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Hickson SE, Hyde JL. RNA structures within Venezuelan equine encephalitis virus E1 alter macrophage replication fitness and contribute to viral emergence. bioRxiv 2024:2024.04.09.588743. [PMID: 38645187 PMCID: PMC11030350 DOI: 10.1101/2024.04.09.588743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Venezuelan equine encephalitis virus (VEEV) is a mosquito-borne +ssRNA virus belonging to the Togaviridae . VEEV is found throughout Central and South America and is responsible for periodic epidemic/epizootic outbreaks of febrile and encephalitic disease in equines and humans. Endemic/enzootic VEEV is transmitted between Culex mosquitoes and sylvatic rodents, whereas epidemic/epizootic VEEV is transmitted between mosquitoes and equids, which serve as amplification hosts during outbreaks. Epizootic VEEV emergence has been shown to arise from mutation of enzootic VEEV strains. Specifically, epizootic VEEV has been shown to acquire amino acid mutations in the E2 viral glycoprotein that facilitate viral entry and equine amplification. However, the abundance of synonymous mutations which accumulate across the epizootic VEEV genome suggests that other viral determinants such as RNA secondary structure may also play a role in VEEV emergence. In this study we identify novel RNA structures in the E1 gene which specifically alter replication fitness of epizootic VEEV in macrophages but not other cell types. We show that SNPs are conserved within epizootic lineages and that RNA structures are conserved across different lineages. We also identified several novel RNA-binding proteins that are necessary for altered macrophage replication. These results suggest that emergence of VEEV in nature requires multiple mutations across the viral genome, some of which alter cell-type specific replication fitness in an RNA structure-dependent manner. AUTHOR SUMMARY Understanding how viral pathogens emerge is critical for ongoing surveillance and outbreak preparedness. However, our understanding of the molecular mechanisms that drive viral emergence are still not completely understood. Emergence of the mosquito-borne virus Venezuelan equine encephalitis virus (VEEV) is known to require mutations in the viral attachment protein (E2), which drive viremia and transmission. We have observed that emergent strains (epizootic VEEV) also accumulate many silent mutations, suggesting that other determinants independent of protein sequence also contributes to emergence. In this study we identify novel RNA secondary structures associated with epizootic VEEV that alters viral replication in a cell-type dependent manner. We show that these RNA structures are conserved across epizootic viruses and identify host proteins that specifically bind these RNAs. These findings imply that viral emergence requires multiple mutations, a number of which likely alter viral structure in a manner that benefits viral replication and transmission.
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Choi R, Zhou M, Shek R, Wilson JW, Tillery L, Craig JK, Salukhe IA, Hickson SE, Kumar N, James RM, Buchko GW, Wu R, Huff S, Nguyen TT, Hurst BL, Cherry S, Barrett LK, Hyde JL, Van Voorhis WC. High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV-2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity. PLoS One 2021; 16:e0250019. [PMID: 33886614 PMCID: PMC8062000 DOI: 10.1371/journal.pone.0250019] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 μM range in vitro. Furthermore, Exebryl-1, a ß-amyloid anti-aggregation molecule for Alzheimer's therapy, was shown to have antiviral activity between 10 to 66 μM, in Vero 76, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.
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Affiliation(s)
- Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Roger Shek
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jesse W. Wilson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Logan Tillery
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Justin K. Craig
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Indraneel A. Salukhe
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Sarah E. Hickson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Neeraj Kumar
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Rhema M. James
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
| | - Garry W. Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), Richland, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- School of Molecular Bioscience, Washington State University, Pullman, WA, United States of America
| | - Ruilian Wu
- Bioenergy and Biome Sciences, Los Alamos National Laboratory (LANL), Los Alamos, NM, United States of America
| | - Sydney Huff
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
| | - Tu-Trinh Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, United States of America
| | - Brett L. Hurst
- Institute for Antiviral Research, Utah State University, Logan, UT, United States of America
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Lynn K. Barrett
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
| | - Jennifer L. Hyde
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Wesley C. Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington School of Medicine, Seattle, WA, United States of America
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, United States of America
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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Hickson SE, Margineantu D, Hockenbery DM, Simon JA, Geballe AP. Inhibition of vaccinia virus replication by nitazoxanide. Virology 2018; 518:398-405. [PMID: 29625403 DOI: 10.1016/j.virol.2018.03.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/27/2022]
Abstract
Nitazoxanide (NTZ) is an FDA-approved anti-protozoal drug that inhibits several bacteria and viruses as well. However, its effect on poxviruses is unknown. Therefore, we investigated the impact of NTZ on vaccinia virus (VACV). We found that NTZ inhibits VACV production with an EC50 of ~2 μM, a potency comparable to that reported for several other viruses. The inhibitory block occurs early during the viral life cycle, prior to viral DNA replication. The mechanism of viral inhibition is likely not due to activation of intracellular innate immune pathways, such as protein kinase R (PKR) or interferon signaling, contrary to what has been suggested to mediate the effects of NTZ against some other viruses. Rather, our finding that addition of exogenous palmitate partially rescues VACV production from the inhibitory effect of NTZ suggests that NTZ impedes adaptations in cellular metabolism that are needed for efficient completion of the VACV replication cycle.
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Affiliation(s)
- Sarah E Hickson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States; Department of Microbiology, University of Washington, Seattle, WA 98115, United States
| | - Daciana Margineantu
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States
| | - David M Hockenbery
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States; Department of Medicine, University of Washington, Seattle, WA 98115, United States
| | - Julian A Simon
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States
| | - Adam P Geballe
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States; Department of Microbiology, University of Washington, Seattle, WA 98115, United States; Department of Medicine, University of Washington, Seattle, WA 98115, United States.
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