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Friedhoff R, Elfayres G, Mérindol N, Desgagné-Penix I, Berthoux L. RNA replication-independent, DNA linearization-dependent expression of reporter genes from a SARS-CoV-2 replicon-encoding DNA in human cells. PLoS One 2024; 19:e0300491. [PMID: 39150942 PMCID: PMC11329111 DOI: 10.1371/journal.pone.0300491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/13/2024] [Indexed: 08/18/2024] Open
Abstract
Replicons, derived from RNA viruses, are genetic constructs retaining essential viral enzyme genes while lacking key structural protein genes. Upon introduction into cells, the genes carried by the replicon RNA are expressed, and the RNA self-replicates, yet viral particle production does not take place. Typically, RNA replicons are transcribed in vitro and are then electroporated in cells. However, it would be advantageous for the replicon to be generated in cells following DNA transfection instead of RNA. In this study, a bacterial artificial chromosome (BAC) DNA encoding a SARS-CoV-2 replicon under control of a T7 promoter was transfected into HEK293T cells engineered to functionally express the T7 RNA polymerase (T7 RNAP). Upon transfection of the BAC DNA, we observed low, but reproducible expression of reporter proteins GFP and luciferase carried by this replicon. Expression of the reporter proteins required linearization of the BAC DNA prior to transfection. Moreover, expression occurred independently of T7 RNAP. Gene expression was also insensitive to remdesivir treatment, suggesting that it did not involve self-replication of replicon RNA. Similar results were obtained in highly SARS-CoV-2 infection-permissive Calu-3 cells. Strikingly, prior expression of the SARS-CoV-2 N protein boosted expression from transfected SARS-CoV-2 RNA replicon but not from the replicon BAC DNA. In conclusion, transfection of a large DNA encoding a coronaviral replicon led to reproducible replicon gene expression through an unidentified mechanism. These findings highlight a novel pathway toward replicon gene expression from transfected replicon cDNA, offering valuable insights for the development of methods for DNA-based RNA replicon applications.
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Affiliation(s)
- Ronja Friedhoff
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Ghada Elfayres
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Natacha Mérindol
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Lionel Berthoux
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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2
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Mani M, Vellusamy M, Rathinavel T, Vadivel P, Dauchez M, Khan R, Aroulmoji V. In silico validation of hyaluronic acid - drug conjugates based targeted drug delivery for the treatment of COVID-19. J Biomol Struct Dyn 2024:1-15. [PMID: 38533826 DOI: 10.1080/07391102.2024.2328745] [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: 09/11/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The impact of COVID-19 urges scientists to develop targeted drug delivery to manage Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral infections with a fast recovery rate. The aim of the study is to develop Hyaluronic Acid (HA) drug conjugates of viral drugs to target two important enzymes (Mpro and PLpro) of SARS-CoV-2. Three antiviral drugs, namely Dexamethasone (DEX), Favipiravir (FAV), and Remdesivir (REM), were chosen for HA conjugation due to their reactive functional groups. Free forms of drugs (DEX, FAV, REM) and HA drug conjugates (HA-DEX, HA-FAV, HA-REM, HA-RHA, HA-RHE) were validated against Mpro (PDB ID 6LU7) and PLpro (PDB 7LLZ), which play an essential role in the replication and reproduction of the SARS-CoV-2 virus. The results of the present study revealed that HA-drug conjugates possess higher binding affinity and the best docking score towards the Mpro and PLpro target proteins of SARS-CoV-2 than their free forms of drugs. ADMET screening resulted that HA-drug conjugates exhibited better pharmacokinetic profiles than their pure forms of drugs. Further, molecular dynamic simulation studies, essential dynamics and free energy landscape analyses show that HA antiviral drug conjugates possess good trajectories and energy status, with the PLpro target protein (PDB 7LLZ) of SARS-CoV-2 through long-distance (500 ns) simulation screening. The research work recorded the best drug candidate for Cell-Targeted Drug Delivery (CTDD) for SARS-CoV-2-infected cells through hyaluronic acid conjugates of antiviral drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohan Mani
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal (Dt.), Tamil Nadu, India
| | - Mahesh Vellusamy
- Universite ́ de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | | | - Pullar Vadivel
- Department of Chemistry, Salem Sowdeswari College for Women, Salem (Dt.), Tamil Nadu, India
| | - Manuel Dauchez
- Universite ́ de Reims Champagne Ardenne, CNRS, MEDyC UMR 7369, Reims, France
| | - Riaz Khan
- Department of Chemistry, Rumsey, Sonning, Berkshire, UK
| | - Vincent Aroulmoji
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal (Dt.), Tamil Nadu, India
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3
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Su WC, Chen ZY, Chang YS, Jeng KS, Le UNP, Chou YC, Kuo LL, Melano I, Jesse, Wang WJ, Song YC, Li SR, Hung MC, Lai MMC, Lin CW. Functional assessments of SARS-CoV-2 single-round infectious particles with variant-specific spike proteins on infectivity, drug sensitivity, and antibody neutralization. Antiviral Res 2023; 220:105744. [PMID: 37944823 DOI: 10.1016/j.antiviral.2023.105744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
Working with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is restricted to biosafety level III (BSL-3) laboratory. The study used a trans-complementation system consisting of virus-like particles (VLPs) and DNA-launched replicons to generate SARS-CoV-2 single-round infectious particles (SRIPs) with variant-specific spike (S) proteins. S gene of Wuhan-Hu-1 strain (SWH1) or Omicron BA.1 variant (SBA.1), along with the envelope (E) and membrane (M) genes, were cloned into a tricistronic vector, co-expressed in the cells to produce variant-specific S-VLPs. Additionally, the replicon of the WH1-like strain without S, E, M and accessory genes, was engineered under the control by a CMV promoter to produce self-replicating RNAs within VLP-producing cells, led to create SWH1- and SBA.1-based SARS-CoV-2 SRIPs. The SBA.1-based SRIP showed lower virus yield, replication, N protein expression, fusogenicity, and infectivity compared to SWH1-based SRIPs. SBA.1-based SRIP also exhibited intermediate resistance to neutralizing antibodies produced by SWH1-based vaccines, but were effective at infecting cells with low ACE2 expression. Importantly, both S-based SRIPs responded similarly to remdesivir and GC376, with EC50 values ranging from 0.17 to 1.46 μM, respectively. The study demonstrated that this trans-complementation system is a reliable and efficient tool for generating SARS-CoV-2 SRIPs with variant-specific S proteins. SARS-CoV-2 SRIPs, mimicking authentic live viruses, facilitate comprehensive analysis of variant-specific virological characteristics, including antibody neutralization, and drug sensitivity in non-BSL-3 laboratories.
