1
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Moore PS, Chang Y. Are There More Human Cancer Viruses Left to Be Found? Annu Rev Virol 2024; 11:239-259. [PMID: 39326883 DOI: 10.1146/annurev-virology-111821-103721] [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: 09/28/2024]
Abstract
Of the thousands of viruses infecting humans, only seven cause cancer in the general population. Tumor sequencing is now a common cancer medicine procedure, and so it seems likely that more human cancer viruses already would have been found if they exist. Here, we review cancer characteristics that can inform a dedicated search for new cancer viruses, focusing on Kaposi sarcoma herpesvirus and Merkel cell polyomavirus as the most recent examples of successful genomic and transcriptomic searches. We emphasize the importance of epidemiology in determining which cancers to examine and describe approaches to virus discovery. Barriers to virus discovery, such as novel genomes and viral suppression of messenger RNA expression, may exist that prevent virus discovery using existing approaches. Optimally virus hunting should be performed in such a way that if no virus is found, the tumor can be reasonably excluded from having an infectious etiology and new information about the biology of the tumor can be found.
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Affiliation(s)
- Patrick S Moore
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; ,
| | - Yuan Chang
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; ,
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2
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Raguette LE, Gunasekera SS, Diaz Ventura RI, Aminov E, Linzer JT, Parwana D, Wu Q, Simmerling C, Nagan MC. Adjusting the Energy Profile for CH-O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations. J Phys Chem B 2024; 128:7921-7933. [PMID: 39110091 DOI: 10.1021/acs.jpcb.4c01910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.
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Affiliation(s)
- Lauren E Raguette
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Sarah S Gunasekera
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Rebeca I Diaz Ventura
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Ethan Aminov
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jason T Linzer
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Diksha Parwana
- Biochemistry & Structural Biology Program, Stony Brook University, Stony Brook, New York 11794, United States
| | - Qin Wu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria C Nagan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
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3
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Allan MF, Aruda J, Plung JS, Grote SL, des Taillades YJM, de Lajarte AA, Bathe M, Rouskin S. Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA. RESEARCH SQUARE 2024:rs.3.rs-4814547. [PMID: 39149495 PMCID: PMC11326378 DOI: 10.21203/rs.3.rs-4814547/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.
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Affiliation(s)
- Matthew F. Allan
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 02139
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 02139
| | - Justin Aruda
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
- Harvard Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA 02115
| | - Jesse S. Plung
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA 02115
| | - Scott L. Grote
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
| | | | - Albéric A. de Lajarte
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 02139
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA 02115
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4
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Allan MF, Aruda J, Plung JS, Grote SL, Martin des Taillades YJ, de Lajarte AA, Bathe M, Rouskin S. Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591762. [PMID: 38746332 PMCID: PMC11092567 DOI: 10.1101/2024.04.29.591762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.
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5
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Morris R, Wang S. Building a pathway to One Health surveillance and response in Asian countries. SCIENCE IN ONE HEALTH 2024; 3:100067. [PMID: 39077383 PMCID: PMC11262298 DOI: 10.1016/j.soh.2024.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/27/2024] [Indexed: 07/31/2024]
Abstract
To detect and respond to emerging diseases more effectively, an integrated surveillance strategy needs to be applied to both human and animal health. Current programs in Asian countries operate separately for the two sectors and are principally concerned with detection of events that represent a short-term disease threat. It is not realistic to either invest only in efforts to detect emerging diseases, or to rely solely on event-based surveillance. A comprehensive strategy is needed, concurrently investigating and managing endemic zoonoses, studying evolving diseases which change their character and importance due to influences such as demographic and climatic change, and enhancing understanding of factors which are likely to influence the emergence of new pathogens. This requires utilisation of additional investigation tools that have become available in recent years but are not yet being used to full effect. As yet there is no fully formed blueprint that can be applied in Asian countries. Hence a three-step pathway is proposed to move towards the goal of comprehensive One Health disease surveillance and response.
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Affiliation(s)
- Roger Morris
- Massey University EpiCentre and EpiSoft International Ltd, 76/100 Titoki Street, Masterton 5810, New Zealand
| | - Shiyong Wang
- Health, Nutrition and Population, World Bank Group, Washington, DC, USA
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6
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Wang Z, Wei P. Shifting the paradigm in RNA virus detection: integrating nucleic acid testing and immunoassays through single-molecule digital ELISA. Front Immunol 2024; 14:1331981. [PMID: 38235132 PMCID: PMC10791976 DOI: 10.3389/fimmu.2023.1331981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
In this review article, we explore the characteristics of RNA viruses and their potential threats to humanity. We also provide a brief overview of the primary contemporary techniques used for the early detection of such viruses. After thoroughly analyzing the strengths and limitations of these methods, we highlight the importance of integrating nucleic acid testing with immunological assays in RNA virus detection. Although notable methodological differences between nucleic acid testing and immune assays pose challenges, the emerging single-molecule immunoassay-digital ELISA may be applied to technically integrate these techniques. We emphasize that the greatest value of digital ELISA is its extensive compatibility, which creates numerous opportunities for real-time, large-scale testing of RNA viruses. Furthermore, we describe the possible developmental trends of digital ELISA in various aspects, such as reaction carriers, identification elements, signal amplification, and data reading, thus revealing the remarkable potential of single-molecule digital ELISA in future RNA virus detection.
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Affiliation(s)
| | - Pei Wei
- Department of Immunology, Zunyi Medical University, Zhuhai, China
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7
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Lu L, Zhang F, Brierley L, Robertson G, Chase-Topping M, Lycett S, Woolhouse M. Temporal Dynamics, Discovery, and Emergence of Human-Transmissible RNA Viruses. Mol Biol Evol 2024; 41:msad272. [PMID: 38241079 PMCID: PMC10797954 DOI: 10.1093/molbev/msad272] [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: 08/21/2023] [Revised: 11/03/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024] Open
Abstract
Transmissibility, the ability to spread within host populations, is a prerequisite for a pathogen to have epidemic or pandemic potential. Here, we estimate the phylogenies of human infectivity and transmissibility using 1,408 genome sequences from 743 distinct RNA virus species/types in 59 genera. By repeating this analysis using data sets censored by virus discovery date, we explore how temporal changes in the known diversity of RNA viruses-especially recent increases in recognized nonhuman viruses-have altered these phylogenies. Over time, we find significant increases in the proportion of RNA virus genera estimated to have a nonhuman-infective ancestral state, in the fraction of distinct human virus lineages that are purely human-transmissible or strictly zoonotic (compared to mixed lineages), and in the number of human viruses with nearest relatives known not to infect humans. Our results are consistent with viruses that are capable of spreading in human populations commonly emerging from a nonhuman reservoir. This is more likely in lineages that already contain human-transmissible viruses but is rare in lineages that contain only strictly zoonotic viruses.
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Affiliation(s)
- Lu Lu
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- National Institute of Health Data Science at Peking University, Beijing, China
| | - Liam Brierley
- Institute of Population Health, University of Liverpool, Liverpool, Unitied Kingdom
| | - Gail Robertson
- Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | | | - Samantha Lycett
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
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8
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Keng CT, Yogarajah T, Lee RCH, Muhammad IBH, Chia BS, Vasandani SR, Lim DS, Guo K, Wong YH, Mok CK, Chu JJH, Chew WL. AAV-CRISPR-Cas13 eliminates human enterovirus and prevents death of infected mice. EBioMedicine 2023; 93:104682. [PMID: 37390772 PMCID: PMC10363442 DOI: 10.1016/j.ebiom.2023.104682] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND RNA viruses account for many human diseases and pandemic events but are often not targetable by traditional therapeutics modalities. Here, we demonstrate that adeno-associated virus (AAV) -delivered CRISPR-Cas13 directly targets and eliminates the positive-strand EV-A71 RNA virus in cells and infected mice. METHODS We developed a Cas13gRNAtor bioinformatics pipeline to design CRISPR guide RNAs (gRNAs) that cleave conserved viral sequences across the virus phylogeny and developed an AAV-CRISPR-Cas13 therapeutics using in vitro viral plaque assay and in vivo EV-A71 lethally-infected mouse model. FINDINGS We show that treatment with a pool of AAV-CRISPR-Cas13-gRNAs designed using the bioinformatics pipeline effectively blocks viral replication and reduces viral titers in cells by >99.99%. We further demonstrate that AAV-CRISPR-Cas13-gRNAs prophylactically and therapeutically inhibited viral replication in infected mouse tissues and prevented death in a lethally challenged EV-A71-infected mouse model. INTERPRETATION Our results show that the bioinformatics pipeline designs efficient CRISPR-Cas13 gRNAs for direct viral RNA targeting to reduce viral loads. Additionally, this new antiviral AAV-CRISPR-Cas13 modality represents an effective direct-acting prophylactic and therapeutic agent against lethal RNA viral infections. FUNDING Agency for Science, Technology and Research (A∗STAR) Assured Research Budget, A∗STAR Central Research Fund UIBR SC18/21-1089UI, A∗STAR Industrial Alignment Fund Pre-Positioning (IAF-PP) grant H17/01/a0/012, MOE Tier 2 2017 (MOE2017-T2-1-078; MOE-T2EP30221-0005), and NUHSRO/2020/050/RO5+5/NUHS-COVID/4.
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Affiliation(s)
- Choong Tat Keng
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Irfan Bin Hajis Muhammad
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Bing Shao Chia
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Suraj Rajan Vasandani
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Daryl Shern Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Ke Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yi Hao Wong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Chee Keng Mok
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Justin Jang Hann Chu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos #06-05, 138673, Singapore; Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore; NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore.
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore.
