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Ullah A, Waqas M, Aziz S, Rahman SU, Khan S, Khalid A, Abdalla AN, Uddin J, Halim SA, Khan A, Al-Harrasi A. Bioinformatics and immunoinformatics approach to develop potent multi-peptide vaccine for coxsackievirus B3 capable of eliciting cellular and humoral immune response. Int J Biol Macromol 2023; 239:124320. [PMID: 37004935 DOI: 10.1016/j.ijbiomac.2023.124320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
Coxsackievirus B3 (CVB3) is a viral pathogen of various human disorders with no effective preventative interventions. Herein, we aimed to design a chimeric vaccine construct for CVB3 using reverse vaccinology and immunoinformatics approaches by screening the whole viral polyprotein sequence. Firstly, screening and mapping of viral polyprotein to predict 21 immunodominant epitopes (B-cell, CD8+ and CD4+ T-cell epitopes), fused with an adjuvant (Resuscitation-promoting factor), appropriate linkers, HIV-TAT peptide, Pan DR epitope, and 6His-tag to assemble a multi-epitope vaccine construct. The chimeric construct is predicted as probable antigen, non-allergen, stable, possess encouraging physicochemical features, and indicates a broader population coverage (98 %). The tertiary structure of the constructed vaccine was predicted and refined, and its interaction with the Toll-like receptor 4 (TLR4) was investigated through molecular docking and dynamics simulation. Computational cloning of the construct was carried out in pET28a (+) plasmid to guarantee the higher expression of the vaccine protein. Lastly, in silico immune simulation foreseen that humoral and cellular immune responses would be elicited in response to the administration of such a potent chimeric construct. Thus, the design constructed could vaccinate against CVB3 infection and various CVB serotypes. However, further in vitro/in vivo research must assess its safety and effectiveness.
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Huang S, Zhang C, Li J, Dai Z, Huang J, Deng F, Wang X, Yue X, Hu X, Li Y, Deng Y, Wang Y, Zhao W, Zhong Z, Wang Y. Designing a multi-epitope vaccine against coxsackievirus B based on immunoinformatics approaches. Front Immunol 2022; 13:933594. [PMID: 36439191 PMCID: PMC9682020 DOI: 10.3389/fimmu.2022.933594] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/18/2022] [Indexed: 12/11/2023] Open
Abstract
Coxsackievirus B (CVB) is one of the major viral pathogens of human myocarditis and cardiomyopathy without any effective preventive measures; therefore, it is necessary to develop a safe and efficacious vaccine against CVB. Immunoinformatics methods are both economical and convenient as in-silico simulations can shorten the development time. Herein, we design a novel multi-epitope vaccine for the prevention of CVB by using immunoinformatics methods. With the help of advanced immunoinformatics approaches, we predicted different B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes, respectively. Subsequently, we constructed the multi-epitope vaccine by fusing all conserved epitopes with appropriate linkers and adjuvants. The final vaccine was found to be antigenic, non-allergenic, and stable. The 3D structure of the vaccine was then predicted, refined, and evaluated. Molecular docking and dynamics simulation were performed to reveal the interactions between the vaccine with the immune receptors MHC-I, MHC-II, TLR3, and TLR4. Finally, to ensure the complete expression of the vaccine protein, the sequence of the designed vaccine was optimized and further performed in-silico cloning. In conclusion, the molecule designed in this study could be considered a potential vaccine against CVB infection and needed further experiments to evaluate its safety and efficacy.