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Affiliation(s)
- Wen-Chi Su
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; International Master's Program of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan; Drug Development Center, China Medical University, Taichung, 404333, Taiwan
| | - Zan-Yu Chen
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan
| | - Young-Sheng Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan
| | - King-Song Jeng
- Department of Medical Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Uyen Nguyen Phuong Le
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Li-Lan Kuo
- International Master's Program of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Ivonne Melano
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Jesse
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan
| | - Ying-Chyi Song
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Sin-Rong Li
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Research Center for Cancer Biology, China Medical University, Taichung, 404327, Taiwan; Center for Molecular Medicine, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Michael M C Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei, 115201, Taiwan.
| | - Cheng-Wen Lin
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 404333, Taiwan; Drug Development Center, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, 404333, Taiwan; Department of Biological Science and Technology, China Medical University, Taichung, 404333, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Wufeng, Taichung, 413305, Taiwan.
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4
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Cai HL, Huang YW. Reverse genetics systems for SARS-CoV-2: Development and applications. Virol Sin 2023; 38:837-850. [PMID: 37832720 PMCID: PMC10786661 DOI: 10.1016/j.virs.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.
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Affiliation(s)
- Hou-Li Cai
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yao-Wei Huang
- Department of Veterinary Medicine, Zhejiang University, Hangzhou, 310058, China; State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.
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5
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Wang L, Guzman M, Muñoz-Santos D, Honrubia JM, Ripoll-Gomez J, Delgado R, Sola I, Enjuanes L, Zuñiga S. Cell type dependent stability and virulence of a recombinant SARS-CoV-2, and engineering of a propagation deficient RNA replicon to analyze virus RNA synthesis. Front Cell Infect Microbiol 2023; 13:1268227. [PMID: 37942479 PMCID: PMC10628495 DOI: 10.3389/fcimb.2023.1268227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool for the study of virus life cycle, virus-host interactions and pathogenesis, as well as for the development of effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent human coronavirus that has caused the coronavirus disease (COVID-19) pandemic. The engineering of a full-length infectious cDNA clone and a fluorescent replicon of SARS-CoV-2 Wuhan-Hu-1, using a bacterial artificial chromosome, is reported. Viral growth and genetic stability in eleven cell lines were analyzed, showing that both VeroE6 cells overexpressing transmembrane serin protease 2 (TMPRSS2) and human lung derived cells resulted in the optimization of a cell system to preserve SARS-CoV-2 genetic stability. The recombinant SARS-CoV-2 virus and a point mutant expressing the D614G spike protein variant were virulent in a mouse model. The RNA replicon was propagation-defective, allowing its use in BSL-2 conditions to analyze viral RNA synthesis. The SARS-CoV-2 reverse genetics systems developed constitute a useful tool for studying the molecular biology of the virus, the development of genetically defined vaccines and to establish systems for antiviral compounds screening.
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Affiliation(s)
- Li Wang
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - María Guzman
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jose Manuel Honrubia
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gomez
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Rafael Delgado
- Laboratory of Molecular Microbiology, Instituto de Investigación Hospital 12 de Octubre (Imas12), Madrid, Spain
| | - Isabel Sola
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Sonia Zuñiga
- Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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6
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Takazawa S, Kotaki T, Nakamura S, Utsubo C, Kameoka M. Construction of Fosmid-based SARS-CoV-2 replicons for antiviral drug screening and replication analyses in biosafety level 2 facilities. Virus Res 2023; 334:199176. [PMID: 37473963 PMCID: PMC10374963 DOI: 10.1016/j.virusres.2023.199176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has necessitated the global development of countermeasures since its outbreak. However, current therapeutics and vaccines to stop the pandemic are insufficient and this is mainly because of the emergence of resistant variants, which requires the urgent development of new countermeasures, such as antiviral drugs. Replicons, self-replicating RNAs that do not produce virions, are a promising system for this purpose because they safely recreate viral replication, enabling antiviral screening in biosafety level (BSL)-2 facilities. We herein constructed three pCC2Fos-based RNA replicons lacking some open reading frames (ORF) of SARS-CoV-2: the Δorf2-8, Δorf2.4, and Δorf2 replicons, and validated their replication in Huh-7 cells. The functionalities of the Δorf2-8 and Δorf2.4 replicons for antiviral drug screening were also confirmed. We conducted puromycin selection following the construction of the Δorf2.4-puro replicon by inserting a puromycin-resistant gene into the Δorf2.4 replicon. We observed the more sustained replication of the Δorf2.4-puro replicon by puromycin pressure. The present results will contribute to the establishment of a safe and useful replicon system for analyzing SARS-CoV-2 replication mechanisms as well as the development of novel antiviral drugs in BSL-2 facilities.