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9
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Kurhade C, Kang S, Biering SB, Hwang S, Randall G. CAPRIN1 Is Required for Control of Viral Replication Complexes by Interferon Gamma. mBio 2023; 14:e0017223. [PMID: 37052473 PMCID: PMC10294620 DOI: 10.1128/mbio.00172-23] [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: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 04/14/2023] Open
Abstract
Replication complexes (RCs), formed by positive-strand (+) RNA viruses through rearrangements of host endomembranes, protect their replicating RNA from host innate immune defenses. We have shown that two evolutionarily conserved defense systems, autophagy and interferon (IFN), target viral RCs and inhibit viral replication collaboratively. However, the mechanism by which autophagy proteins target viral RCs and the role of IFN-inducible GTPases in the disruption of RCs remains poorly understood. Here, using murine norovirus (MNV) as a model (+) RNA virus, we show that the guanylate binding protein 1 (GBP1) is the human GTPase responsible for inhibiting RCs. Furthermore, we found that ATG16L1 mediates the LC3 targeting of MNV RC by binding to WIPI2B and CAPRIN1, and that IFN gamma-mediated control of MNV replication was dependent on CAPRIN1. Collectively, this study identifies a novel mechanism for the autophagy machinery-mediated recognition and inhibition of viral RCs, a hallmark of (+) RNA virus replication. IMPORTANCE Replication complexes provide a microenvironment important for (+) RNA virus replication and shield it from host immune response. Previously we have shown that interferon gamma (IFNG) disrupts the RC of MNV via evolutionarily conserved autophagy proteins and IFN-inducible GTPases. Elucidating the mechanism of targeting of viral RC by ATG16L1 and IFN-induced GTPase will pave the way for development of therapeutics targeting the viral replication complexes. Here, we have identified GBP1 as the sole GBP targeting viral RC and uncovered the novel role of CAPRIN1 in recruiting ATG16L1 to the viral RC.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Soowon Kang
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Seungmin Hwang
- Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, Illinois, USA
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10
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Poisot T, Ouellet MA, Mollentze N, Farrell MJ, Becker DJ, Brierley L, Albery GF, Gibb RJ, Seifert SN, Carlson CJ. Network embedding unveils the hidden interactions in the mammalian virome. PATTERNS (NEW YORK, N.Y.) 2023; 4:100738. [PMID: 37409053 PMCID: PMC10318366 DOI: 10.1016/j.patter.2023.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 01/19/2023] [Accepted: 03/31/2023] [Indexed: 07/07/2023]
Abstract
Predicting host-virus interactions is fundamentally a network science problem. We develop a method for bipartite network prediction that combines a recommender system (linear filtering) with an imputation algorithm based on low-rank graph embedding. We test this method by applying it to a global database of mammal-virus interactions and thus show that it makes biologically plausible predictions that are robust to data biases. We find that the mammalian virome is under-characterized anywhere in the world. We suggest that future virus discovery efforts could prioritize the Amazon Basin (for its unique coevolutionary assemblages) and sub-Saharan Africa (for its poorly characterized zoonotic reservoirs). Graph embedding of the imputed network improves predictions of human infection from viral genome features, providing a shortlist of priorities for laboratory studies and surveillance. Overall, our study indicates that the global structure of the mammal-virus network contains a large amount of information that is recoverable, and this provides new insights into fundamental biology and disease emergence.
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Affiliation(s)
- Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Marie-Andrée Ouellet
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - Nardus Mollentze
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
- MRC – University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | | | - Rory J. Gibb
- Center for Biodiversity & Environment Research, University College, London, UK
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
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11
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Ratcliff J, Simmonds P. The roles of nucleic acid editing in adaptation of zoonotic viruses to humans. Curr Opin Virol 2023; 60:101326. [PMID: 37031485 PMCID: PMC10155873 DOI: 10.1016/j.coviro.2023.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023]
Abstract
Following spillover, viruses must adapt to new selection pressures exerted by antiviral responses in their new hosts. In mammals, cellular defense mechanisms often include viral nucleic acid editing pathways mediated through protein families apolipoprotein-B mRNA-editing complex (APOBEC) and Adenosine Deaminase Acting on ribonucleic acid (ADAR). APOBECs induce C→U transitions in viral genomes; the APOBEC locus is highly polymorphic with variable numbers of APOBEC3 paralogs and target preferences in humans and other mammals. APOBEC3 paralogs have shaped the evolutionary history of human immunodeficiency virus, with compelling bioinformatic evidence also for its mutagenic impact on monkeypox virus and severe acute respiratory syndrome coronavirus 2. ADAR-1 induces adenose-to-inosine (A→I) substitutions in double-stranded ribonucleic acid (RNA); its role in virus adaptation is less clear, as are epigenetic modifications to viral genomes, such as methylation. Nucleic acid editing restricts evolutionary space in which viruses can explore and may restrict viral-host range.
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Affiliation(s)
- Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
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12
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Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. In vivo secondary structural analysis of Influenza A virus genomic RNA. Cell Mol Life Sci 2023; 80:136. [PMID: 37131079 PMCID: PMC10153785 DOI: 10.1007/s00018-023-04764-1] [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: 10/28/2022] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 05/04/2023]
Abstract
Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.
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Affiliation(s)
- Barbara Mirska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Tomasz Woźniak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland
| | - Dagny Lorent
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
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13
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Kelley EJ, Henson SN, Rahee F, Boyle AS, Engelbrektson AL, Nelson GA, Mead HL, Anderson NL, Razavi M, Yip R, Ladner JT, Scriba TJ, Altin JA. Virome-wide detection of natural infection events and the associated antibody dynamics using longitudinal highly-multiplexed serology. Nat Commun 2023; 14:1783. [PMID: 36997517 PMCID: PMC10062260 DOI: 10.1038/s41467-023-37378-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
Current methods for detecting infections either require a sample collected from an actively infected site, are limited in the number of agents they can query, and/or yield no information on the immune response. Here we present an approach that uses temporally coordinated changes in highly-multiplexed antibody measurements from longitudinal blood samples to monitor infection events at sub-species resolution across the human virome. In a longitudinally-sampled cohort of South African adolescents representing >100 person-years, we identify >650 events across 48 virus species and observe strong epidemic effects, including high-incidence waves of Aichivirus A and the D68 subtype of Enterovirus D earlier than their widespread circulation was appreciated. In separate cohorts of adults who were sampled at higher frequency using self-collected dried blood spots, we show that such events temporally correlate with symptoms and transient inflammatory biomarker elevations, and observe the responding antibodies to persist for periods ranging from ≤1 week to >5 years. Our approach generates a rich view of viral/host dynamics, supporting novel studies in immunology and epidemiology.
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Affiliation(s)
- Erin J Kelley
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Sierra N Henson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Fatima Rahee
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Annalee S Boyle
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Anna L Engelbrektson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Georgia A Nelson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Heather L Mead
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | | | | | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - John A Altin
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA.
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14
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Iuchi H, Kawasaki J, Kubo K, Fukunaga T, Hokao K, Yokoyama G, Ichinose A, Suga K, Hamada M. Bioinformatics approaches for unveiling virus-host interactions. Comput Struct Biotechnol J 2023; 21:1774-1784. [PMID: 36874163 PMCID: PMC9969756 DOI: 10.1016/j.csbj.2023.02.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has elucidated major limitations in the capacity of medical and research institutions to appropriately manage emerging infectious diseases. We can improve our understanding of infectious diseases by unveiling virus-host interactions through host range prediction and protein-protein interaction prediction. Although many algorithms have been developed to predict virus-host interactions, numerous issues remain to be solved, and the entire network remains veiled. In this review, we comprehensively surveyed algorithms used to predict virus-host interactions. We also discuss the current challenges, such as dataset biases toward highly pathogenic viruses, and the potential solutions. The complete prediction of virus-host interactions remains difficult; however, bioinformatics can contribute to progress in research on infectious diseases and human health.
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Affiliation(s)
- Hitoshi Iuchi
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan
| | - Junna Kawasaki
- Faculty of Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kento Kubo
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Nishi Waseda, Shinjuku-ku, Tokyo 169-0051, Japan
| | - Koki Hokao
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Gentaro Yokoyama
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Akiko Ichinose
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kanta Suga
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Michiaki Hamada
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.,Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
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15
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Borghei YS, Samadikhah HR, Hosseinkhani S. Exploitation of N-Gene of SARS-CoV-2 to Develop a New Rapid Assay by ASOs@AuNPs. Anal Chem 2022; 94:13616-13622. [PMID: 36130119 PMCID: PMC9514053 DOI: 10.1021/acs.analchem.2c03544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
A naked-eye (equipment-free), label-free (cost-effective), and RNA extraction-free (to speed up) method for SARS-CoV-2 (as a case study of RNA viruses) detection is developed. Here, the DNA is being used as a template for in situ formation of anisotropic gold nanoparticles (AuNPs) without any chemical modification or DNA labeling. In this study, synthesized AuNPs for the direct detection of N-gene (nucleocapsid phosphoprotein) of SARS-CoV-2 are exploited. To this aim, antisense oligonucleotides (ASOs) with an extra poly guanine tail (G12) were designed. Thus, in the presence of its viral target RNA gene and ASOs@AuNPs-RNA hybridization, there was a red shift in its localized surface plasmon resonance (LSPR), and the intensity of the LSPR peak at 690 nm of throat swab samples was compared to the threshold cycle (Ct) of a reverse-transcriptase real-time polymerase chain reaction (RT-qPCR) (as a gold standard). Results suggested that the plasmonic biosensor can detect a very low amount of SARS-CoV-2 with a detection limit close to RT-qPCR. Simplicity of the new conjugation method with hybridization and annealing without amplification and denaturation steps enabled it to perform in a microfluidic paper-based analytical device.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Institute
for Convergent Science and Technology, Sharif
University of Technology, Tehran 11155-8639, Iran
| | - Hamid Reza Samadikhah
- Department
of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran 19585-466, Iran
| | - Saman Hosseinkhani
- Department
of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
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16
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A Novel Approach of Antiviral Drugs Targeting Viral Genomes. Microorganisms 2022; 10:microorganisms10081552. [PMID: 36013970 PMCID: PMC9414836 DOI: 10.3390/microorganisms10081552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Outbreaks of viral diseases, which cause morbidity and mortality in animals and humans, are increasing annually worldwide. Vaccines, antiviral drugs, and antibody therapeutics are the most effective tools for combating viral infection. The ongoing coronavirus disease 2019 pandemic, in particular, raises an urgent need for the development of rapid and broad-spectrum therapeutics. Current antiviral drugs and antiviral antibodies, which are mostly specific at protein levels, have encountered difficulties because the rapid evolution of mutant viral strains resulted in drug resistance. Therefore, degrading viral genomes is considered a novel approach for developing antiviral drugs. The current article highlights all potent candidates that exhibit antiviral activity by digesting viral genomes such as RNases, RNA interference, interferon-stimulated genes 20, and CRISPR/Cas systems. Besides that, we introduce a potential single-chain variable fragment (scFv) that presents antiviral activity against various DNA and RNA viruses due to its unique nucleic acid hydrolyzing characteristic, promoting it as a promising candidate for broad-spectrum antiviral therapeutics.