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Affiliation(s)
- Sichao Huang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Congcong Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Jianing Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zongmao Dai
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Jingjing Huang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Fengzhen Deng
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xumeng Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xinxin Yue
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xinnan Hu
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yuxuan Li
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yushu Deng
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yanhang Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
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Torii S, Itamochi M, Katayama H. Inactivation kinetics of waterborne virus by ozone determined by a continuous quench flow system. WATER RESEARCH 2020; 186:116291. [PMID: 32836147 DOI: 10.1016/j.watres.2020.116291] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 05/22/2023]
Abstract
Ozone has a strong oxidation power that allows effective inactivation of waterborne viruses. Few studies have accurately measured the kinetic relationship between virus inactivation and ozone exposure, because the high reactivity of ozone makes it difficult to measure them simultaneously. A continuous quench flow system (CQFS) is a possible solution for analyzing such a fast reaction; however, previous studies reported that CQFS provided different results of inactivation rate constants from the batch system. The objectives of this study were (1) to develop a CQFS to evaluate the kinetics of microbial inactivation accurately, (2) to evaluate the inactivation rate constants of waterborne virus by ozone, and (3) to compare the results with previous studies. The results indicated that the simple plug flow assumption in the reaction tube of CQFS led to underestimation of the rate constants. The accurate measurement of rate constants was achieved by the pseudo-first-order reaction model that takes the residence time distribution (RTD; i.e., the laminar flow assumption) into account. The results of inactivation experiments suggested that the resistance of viruses were getting higher in the following order: Qβ < MS2, fr, GA < CVB5 Faulkner, φX-174, PV1 Sabin, CVB3 Nancy. The environmental isolates of CVB3 and CVB5 had a 2-fold higher resistance compared with their lab strains. Predicted CT values for 4-log inactivation ranged from 0.018 mg sec L-1 (Qβ) to 0.31 mg sec L-1 (CVB3 Environmental strain). The required CT values for 4-log PV1 inactivation was 0.15 mg sec L-1, which was 166-fold smaller than those reported in the United States Environmental Protection Agency guidance manuals. The overestimation in previous studies was due to the sparse assumption of RTD in the reactor. Consequently, the required ozone CT values for virus inactivation should be reconsidered to minimize the health risks and environmental costs in water treatment.
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Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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Two Natural Recombination gave rise to the Coxsackievirus B3 GV that triggered outbreaks in China in 2006 - 2012. Infect Dis Now 2020; 51:81-85. [PMID: 33007404 DOI: 10.1016/j.medmal.2020.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
Coxsackievirus B3 serotype GV caused the epidemic of Coxsackievirus B3 infection in China from 2006 to 2012. To study the evolution and recombination of Coxsackievirus B3 serotype GV, we performed recombination and phylogenetic analysis of 499 complete genomes of Enterovirus B available in GenBank, dated April 2019. Results indicated that most of the strains of Coxsackievirus B3 GV in P1 region were derived from a Coxsackievirus B3 GVI parent, and in P2-3 region from EchoV E25 strain, with nucleotide identities of 97.2% and 94.7%, respectively. Other strains of Coxsackievirus B3 GV-C1 in P1-P2 regions were derived from Coxsackievirus B3 GV-C3, whereas those in P3 regions were from CVB5. These naturally occurring recombination events were confirmed by phylogenetic analysis. This study indicates that two naturally occurring recombination gave rise to the coxsackievirus B3 GV that triggered outbreaks in China in 2006 - 2012.
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Fu X, Mao L, Wan Z, Xu R, Ma Y, Shen L, Jin X, Zhang C. High proportion of coxsackievirus B3 genotype A in hand, foot and mouth disease in Zhenjiang, China, 2011–2016. Int J Infect Dis 2019; 87:1-7. [DOI: 10.1016/j.ijid.2019.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/27/2022] Open
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Han Z, Zhang Y, Huang K, Wang J, Tian H, Song Y, Yang Q, Yan D, Zhu S, Yao M, Wang X, Xu W. Two Coxsackievirus B3 outbreaks associated with hand, foot, and mouth disease in China and the evolutionary history worldwide. BMC Infect Dis 2019; 19:466. [PMID: 31126252 PMCID: PMC6534883 DOI: 10.1186/s12879-019-4107-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/17/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Coxsackievirus B3 (CV-B3) is usually associated with aseptic meningitis and myocarditis; however, the association between CV-B3 and hand, foot, and mouth disease (HFMD) has not been clearly demonstrated, and the phylogenetic dynamics and transmission history of CV-B3 have not been well summarized. METHOD Two HFMD outbreaks caused by CV-B3 were described in Hebei Province in 2012 and in Shandong Province in 2016 in China. To analyze the epidemiological features of two CV-B3 outbreaks, a retrospective analysis was conducted. All clinical specimens from CV-B3 outbreaks were collected and disposed according to the standard procedures supported by the WHO Global Poliovirus Specialized Laboratory. EV genotyping and phylogenetic analysis were performed to illustrate the genetic characteristics of CV-B3 in China and worldwide. RESULTS Two transmissible lineages (lineage 2 and 3) were observed in Northern China, which acted as an important "reservoir" for the transmission of CV-B3. Sporadic exporting and importing of cases were observed in almost all regions. In addition, the global sequences of CV-B3 showed a tendency of geographic-specific clustering, indicating that geographic-driven adaptation plays a major role in the diversification and evolution of CV-B3. CONCLUSIONS Overall, our study indicated that CV-B3 is a causative agent of HFMD outbreak and revealed the phylogenetic dynamics of CV-B3 worldwide, as well as provided an insight on CV-B3 outbreaks for effective intervention and countermeasures.