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Affiliation(s)
- Shunta Takazawa
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Hyogo, Japan; Department of Clinical Laboratory, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.
| | - Satsuki Nakamura
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Hyogo, Japan
| | - Chie Utsubo
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Hyogo, Japan
| | - Masanori Kameoka
- Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Hyogo, Japan.
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7
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von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 2023; 22:585-603. [PMID: 37173515 PMCID: PMC10176316 DOI: 10.1038/s41573-023-00692-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, a wave of rapid and collaborative drug discovery efforts took place in academia and industry, culminating in several therapeutics being discovered, approved and deployed in a 2-year time frame. This article summarizes the collective experience of several pharmaceutical companies and academic collaborations that were active in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral discovery. We outline our opinions and experiences on key stages in the small-molecule drug discovery process: target selection, medicinal chemistry, antiviral assays, animal efficacy and attempts to pre-empt resistance. We propose strategies that could accelerate future efforts and argue that a key bottleneck is the lack of quality chemical probes around understudied viral targets, which would serve as a starting point for drug discovery. Considering the small size of the viral proteome, comprehensively building an arsenal of probes for proteins in viruses of pandemic concern is a worthwhile and tractable challenge for the community.
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Affiliation(s)
- Annette von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK.
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | | | | | | | - Alpha A Lee
- PostEra, Inc., Cambridge, MA, USA.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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8
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Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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9
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Shang W, Dai W, Yao C, Xu L, Tao X, Su H, Li J, Xie X, Xu Y, Hu M, Xie D, Jiang H, Zhang L, Liu H. In vitro and in vivo evaluation of the main protease inhibitor FB2001 against SARS-CoV-2. Antiviral Res 2022; 208:105450. [PMID: 36354082 PMCID: PMC9617675 DOI: 10.1016/j.antiviral.2022.105450] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/26/2022]
Abstract
FB2001 is a drug candidate that targets the main protease of SARS-CoV-2 via covalently binding to cysteine 145. In this study, we evaluated the inhibitory activities of FB2001 against several SARS-CoV-2 variants in vitro and in vivo (in mice), and we also evaluated the histopathological analysis and immunostaining of FB2001 on lung and brain which have been rarely reported. The results showed that FB2001 exhibited potent antiviral efficacy against several current SARS-CoV-2 variants in Vero E6 cells, namely, B.1.1.7 (Alpha): EC50 = 0.39 ± 0.01 μM, EC90 = 0.75 ± 0.01 μM; B.1.351 (Beta): EC50 = 0.28 ± 0.11 μM, EC90 = 0.57 ± 0.21 μM; B.1.617.2 (Delta): EC50 = 0.27 ± 0.05 μM, EC90 = 0.81 ± 0.20 μM; B.1.1.529 (Omicron): EC50 = 0.26 ± 0.06 μM and EC50 = 0.042 ± 0.007 μM (in the presence of a P-glycoprotein inhibitor). FB2001 remained potent against SARS-CoV-2 replication in the presence of high concentrations of human serum, which indicating that human serum had no significant effect on the in vitro inhibitory activity. Additionally, this inhibitor exhibited an additive effect against SARS-CoV-2 when combined with Remdesivir. Furthermore, FB2001 significantly reduced the SARS-CoV-2 copy numbers and titers in the lungs and brains in vivo, and alleviated the pathological symptoms. In addition, FB2001 could alleviated local bleeding, erythrocyte overflow, edema, and inflammatory cell infiltration in brain tissue, and inhibitors reducing viral titers and improving inflammation in the brain have been rarely reported. A physiologically based pharmacokinetic model was established and verified to predict the FB2001 concentration in human lungs. When FB2001 was administered at 200 mg twice a day for 5 days, the observed Ctrough ss in plasma and predicted Ctrough ss of lung total concentration were 0.163 and 2.5 μg/mL, which were approximately 9 and 132-fold higher than the EC50 of 0.019 μg/mL (0.042 μM) against Omicron variant. Taken together, our study suggests that FB2001 is a promising therapeutic agent in COVID-19 treatment and can be combined with remdesivir to achieve improved clinical outcomes. Owing to its good safety and tolerability in healthy human (NCT05197179 and NCT04766931), FB2001 has been approved for Phase II/III clinical trial (NCT05445934).
