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Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. eLife 2023; 12:RP89035. [PMID: 37988285 PMCID: PMC10662946 DOI: 10.7554/elife.89035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the coronavirus disease 2019 pandemic, already established methods were challenged by the large genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Tatjana Kipfer
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Martin J Lett
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Christopher MR Lang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, MattenstrasseBaselSwitzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
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Kipfer E, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. bioRxiv 2023:2023.05.11.540343. [PMID: 37292682 PMCID: PMC10245781 DOI: 10.1101/2023.05.11.540343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Kipfer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Martin J. Lett
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Christopher M. R. Lang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Mittelholzer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
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Seeburg U, Urda L, Otte F, Lett MJ, Caimi S, Mittelholzer C, Klimkait T. Virus Inactivation by Formaldehyde and Common Lysis Buffers. Viruses 2023; 15:1693. [PMID: 37632035 PMCID: PMC10458352 DOI: 10.3390/v15081693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Numerous mammalian viruses are routinely analyzed in clinical diagnostic laboratories around the globe or serve as indispensable model systems in viral research. Potentially infectious viral entities are handled as blood, biopsies, or cell and tissue culture samples. Countless protocols describe methods for virus fixation and inactivation, yet for many, a formal proof of safety and completeness of inactivation remains to be shown. While modern nucleic acid extraction methods work quite effectively, data are largely lacking on possible residual viral infectivity, e.g., when assessed after extended culture times, which maximizes the sensitivity for low levels of residual infectiousness. Therefore, we examined the potency and completeness of inactivation procedures on virus-containing specimens when applying commonly used fixatives like formaldehyde or nucleic acid extraction/lysis buffers. Typical representatives of different virus classes, including RNA and DNA viruses, enveloped and non-enveloped, such as adenovirus, enterovirus, lentivirus, and coronavirus, were used, and the reduction in the in vitro infectiousness was assessed for standard protocols. Overall, a 30-minute incubation with formaldehyde at room temperature effectively inactivated all tested enveloped and non-enveloped viruses. Full inactivation of HIV-1 and ECHO-11 was also achieved with all buffers in the test, whereas for SARS-CoV-2 and AdV-5, only five of the seven lysis buffers were fully effective under the tested conditions.
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Urda L, Kreuter MH, Drewe J, Boonen G, Butterweck V, Klimkait T. The Petasites hybridus CO 2 Extract (Ze 339) Blocks SARS-CoV-2 Replication In Vitro. Viruses 2022; 14:v14010106. [PMID: 35062310 PMCID: PMC8781559 DOI: 10.3390/v14010106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), has spread worldwide, affecting over 250 million people and resulting in over five million deaths. Antivirals that are effective are still limited. The antiviral activities of the Petasites hybdridus CO2 extract Ze 339 were previously reported. Thus, to assess the anti-SARS-CoV-2 activity of Ze 339 as well as isopetasin and neopetasin as major active compounds, a CPE and plaque reduction assay in Vero E6 cells was used for viral output. Antiviral effects were tested using the original virus (Wuhan) and the Delta variant of SARS-CoV-2. The antiviral drug remdesivir was used as control. Pre-treatment with Ze 339 in SARS-CoV-2-infected Vero E6 cells with either virus variant significantly inhibited virus replication with IC50 values of 0.10 and 0.40 μg/mL, respectively. The IC50 values obtained for isopetasin ranged between 0.37 and 0.88 μM for both virus variants, and that of remdesivir ranged between 1.53 and 2.37 μM. In conclusion, Ze 339 as well as the petasins potently inhibited SARS-CoV-2 replication in vitro of the Wuhan and Delta variants. Since time is of essence in finding effective treatments, clinical studies will have to demonstrate if Ze339 can become a therapeutic option to treat SARS-CoV-2 infections.
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Affiliation(s)
- Lorena Urda
- Department Biomedicine, University of Basel, Petersplatz 10, 4051 Basel, Switzerland
| | | | - Jürgen Drewe
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Georg Boonen
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Veronika Butterweck
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Thomas Klimkait
- Department Biomedicine, University of Basel, Petersplatz 10, 4051 Basel, Switzerland
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Brown JA, Nsakala BL, Mokhele K, Rakuoane I, Muhairwe J, Urda L, Amstutz A, Tschumi N, Klimkait T, Labhardt ND. Viral suppression after transition from nonnucleoside reverse transcriptase inhibitor- to dolutegravir-based antiretroviral therapy: A prospective cohort study in Lesotho (DO-REAL study). HIV Med 2021; 23:287-293. [PMID: 34632682 PMCID: PMC9293184 DOI: 10.1111/hiv.13189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Since 2018, the World Health Organization has recommended dolutegravir (DTG)-containing antiretroviral therapy (ART) for most people living with HIV. Country programmes across Africa have subsequently transitioned from other, mostly nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART to DTG-based ART. This study aims to assess the virological impact of programmatic transitioning to DTG-based ART in Lesotho. METHODS The prospective Dolutegravir in Real-Life in Lesotho (DO-REAL) cohort enrols people living with HIV initiating or transitioning to DTG-based ART in Lesotho. Here, we present data from participants who transitioned from NNRTI- to DTG-based ART between February and December 2020. Blood samples collected at transition and at 16 weeks' follow-up (window 8-32 weeks) were used for viral load (VL) and resistance testing. RESULTS Among 1347 participants, follow-up data was available for 1225. The majority (60%) were female, median age at transition was 47 years [interquartile range (IQR): 38-56], and median (IQR) time since ART initiation was 5.9 (3.5-9.0) years. Among those with complete VL data, the rate of viral suppression to < 100 copies/mL was 1093/1116 (98%) before, 1073/1116 (96%) at, and 1098/1116 (98%) after transition. Even among those with a VL ≥ 100 copies/mL at transition, 42/44 (95%) achieved suppression to < 100 copies/mL at follow-up. Seven participants had a VL ≥ 1000 copies/mL at follow-up and did not harbour any integrase mutations associated with resistance to DTG. CONCLUSIONS The high levels of viral suppression observed are encouraging regarding virological outcomes upon programmatic transitioning from NNRTI- to DTG-based ART.
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Affiliation(s)
- Jennifer A Brown
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Kuena Mokhele
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | | | - Lorena Urda
- Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Nadine Tschumi
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus D Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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Aeschlimann SH, Graf C, Mayilo D, Lindecker H, Urda L, Kappes N, Burr AL, Simonis M, Splinter E, Min M, Laux H. Enhanced CHO Clone Screening: Application of Targeted Locus Amplification and Next‐Generation Sequencing Technologies for Cell Line Development. Biotechnol J 2019; 14:e1800371. [DOI: 10.1002/biot.201800371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/20/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Samuel H. Aeschlimann
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Christian Graf
- Novartis Technical R&D, Technical Development BiosimilarsHexal AG, Keltenring 1+3 82041 Oberhaching Germany
| | - Dmytro Mayilo
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Hélène Lindecker
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Lorena Urda
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Nora Kappes
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | - Alicia Leone Burr
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
| | | | - Erik Splinter
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Max Min
- Cergentis B.VYalelaan 62 3584 CM Utrecht The Netherlands
| | - Holger Laux
- Novartis Institutes for BioMedical Research, Integrated Biologics Profiling UnitCH‐4002 Basel Switzerland
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