necessary to stabilize the complex and promote the catalytically active state of the NS5. By contrast, we show that a serotype-specific binding is driven by specific interactions involving conformational changes within the SLA RNA.
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Affiliation(s)
- Karl Brillet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000, Strasbourg, France
| | | | - Amanda Poon
- Creoptix AG (a Malvern Panalytical Brand), CH-8820, Wädenswil, Switzerland
| | | | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Isabelle Lebars
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000, Strasbourg, France.
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2
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Hasan ME, Samir A, Khalil MM, Shafaa MW. Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus. J Genet Eng Biotechnol 2024; 22:100336. [PMID: 38494248 PMCID: PMC10860876 DOI: 10.1016/j.jgeb.2023.100336] [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: 03/19/2024]
Abstract
BACKGROUND The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure-function/evolution links to both previously known and recently discovered protein structures.
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Affiliation(s)
- Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
| | - Aya Samir
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Magdy M Khalil
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt; School of Biotechnology, Badr University in Cairo, Egypt
| | - Medhat W Shafaa
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
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3
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Abram QH, Landry BN, Wang AB, Kothe RF, Hauch HC, Sagan SM. The myriad roles of RNA structure in the flavivirus life cycle. RNA Biol 2024; 21:14-30. [PMID: 38797925 PMCID: PMC11135854 DOI: 10.1080/15476286.2024.2357857] [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] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
As positive-sense RNA viruses, the genomes of flaviviruses serve as the template for all stages of the viral life cycle, including translation, replication, and infectious particle production. Yet, they encode just 10 proteins, suggesting that the structure and dynamics of the viral RNA itself helps shepherd the viral genome through these stages. Herein, we highlight advances in our understanding of flavivirus RNA structural elements through the lens of their impact on the viral life cycle. We highlight how RNA structures impact translation, the switch from translation to replication, negative- and positive-strand RNA synthesis, and virion assembly. Consequently, we describe three major themes regarding the roles of RNA structure in flavivirus infections: 1) providing a layer of specificity; 2) increasing the functional capacity; and 3) providing a mechanism to support genome compaction. While the interactions described herein are specific to flaviviruses, these themes appear to extend more broadly across RNA viruses.
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Affiliation(s)
- Quinn H. Abram
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Breanna N. Landry
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Alex B. Wang
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ronja F. Kothe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Hannah C.H. Hauch
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
| | - Selena M. Sagan
- Department of Biochemistry, McGill University, Montreal, QC, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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4
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Scott S, Li Y, Bermek O, Griffith JD, Lemon SM, Choi K. Binding of microRNA-122 to the hepatitis C virus 5' untranslated region modifies interactions with poly(C) binding protein 2 and the NS5B viral polymerase. Nucleic Acids Res 2023; 51:12397-12413. [PMID: 37941151 PMCID: PMC10711565 DOI: 10.1093/nar/gkad1000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Hepatitis C virus (HCV) requires two cellular factors, microRNA-122 (miR-122) and poly(C) binding protein 2 (PCBP2), for optimal replication. These host factors compete for binding to the 5' end of the single-stranded RNA genome to regulate the viral replication cycle. To understand how they interact with the RNA, we measured binding affinities of both factors for an RNA probe representing the 5' 45 nucleotides of the HCV genome (HCV45). Isothermal titration calorimetry revealed two, unequal miR-122 binding sites in HCV45, high-affinity (S1) and low-affinity (S2), differing roughly 100-fold in binding affinity. PCBP2 binds a site overlapping S2 with affinity similar to miR-122 binding to S2. PCBP2 circularizes the genome by also binding to the 3' UTR, bridging the 5' and 3' ends of the genome. By competing with PCBP2 for binding at S2, miR-122 disrupts PCBP2-mediated genome circularization. We show that the viral RNA-dependent RNA polymerase, NS5B, also binds to HCV45, and that the binding affinity of NS5B is increased in the presence of miR-122, suggesting miR-122 promotes recruitment of the polymerase. We propose that competition between miR-122 and PCBP2 for HCV45 functions as a translation-to-replication switch, determining whether the RNA genome templates protein synthesis or RNA replication.
