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Chen Y, Li X, Han F, Ji B, Li Y, Yan J, Wang M, Fan J, Zhang S, Lu L, Zou P. The nucleoside analog 4'-fluorouridine suppresses the replication of multiple enteroviruses by targeting 3D polymerase. Antimicrob Agents Chemother 2024:e0005424. [PMID: 38687016 DOI: 10.1128/aac.00054-24] [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: 01/17/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Human enteroviruses are the major pathogens causing hand-foot-and-mouth disease in infants and young children throughout the world, and infection with enterovirus is also associated with severe complications, such as aseptic meningitis and myocarditis. However, there are no antiviral drugs available to treat enteroviruses infection at present. In this study, we found that 4'-fluorouridine (4'-FlU), a nucleoside analog with low cytotoxicity, exhibited broad-spectrum activity against infections of multiple enteroviruses with EC50 values at low micromolar levels, including coxsackievirus A10 (CV-A10), CV-A16, CV-A6, CV-A7, CV-B3, enterovirus A71 (EV-A71), EV-A89, EV-D68, and echovirus 6. With further investigation, the results indicated that 4'-FlU directly interacted with the RNA-dependent RNA polymerase of enterovirus, the 3D pol, and impaired the polymerase activity of 3D pol, hence inhibiting viral RNA synthesis and significantly suppressing viral replication. Our findings suggest that 4'-FlU could be promisingly developed as a broad-spectrum direct-acting antiviral agent for anti-enteroviruses therapy.
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Affiliation(s)
- Yongkang Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaohong Li
- Clinical Center for BioTherapy, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fengyang Han
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Beihong Ji
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuan Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jingjing Yan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Fan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shuye Zhang
- Clinical Center for BioTherapy, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Peng Zou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Rai A, Ammi Z, Anes-Boulahbal DL, Assadi AA, Amrane A, Baaloudj O, Mouni L. Molecular Amplification and Cell Culturing Efficiency for Enteroviruses' Detection in Cerebrospinal Fluids of Algerian Patients Suffering from Meningitis. Viruses 2024; 16:170. [PMID: 38399946 PMCID: PMC10891896 DOI: 10.3390/v16020170] [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: 01/05/2024] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/25/2024] Open
Abstract
Enteroviruses (EVs) represent a major cause of viral meningitis, being responsible for nearly 1 billion infections each year worldwide. Several techniques were developed to obtain better diagnostic results of EV infections. Herein, we evaluated the efficiency of EV detection through isolation on both Rhabdomyosarcoma (RD) and Vero cell line cultures, conventional reverse transcription-polymerase chain reaction (RT-PCR) and real-time RT-PCR. Thus, 50 cerebrospinal fluid (CSF) samples belonging to patients suspected to have viral meningitis in northern Algeria were collected, anonymously numbered from 1 to 50 and subjected to the above-mentioned techniques for EV detection. Using real-time RT-PCR, 34 CSF samples were revealed to be positive for viral origin of meningitis (68%). Thirteen of them were positive when the conventional RT-PCR was used (26%), and only three samples gave positive results when the cell culture technique was used (6%). Surprisingly, two cell culture-positive CSF samples, namely, 31 and 39, were negative using RT-PCR directly on the original samples. However, they turned to be positive when amplification was carried out on their corresponding cell culture supernatant. The cell-cultured viral isolates were then identified by sequencing their viral genome's VP1 regions. All of them were revealed to belong to the echovirus 27 strain. This investigation demonstrates that RT-PCR techniques are often more sensitive, accurate and much faster, providing reliable results within a clinically acceptable timeframe. However, viral isolation on cell cultures remains crucial to obtain enough viral load for serological tests or even to avoid the rare, but existing, false negative PCR.
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Affiliation(s)
- Abdelwahab Rai
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Zohra Ammi
- Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
| | - Dahbia Leila Anes-Boulahbal
- Laboratoire des Entérovirus, Département de Virologie, Institut Pasteur d’Alger, Annexe de Sidi-Fredj, Alger 16000, Algeria;
| | - Aymen Amin Assadi
- College of Engineering, Imam Mohammad Ibn Saud Islamic University, IMSIU, Riyadh 11432, Saudi Arabia;
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Abdeltif Amrane
- Ecole Nationale Supérieure de Chimie de Rennes, University Rennes, CNRS, ISCR-UMR 6226, 35000 Rennes, France;
| | - Oussama Baaloudj
- Laboratory of Reaction Engineering, Faculty of Mechanical Engineering and Process Engineering, Université des Sciences et de la Technologie Houari Boumediene, BP 32, Algiers 16111, Algeria;
| | - Lotfi Mouni
- Laboratoire de Gestion et Valorisation des Ressources Naturelles et Assurance Qualité, Faculté SNVST, Université de Bouira, Bouira 10000, Algeria;
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Soria-Villalba A, Pesantes N, Jiménez-Hernández N, Pons J, Moya A, Pérez-Brocal V. Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome. Microorganisms 2024; 12:162. [PMID: 38257988 PMCID: PMC10820677 DOI: 10.3390/microorganisms12010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.
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Affiliation(s)
| | - Nicole Pesantes
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Nuria Jiménez-Hernández
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Javier Pons
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), 46020 Valencia, Spain; (N.P.); (N.J.-H.); (J.P.); (A.M.)
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
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Noisumdaeng P, Puthavathana P. Molecular evolutionary dynamics of enterovirus A71, coxsackievirus A16 and coxsackievirus A6 causing hand, foot and mouth disease in Thailand, 2000-2022. Sci Rep 2023; 13:17359. [PMID: 37833525 PMCID: PMC10576028 DOI: 10.1038/s41598-023-44644-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/11/2023] [Indexed: 10/15/2023] Open
Abstract
Hand, foot and mouth disease (HFMD) is a public health threat worldwide, particularly in the Asia-Pacific region. Enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16), and CVA6 are the major pathogens causing HFMD outbreaks in several countries, including Thailand. We retrieved 385 VP1 nucleotide sequences, comprising 228 EV-A71, 33 CVA16, and 124 CVA6, deposited in the databases between 2000 and 2022 for molecular evolutionary characterization using Bayesian phylogeny. All EV-A71 identified belonged to genotype B, subgenotypes B4, and B5, and to genotype C, subgenotypes C1, C2, C4a, C4b, and C5. The analyzes demonstrated these viruses' co-circulation and subgenotypic changes throughout the past two decades. The CVA16 was grouped in genotype B1, predominantly subgenotype B1a, and the CVA6 was grouped in subgenotype D3, clades 1-4. The tMRCA of EV-A71 genotypes B and C, CVA16 B1, and CVA6 D3 dated 1993.79, 1982.62, 1995.86, and 2007.31, respectively, suggesting that the viruses were likely introduced and cryptically circulated in Thailand before the HFMD cases were recognized. We demonstrated these viruses' fluctuation and cyclical pattern throughout the two decades of observation. This study provided insight into evolutionary dynamics concerning molecular epidemiology and supported the selection of current genotype-matched vaccines, vaccine development, and implementation.
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Affiliation(s)
- Pirom Noisumdaeng
- Faculty of Public Health, Thammasat University, Pathum Thani, 12120, Thailand.
- Thammasat University Research Unit in Modern Microbiology and Public Health Genomics, Thammasat University, Pathum Thani, 12120, Thailand.
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