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10
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Feng X, Zhang X, Jiang S, Tang Y, Cheng C, Krishna PA, Wang X, Dai J, Zhao D, Xia T, Zeng J. A DNA-based non-infectious replicon system to study SARS-CoV-2 RNA synthesis. Comput Struct Biotechnol J 2022; 20:5193-5202. [PMID: 36059866 PMCID: PMC9424123 DOI: 10.1016/j.csbj.2022.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/02/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seriously affected public health around the world. In-depth studies on the pathogenic mechanisms of SARS-CoV-2 is urgently necessary for pandemic prevention. However, most laboratory studies on SARS-CoV-2 have to be carried out in bio-safety level 3 (BSL-3) laboratories, greatly restricting the progress of relevant experiments. In this study, we used a bacterial artificial chromosome (BAC) method to assemble a SARS-CoV-2 replication and transcription system in Vero E6 cells without virion envelope formation, thus avoiding the risk of coronavirus exposure. Furthermore, an improved real-time quantitative reverse transcription PCR (RT-qPCR) approach was used to distinguish the replication of full-length replicon RNAs and transcription of subgenomic RNAs (sgRNAs). Using the SARS-CoV-2 replicon, we demonstrated that the nucleocapsid (N) protein of SARS-CoV-2 facilitates the transcription of sgRNAs in the discontinuous synthesis process. Moreover, two high-frequency mutants of N protein, R203K and S194L, can obviously enhance the transcription level of the replicon, hinting that these mutations likely allow SARS-CoV-2 to spread and reproduce more quickly. In addition, remdesivir and chloroquine, two well-known drugs demonstrated to be effective against coronavirus in previous studies, also inhibited the transcription of our replicon, indicating the potential applications of this system in antiviral drug discovery. Overall, we developed a bio-safe and valuable replicon system of SARS-CoV-2 that is useful to study the mechanisms of viral RNA synthesis and has potential in novel antiviral drug screening.
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Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Kurhade C, Plante JA, Bopp NE, Kalveram B, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. Nat Commun 2022; 13:4337. [PMID: 35896528 PMCID: PMC9326133 DOI: 10.1038/s41467-022-31930-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/08/2022] [Indexed: 12/27/2022] Open
Abstract
We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcription regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (∆3678). The ∆3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The ∆3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the ∆3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the ∆3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter ∆3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that ∆3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Birte Kalveram
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander Bukreyev
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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12
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Tian L, Liu Q, Pei R, Chen Y, Xu C, Tang J, Sun H, Liu K, Yang Q, Yang L, Li L, Zhang Y, Zhou Y, Shan C, Hu X, Chen X, Wang Y. Comparison of viral propagation and drug response among SARS-CoV-2 VOCs using replicons capable of recapitulating virion assembly and release. Virol Sin 2022; 37:695-703. [PMID: 35781091 PMCID: PMC9247232 DOI: 10.1016/j.virs.2022.06.008] [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: 03/29/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Several variants of concern (VOCs) have emerged since the WIV04 strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first isolated in January 2020. Due to mutations in the spike (S) protein, these VOCs have evolved to enhance viral infectivity and immune evasion. However, whether mutations of the other viral proteins lead to altered viral propagation and drug resistance remains obscure. The replicon is a noninfectious viral surrogate capable of recapitulating certain steps of the viral life cycle. Although several SARS-CoV-2 replicons have been developed, none of them were derived from emerging VOCs and could only recapitulate viral genome replication and subgenomic RNA (sgRNA) transcription. In this study, SARS-CoV-2 replicons derived from the WIV04 strain and two VOCs (the Beta and Delta variants) were prepared by removing the S gene from their genomes, while other structural genes remained untouched. These replicons not only recapitulate viral genome replication and sgRNA transcription but also support the assembly and release of viral-like particles, as manifested by electron microscopic assays. Thus, the S-deletion replicon could recapitulate virtually all the post-entry steps of the viral life cycle and provides a versatile tool for measuring viral intracellular propagation and screening novel antiviral drugs, including inhibitors of virion assembly and release. Through the quantification of replicon RNA released into the supernatant, we demonstrate that viral intracellular propagation and drug response to remdesivir have not yet substantially changed during the evolution of SARS-CoV-2 from the WIV04 strain to the Beta and Delta VOCs.
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Affiliation(s)
- Lingqian Tian
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuhong Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yingshan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chonghui Xu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jielin Tang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Hao Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunpeng Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Yang
- Department of Gastroenterology, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Lei Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leshan Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongli Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yuan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Chao Shan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xue Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China; Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, 510320, China.