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Affiliation(s)
- Seth Scott
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - You Li
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Oya Bermek
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Stanley M Lemon
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA
| | - Kyung H Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
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Zhou P, Ma B, Gao Y, Xu Y, Li Z, Jin H, Luo R. Epidemiology, genetic diversity, and evolutionary dynamics of Tembusu virus. Arch Virol 2023; 168:262. [PMID: 37773423 DOI: 10.1007/s00705-023-05885-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/02/2023] [Indexed: 10/01/2023]
Abstract
Tembusu virus (TMUV) is an emerging pathogenic flavivirus associated with acute egg-drop and fatal encephalitis in domestic waterfowl. Since its initial identification in mosquitoes in 1955, TMUV has been confirmed to infect ducks, pigeons, sparrows, geese, and chickens, posing a significant threat to the poultry industry. Here, we sequenced two DTMUV strains isolated in 2019 and systematically investigated the possible origin, genetic relationships, evolutionary dynamics, and transmission patterns of TMUV based on complete virus genome sequences in the public database. We found that TMUV can be divided into four major clusters: TMUV, cluster 1, cluster 2, and cluster 3. Interestingly, we found that cluster 2.2 (within cluster 2) is the most commonly involved in interspecies transmission events, and subcluster 2.1.2 (within cluster 2.1) is currently the most prevalent cluster circulating in Asia. Notably, we also identified three positively selected sites in the E and NS1 proteins, which may be involved in virus replication, immune evasion, and host adaptation. Finally, phylogeographic analysis revealed that cluster dispersal originated in Southeast Asia and that short-distance transmission events have occurred frequently. Altogether, these data provide novel insights into the evolution and dispersal of TMUV, facilitating the development of rapid diagnostics, vaccines, and therapeutics against TMUV infection.
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Affiliation(s)
- Peng Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Bin Ma
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yuan Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Yumin Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Zhuofei Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, No.1 Shizishan Road, Wuhan, 430070, Hubei, China.
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, Hubei, China.
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Li D, Lu HT, Ding YZ, Wang HJ, Ye JL, Qin CF, Liu ZY. Specialized cis-Acting RNA Elements Balance Genome Cyclization to Ensure Efficient Replication of Yellow Fever Virus. J Virol 2023; 97:e0194922. [PMID: 37017533 PMCID: PMC10134800 DOI: 10.1128/jvi.01949-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/13/2023] [Indexed: 04/06/2023] Open
Abstract
Genome cyclization is essential for viral RNA (vRNA) replication of the vertebrate-infecting flaviviruses, and yet its regulatory mechanisms are not fully understood. Yellow fever virus (YFV) is a notorious pathogenic flavivirus. Here, we demonstrated that a group of cis-acting RNA elements in YFV balance genome cyclization to govern efficient vRNA replication. It was shown that the downstream of the 5'-cyclization sequence hairpin (DCS-HP) is conserved in the YFV clade and is important for efficient YFV propagation. By using two different replicon systems, we found that the function of the DCS-HP is determined primarily by its secondary structure and, to a lesser extent, by its base-pair composition. By combining in vitro RNA binding and chemical probing assays, we found that the DCS-HP orchestrates the balance of genome cyclization through two different mechanisms, as follows: the DCS-HP assists the correct folding of the 5' end in a linear vRNA to promote genome cyclization, and it also limits the overstabilization of the circular form through a potential crowding effect, which is influenced by the size and shape of the DCS-HP structure. We also provided evidence that an A-rich sequence downstream of the DCS-HP enhances vRNA replication and contributes to the regulation of genome cyclization. Interestingly, diversified regulatory mechanisms of genome cyclization, involving both the downstream of the 5'-cyclization sequence (CS) and the upstream of the 3'-CS elements, were identified among different subgroups of the mosquito-borne flaviviruses. In summary, our work highlighted how YFV precisely controls the balance of genome cyclization to ensure viral replication. IMPORTANCE Yellow fever virus (YFV), the prototype of the Flavivirus genus, can cause devastating yellow fever disease. Although it is preventable by vaccination, there are still tens of thousands of yellow fever cases per year, and no approved antiviral medicine is available. However, the understandings about the regulatory mechanisms of YFV replication are obscure. In this study, by a combination of bioinformatics, reverse genetics, and biochemical approaches, it was shown that the downstream of the 5'-cyclization sequence hairpin (DCS-HP) promotes efficient YFV replication by modulating the conformational balance of viral RNA. Interestingly, we found specialized combinations for the downstream of the 5'-cyclization sequence (CS) and upstream of the 3'-CS elements in different groups of the mosquito-borne flaviviruses. Moreover, possible evolutionary relationships among the various downstream of the 5'-CS elements were implied. This work highlighted the complexity of RNA-based regulatory mechanisms in the flaviviruses and will facilitate the design of RNA structure-targeted antiviral therapies.
