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Scroggs SLP, Gass JT, Chinnasamy R, Widen SG, Azar SR, Rossi SL, Arterburn JB, Vasilakis N, Hanley KA. Evolution of resistance to fluoroquinolones by dengue virus serotype 4 provides insight into mechanism of action and consequences for viral fitness. Virology 2020; 552:94-106. [PMID: 33120225 PMCID: PMC7528753 DOI: 10.1016/j.virol.2020.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
Drugs against flaviviruses such as dengue (DENV) and Zika (ZIKV) virus are urgently needed. We previously demonstrated that three fluoroquinolones, ciprofloxacin, enoxacin, and difloxacin, suppress replication of six flaviviruses. To investigate the barrier to resistance and mechanism(s) of action of these drugs, DENV-4 was passaged in triplicate in HEK-293 cells in the presence or absence of each drug. Resistance to ciprofloxacin was detected by the seventh passage and to difloxacin by the tenth, whereas resistance to enoxacin did not occur within ten passages. Two putative resistance-conferring mutations were detected in the envelope gene of ciprofloxacin and difloxacin-resistant DENV-4. In the absence of ciprofloxacin, ciprofloxacin-resistant viruses sustained a significantly higher viral titer than control viruses in HEK-293 and HuH-7 cells and resistant viruses were more stable than control viruses at 37 °C. These results suggest that the mechanism of action of ciprofloxacin and difloxacin involves interference with virus binding or entry.
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Affiliation(s)
- Stacey L P Scroggs
- Department of Biology, New Mexico State University, Las Cruces, NM, USA.
| | - Jordan T Gass
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Ramesh Chinnasamy
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Steven G Widen
- Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sasha R Azar
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Shannan L Rossi
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Jeffrey B Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA
| | - Nikos Vasilakis
- Department of Pathology, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Biodefense and Emerging Infectious Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Center for Tropical Diseases, The University of University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, The University of University of Texas Medical Branch, Galveston, TX, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
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SuPReMe: a rapid reverse genetics method to generate clonal populations of recombinant RNA viruses. Emerg Microbes Infect 2018; 7:40. [PMID: 29559627 PMCID: PMC5861084 DOI: 10.1038/s41426-018-0040-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 11/26/2022]
Abstract
Reverse genetics systems enable the manipulation of viral genomes and are proving to be essential for studying RNA viruses. Methods for generating clonal virus populations are particularly useful for studying the impact of genomic modifications on viral properties. Here, by exploiting a chikungunya virus model, we compare viral populations and their replicative fitness when generated using either the rapid and user-friendly PCR-based ISA (Infectious Subgenomic Amplicons) method or classical infectious clone technology. As anticipated, the ISA method resulted in greater genetic diversity of the viral populations, but no significant difference in viral fitness in vitro was observed. On the basis of these results, a new ISA-derived reverse genetics procedure was developed. This method, designated ‘SuPReMe’ (Subgenomic Plasmids Recombination Method), in which digested plasmids containing subgenomic DNA fragments were directly transfected into permissive cells, retains the following major advantages of the ISA method: it is rapid, flexible and does not require the cloning of complete genomes. Moreover, SuPReMe has been shown to produce virus populations with genetic diversity and replicative fitness similar to those obtained using conventional infectious clone technology. SuPReMe, therefore, represents an effective and promising option for the rapid generation of clonal recombinant populations of single-stranded positive-sense RNA viruses.
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Zhu Z, Chan JFW, Tee KM, Choi GKY, Lau SKP, Woo PCY, Tse H, Yuen KY. Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic. Emerg Microbes Infect 2016; 5:e22. [PMID: 26980239 PMCID: PMC4820678 DOI: 10.1038/emi.2016.48] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/21/2022]
Abstract
Less than 20 sporadic cases of human Zika virus (ZIKV) infection were reported in Africa and Asia before 2007, but large outbreaks involving up to 73% of the populations on the Pacific islands have started since 2007, and spread to the Americas in 2014. Moreover, the clinical manifestation of ZIKV infection has apparently changed, as evident by increasing reports of neurological complications, such as Guillain-Barré syndrome in adults and congenital anomalies in neonates. We comprehensively compared the genome sequences of pre-epidemic and epidemic ZIKV strains with complete genome or complete polyprotein sequences available in GenBank. Besides the reported phylogenetic clustering of the epidemic strains with the Asian lineage, we found that the topology of phylogenetic tree of all coding regions is the same except that of the non-structural 2B (NS2B) coding region. This finding was confirmed by bootscan analysis and multiple sequence alignment, which suggested the presence of a fragment of genetic recombination at NS2B with that of Spondweni virus. Moreover, the representative epidemic strain possesses one large bulge of nine bases instead of an external loop on the first stem-loop structure at the 3'-untranslated region just distal to the stop codon of the NS5 in the 1947 pre-epidemic prototype strain. Fifteen amino acid substitutions are found in the epidemic strains when compared with the pre-epidemic strains. As mutations in other flaviviruses can be associated with changes in virulence, replication efficiency, antigenic epitopes and host tropism, further studies would be important to ascertain the biological significance of these genomic changes.
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Affiliation(s)
- Zheng Zhu
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kah-Meng Tee
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Garnet Kwan-Yue Choi
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
| | - Susanna Kar-Pui Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Patrick Chiu-Yat Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Herman Tse
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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