| | - Yun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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13
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Chou JM, Tsai JL, Hung JN, Chen IH, Chen ST, Tsai MH. The ORF8 Protein of SARS-CoV-2 Modulates the Spike Protein and Its Implications in Viral Transmission. Front Microbiol 2022; 13:883597. [PMID: 35663899 PMCID: PMC9161165 DOI: 10.3389/fmicb.2022.883597] [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: 02/25/2022] [Accepted: 04/01/2022] [Indexed: 01/09/2023] Open
Abstract
COVID-19 is currently global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Accompanying the rapid spread of the error-prone RNA-based genome, several dominant SARS-CoV-2 variants have been genetically identified. The mutations in the spike protein, which are essential for receptor binding and fusion, have been intensively investigated for their contributions to viral transmission. Nevertheless, the importance of other viral proteins and their mutations in SARS-CoV-2 lifecycle and transmission remains fairly understood. Here, we report the strong potency of an accessory protein ORF8 in modulating the level and processing of the spike protein. The expression of ORF8 protein does not affect propagation but expression of spike protein, which may lead to pseudovirions with less spike protein on the surface, therefore less infection potential. At the protein level, ORF8 expression led to downregulation and insufficient S1/S2 cleavage of the spike protein in a dose-dependent manner. ORF8 exhibits a strong interaction with the spike protein mainly at S1 domains and mediates its degradation through multiple pathways. The dominant clinical isolated ORF8 variants with the reduced protein stability exhibited the increased capacity of viral transmission without compromising their inhibitory effects on HLA-A2. Although the increase in spike protein level and Spike pseudovirus production observed by using highly transmissible clinical spike variants, there was no significant compromise in ORF8-mediated downregulation. Because ORF8 is important for immune surveillance and might be required for viral fitness in vivo, the alteration of the spike protein might be an optional strategy used by SARS-CoV-2 to promote viral transmission by escaping the inhibitory effects of ORF8. Therefore, our report emphasized the importance of ORF8 in SARS-CoV-2 spike protein production, maturation, and possible evolution.
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Affiliation(s)
- Jen-Mei Chou
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ling Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Jo-Ning Hung
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - I-Hua Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Szu-Ting Chen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Han Tsai
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Research Center for Epidemic Prevention, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- *Correspondence: Ming-Han Tsai,
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14
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Liu Y, Li L, Timani KA, He JJ. A Unique Robust Dual-Promoter-Driven and Dual-Reporter-Expressing SARS-CoV-2 Replicon: Construction and Characterization. Viruses 2022; 14:974. [PMID: 35632716 PMCID: PMC9143625 DOI: 10.3390/v14050974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs, even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe, and readily scalable platform for high-throughput screening, identification, and evaluation of antiviral drugs against positive-stranded RNA viruses. In the study, we report a unique robust HIV long terminal repeat (LTR)/T7 dual-promoter-driven and dual-reporter firefly luciferase (fLuc) and green fluorescent protein (GFP)-expressing SARS2 replicon. The genomic organization of the replicon was designed with quite a few features that were to ensure the replication fidelity of the replicon, to maximize the expression of the full-length replicon, and to offer the monitoring flexibility of the replicon replication. We showed the success of the construction of the replicon and expression of reporter genes fLuc and GFP and SARS structural N from the replicon DNA or the RNA that was in vitro transcribed from the replicon DNA. We also showed detection of the negative-stranded genomic RNA (gRNA) and subgenomic RNA (sgRNA) intermediates, a hallmark of replication of positive-stranded RNA viruses from the replicon. Lastly, we showed that expression of the reporter genes, N gene, gRNA, and sgRNA from the replicon was sensitive to inhibition by Remdesivir. Taken together, our results support use of the replicon for identification of anti-SARS2 drugs and development of new anti-SARS strategies targeted at the step of virus replication.
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Affiliation(s)
- Ying Liu
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Lu Li
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Khalid A. Timani
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J. He
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, North Chicago, IL 60064, USA; (Y.L.); (L.L.); (K.A.T.)
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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15
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Tanaka T, Saito A, Suzuki T, Miyamoto Y, Takayama K, Okamoto T, Moriishi K. Establishment of a stable SARS-CoV-2 replicon system for application in high-throughput screening. Antiviral Res 2022; 199:105268. [PMID: 35271914 PMCID: PMC8900913 DOI: 10.1016/j.antiviral.2022.105268] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
Experiments with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are limited by the need for biosafety level 3 (BSL3) conditions. A SARS-CoV-2 replicon system rather than an in vitro infection system is suitable for antiviral screening since it can be handled under BSL2 conditions and does not produce infectious particles. However, the reported replicon systems are cumbersome because of the need for transient transfection in each assay. In this study, we constructed a bacterial artificial chromosome vector (the replicon-BAC vector) including the SARS-CoV-2 replicon and a fusion gene encoding Renilla luciferase and neomycin phosphotransferase II, examined the antiviral effects of several known compounds, and then established a cell line stably harboring the replicon-BAC vector. Several cell lines transiently transfected with the replicon-BAC vector produced subgenomic replicon RNAs (sgRNAs) and viral proteins, and exhibited luciferase activity. In the transient replicon system, treatment with remdesivir or interferon-β but not with camostat or favipiravir suppressed the production of viral agents and luciferase, indicating that luciferase activity corresponds to viral replication. VeroE6/Rep3, a stable replicon cell line based on VeroE6 cells, was successfully established and continuously produced viral proteins, sgRNAs and luciferase, and their production was suppressed by treatment with remdesivir or interferon-β. Molnupiravir, a novel coronavirus RdRp inhibitor, inhibited viral replication more potently in VeroE6/Rep3 cells than in VeroE6-based transient replicon cells. In summary, our stable replicon system will be a powerful tool for the identification of SARS-CoV-2 antivirals through high-throughput screening.
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Affiliation(s)
- Tomohisa Tanaka
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Yamanashi, 409-3898, Japan; Center for Life Science Research, University of Yamanashi, Yamanashi, 409-3898, Japan; Division of Hepatitis Virology, Institute for Genetic Medicine, Hokkaido University, Hokkaido, 060-0808, Japan.