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Affiliation(s)
- Dan Li
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hai-Tao Lu
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yu-Zhen Ding
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Hong-Jiang Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
- The Chinese People’s Liberation Army Strategic Support Force Characteristic Medical Center, Beijing, China
| | - Jing-Long Ye
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Zhong-Yu Liu
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
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Structure-Based Regulatory Role for the 5′UTR of RCNMV RNA2. Viruses 2023; 15:v15030722. [PMID: 36992432 PMCID: PMC10057905 DOI: 10.3390/v15030722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Red clover necrotic mosaic virus (RCNMV) is a segmented positive-strand RNA virus consisting of RNA1 and RNA2. Previous studies demonstrated that efficient translation of RCNMV RNA2 requires de novo synthesis of RNA2 during infections, suggesting that RNA2 replication is required for its translation. We explored a potential mechanism underlying the regulation of replication-associated translation of RNA2 by examining RNA elements in its 5′ untranslated region (5′UTR). Structural analysis of the 5′UTR suggested that it can form two mutually exclusive configurations: a more thermodynamically stable conformation, termed the 5′-basal stem structure (5′BS), in which 5′-terminal sequences are base paired, and an alternative conformation, where the 5′-end segment is single stranded. Functional mutational analysis of the 5′UTR structure indicated that (i) 43S ribosomal subunits enter at the very 5′-end of RNA2; (ii) the alternative conformation, containing unpaired 5′-terminal nucleotides, mediates efficient translation; (iii) the 5′BS conformation, with a paired 5′-end segment, supresses translation; and (iv) the 5′BS conformation confers stability to RNA2 from 5′-to-3′ exoribonuclease Xrn1. Based on our results, we suggest that during infections, newly synthesized RNA2s transiently adopt the alternative conformation to allow for efficient translation, then refold into the 5′BS conformation, which supresses translation and promotes efficient RNA2 replication. The potential advantages of this proposed 5′UTR-based regulatory mechanism for coordinating RNA2 translation and replication are discussed.
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8
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Identification of West Nile virus RNA-dependent RNA polymerase non-nucleoside inhibitors by real-time high throughput fluorescence screening. Antiviral Res 2023; 212:105568. [PMID: 36842536 DOI: 10.1016/j.antiviral.2023.105568] [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: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 02/28/2023]
Abstract
West Nile virus (WNV) is a re-emergent mosquito-borne RNA virus that causes major outbreaks of encephalitis around the world. However, there is no therapeutic treatment to struggle against WNV, and the current treatment relies on alleviating symptoms. Therefore, due to the threat virus poses to animal and human health, there is an urgent need to come up with fast strategies to identify and assess effective antiviral compounds. A relevant target when developing drugs against RNA viruses is the viral RNA-dependent RNA polymerase (RdRp), responsible for the replication of the viral genome within a host cell. RdRps are key therapeutic targets based on their specificity for RNA and their essential role in the propagation of the infection. We have developed a fluorescence-based method to measure WNV RdRp activity in a fast and reliable real-time way. Interestingly, rilpivirine has shown in our assay inhibition of the WNV RdRp activity with an IC50 value of 3.3 μM and its antiviral activity was confirmed in cell cultures. Furthermore, this method has been extended to build up a high-throughput screening platform to identify WNV polymerase inhibitors. By screening a small chemical library, novel RdRp inhibitors 1-4 have been identified. When their antiviral activity was tested against WNV in cell culture, 4 exhibited an EC50 value of 2.5 μM and a selective index of 12.3. Thus, rilpivirine shows up as an interesting candidate for repurposing against flavivirus. Moreover, the here reported method allows the rapid identification of new WNV RdRp inhibitors.