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17
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Qin B, Craven GB, Hou P, Chesti J, Lu X, Child ES, Morgan RML, Niu W, Zhao L, Armstrong A, Mann DJ, Cui S. Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease. Acta Pharm Sin B 2022; 12:3924-3933. [PMID: 35702321 PMCID: PMC9181371 DOI: 10.1016/j.apsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are critically dependent upon virally encoded proteases to cleave the viral polyproteins into functional proteins. Many of these proteases exhibit a similar fold and contain an essential catalytic cysteine, offering the opportunity to inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold and a similar active site. The hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. We demonstrate that targeting the active site cysteine of Mpro can have profound allosteric effects, distorting secondary structures to disrupt the active dimeric unit.
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Affiliation(s)
- Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
| | - Gregory B Craven
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Pengjiao Hou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
| | - Julian Chesti
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Xinran Lu
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - Emma S Child
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Wenchao Niu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK
| | - David J Mann
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100076, China
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18
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Zhang F, Chase-Topping M, Guo CG, Woolhouse MEJ. Predictors of human-infective RNA virus discovery in the United States, China, and Africa, an ecological study. eLife 2022; 11:e72123. [PMID: 35666108 PMCID: PMC9278958 DOI: 10.7554/elife.72123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background The variation in the pathogen type as well as the spatial heterogeneity of predictors make the generality of any associations with pathogen discovery debatable. Our previous work confirmed that the association of a group of predictors differed across different types of RNA viruses, yet there have been no previous comparisons of the specific predictors for RNA virus discovery in different regions. The aim of the current study was to close the gap by investigating whether predictors of discovery rates within three regions-the United States, China, and Africa-differ from one another and from those at the global level. Methods Based on a comprehensive list of human-infective RNA viruses, we collated published data on first discovery of each species in each region. We used a Poisson boosted regression tree (BRT) model to examine the relationship between virus discovery and 33 predictors representing climate, socio-economics, land use, and biodiversity across each region separately. The discovery probability in three regions in 2010-2019 was mapped using the fitted models and historical predictors. Results The numbers of human-infective virus species discovered in the United States, China, and Africa up to 2019 were 95, 80, and 107 respectively, with China lagging behind the other two regions. In each region, discoveries were clustered in hotspots. BRT modelling suggested that in all three regions RNA virus discovery was better predicted by land use and socio-economic variables than climatic variables and biodiversity, although the relative importance of these predictors varied by region. Map of virus discovery probability in 2010-2019 indicated several new hotspots outside historical high-risk areas. Most new virus species since 2010 in each region (6/6 in the United States, 19/19 in China, 12/19 in Africa) were discovered in high-risk areas as predicted by our model. Conclusions The drivers of spatiotemporal variation in virus discovery rates vary in different regions of the world. Within regions virus discovery is driven mainly by land-use and socio-economic variables; climate and biodiversity variables are consistently less important predictors than at a global scale. Potential new discovery hotspots in 2010-2019 are identified. Results from the study could guide active surveillance for new human-infective viruses in local high-risk areas. Funding FFZ is funded by the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk/). MEJW has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 874735 (VEO) (https://www.veo-europe.eu/).
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
| | - Margo Chase-Topping
- Usher Institute, University of EdinburghEdinburghUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghEdinburghUnited Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong KongHong KongChina
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19
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Fagre AC, Cohen LE, Eskew EA, Farrell M, Glennon E, Joseph MB, Frank HK, Ryan SJ, Carlson CJ, Albery GF. Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health. Ecol Lett 2022; 25:1534-1549. [PMID: 35318793 PMCID: PMC9313783 DOI: 10.1111/ele.14003] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human-to-wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non-human primates or large, long-lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent "secondary spillover" back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non-human primates and human-proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human-to-wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human-to-wildlife pathogen transmission.
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Affiliation(s)
- Anna C. Fagre
- Department of Microbiology, Immunology, and PathologyCollege of Veterinary Medicine and Biomedical SciencesColorado State UniversityFort CollinsColoradoUSA
- Bat Health FoundationFort CollinsColoradoUSA
| | - Lily E. Cohen
- Icahn School of Medicine at Mount SinaiNew YorkNew York CityUSA
| | - Evan A. Eskew
- Department of BiologyPacific Lutheran UniversityTacomaWashingtonUSA
| | - Max Farrell
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Emma Glennon
- Disease Dynamics UnitDepartment of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | | | - Hannah K. Frank
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisinaUSA
| | - Sadie J. Ryan
- Quantitative Disease Ecology and Conservation (QDEC) Lab GroupDepartment of GeographyUniversity of FloridaGainesvilleFloridaUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Colin J Carlson
- Center for Global Health Science and SecurityGeorgetown University Medical CenterWashingtonDistrict of ColumbiaUSA
- Department of Microbiology and ImmunologyGeorgetown University Medical CenterWashingtonDistrict of ColumbiaUSA
| | - Gregory F. Albery
- Department of BiologyGeorgetown UniversityWashingtonDistrict of ColumbiaUSA
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20
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Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J, Mohssen M, Tian F, Pratama AA, Bolduc B, Zablocki O, Cronin D, Solden L, Delage E, Alberti A, Aury JM, Carradec Q, da Silva C, Labadie K, Poulain J, Ruscheweyh HJ, Salazar G, Shatoff E, Coordinators TO, Bundschuh R, Fredrick K, Kubatko LS, Chaffron S, Culley AI, Sunagawa S, Kuhn JH, Wincker P, Sullivan MB. Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome. Science 2022; 376:156-162. [PMID: 35389782 PMCID: PMC10990476 DOI: 10.1126/science.abm5847] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.
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Affiliation(s)
- Ahmed A. Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - James M. Wainaina
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Guillermo Dominguez-Huerta
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jiarong Guo
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Mohamed Mohssen
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
| | - Funing Tian
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Akbar Adjie Pratama
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
| | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Olivier Zablocki
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Dylan Cronin
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
| | - Lindsey Solden
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Erwan Delage
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Corinne da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Elan Shatoff
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ralf Bundschuh
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, Ohio State University, Columbus, OH 43210, USA
| | - Kurt Fredrick
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Laura S. Kubatko
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, Ohio State University, Columbus, OH 43210, USA
| | - Samuel Chaffron
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Nantes Université, CNRS UMR 6004, LS2N, F-44000 Nantes, France
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91000 Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Matthew B. Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
- EMERGE Biology Integration Institute, Ohio State University, Columbus, OH 43210, USA
- Center of Microbiome Science, Ohio State University, Columbus, OH 43210, USA
- The Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, OH 43210, USA
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA
- Department of Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
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21
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Tian L, Pang Z, Li M, Lou F, An X, Zhu S, Song L, Tong Y, Fan H, Fan J. Molnupiravir and Its Antiviral Activity Against COVID-19. Front Immunol 2022; 13:855496. [PMID: 35444647 PMCID: PMC9013824 DOI: 10.3389/fimmu.2022.855496] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) constitutes a major worldwide public health threat and economic burden. The pandemic is still ongoing and the SARS-CoV-2 variants are still emerging constantly, resulting in an urgent demand for new drugs to treat this disease. Molnupiravir, a biological prodrug of NHC (β-D-N(4)-hydroxycytidine), is a novel nucleoside analogue with a broad-spectrum antiviral activity against SARS-CoV, SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), influenza virus, respiratory syncytial virus (RSV), bovine viral diarrhea virus (BVDV), hepatitis C virus (HCV) and Ebola virus (EBOV). Molnupiravir showed potent therapeutic and prophylactic activity against multiple coronaviruses including SARS-CoV-2, SARS-CoV, and MERS-CoV in animal models. In clinical trials, molnupiravir showed beneficial effects for mild to moderate COVID-19 patients with a favorable safety profile. The oral bioavailability and potent antiviral activity of molnupiravir highlight its potential utility as a therapeutic candidate against COVID-19. This review presents the research progress of molnupiravir starting with its discovery and synthesis, broad-spectrum antiviral effects, and antiviral mechanism. In addition, the preclinical studies, antiviral resistance, clinical trials, safety, and drug tolerability of molnupiravir are also summarized and discussed, aiming to expand our knowledge on molnupiravir and better deal with the COVID-19 epidemic.