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16
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Liu Y, Zhang X, Liu J, Xia H, Zou J, Muruato AE, Periasamy S, Plante JA, Bopp NE, Kurhade C, Bukreyev A, Ren P, Wang T, Menachery VD, Plante KS, Xie X, Weaver SC, Shi PY. A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.14.480460. [PMID: 35194609 PMCID: PMC8863145 DOI: 10.1101/2022.02.14.480460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcriptional regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 (Δ3678). The Δ3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The Δ3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the Δ3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the Δ3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter Δ3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that Δ3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Antonio E. Muruato
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Sivakumar Periasamy
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, Texas, USA
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E. Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Alexander Bukreyev
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Galveston National Laboratory, Galveston, Texas, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tian Wang
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology,University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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17
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Galkin SO, Anisenko AN, Shadrina OA, Gottikh MB. Genetic Engineering Systems to Study Human Viral Pathogens from the Coronaviridae Family. Mol Biol 2022; 56:72-89. [PMID: 35194246 PMCID: PMC8853348 DOI: 10.1134/s0026893322010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022]
Abstract
The COVID-19 pandemic caused by the previously unknown SARS-CoV-2 Betacoronavirus made it extremely important to develop simple and safe cellular systems which allow manipulation of the viral genome and high-throughput screening of its potential inhibitors. In this review, we made an attempt at summarizing the currently existing data on genetic engineering systems used to study not only SARS-CoV-2, but also other viruses from the Coronaviridae family. In addition, the review covers the basic knowledge about the structure and the life cycle of coronaviruses.
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Affiliation(s)
- S. O. Galkin
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
| | - A. N. Anisenko
- Bioengineering and Bioinformatics Department, Moscow State University, 119991 Moscow, Russia
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - O. A. Shadrina
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
| | - M. B. Gottikh
- Chemistry Department, Moscow State University, 119991 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
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18
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Zhang H, Fischer DK, Shuda M, Moore PS, Gao SJ, Ambrose Z, Guo H. Construction and characterization of two SARS-CoV-2 minigenome replicon systems. J Med Virol 2022; 94:2438-2452. [PMID: 35137972 PMCID: PMC9088700 DOI: 10.1002/jmv.27650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/10/2022]
Abstract
The ongoing COVID-19 pandemic severely impacts global public health and economies. In order to facilitate research on SARS-CoV-2 virology and antiviral discovery, a non-infectious viral replicon system operating under biosafety level 2 containment is warranted. We report herein the construction and characterization of two SARS-CoV-2 minigenome replicon systems. First, we constructed the IVT-CoV2-Rep cDNA template to generate a replicon mRNA with nanoluciferase (NLuc) reporter via in vitro transcription (IVT). The replicon mRNA transfection assay demonstrated a rapid and transient replication of IVT-CoV2-Rep in a variety of cell lines, which could be completely abolished by known SARS-CoV-2 replication inhibitors. Our data also suggests that the transient phenotype of IVT-CoV2-Rep is not due to host innate antiviral responses. In addition, we have developed a DNA-launched replicon BAC-CoV2-Rep, which supports the in-cell transcription of a replicon mRNA as initial replication template. The BAC-CoV2-Rep transient transfection system exhibited a much stronger and longer replicon signal compared to the IVT-CoV2-Rep version. We also found that a portion of the NLuc reporter signal was derived from the spliced BAC-CoV2-Rep mRNA and was resistant to antiviral treatment, especially during the early phase after transfection. In summary, the established SARS-CoV-2 transient replicon systems are suitable for basic and antiviral research, and hold promise for stable replicon cell line development with further optimization. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hu Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Douglas K Fischer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Masahiro Shuda
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Patrick S Moore
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Shou-Jiang Gao
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Zandrea Ambrose
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine.,Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh Medical Center
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19
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Abstract
The development of antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been hampered by the lack of efficient cell-based replication systems that are amenable to high-throughput screens in biosafety level 2 laboratories. Here we report that stable cell clones harboring autonomously replicating SARS-CoV-2 RNAs without spike (S), membrane (M), and envelope (E) genes can be efficiently derived from the baby hamster kidney (BHK-21) cell line when a pair of mutations were introduced into the non-structural protein 1 (Nsp1) of SARS-CoV-2 to ameliorate cellular toxicity associated with virus replication. In a proof-of-concept experiment we screened a 273-compound library using replicon cells and identified three compounds as novel inhibitors of SARS-CoV-2 replication. Altogether, this work establishes a robust, cell-based system for genetic and functional analyses of SARS-CoV-2 replication and for the development of antiviral drugs. IMPORTANCE SARS-CoV-2 replicon systems that have been reported up to date were unsuccessful in deriving stable cell lines harboring non-cytopathic replicons. The transient expression of viral sgmRNA or a reporter gene makes it impractical for industry-scale screening of large compound libraries using these systems. Here, for the first time, we derived stable cell clones harboring the SARS-CoV-2 replicon. These clones may now be conveniently cultured in a standard BSL-2 laboratory for high throughput screen of compound libraries. Additionally, our stable replicon cells represent a new model system to study SARS-CoV-2 replication.