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Bulstrode H, Girdler GC, Gracia T, Aivazidis A, Moutsopoulos I, Young AMH, Hancock J, He X, Ridley K, Xu Z, Stockley JH, Finlay J, Hallou C, Fajardo T, Fountain DM, van Dongen S, Joannides A, Morris R, Mair R, Watts C, Santarius T, Price SJ, Hutchinson PJA, Hodson EJ, Pollard SM, Mohorianu I, Barker RA, Sweeney TR, Bayraktar O, Gergely F, Rowitch DH. Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells. Neuron 2022; 110:3936-3951.e10. [PMID: 36174572 PMCID: PMC7615581 DOI: 10.1016/j.neuron.2022.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 02/02/2023]
Abstract
Zika virus (ZIKV) can infect human developing brain (HDB) progenitors resulting in epidemic microcephaly, whereas analogous cellular tropism offers treatment potential for the adult brain cancer, glioblastoma (GBM). We compared productive ZIKV infection in HDB and GBM primary tissue explants that both contain SOX2+ neural progenitors. Strikingly, although the HDB proved uniformly vulnerable to ZIKV infection, GBM was more refractory, and this correlated with an innate immune expression signature. Indeed, GBM-derived CD11b+ microglia/macrophages were necessary and sufficient to protect progenitors against ZIKV infection in a non-cell autonomous manner. Using SOX2+ GBM cell lines, we found that CD11b+-conditioned medium containing type 1 interferon beta (IFNβ) promoted progenitor resistance to ZIKV, whereas inhibition of JAK1/2 signaling restored productive infection. Additionally, CD11b+ conditioned medium, and IFNβ treatment rendered HDB progenitor lines and explants refractory to ZIKV. These findings provide insight into neuroprotection for HDB progenitors as well as enhanced GBM oncolytic therapies.
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Affiliation(s)
- Harry Bulstrode
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Gemma C Girdler
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tannia Gracia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Ilias Moutsopoulos
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adam M H Young
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John Hancock
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaoling He
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Katherine Ridley
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Zhaoyang Xu
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John H Stockley
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John Finlay
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Clement Hallou
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Teodoro Fajardo
- Department of Virology, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Virology, Royal London Hospital, Barts Health NHS Trust, London E1 2ES, UK
| | | | | | - Alexis Joannides
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Robert Morris
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Richard Mair
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK
| | - Thomas Santarius
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stephen J Price
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Peter J A Hutchinson
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Emma J Hodson
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Irina Mohorianu
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Roger A Barker
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Trevor R Sweeney
- Department of Virology, University of Cambridge, Cambridge CB2 0QQ, UK; The Pirbright Institute, Guildford, Surrey GU24 0NF, UK
| | | | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - David H Rowitch
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK.
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The RNA polymerase of cytoplasmically replicating Zika virus binds with chromatin DNA in nuclei and regulates host gene transcription. Proc Natl Acad Sci U S A 2022; 119:e2205013119. [PMID: 36442102 PMCID: PMC9894162 DOI: 10.1073/pnas.2205013119] [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: 11/29/2022] Open
Abstract
Zika virus (ZIKV) targets the neural progenitor cells (NPCs) in brain during intrauterine infections and consequently causes severe neurological disorders, such as microcephaly in neonates. Although replicating in the cytoplasm, ZIKV dysregulates the expression of thousands of host genes, yet the detailed mechanism remains elusive. Herein, we report that ZIKV encodes a unique DNA-binding protein to regulate host gene transcription in the nucleus. We found that ZIKV NS5, the viral RNA polymerase, associates tightly with host chromatin DNA through its methyltransferase domain and this interaction could be specifically blocked by GTP. Further study showed that expression of ZIKV NS5 in human NPCs markedly suppressed the transcription of its target genes, especially the genes involved in neurogenesis. Mechanistically, ZIKV NS5 binds onto the gene body of its target genes and then blocks their transcriptional elongation. The utero electroporation in pregnant mice showed that NS5 expression significantly disrupts the neurogenesis by reducing the number of Sox2- and Tbr2-positive cells in the fetal cortex. Together, our findings demonstrate a molecular clue linking to the abnormal neurodevelopment caused by ZIKV infection and also provide intriguing insights into the interaction between the host cell and the pathogenic RNA virus, where the cytoplasmic RNA virus encodes a DNA-binding protein to control the transcription of host cell in the nuclei.