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Affiliation(s)
- Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fuxing Lou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shaozhou Zhu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Junfen Fan, ; Huahao Fan, ; Yigang Tong, ; Lihua Song,
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Junfen Fan, ; Huahao Fan, ; Yigang Tong, ; Lihua Song,
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Junfen Fan, ; Huahao Fan, ; Yigang Tong, ; Lihua Song,
| | - Junfen Fan
- Department of Neurology, Institute of Cerebrovascular Disease Research, Xuanwu Hospital, Capital Medical University, Beijing, China
- *Correspondence: Junfen Fan, ; Huahao Fan, ; Yigang Tong, ; Lihua Song,
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22
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Recent Advances in Influenza, HIV and SARS-CoV-2 Infection Prevention and Drug Treatment—The Need for Precision Medicine. CHEMISTRY 2022. [DOI: 10.3390/chemistry4020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Viruses, and in particular, RNA viruses, dominate the WHO’s current list of ten global health threats. Of these, we review the widespread and most common HIV, influenza virus, and SARS-CoV-2 infections, as well as their possible prevention by vaccination and treatments by pharmacotherapeutic approaches. Beyond the vaccination, we discuss the virus-targeting and host-targeting drugs approved in the last five years, in the case of SARS-CoV-2 in the last one year, as well as new drug candidates and lead molecules that have been published in the same periods. We share our views on vaccination and pharmacotherapy, their mutually reinforcing strategic significance in combating pandemics, and the pros and cons of host and virus-targeted drug therapy. The COVID-19 pandemic has provided evidence of our limited armamentarium to fight emerging viral diseases. Novel broad-spectrum vaccines as well as drugs that could even be applied as prophylactic treatments or in early phases of the viremia, possibly through oral administration, are needed in all three areas. To meet these needs, the use of multi-data-based precision medicine in the practice and innovation of vaccination and drug therapy is inevitable.
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23
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Zhu W, Yang J, Lu S, Jin D, Pu J, Wu S, Luo XL, Liu L, Li Z, Xu J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front Microbiol 2022; 13:780651. [PMID: 35250920 PMCID: PMC8894885 DOI: 10.3389/fmicb.2022.780651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai–Tibet Plateau.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- *Correspondence: Jianguo Xu,
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24
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van Heuvel Y, Schatz S, Rosengarten JF, Stitz J. Infectious RNA: Human Immunodeficiency Virus (HIV) Biology, Therapeutic Intervention, and the Quest for a Vaccine. Toxins (Basel) 2022; 14:toxins14020138. [PMID: 35202165 PMCID: PMC8876946 DOI: 10.3390/toxins14020138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022] Open
Abstract
Different mechanisms mediate the toxicity of RNA. Genomic retroviral mRNA hijacks infected host cell factors to enable virus replication. The viral genomic RNA of the human immunodeficiency virus (HIV) encompasses nine genes encoding in less than 10 kb all proteins needed for replication in susceptible host cells. To do so, the genomic RNA undergoes complex alternative splicing to facilitate the synthesis of the structural, accessory, and regulatory proteins. However, HIV strongly relies on the host cell machinery recruiting cellular factors to complete its replication cycle. Antiretroviral therapy (ART) targets different steps in the cycle, preventing disease progression to the acquired immunodeficiency syndrome (AIDS). The comprehension of the host immune system interaction with the virus has fostered the development of a variety of vaccine platforms. Despite encouraging provisional results in vaccine trials, no effective vaccine has been developed, yet. However, novel promising vaccine platforms are currently under investigation.
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Affiliation(s)
- Yasemin van Heuvel
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Stefanie Schatz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jamila Franca Rosengarten
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Institute of Technical Chemistry, Leibniz University Hannover, Callinstraße 3-9, 30167 Hannover, Germany
| | - Jörn Stitz
- Research Group Pharmaceutical Biotechnology, Faculty of Applied Natural Sciences, TH Köln—University of Applied Sciences, Chempark Leverkusen, Kaiser-Wilhelm-Allee, 51368 Leverkusen, Germany; (Y.v.H.); (S.S.); (J.F.R.)
- Correspondence:
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25
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Abstract
Infectious diseases emerge via many routes and may need to overcome stepwise bottlenecks to burgeon into epidemics and pandemics. About 60% of human infections have animal origins, whereas 40% either co-evolved with humans or emerged from non-zoonotic environmental sources. Although the dynamic interaction between wildlife, domestic animals, and humans is important for the surveillance of zoonotic potential, exotic origins tend to be overemphasized since many zoonoses come from anthropophilic wild species (for example, rats and bats). We examine the equivocal evidence of whether the appearance of novel infections is accelerating and relate technological developments to the risk of novel disease outbreaks. Then we briefly compare selected epidemics, ancient and modern, from the Plague of Athens to COVID-19.
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Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, London, UK
| | - Neeraja Sankaran
- The Descartes Centre for the History and Philosophy of the Sciences and the Humanities, Utrecht University, Utrecht, The Netherlands
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26
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Owen L, Laird K, Shivkumar M. Antiviral plant-derived natural products to combat RNA viruses: Targets throughout the viral life cycle. Lett Appl Microbiol 2021; 75:476-499. [PMID: 34953146 PMCID: PMC9544774 DOI: 10.1111/lam.13637] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/08/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022]
Abstract
There is a need for new effective antivirals, particularly in response to the development of antiviral drug resistance and emerging RNA viruses such as SARS‐CoV‐2. Plants are a significant source of structurally diverse bioactive compounds for drug discovery suggesting that plant‐derived natural products could be developed as antiviral agents. This article reviews the antiviral activity of plant‐derived natural products against RNA viruses, with a focus on compounds targeting specific stages of the viral life cycle. A range of plant extracts and compounds have been identified with antiviral activity, often against multiple virus families suggesting they may be useful as broad‐spectrum antiviral agents. The antiviral mechanism of action of many of these phytochemicals is not fully understood and there are limited studies and clinical trials demonstrating their efficacy and toxicity in vivo. Further research is needed to evaluate the therapeutic potential of plant‐derived natural products as antiviral agents.
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Affiliation(s)
- Lucy Owen
- Infectious Disease Research Group, The Leicester School of Pharmacy, De Montfort University, Leicester, UK
| | - Katie Laird
- Infectious Disease Research Group, The Leicester School of Pharmacy, De Montfort University, Leicester, UK
| | - Maitreyi Shivkumar
- Infectious Disease Research Group, The Leicester School of Pharmacy, De Montfort University, Leicester, UK
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27
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Bayoumi M, Munir M. Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction. Front Microbiol 2021; 12:743580. [PMID: 34899631 PMCID: PMC8664230 DOI: 10.3389/fmicb.2021.743580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes have evolutionarily acquired an immune system to fend off invading mobile genetic elements, including viral phages and plasmids. Through recognizing specific sequences of the invading nucleic acid, prokaryotes mediate a subsequent degradation process collectively referred to as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) (CRISPR-Cas) system. The CRISPR-Cas systems are divided into two main classes depending on the structure of the effector Cas proteins. Class I systems have effector modules consisting of multiple proteins, while class II systems have a single multidomain effector. Additionally, the CRISPR-Cas systems can also be categorized into types depending on the spacer acquisition components and their evolutionary features, namely, types I-VI. Among CRISPR/Cas systems, Cas9 is one of the most common multidomain nucleases that identify, degrade, and modulate DNA. Importantly, variants of Cas proteins have recently been found to target RNA, especially the single-effector Cas13 nucleases. The Cas13 has revolutionized our ability to study and perturb RNAs in endogenous microenvironments. The Cas13 effectors offer an excellent candidate for developing novel research tools in virological and biotechnological fields. Herein, in this review, we aim to provide a comprehensive summary of the recent advances of Cas13s for targeting viral RNA for either RNA-mediated degradation or CRISPR-Cas13-based diagnostics. Additionally, we aim to provide an overview of the proposed applications that could revolutionize our understanding of viral-host interactions using Cas13-mediated approaches.
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Affiliation(s)
- Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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28
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Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infect Immun 2021; 90:e0033421. [PMID: 34780277 PMCID: PMC9119117 DOI: 10.1128/iai.00334-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To identify sequences with a role in microbial pathogenesis, we assessed the adequacy of their annotation by existing controlled vocabularies and sequence databases. Our goal was to regularize descriptions of microbial pathogenesis for improved integration with bioinformatic applications. Here, we review the challenges of annotating sequences for pathogenic activity. We relate the categorization of more than 2,750 sequences of pathogenic microbes through a controlled vocabulary called Functions of Sequences of Concern (FunSoCs). These allow for an ease of description by both humans and machines. We provide a subset of 220 fully annotated sequences in the supplemental material as examples. The use of this compact (∼30 terms), controlled vocabulary has potential benefits for research in microbial genomics, public health, biosecurity, biosurveillance, and the characterization of new and emerging pathogens.