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20
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Versatile SARS-CoV-2 Reverse-Genetics Systems for the Study of Antiviral Resistance and Replication. Viruses 2022; 14:v14020172. [PMID: 35215765 PMCID: PMC8878408 DOI: 10.3390/v14020172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 01/02/2023] Open
Abstract
The COVID-19 pandemic continues to threaten healthcare systems worldwide due to the limited access to vaccines, suboptimal treatment options, and the continuous emergence of new and more transmissible SARS-CoV-2 variants. Reverse-genetics studies of viral genes and mutations have proven highly valuable in advancing basic virus research, leading to the development of therapeutics. We developed a functional and highly versatile full-length SARS-CoV-2 infectious system by cloning the sequence of a COVID-19 associated virus isolate (DK-AHH1) into a bacterial artificial chromosome (BAC). Viruses recovered after RNA-transfection of in vitro transcripts into Vero E6 cells showed growth kinetics and remdesivir susceptibility similar to the DK-AHH1 virus isolate. Insertion of reporter genes, green fluorescent protein, and nanoluciferase into the ORF7 genomic region led to high levels of reporter activity, which facilitated high throughput treatment experiments. We found that putative coronavirus remdesivir resistance-associated substitutions F480L and V570L—and naturally found polymorphisms A97V, P323L, and N491S, all in nsp12—did not decrease SARS-CoV-2 susceptibility to remdesivir. A nanoluciferase reporter clone with deletion of spike (S), envelope (E), and membrane (M) proteins exhibited high levels of transient replication, was inhibited by remdesivir, and therefore could function as an efficient non-infectious subgenomic replicon system. The developed SARS-CoV-2 reverse-genetics systems, including recombinants to modify infectious viruses and non-infectious subgenomic replicons with autonomous genomic RNA replication, will permit high-throughput cell culture studies—providing fundamental understanding of basic biology of this coronavirus. We have proven the utility of the systems in rapidly introducing mutations in nsp12 and studying their effect on the efficacy of remdesivir, which is used worldwide for the treatment of COVID-19. Our system provides a platform to effectively test the antiviral activity of drugs and the phenotype of SARS-CoV-2 mutants.
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21
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A structurally conserved RNA element within SARS-CoV-2 ORF1a RNA and S mRNA regulates translation in response to viral S protein-induced signaling in human lung cells. J Virol 2021; 96:e0167821. [PMID: 34757848 PMCID: PMC8791291 DOI: 10.1128/jvi.01678-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The positive-sense, single-stranded RNA genome SARS-CoV-2 harbors functionally important cis-acting elements governing critical aspects of viral gene expression. However, insights on how these elements sense various signals from the host cell and regulate viral protein synthesis are lacking. Here, we identified two novel cis-regulatory elements in SARS-CoV-2 ORF1a and S RNAs and describe their role in translational control of SARS-CoV-2. These elements are sequence-unrelated but form conserved hairpin structures (validated by NMR) resembling Gamma Activated Inhibitor of Translation (GAIT) elements that are found in a cohort of human mRNAs directing translational suppression in myeloid cells in response to IFN-γ. Our studies show that treatment of human lung cells with receptor-binding S1 subunit, S protein pseudotyped lentivirus, and S protein-containing virus-like particles triggers a signaling pathway involving DAP-kinase1 that leads to phosphorylation and release of the ribosomal protein L13a from the large ribosomal subunit. Released L13a forms a Virus Activated Inhibitor of Translation (VAIT) complex that binds to ORF1a and S VAIT elements, causing translational silencing. Translational silencing requires extracellular S protein (and its interaction with host ACE2 receptor), but not its intracellular synthesis. RNA-protein interaction analyses and in vitro translation experiments showed that GAIT and VAIT elements do not compete with each other, highlighting differences between the two pathways. Sequence alignments of SARS-CoV-2 genomes showed a high level of conservation of VAIT elements, suggesting their functional importance. This VAIT-mediated translational control mechanism of SARS-CoV-2 may provide novel targets for small molecule intervention and/or facilitate development of more effective mRNA vaccines. Importance Specific RNA elements in the genomes of RNA viruses play important roles in host-virus interaction. For SARS-CoV-2, the mechanistic insights on how these RNA elements could sense the signals from the host cell are lacking. Here we report a novel relationship between the GAIT-like SARS-CoV-2 RNA element (called VAITs) and the signal generated from the host cell. We show that for SARS-CoV-2, the interaction of spike protein with ACE2 not only serves the purpose for viral entry into the host cell, but also transduces signals that culminate into the phosphorylation and the release of L13a from the large ribosomal subunit. We also show that this event leads to the translational arrest of ORF1a and S mRNAs in a manner dependent on the structure of the RNA elements. Translational control of viral mRNA by a host-cell generated signal triggered by viral protein is a new paradigm in the host-virus relationship.