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11
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Yang C, Xie W, Zhang H, Xie W, Tian T, Qin Z. Recent two-year advances in anti-dengue small-molecule inhibitors. Eur J Med Chem 2022; 243:114753. [PMID: 36167010 DOI: 10.1016/j.ejmech.2022.114753] [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: 07/31/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/04/2022]
Abstract
Dengue is an acute tropical infectious disease transmitted by mosquitoes, which has posed a major challenge to global public health. Unfortunately, there is a lack of clinically proven dengue-specific drugs for its prevention and treatment. As the pathogenesis of dengue has not been fully elucidated, the development of specific drugs is seriously hindered. This article briefly describes the pathogenesis of dengue fever, the molecular characteristics, and epidemiology of dengue virus, and focuses on the potential small-molecule inhibitors of dengue virus, including on-target and multi-targeted inhibitors, which have been reported in the past two years.
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Affiliation(s)
- Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macao University of Science and Technology, Macao, 999078, China
| | - Wansheng Xie
- Hainan Center for Drug and Medical Device Evaluation and Service, Hainan Provincial Drug Administration, Haikou, Hainan, 570206, China
| | - Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China
| | - Wenjian Xie
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, PR China
| | - Tiantian Tian
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China.
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, 519087, China.
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12
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Ding P, Summers MF. Sequestering the 5′‐cap for viral RNA packaging. Bioessays 2022; 44:e2200104. [PMID: 36101513 DOI: 10.1002/bies.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/11/2022]
Abstract
Many viruses evolved mechanisms for capping the 5'-ends of their plus-strand RNAs as a means of hijacking the eukaryotic messenger RNA (mRNA) splicing/translation machinery. Although capping is critical for replication, the RNAs of these viruses have other essential functions including their requirement to be packaged as either genomes or pre-genomes into progeny viruses. Recent studies indicate that human immunodeficiency virus type-1 (HIV-1) RNAs are segregated between splicing/translation and packaging functions by a mechanism that involves structural sequestration of the 5'-cap. Here, we examined studies reported for other viruses and retrotransposons that require both selective packaging of their RNAs and 5'-RNA capping for host-mediated translation. Our findings suggest that viruses and retrotransposons have evolved multiple mechanisms to control 5'-cap accessibility, consistent with the hypothesis that removal or sequestration of the 5' cap enables packageable RNAs to avoid capture by the cellular RNA processing and translation machinery.
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Affiliation(s)
- Pengfei Ding
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
| | - Michael F. Summers
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County Baltimore Maryland USA
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13
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Bonnet E, van Jaarsveldt D, Burt FJ. Rapid reverse transcriptase recombinase polymerase amplification assay for flaviviruses using non-infectious in vitro transcribed RNA as positive controls. J Virol Methods 2021; 299:114351. [PMID: 34748816 DOI: 10.1016/j.jviromet.2021.114351] [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: 08/11/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/26/2022]
Abstract
West Nile virus (WNV) and Wesselsbron virus (WSLV) are mosquito-borne viruses belonging to the Flavivirus genus, family Flaviviridae and cause outbreaks in southern Africa after heavy rain. Isothermal assays have been proposed for application in field situations as well as low resource settings and hence we developed a reverse-transcriptase recombinase polymerase amplification (RT-RPA) to detect WNV and WSLV known to occur in South Africa, causing sporadic outbreaks usually associated with good rainfall favouring mosquito breeding. Infectious virus can only be handled within a biosafety level (BSL) 3 facility, hence we opted to validate the assay with transcribed RNA. Specific RT-RPA primers and probes were designed for detection of WNV and WSLV and products detected using a rapid lateral flow device. The assay was performed in 30 min and detected 1.9 × 10¹ copies of WNV and 3.5 × 10° copies WSLV using noninfectious transcribed RNA controls. In addition, the assay was not inhibited by the presence of mosquito extracts in spiked samples. Mismatches between the WNV and WSLV probes and other flaviviruses will likely prevent cross reactivity. The sensitivity, low RPA incubation temperature and rapid processing time makes assay systems based on RPA technology ideally suited for fieldable diagnostics.
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Affiliation(s)
- Elise Bonnet
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Danelle van Jaarsveldt
- Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Felicity Jane Burt
- Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa; Division of Virology, National Health Laboratory Service, Universitas, Bloemfontein, South Africa.