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29
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Adetunji SA, Smolensky D, Mitzel DN, Owens JL, Chitko-McKown CG, Cernicchiaro N, Noronha LE. In Vitro Infection Dynamics of Japanese Encephalitis Virus in Established Porcine Cell Lines. Pathogens 2021; 10:pathogens10111468. [PMID: 34832623 PMCID: PMC8618157 DOI: 10.3390/pathogens10111468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/16/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Japanese encephalitis virus (JEV) is a zoonotic mosquito-borne pathogen that regularly causes severe neurological disease in humans in Southeast Asia and the Western Pacific region. Pigs are one of the main amplifying hosts of JEV and play a central role in the virus transmission cycle. The objective of this study was to identify in vitro cell systems to investigate early effects of JEV infection including viral replication and host cell death. Here, we demonstrate the susceptibility of several porcine cell lines to the attenuated genotype III JEV strain SA14-14-2. Monolayers of porcine nasal turbinate (PT-K75), kidney (SK-RST), testis (ST), and monocyte-derived macrophage (CΔ2+) cells were infected with SA14-14-2 for up to five days at a multiplicity of infection (MOI) of 0.1. The hamster kidney cell line BHK-21, previously shown to be susceptible to SA14-14-2, was used as a positive control. Culture supernatants and cells were collected between 0 and 120 h post infection (hpi), and monolayers were observed for cytopathic effect (CPE) using brightfield microscopy. The number of infectious virus particles was quantified by plaque assay and cell viability was determined using trypan blue staining. An indirect immunofluorescence assay was used to detect the presence of JEV NS1 antigens in cells infected at 1 MOI. All four porcine cell lines demonstrated susceptibility to SA14-14-2 and produced infectious virus by 12 hpi. Virus titers peaked at 48 hpi in CΔ2+, BHK-21, and SK-RST cells, at 72 hpi in PT-K75, and at 120 hpi in ST cells. CPE was visible in infected CΔ2+ and BHK-21 cells, but not the other three cell lines. The proportion of viable cells, as measured by trypan blue exclusion, declined after 24 hpi in BHK-21 and 48 hpi in CΔ2+ cells, but did not substantially decline in SK-RST, PT-K75 or ST cells. At 48 hpi, JEV NS1 was detected in all infected cell lines by fluorescence microscopy. These findings demonstrate several porcine cell lines which have the potential to serve as useful research tools for investigating JEV infection dynamics and host cell mechanisms in a natural amplifying host species, such as pigs, in vitro.
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Affiliation(s)
- Shakirat A. Adetunji
- Center for Outcomes Research and Epidemiology, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (S.A.A.); (N.C.)
| | - Dmitriy Smolensky
- Center for Grain and Animal Health Research, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA;
| | - Dana N. Mitzel
- National Bio and Agro-Defense Facility, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA; (D.N.M.); (J.L.O.)
| | - Jeana L. Owens
- National Bio and Agro-Defense Facility, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA; (D.N.M.); (J.L.O.)
| | - Carol G. Chitko-McKown
- Roman L. Hruska U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NE 68933, USA;
| | - Natalia Cernicchiaro
- Center for Outcomes Research and Epidemiology, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA; (S.A.A.); (N.C.)
| | - Leela E. Noronha
- National Bio and Agro-Defense Facility, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66502, USA; (D.N.M.); (J.L.O.)
- Correspondence:
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30
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Painter GR, Natchus MG, Cohen O, Holman W, Painter WP. Developing a direct acting, orally available antiviral agent in a pandemic: the evolution of molnupiravir as a potential treatment for COVID-19. Curr Opin Virol 2021; 50:17-22. [PMID: 34271264 PMCID: PMC8277160 DOI: 10.1016/j.coviro.2021.06.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 01/22/2023]
Abstract
Despite the availability of vaccines, there remains an urgent need for antiviral drugs with potent activity against SARS-CoV-2, the cause of COVID-19. Millions of people are immune-suppressed and may not be able to mount a fully protective immune response after vaccination. There is also an increasingly critical need for a drug to cover emerging SARS-CoV-2 variants, against which existing vaccines may be less effective. Here, we describe the evolution of molnupiravir (EIDD-2801, MK-4482), a broad-spectrum antiviral agent originally designed for the treatment of Alphavirus infections, into a potential drug for the prevention and treatment of COVID-19. When the pandemic began, molnupiravir was in pre-clinical development for the treatment of seasonal influenza. As COVID-19 spread, the timeline for the development program was moved forward significantly, and focus shifted to treatment of coronavirus infections. Real time consultation with regulatory authorities aided in making the acceleration of the program possible.
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Affiliation(s)
- George R Painter
- Emory Institute for Drug Development (EIDD), Emory University, Atlanta, GA, USA; Drug Innovation Ventures at Emory (DRIVE), Atlanta, GA, USA; Department of Pharmacology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Michael G Natchus
- Emory Institute for Drug Development (EIDD), Emory University, Atlanta, GA, USA
| | - Oren Cohen
- Covance Clinical Research Unit Ltd., Springfield House, Hyde Street, Leeds LS2 9LH, UK
| | - Wendy Holman
- Ridgeback Biotherapeutics LP, 3480 Main Highway, Unit 402, Miami, Florida 33133, USA
| | - Wendy P Painter
- Ridgeback Biotherapeutics LP, 3480 Main Highway, Unit 402, Miami, Florida 33133, USA
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31
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Spruill-Harrell B, Pérez-Umphrey A, Valdivieso-Torres L, Cao X, Owen RD, Jonsson CB. Impact of Predator Exclusion and Habitat on Seroprevalence of New World Orthohantavirus Harbored by Two Sympatric Rodents within the Interior Atlantic Forest. Viruses 2021; 13:1963. [PMID: 34696393 PMCID: PMC8538774 DOI: 10.3390/v13101963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Understanding how perturbations to trophic interactions influence virus-host dynamics is essential in the face of ongoing biodiversity loss and the continued emergence of RNA viruses and their associated zoonoses. Herein, we investigated the role of predator exclusion on rodent communities and the seroprevalence of hantaviruses within the Reserva Natural del Bosque Mbaracayú (RNBM), which is a protected area of the Interior Atlantic Forest (IAF). In the IAF, two sympatric rodent reservoirs, Akodon montensis and Oligoryzomys nigripes, harbor Jaborá and Juquitiba hantavirus (JABV, JUQV), respectively. In this study, we employed two complementary methods for predator exclusion: comprehensive fencing and trapping/removal. The goal of exclusion was to preclude the influence of predation on small mammals on the sampling grids and thereby potentially reduce rodent mortality. Following baseline sampling on three grid pairs with different habitats, we closed the grids and began predator removal. By sampling three habitat types, we controlled for habitat-specific effects, which is important for hantavirus-reservoir dynamics in neotropical ecosystems. Our six-month predator exclusion experiment revealed that the exclusion of terrestrial mammalian predators had little influence on the rodent community or the population dynamics of A. montensis and O. nigripes. Instead, fluctuations in species diversity and species abundances were influenced by sampling session and forest degradation. These results suggest that seasonality and landscape composition play dominant roles in the prevalence of hantaviruses in rodent reservoirs in the IAF ecosystem.
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Affiliation(s)
- Briana Spruill-Harrell
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Anna Pérez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Building, Baton Rouge, LA 70803, USA;
| | | | - Xueyuan Cao
- Department of Nursing-Acute/Tert Care, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Robert D. Owen
- Centro para el Desarrollo de la Investigación Científica, Asunción C.P. 1371, Paraguay;
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
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32
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Mollentze N, Babayan SA, Streicker DG. Identifying and prioritizing potential human-infecting viruses from their genome sequences. PLoS Biol 2021; 19:e3001390. [PMID: 34582436 PMCID: PMC8478193 DOI: 10.1371/journal.pbio.3001390] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
Determining which animal viruses may be capable of infecting humans is currently intractable at the time of their discovery, precluding prioritization of high-risk viruses for early investigation and outbreak preparedness. Given the increasing use of genomics in virus discovery and the otherwise sparse knowledge of the biology of newly discovered viruses, we developed machine learning models that identify candidate zoonoses solely using signatures of host range encoded in viral genomes. Within a dataset of 861 viral species with known zoonotic status, our approach outperformed models based on the phylogenetic relatedness of viruses to known human-infecting viruses (area under the receiver operating characteristic curve [AUC] = 0.773), distinguishing high-risk viruses within families that contain a minority of human-infecting species and identifying putatively undetected or so far unrealized zoonoses. Analyses of the underpinnings of model predictions suggested the existence of generalizable features of viral genomes that are independent of virus taxonomic relationships and that may preadapt viruses to infect humans. Our model reduced a second set of 645 animal-associated viruses that were excluded from training to 272 high and 41 very high-risk candidate zoonoses and showed significantly elevated predicted zoonotic risk in viruses from nonhuman primates, but not other mammalian or avian host groups. A second application showed that our models could have identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as a relatively high-risk coronavirus strain and that this prediction required no prior knowledge of zoonotic Severe Acute Respiratory Syndrome (SARS)-related coronaviruses. Genome-based zoonotic risk assessment provides a rapid, low-cost approach to enable evidence-driven virus surveillance and increases the feasibility of downstream biological and ecological characterization of viruses.
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Affiliation(s)
- Nardus Mollentze
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon A. Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Daniel G. Streicker
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Lu L, Ashworth J, Nguyen D, Li K, Smith DB, Woolhouse M. No Exchange of Picornaviruses in Vietnam between Humans and Animals in a High-Risk Cohort with Close Contact despite High Prevalence and Diversity. Viruses 2021; 13:v13091709. [PMID: 34578290 PMCID: PMC8473303 DOI: 10.3390/v13091709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 02/03/2023] Open
Abstract
Hospital-based and community-based 'high-risk cohort' studies investigating humans at risk of zoonotic infection due to occupational or residential exposure to animals were conducted in Vietnam, with diverse viruses identified from faecal samples collected from humans, domestic and wild animals. In this study, we focus on the positive-sense RNA virus family Picornaviridae, investigating the prevalence, diversity, and potential for cross-species transmission. Through metagenomic sequencing, we found picornavirus contigs in 23% of samples, belonging to 15 picornavirus genera. Prevalence was highest in bats (67%) while diversity was highest in rats (nine genera). In addition, 22% of the contigs were derived from novel viruses: Twelve phylogenetically distinct clusters were observed in rats of which seven belong to novel species or types in the genera Hunnivirus, Parechovirus, Cardiovirus, Mosavirus and Mupivirus; four distinct clusters were found in bats, belonging to one novel parechovirus species and one related to an unclassified picornavirus. There was no evidence for zoonotic transmission in our data. Our study provides an improved knowledge of the diversity and prevalence of picornaviruses, including a variety of novel picornaviruses in rats and bats. We highlight the importance of monitoring the human-animal interface for possible spill-over events.