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22
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Wang B, Zhang C, Lei X, Ren L, Zhao Z, Wang J, Huang H. Construction of Non-infectious SARS-CoV-2 Replicons and Their Application in Drug Evaluation. Virol Sin 2021; 36:890-900. [PMID: 33835389 PMCID: PMC8034055 DOI: 10.1007/s12250-021-00369-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a devastating pandemic worldwide. Vaccines and antiviral drugs are the most promising candidates for combating this global epidemic, and scientists all over the world have made great efforts to this end. However, manipulation of the SARS-CoV-2 should be performed in the biosafety level 3 laboratory. This makes experiments complicated and time-consuming. Therefore, a safer system for working with this virus is urgently needed. Here, we report the construction of plasmid-based, non-infectious SARS-CoV-2 replicons with turbo-green fluorescent protein and/or firefly luciferase reporters by reverse genetics using transformation-associated recombination cloning in Saccharomyces cerevisiae. Replication of these replicons was achieved simply by direct transfection of cells with the replicon plasmids as evident by the expression of reporter genes. Using SARS-CoV-2 replicons, the inhibitory effects of E64-D and remdesivir on SARS-CoV-2 replication were confirmed, and the half-maximal effective concentration (EC50) value of remdesivir and E64-D was estimated by different quantification methods respectively, indicating that these SARS-CoV-2 replicons are useful tools for antiviral drug evaluation.
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Affiliation(s)
- Bei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Chongyang Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Xiaobo Lei
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China
| | - Zhendong Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China.
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China.
| | - He Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100176, China.
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23
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Hall MD, Anderson JM, Anderson A, Baker D, Bradner J, Brimacombe KR, Campbell EA, Corbett KS, Carter K, Cherry S, Chiang L, Cihlar T, de Wit E, Denison M, Disney M, Fletcher CV, Ford-Scheimer SL, Götte M, Grossman AC, Hayden FG, Hazuda DJ, Lanteri CA, Marston H, Mesecar AD, Moore S, Nwankwo JO, O’Rear J, Painter G, Singh Saikatendu K, Schiffer CA, Sheahan TP, Shi PY, Smyth HD, Sofia MJ, Weetall M, Weller SK, Whitley R, Fauci AS, Austin CP, Collins FS, Conley AJ, Davis MI. Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit. J Infect Dis 2021; 224:S1-S21. [PMID: 34111271 PMCID: PMC8280938 DOI: 10.1093/infdis/jiab305] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The NIH Virtual SARS-CoV-2 Antiviral Summit, held on 6 November 2020, was organized to provide an overview on the status and challenges in developing antiviral therapeutics for coronavirus disease 2019 (COVID-19), including combinations of antivirals. Scientific experts from the public and private sectors convened virtually during a live videocast to discuss severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) targets for drug discovery as well as the preclinical tools needed to develop and evaluate effective small-molecule antivirals. The goals of the Summit were to review the current state of the science, identify unmet research needs, share insights and lessons learned from treating other infectious diseases, identify opportunities for public-private partnerships, and assist the research community in designing and developing antiviral therapeutics. This report includes an overview of therapeutic approaches, individual panel summaries, and a summary of the discussions and perspectives on the challenges ahead for antiviral development.
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Affiliation(s)
- Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - James M Anderson
- Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Annaliesa Anderson
- Pfizer Vaccine Research and Development, Pfizer, Pearl River, New York, USA
| | - David Baker
- University of Washington, Seattle, Washington, USA
| | - Jay Bradner
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Kyle R Brimacombe
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Sara Cherry
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | | | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mark Denison
- Vanderbilt University, Nashville, Tennessee, USA
| | | | | | - Stephanie L Ford-Scheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | - Abigail C Grossman
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | | | | | | | - Hilary Marston
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Stephanie Moore
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Jules O’Rear
- US Food and Drug Administration, Silver Spring, Maryland, USA
| | | | | | - Celia A Schiffer
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Timothy P Sheahan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, Texas, USA
| | - Hugh D Smyth
- University of Texas at Austin, Austin, Texas, USA
| | | | - Marla Weetall
- PTC Therapeutics, Inc, South Plainfield, New Jersey, USA
| | - Sandra K Weller
- University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Richard Whitley
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher P Austin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Francis S Collins
- Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony J Conley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Mindy I Davis
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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24
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Zhang X, Liu Y, Liu J, Bailey AL, Plante KS, Plante JA, Zou J, Xia H, Bopp NE, Aguilar PV, Ren P, Menachery VD, Diamond MS, Weaver SC, Xie X, Shi PY. A trans-complementation system for SARS-CoV-2 recapitulates authentic viral replication without virulence. Cell 2021; 184:2229-2238.e13. [PMID: 33691138 PMCID: PMC7901297 DOI: 10.1016/j.cell.2021.02.044] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/25/2022]
Abstract
The biosafety level 3 (BSL-3) requirement to culture severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a bottleneck for research. Here, we report a trans-complementation system that produces single-round infectious SARS-CoV-2 that recapitulates authentic viral replication. We demonstrate that the single-round infectious SARS-CoV-2 can be used at BSL-2 laboratories for high-throughput neutralization and antiviral testing. The trans-complementation system consists of two components: a genomic viral RNA containing ORF3 and envelope gene deletions, as well as mutated transcriptional regulator sequences, and a producer cell line expressing the two deleted genes. Trans-complementation of the two components generates virions that can infect naive cells for only one round but does not produce wild-type SARS-CoV-2. Hamsters and K18-hACE2 transgenic mice inoculated with the complementation-derived virions exhibited no detectable disease, even after intracranial inoculation with the highest possible dose. Thus, the trans-complementation platform can be safely used at BSL-2 laboratories for research and countermeasure development.
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Affiliation(s)
- Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Adam L Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nathen E Bopp
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Patricia V Aguilar
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Michael S Diamond
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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