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14
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Blahove MR, Carter JR. Flavivirus Persistence in Wildlife Populations. Viruses 2021; 13:v13102099. [PMID: 34696529 PMCID: PMC8541186 DOI: 10.3390/v13102099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
A substantial number of humans are at risk for infection by vector-borne flaviviruses, resulting in considerable morbidity and mortality worldwide. These viruses also infect wildlife at a considerable rate, persistently cycling between ticks/mosquitoes and small mammals and reptiles and non-human primates and humans. Substantially increasing evidence of viral persistence in wildlife continues to be reported. In addition to in humans, viral persistence has been shown to establish in mammalian, reptile, arachnid, and mosquito systems, as well as insect cell lines. Although a considerable amount of research has centered on the potential roles of defective virus particles, autophagy and/or apoptosis-induced evasion of the immune response, and the precise mechanism of these features in flavivirus persistence have yet to be elucidated. In this review, we present findings that aid in understanding how vector-borne flavivirus persistence is established in wildlife. Research studies to be discussed include determining the critical roles universal flavivirus non-structural proteins played in flaviviral persistence, the advancement of animal models of viral persistence, and studying host factors that allow vector-borne flavivirus replication without destructive effects on infected cells. These findings underscore the viral–host relationships in wildlife animals and could be used to elucidate the underlying mechanisms responsible for the establishment of viral persistence in these animals.
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15
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5'-Cap sequestration is an essential determinant of HIV-1 genome packaging. Proc Natl Acad Sci U S A 2021; 118:2112475118. [PMID: 34493679 PMCID: PMC8449379 DOI: 10.1073/pnas.2112475118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
HIV-1 selectively packages two copies of its 5'-capped RNA genome (gRNA) during virus assembly, a process mediated by the nucleocapsid (NC) domain of the viral Gag polyprotein and encapsidation signals located within the dimeric 5' leader of the viral RNA. Although residues within the leader that promote packaging have been identified, the determinants of authentic packaging fidelity and efficiency remain unknown. Here, we show that a previously characterized 159-nt region of the leader that possesses all elements required for RNA dimerization, high-affinity NC binding, and packaging in a noncompetitive RNA packaging assay (ΨCES) is unexpectedly poorly packaged when assayed in competition with the intact 5' leader. ΨCES lacks a 5'-tandem hairpin element that sequesters the 5' cap, suggesting that cap sequestration may be important for packaging. Consistent with this hypothesis, mutations within the intact leader that expose the cap without disrupting RNA structure or NC binding abrogated RNA packaging, and genetic addition of a 5' ribozyme to ΨCES to enable cotranscriptional shedding of the 5' cap promoted ΨCES-mediated RNA packaging to wild-type levels. Additional mutations that either block dimerization or eliminate subsets of NC binding sites substantially attenuated competitive packaging. Our studies indicate that packaging is achieved by a bipartite mechanism that requires both sequestration of the 5' cap and exposure of NC binding sites that reside fully within the ΨCES region of the dimeric leader. We speculate that cap sequestration prevents irreversible capture by the cellular RNA processing and translation machinery, a mechanism likely employed by other viruses that package 5'-capped RNA genomes.
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16
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Samanta B. Structural evolution of SLA promoter in mosquito-borne flaviviruses: A sequence-structure based phylogenetic framework. Virology 2021; 562:110-120. [PMID: 34311294 DOI: 10.1016/j.virol.2021.07.007] [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: 03/12/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 11/18/2022]
Abstract
All the flaviviruses have a Y-shaped stem-loop secondary structure known as the SLA element, and the structural features of this element are crucial to initiating the infection cycle. The present study particularly investigated how flaviviruses retained the common core SLA element secondary structure during the species evolution by selecting mosquito-borne flaviviruses (MBFVs) as a case study. The detailed search of nucleotide substitutions in species-wise consensus SLA secondary structure models suggested that the compensatory and hemi-compensatory base changes in the helices are crucial to preserving the common core secondary structure. In contrast to the coding region-based phylogeny, the SLA sequence-structure-based phylogenetic tree revealed an intriguing evolutionary relationship among MBFVs. Overall, this paper demonstrated for the first time the efficacy of RNA secondary structures as a phylogenetic marker to study the RNA virus evolution.
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Affiliation(s)
- Brajogopal Samanta
- Department of Microbiology and FST, GITAM Institute of Science, GITAM (Deemed to be University), Rushikonda, Visakhapatnam, 530045, Andhra Pradesh, India.