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Affiliation(s)
- Lu Lu
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
- Correspondence:
| | - Jordan Ashworth
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
| | - Dung Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
| | - Kejin Li
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (D.N.); (D.B.S.)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Mark Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh EH9 3FL, UK; (J.A.); (M.W.)
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Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
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Shivaprakash KN, Sen S, Paul S, Kiesecker JM, Bawa KS. Mammals, wildlife trade, and the next global pandemic. Curr Biol 2021; 31:3671-3677.e3. [PMID: 34237267 DOI: 10.1016/j.cub.2021.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/09/2021] [Accepted: 06/02/2021] [Indexed: 12/23/2022]
Abstract
Most new infectious diseases emerge when pathogens transfer from animals to humans.1,2 The suspected origin of the COVID pandemic in a wildlife wet market has resurfaced debates on the role of wildlife trade as a potential source of emerging zoonotic diseases.3-5 Yet there are no studies quantitatively assessing zoonotic disease risk associated with wildlife trade. Combining data on mammal species hosting zoonotic viruses and mammals known to be in current and future wildlife trade,6 we found that one-quarter (26.5%) of the mammals in wildlife trade harbor 75% of known zoonotic viruses, a level much higher than domesticated and non-traded mammals. The traded mammals also harbor distinct compositions of zoonotic viruses and different host reservoirs from non-traded and domesticated mammals. Furthermore, we highlight that primates, ungulates, carnivores, and bats represent significant zoonotic disease risks as they host 132 (58%) of 226 known zoonotic viruses in present wildlife trade, whereas species of bats, rodents, and marsupials represent significant zoonotic disease risks in future wildlife trade. Thus, the risk of carrying zoonotic diseases is not equal for all mammal species in wildlife trade. Overall, our findings strengthen the evidence that wildlife trade and zoonotic disease risks are strongly associated, and that mitigation measures should prioritize species with the highest risk of carrying zoonotic viruses. Curbing the sales of wildlife products and developing principles that support the sustainable and healthy trade of wildlife could be cost-effective investments given the potential risk and consequences of zoonotic outbreaks.
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Affiliation(s)
| | - Sandeep Sen
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Sriramapura, Jakkur Post, Bangalore, Karnataka 560064, India
| | - Seema Paul
- The Nature Conservancy Center, Lajpat Nagar III, New Delhi 110024, India
| | - Joseph M Kiesecker
- Global Lands Program, The Nature Conservancy, Fort Collins, CO 80524, USA
| | - Kamaljit S Bawa
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Sriramapura, Jakkur Post, Bangalore, Karnataka 560064, India; Department of Biology, University of Massachusetts, 100 Morrissey Boulevard, Boston, MA 02125, USA
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36
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High-Throughput Fluorescent Assay for Inhibitor Screening of Proteases from RNA Viruses. Molecules 2021; 26:molecules26133792. [PMID: 34206406 PMCID: PMC8270262 DOI: 10.3390/molecules26133792] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023] Open
Abstract
Spanish flu, polio epidemics, and the ongoing COVID-19 pandemic are the most profound examples of severe widespread diseases caused by RNA viruses. The coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands affordable and reliable assays for testing antivirals. To test inhibitors of viral proteases, we have developed an inexpensive high-throughput assay based on fluorescent energy transfer (FRET). We assayed an array of inhibitors for papain-like protease from SARS-CoV-2 and validated it on protease from the tick-borne encephalitis virus to emphasize its versatility. The reaction progress is monitored as loss of FRET signal of the substrate. This robust and reproducible assay can be used for testing the inhibitors in 96- or 384-well plates.
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37
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Grange ZL, Goldstein T, Johnson CK, Anthony S, Gilardi K, Daszak P, Olival KJ, O'Rourke T, Murray S, Olson SH, Togami E, Vidal G, Mazet JAK. Ranking the risk of animal-to-human spillover for newly discovered viruses. Proc Natl Acad Sci U S A 2021; 118:e2002324118. [PMID: 33822740 PMCID: PMC8053939 DOI: 10.1073/pnas.2002324118] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The death toll and economic loss resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are stark reminders that we are vulnerable to zoonotic viral threats. Strategies are needed to identify and characterize animal viruses that pose the greatest risk of spillover and spread in humans and inform public health interventions. Using expert opinion and scientific evidence, we identified host, viral, and environmental risk factors contributing to zoonotic virus spillover and spread in humans. We then developed a risk ranking framework and interactive web tool, SpillOver, that estimates a risk score for wildlife-origin viruses, creating a comparative risk assessment of viruses with uncharacterized zoonotic spillover potential alongside those already known to be zoonotic. Using data from testing 509,721 samples from 74,635 animals as part of a virus discovery project and public records of virus detections around the world, we ranked the spillover potential of 887 wildlife viruses. Validating the risk assessment, the top 12 were known zoonotic viruses, including SARS-CoV-2. Several newly detected wildlife viruses ranked higher than known zoonotic viruses. Using a scientifically informed process, we capitalized on the recent wealth of virus discovery data to systematically identify and prioritize targets for investigation. The publicly accessible SpillOver platform can be used by policy makers and health scientists to inform research and public health interventions for prevention and rapid control of disease outbreaks. SpillOver is a living, interactive database that can be refined over time to continue to improve the quality and public availability of information on viral threats to human health.
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Affiliation(s)
- Zoë L Grange
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616;
| | - Tracey Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Christine K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Simon Anthony
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
- EcoHealth Alliance, New York, NY 1001
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Kirsten Gilardi
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
| | | | | | | | - Suzan Murray
- Global Health, Smithsonian Conservation Biology Institute, Washington, DC 20008
| | | | - Eri Togami
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Gema Vidal
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Jonna A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616;
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Riaz N, Leung P, Barton K, Smith MA, Carswell S, Bull R, Lloyd AR, Rodrigo C. Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants. BMC Genomics 2021; 22:148. [PMID: 33653280 PMCID: PMC7923462 DOI: 10.1186/s12864-021-07460-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 02/19/2021] [Indexed: 01/23/2023] Open
Abstract
Background Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. With the advent of third generation long read sequencing technologies, including Oxford Nanopore Technology (ONT) and PacBio platforms, this problem is potentially surmountable. ONT is particularly attractive in this regard due to the portable nature of the MinION sequencer, which makes real-time sequencing in remote and resource-limited locations possible. However, this technology (termed here ‘nanopore sequencing’) has a comparatively high technical error rate. The present study aimed to assess the utility, accuracy and cost-effectiveness of nanopore sequencing for HCV genomes. We also introduce a new bioinformatics tool (Nano-Q) to differentiate within-host variants from nanopore sequencing. Results The Nanopore platform, when the coverage exceeded 300 reads, generated comparable consensus sequences to Illumina sequencing. Using HCV Envelope plasmids (~ 1800 nt) mixed in known proportions, the capacity of nanopore sequencing to reliably identify variants with an abundance as low as 0.1% was demonstrated, provided the autologous reference sequence was available to identify the matching reads. Successful pooling and nanopore sequencing of 52 samples from patients with HCV infection demonstrated its cost effectiveness (AUD$ 43 per sample with nanopore sequencing versus $100 with paired-end short read technology). The Nano-Q tool successfully separated between-host sequences, including those from the same subtype, by bulk sorting and phylogenetic clustering without an autologous reference sequence (using only a subtype-specific generic reference). The pipeline also identified within-host viral variants and their abundance when the parameters were appropriately adjusted. Conclusion Cost effective HCV whole genome sequencing and within-host variant identification without haplotype reconstruction are potential advantages of nanopore sequencing. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07460-1.
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Affiliation(s)
- Nasir Riaz
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia.,Department of Microbiology, Hazara University, KPK, Maneshra, 21120, Pakistan
| | - Preston Leung
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kirston Barton
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Martin A Smith
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Shaun Carswell
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Rowena Bull
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia.,Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Andrew R Lloyd
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Chaturaka Rodrigo
- Kirby Institute, UNSW Sydney, Sydney, NSW, 2052, Australia. .,Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
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39
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Blanchard EL, Vanover D, Bawage SS, Tiwari PM, Rotolo L, Beyersdorf J, Peck HE, Bruno NC, Hincapie R, Michel F, Murray J, Sadhwani H, Vanderheyden B, Finn MG, Brinton MA, Lafontaine ER, Hogan RJ, Zurla C, Santangelo PJ. Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents. Nat Biotechnol 2021; 39:717-726. [PMID: 33536629 DOI: 10.1038/s41587-021-00822-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
Cas13a has been used to target RNA viruses in cell culture, but efficacy has not been demonstrated in animal models. In this study, we used messenger RNA (mRNA)-encoded Cas13a for mitigating influenza virus A and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in mice and hamsters, respectively. We designed CRISPR RNAs (crRNAs) specific for PB1 and highly conserved regions of PB2 of influenza virus, and against the replicase and nucleocapsid genes of SARS-CoV-2, and selected the crRNAs that reduced viral RNA levels most efficiently in cell culture. We delivered polymer-formulated Cas13a mRNA and the validated guides to the respiratory tract using a nebulizer. In mice, Cas13a degraded influenza RNA in lung tissue efficiently when delivered after infection, whereas in hamsters, Cas13a delivery reduced SARS-CoV-2 replication and reduced symptoms. Our findings suggest that Cas13a-mediated targeting of pathogenic viruses can mitigate respiratory infections.
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Affiliation(s)
- Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Swapnil Subhash Bawage
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Pooja Munnilal Tiwari
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Laura Rotolo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jared Beyersdorf
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hannah E Peck
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Nicholas C Bruno
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Frank Michel
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Jackelyn Murray
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Heena Sadhwani
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Bob Vanderheyden
- Analytics and Data Science Institute, Kennesaw State University, Kennesaw, GA, USA
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Eric R Lafontaine
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Robert J Hogan
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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40
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Nabi G, Wang Y, Lü L, Jiang C, Ahmad S, Wu Y, Li D. Bats and birds as viral reservoirs: A physiological and ecological perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142372. [PMID: 33254850 PMCID: PMC7505891 DOI: 10.1016/j.scitotenv.2020.142372] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/31/2020] [Accepted: 09/11/2020] [Indexed: 05/04/2023]
Abstract
The birds (class Aves) and bats (order Chiroptera, class Mammalia) are well known natural reservoirs of a diverse range of viruses, including some zoonoses. The only extant volant vertebrates, bats and birds have undergone dramatic adaptive radiations that have allowed them to occupy diverse ecological niches and colonize most of the planet. However, few studies have compared the physiology and ecology of these ecologically, and medically, important taxa. Here, we review convergent traits in the physiology, immunology, flight-related ecology of birds and bats that might enable these taxa to act as viral reservoirs and asymptomatic carriers. Many species of birds and bats are well adapted to urban environments and may host more zoonotic pathogens than species that do not colonize anthropogenic habitats. These convergent traits in birds and bats and their ecological interactions with domestic animals and humans increase the potential risk of viral spillover transmission and facilitate the emergence of novel viruses that most likely sources of zoonoses with the potential to cause global pandemics.
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Affiliation(s)
- Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yang Wang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Liang Lü
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chuan Jiang
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shahid Ahmad
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yuefeng Wu
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
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Pahmeier F, Neufeldt CJ, Cerikan B, Prasad V, Pape C, Laketa V, Ruggieri A, Bartenschlager R, Cortese M. A Versatile Reporter System To Monitor Virus-Infected Cells and Its Application to Dengue Virus and SARS-CoV-2. J Virol 2021; 95:e01715-20. [PMID: 33257477 PMCID: PMC7851548 DOI: 10.1128/jvi.01715-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022] Open
Abstract
Positive-strand RNA viruses have been the etiological agents in several major disease outbreaks over the last few decades. Examples of this include flaviviruses, such as dengue virus and Zika virus, which cause millions of yearly infections around the globe, and coronaviruses, such as SARS-CoV-2, the source of the current pandemic. The severity of outbreaks caused by these viruses stresses the importance of research aimed at determining methods to limit virus spread and to curb disease severity. Such studies require molecular tools to decipher virus-host interactions and to develop effective treatments. Here, we describe the generation and characterization of a reporter system that can be used to visualize and identify cells infected with dengue virus or SARS-CoV-2. This system is based on viral protease activity that mediates cleavage and nuclear translocation of an engineered fluorescent protein stably expressed in cells. We show the suitability of this system for live cell imaging, for visualization of single infected cells, and for screening and testing of antiviral compounds. With the integrated modular building blocks, this system is easy to manipulate and can be adapted to any virus encoding a protease, thus offering a high degree of flexibility.IMPORTANCE Reporter systems are useful tools for fast and quantitative visualization of virus-infected cells within a host cell population. Here, we describe a reporter system that takes advantage of virus-encoded proteases expressed in infected cells to cleave an ER-anchored fluorescent protein fused to a nuclear localization sequence. Upon cleavage, the GFP moiety translocates to the nucleus, allowing for rapid detection of the infected cells. Using this system, we demonstrate reliable reporting activity for two major human pathogens from the Flaviviridae and the Coronaviridae families: dengue virus and SARS-CoV-2. We apply this reporter system to live cell imaging and use it for proof-of-concept to validate antiviral activity of a nucleoside analogue. This reporter system is not only an invaluable tool for the characterization of viral replication, but also for the discovery and development of antivirals that are urgently needed to halt the spread of these viruses.
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Affiliation(s)
- Felix Pahmeier
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Costantin Pape
- HCI/IWR, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vibor Laketa
- German Center for Infection Research, Heidelberg partner site, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, Heidelberg, Germany
- Division "Virus-Associated Carcinogenesis", German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
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cDNA-Derived RNA Phage Assembly Reveals Critical Residues in the Maturation Protein of the Pseudomonas aeruginosa Leviphage PP7. J Virol 2021; 95:JVI.01643-20. [PMID: 33177196 DOI: 10.1128/jvi.01643-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
PP7 is a leviphage, with a single-stranded RNA genome, that infects Pseudomonas aeruginosa PAO1. A reverse genetic system for PP7 was previously created by using reverse-transcribed cDNA (PP7O) from a virion-derived RNA genome. Here, we have found that the PP7O cDNA contained 20 nucleotide differences from the PP7 genome sequence deposited in the database. We created another reverse genetic system exploiting chemically synthesized cDNA (PP7S) based on the database sequence. Unlike PP7O, which yielded infectious PP7 virions, PP7S-derived particles were incapable of plaque formation on PAO1 cells, which was restored in the PAO1 cells expressing the maturation protein (MP) from PP7O Using this reverse genetic system, we revealed two amino acid residues involved in the known roles of MP (i.e., adsorption and genome replication), fortuitously providing a lesson that the viral RNA genome sequencing needs functional verification, possibly by a reverse genetic system.IMPORTANCE The biological significance of RNA phages has been largely ignored, ironically, because few studies have focused on RNA phages. As an initial attempt to properly represent RNA phages in the phageome, we previously created, by using reverse-transcribed cDNA, a reverse genetic system for the small RNA phage PP7, which infects the opportunistic human pathogen Pseudomonas aeruginosa We report another system by using chemically synthesized cDNA based on the database genome that has 20 nucleotide differences from the previous cDNA. Investigation of those cDNA-derived phage virions revealed that two amino acids of the maturation protein are crucial for the normal phage lifecycle at different steps. Our study provides insight into the molecular basis for the RNA phage lifecycle and a lesson that the RNA genome sequencing needs to be carefully validated by cDNA-based phage assembly systems.
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43
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Ladner JT, Henson SN, Boyle AS, Engelbrektson AL, Fink ZW, Rahee F, D'ambrozio J, Schaecher KE, Stone M, Dong W, Dadwal S, Yu J, Caligiuri MA, Cieplak P, Bjørås M, Fenstad MH, Nordbø SA, Kainov DE, Muranaka N, Chee MS, Shiryaev SA, Altin JA. Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with endemic human coronaviruses. CELL REPORTS MEDICINE 2021; 2:100189. [PMID: 33495758 PMCID: PMC7816965 DOI: 10.1016/j.xcrm.2020.100189] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Accepted: 12/17/2020] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 proteome shares regions of conservation with endemic human coronaviruses (CoVs), but it remains unknown to what extent these may be cross-recognized by the antibody response. Here, we study cross-reactivity using a highly multiplexed peptide assay (PepSeq) to generate an epitope-resolved view of IgG reactivity across all human CoVs in both COVID-19 convalescent and negative donors. PepSeq resolves epitopes across the SARS-CoV-2 Spike and Nucleocapsid proteins that are commonly targeted in convalescent donors, including several sites also recognized in some uninfected controls. By comparing patterns of homologous reactivity between CoVs and using targeted antibody-depletion experiments, we demonstrate that SARS-CoV-2 elicits antibodies that cross-recognize pandemic and endemic CoV antigens at two Spike S2 subunit epitopes. We further show that these cross-reactive antibodies preferentially bind endemic homologs. Our findings highlight sites at which the SARS-CoV-2 response appears to be shaped by previous CoV exposures and which have the potential to raise broadly neutralizing responses. PepSeq enables fully in vitro, highly multiplexed peptide-based antibody assays Epitope mapping shows preexisting antibody reactivity to SARS-CoV-2 antigens Antibodies cross-recognize endemic and pandemic antigens in the Spike S2 subunit Cross-reactive antibodies raised by SARS-CoV-2 preferentially bind endemic homologs
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Affiliation(s)
- Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Sierra N Henson
- The Translational Genomics Research Institute (TGen), Phoenix and Flagstaff, AZ, USA
| | - Annalee S Boyle
- The Translational Genomics Research Institute (TGen), Phoenix and Flagstaff, AZ, USA
| | - Anna L Engelbrektson
- The Translational Genomics Research Institute (TGen), Phoenix and Flagstaff, AZ, USA
| | - Zane W Fink
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Fatima Rahee
- The Translational Genomics Research Institute (TGen), Phoenix and Flagstaff, AZ, USA
| | | | | | - Mars Stone
- Vitalant Research Institute and Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wenjuan Dong
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Sanjeet Dadwal
- Division of Infectious Diseases, City of Hope National Medical Center, Duarte, CA, USA
| | - Jianhua Yu
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Michael A Caligiuri
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Piotr Cieplak
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mona H Fenstad
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Immunology and Transfusion Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Svein A Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Medical Microbiology, St. Olavs Hospital, Trondheim, Norway
| | - Denis E Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Sergey A Shiryaev
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - John A Altin
- The Translational Genomics Research Institute (TGen), Phoenix and Flagstaff, AZ, USA
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44
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Wieczorek K, Szutkowska B, Kierzek E. Anti-Influenza Strategies Based on Nanoparticle Applications. Pathogens 2020; 9:E1020. [PMID: 33287259 PMCID: PMC7761763 DOI: 10.3390/pathogens9121020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Influenza virus has the potential for being one of the deadliest viruses, as we know from the pandemic's history. The influenza virus, with a constantly mutating genome, is becoming resistant to existing antiviral drugs and vaccines. For that reason, there is an urgent need for developing new therapeutics and therapies. Despite the fact that a new generation of universal vaccines or anti-influenza drugs are being developed, the perfect remedy has still not been found. In this review, various strategies for using nanoparticles (NPs) to defeat influenza virus infections are presented. Several categories of NP applications are highlighted: NPs as immuno-inducing vaccines, NPs used in gene silencing approaches, bare NPs influencing influenza virus life cycle and the use of NPs for drug delivery. This rapidly growing field of anti-influenza methods based on nanotechnology is very promising. Although profound research must be conducted to fully understand and control the potential side effects of the new generation of antivirals, the presented and discussed studies show that nanotechnology methods can effectively induce the immune responses or inhibit influenza virus activity both in vitro and in vivo. Moreover, with its variety of modification possibilities, nanotechnology has great potential for applications and may be helpful not only in anti-influenza but also in the general antiviral approaches.