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17
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C. Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados. Parasit Vectors 2021; 14:343. [PMID: 34187544 PMCID: PMC8244189 DOI: 10.1186/s13071-021-04840-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years before it was identified by the World Health Organization in 2015. Metagenomic detection assays have the potential to detect emerging pathogens without prior knowledge of their genomic nucleic acid sequence. Yet their applicability as vector surveillance tools has been widely limited by the complexity of DNA populations from field-collected mosquito preparations. The aim of this study was to investigate local vector biology and characterize metagenomic arbovirus diversity in Aedes mosquitoes during the ongoing 2015/2016 ZIKV epidemic. Methods We performed a short-term vector screening study on the island of Barbados during the ongoing 2015/2016 ZIKV epidemic, where we sampled local Aedes mosquitoes. We reanalyzed mosquito viral microbiome data derived from standard Illumina MiSeq sequencing to detect arbovirus sequences. Additionally, we employed deep sequencing techniques (Illumina HiSeq) and designed a novel bait capture enrichment assay to increase sequencing efficiency for arbovirus sequences from complex DNA samples. Results We found that Aedes aegypti seemed to be the most likely vector of ZIKV, although it prevailed at a low density during the observed time period. The number of detected viruses increased with sequencing depth. Arbovirus sequence enrichment of metagenomic DNA preparations allowed the detection of arbovirus sequences of two different ZIKV genotypes, including a novel one. To our knowledge, this is the first report of the S3116W mutation in the NS5 gene region of ZIKV polyprotein. Conclusions The metagenomic arbovirus detection approach presented here may serve as a useful tool for the identification of epidemic-causing arboviruses with the additional benefit of enabling the collection of phylogenetic information on the source. Apart from detecting more than 88 viruses using this approach, we also found evidence of novel ZIKV variants circulating in the local mosquito population during the observed time period. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04840-0.
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Affiliation(s)
- J Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - N Rascovan
- Department of Genomes & Genetics, Institut Pasteur, Paris, France
| | - A Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - I Klymiuk
- Department of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - C Zittra
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - H P Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - T Scantlebury-Manning
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | | | - S Austin
- Department of Biological and Chemical Sciences, University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
| | - R C Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown, Barbados
| | - C Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
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18
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Ramos-Lorente S, Romero-López C, Berzal-Herranz A. Information Encoded by the Flavivirus Genomes beyond the Nucleotide Sequence. Int J Mol Sci 2021; 22:3738. [PMID: 33916729 PMCID: PMC8038387 DOI: 10.3390/ijms22073738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/05/2023] Open
Abstract
The genus Flavivirus comprises numerous, small, single positive-stranded RNA viruses, many of which are important human pathogens. To store all the information required for their successful propagation, flaviviruses use discrete structural genomic RNA elements to code for functional information by the establishment of dynamic networks of long-range RNA-RNA interactions that promote specific folding. These structural elements behave as true cis-acting, non-coding RNAs (ncRNAs) and have essential regulatory roles in the viral cycle. These include the control of the formation of subgenomic RNAs, known as sfRNAs, via the prevention of the complete degradation of the RNA genome. These sfRNAs are important in ensuring viral fitness. This work summarizes our current knowledge of the functions performed by the genome conformations and the role of RNA-RNA interactions in these functions. It also reviews the role of RNA structure in the production of sfRNAs across the genus Flavivirus, and their existence in related viruses.
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Affiliation(s)
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
| | - Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), Av. Conocimiento 17, Armilla, 18016 Granada, Spain;
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Shivaprasad S, Sarnow P. The tale of two flaviviruses: subversion of host pathways by RNA shapes in dengue and hepatitis C viral RNA genomes. Curr Opin Microbiol 2020; 59:79-85. [PMID: 33070015 DOI: 10.1016/j.mib.2020.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 01/24/2023]
Abstract
Pathogenic RNA viruses continue to emerge owing to their rapid evolutionary rates. The family of the Flaviviridae contains enveloped, single-stranded, positive-sense RNA viruses that include mosquito borne viruses such as dengue virus and the blood-borne hepatitis C virus. Upon infection, the genomic viral RNA needs to first compete with a sea of host mRNAs for host ribosomes that synthesize the viral proteins. Then, the positive-sense template needs to be amplified and packaged into newly assembled virions. To accomplish these tasks, the virus subverts several biochemical machineries from the host. The participation of specific structures in the viral RNA mediates specific RNA-RNA and RNA-protein interactions that dictate many viral subversion strategies. In this review, we shall focus on the various mechanisms by which RNA elements in the dengue virus and hepatitis C virus untranslated regions aid the viral infectious cycle and contribute to viral fitness.
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Affiliation(s)
- Shwetha Shivaprasad
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter Sarnow
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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