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Affiliation(s)
- Klaudia Wieczorek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (K.W.); (B.S.)
- NanoBioMedical Centre, Adam Mickiewicz University, 61-704 Poznan, Poland
| | - Barbara Szutkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (K.W.); (B.S.)
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland; (K.W.); (B.S.)
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Zhang F, Chase-Topping M, Guo CG, van Bunnik BAD, Brierley L, Woolhouse MEJ. Global discovery of human-infective RNA viruses: A modelling analysis. PLoS Pathog 2020; 16:e1009079. [PMID: 33253277 PMCID: PMC7728385 DOI: 10.1371/journal.ppat.1009079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 12/10/2020] [Accepted: 10/19/2020] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are a leading cause of human infectious diseases and the prediction of where new RNA viruses are likely to be discovered is a significant public health concern. Here, we geocoded the first peer-reviewed reports of 223 human RNA viruses. Using a boosted regression tree model, we matched these virus data with 33 explanatory factors related to natural virus distribution and research effort to predict the probability of virus discovery across the globe in 2010–2019. Stratified analyses by virus transmissibility and transmission mode were also performed. The historical discovery of human RNA viruses has been concentrated in eastern North America, Europe, central Africa, eastern Australia, and north-eastern South America. The virus discovery can be predicted by a combination of socio-economic, land use, climate, and biodiversity variables. Remarkably, vector-borne viruses and strictly zoonotic viruses are more associated with climate and biodiversity whereas non-vector-borne viruses and human transmissible viruses are more associated with GDP and urbanization. The areas with the highest predicted probability for 2010–2019 include three new regions including East and Southeast Asia, India, and Central America, which likely reflect both increasing surveillance and diversity of their virome. Our findings can inform priority regions for investment in surveillance systems for new human RNA viruses. There is a lack of evidence on the factors driving the discovery of RNA viruses in general globally. Here, we recorded the initial discovery sites of all 223 human RNA viruses and revealed its global distribution pattern. By using a machine learning method, we found that the virus discovery was driven by a combination of variables describing socio-economic level, land use, climate and biodiversity, with GDP and GDP growth found to be the two leading predictors. We also predicted the probability of virus discovery in 2010–2019 across the globe, and identified three new areas (East and Southeast Asia, India, and Central America) in addition to the historical high-risk areas. The further stratified analyses (distinguishing viruses transmissible in humans or strictly zoonotic, and vector-borne or non-vector-borne) helped pinpoint the explanatory factors for the discovery of specific categories of viruses and confirm the plausibility of the model. The results of our study further understanding of the spatial distribution of human RNA virus discovery, and map the likelihood of further discoveries across the world. By identifying where new viruses are most likely to be discovered in the near future the study helps identify priority areas for surveillance.
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Affiliation(s)
- Feifei Zhang
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Margo Chase-Topping
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Chuan-Guo Guo
- Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
| | - Bram A. D. van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
| | - Liam Brierley
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Mark E. J. Woolhouse
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, United Kingdom
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Navare AT, Mast FD, Olivier JP, Bertomeu T, Neal M, Carpp LN, Kaushansky A, Coulombe-Huntington J, Tyers M, Aitchison JD. Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020; 221:2020.10.12.336487. [PMID: 33173868 PMCID: PMC7654857 DOI: 10.1101/2020.10.12.336487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viruses co-opt host proteins to carry out their lifecycle. Repurposed host proteins may thus become functionally compromised; a situation analogous to a loss-of-function mutation. We term such host proteins viral-induced hypomorphs. Cells bearing cancer driver loss-of-function mutations have successfully been targeted with drugs perturbing proteins encoded by the synthetic lethal partners of cancer-specific mutations. Synthetic lethal interactions of viral-induced hypomorphs have the potential to be similarly targeted for the development of host-based antiviral therapeutics. Here, we use GBF1, which supports the infection of many RNA viruses, as a proof-of-concept. GBF1 becomes a hypomorph upon interaction with the poliovirus protein 3A. Screening for synthetic lethal partners of GBF1 revealed ARF1 as the top hit, disruption of which, selectively killed cells that synthesize poliovirus 3A. Thus, viral protein interactions can induce hypomorphs that render host cells vulnerable to perturbations that leave uninfected cells intact. Exploiting viral-induced vulnerabilities could lead to broad-spectrum antivirals for many viruses, including SARS-CoV-2. SUMMARY Using a viral-induced hypomorph of GBF1, Navare et al., demonstrate that the principle of synthetic lethality is a mechanism to selectively kill virus-infected cells.
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Affiliation(s)
- Arti T Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Maxwell Neal
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Lindsay N Carpp
- Center for Infectious Disease Research, Seattle, Washington, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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47
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Tan S, Dvorak CMT, Murtaugh MP. Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model. Viruses 2020; 12:v12101136. [PMID: 33036361 PMCID: PMC7600144 DOI: 10.3390/v12101136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases.
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48
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Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 2020; 219:e202006159. [PMID: 32785687 PMCID: PMC7659715 DOI: 10.1083/jcb.202006159] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
With the rapid global spread of SARS-CoV-2, we have become acutely aware of the inadequacies of our ability to respond to viral epidemics. Although disrupting the viral life cycle is critical for limiting viral spread and disease, it has proven challenging to develop targeted and selective therapeutics. Synthetic lethality offers a promising but largely unexploited strategy against infectious viral disease; as viruses infect cells, they abnormally alter the cell state, unwittingly exposing new vulnerabilities in the infected cell. Therefore, we propose that effective therapies can be developed to selectively target the virally reconfigured host cell networks that accompany altered cellular states to cripple the host cell that has been converted into a virus factory, thus disrupting the viral life cycle.
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Affiliation(s)
- Fred D. Mast
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Arti T. Navare
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
| | - Almer M. van der Sloot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | | | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY
| | | | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Canada
| | - John D. Aitchison
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Biochemistry, University of Washington, Seattle, WA
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49
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Sensitive fluorescence detection of SARS-CoV-2 RNA in clinical samples via one-pot isothermal ligation and transcription. Nat Biomed Eng 2020; 4:1168-1179. [PMID: 32948855 PMCID: PMC7499000 DOI: 10.1038/s41551-020-00617-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/27/2020] [Indexed: 01/12/2023]
Abstract
The control of viral outbreaks requires nucleic acid diagnostic tests that are sensitive, simple and fast. Here, we report a highly sensitive and specific one-pot assay for the fluorescence-based detection of RNA from pathogens. The assay, which can be performed within 30-50 min of incubation time and can reach a limit of detection of 0.1-attomolar RNA concentration, relies on a sustained isothermal reaction cascade producing an RNA aptamer that binds to a fluorogenic dye. The RNA aptamer is transcribed by the T7 RNA polymerase from the ligation product of a promoter DNA probe and a reporter DNA probe that hybridize with the target single-stranded RNA sequence via the SplintR ligase (a Chlorella virus DNA ligase). In 40 nasopharyngeal SARS-CoV-2 samples, the assay reached positive and negative predictive values of 95 and 100%, respectively. We also show that the assay can rapidly detect a range of viral and bacterial RNAs.
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50
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Replication of Equine arteritis virus is efficiently suppressed by purine and pyrimidine biosynthesis inhibitors. Sci Rep 2020; 10:10100. [PMID: 32572069 PMCID: PMC7308276 DOI: 10.1038/s41598-020-66944-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/20/2020] [Indexed: 11/23/2022] Open
Abstract
RNA viruses are responsible for a large variety of animal infections. Equine Arteritis Virus (EAV) is a positive single-stranded RNA virus member of the family Arteriviridae from the order Nidovirales like the Coronaviridae. EAV causes respiratory and reproductive diseases in equids. Although two vaccines are available, the vaccination coverage of the equine population is largely insufficient to prevent new EAV outbreaks around the world. In this study, we present a high-throughput in vitro assay suitable for testing candidate antiviral molecules on equine dermal cells infected by EAV. Using this assay, we identified three molecules that impair EAV infection in equine cells: the broad-spectrum antiviral and nucleoside analog ribavirin, and two compounds previously described as inhibitors of dihydroorotate dehydrogenase (DHODH), the fourth enzyme of the pyrimidine biosynthesis pathway. These molecules effectively suppressed cytopathic effects associated to EAV infection, and strongly inhibited viral replication and production of infectious particles. Since ribavirin is already approved in human and small animal, and that several DHODH inhibitors are in advanced clinical trials, our results open new perspectives for the management of EAV outbreaks.
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