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Affiliation(s)
- Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.
| | - Keqiang Huang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan City, Shandong Province, People's Republic of China
| | - Huifang Tian
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang City, Hebei Province, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China
| | - Mingxiao Yao
- Shandong Center for Disease Control and Prevention, Jinan City, Shandong Province, People's Republic of China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan City, Shandong Province, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory of biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, People's Republic of China.,Anhui University of Science and Technology, Hefei City, Anhui Province, People's Republic of China
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Laxmivandana R, Cherian SS, Yergolkar P, Chitambar SD. Genomic characterization of coxsackievirus type B3 strains associated with acute flaccid paralysis in south-western India. J Gen Virol 2016; 97:694-705. [DOI: 10.1099/jgv.0.000391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
| | - Sarah S. Cherian
- Bioinformatics Group, National Institute of Virology, Pune, India
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Molecular epidemiology of coxsackievirus B3 infection in Spain, 2004-2014. Arch Virol 2016; 161:1365-70. [DOI: 10.1007/s00705-016-2783-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
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Huang HW, Chen YS, Chen JYF, Lu PL, Lin YC, Chen BC, Chou LC, Wang CF, Su HJ, Huang YC, Shi YY, Chen HL, Sanno-Duanda B, Huang TS, Lin KH, Tyan YC, Chu PY. Phylodynamic reconstruction of the spatiotemporal transmission and demographic history of coxsackievirus B2. BMC Bioinformatics 2015; 16:302. [PMID: 26390997 PMCID: PMC4578604 DOI: 10.1186/s12859-015-0738-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/11/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013. RESULTS Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region. CONCLUSIONS Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.
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Affiliation(s)
- Hui-Wen Huang
- Department of Anesthesiology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, ROC, Taiwan. .,Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, ROC, Taiwan.
| | - Yao-Shen Chen
- Division of Infectious Diseases, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. .,Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan. .,Department of Internal Medicine, National Yang-Ming Medical University, Taipei, ROC, Taiwan.
| | - Jeff Yi-Fu Chen
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Po-Liang Lu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. .,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Yung-Cheng Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, ROC, Taiwan.
| | - Bao-Chen Chen
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan.
| | - Li-Chiu Chou
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Chu-Feng Wang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Hui-Ju Su
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan.
| | - Yi-Chien Huang
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Yong-Ying Shi
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Hsiu-Lin Chen
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. .,Department of Respiratory Therapy, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Bintou Sanno-Duanda
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan. .,Department of laboratory medicine, Edward Francis Small Teaching Hospital, Banjul, Gambia.
| | - Tsi-Shu Huang
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, ROC, Taiwan.
| | - Kuei-Hsiang Lin
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
| | - Yu-Chang Tyan
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Pei-Yu Chu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, ROC, Taiwan. .,Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, ROC, Taiwan.
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Klein M, Chong P. Is a multivalent hand, foot, and mouth disease vaccine feasible? Hum Vaccin Immunother 2015; 11:2688-704. [PMID: 26009802 DOI: 10.1080/21645515.2015.1049780] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Enterovirus A infections are the primary cause of hand, foot and mouth disease (HFMD) in infants and young children. Although enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) are the predominant causes of HFMD epidemics worldwide, EV-A71 has emerged as a major neurovirulent virus responsible for severe neurological complications and fatal outcomes. HFMD is a serious health threat and economic burden across the Asia-Pacific region. Inactivated EV-A71 vaccines have elicited protection against EV-A71 but not against CV-A16 infections in large efficacy trials. The current development of a bivalent inactivated EV-A71/CV-A16 vaccine is the next step toward that of multivalent HFMD vaccines. These vaccines should ultimately include other prevalent pathogenic coxsackieviruses A (CV-A6 and CV-A10), coxsackieviruses B (B3 and B5) and echovirus 30 that often co-circulate during HFMD epidemics and can cause severe HFMD, aseptic meningitis and acute viral myocarditis. The prospect and challenges for the development of such multivalent vaccines are discussed.
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Affiliation(s)
| | - Pele Chong
- b Vaccine R&D Center; National Health Research Institutes ; Zhunan Town, Miaoli County , Taiwan.,c Graduate Institute of Immunology; China Medical University ; Taichung , Taiwan
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The evolution of Vp1 gene in enterovirus C species sub-group that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99. PLoS One 2014; 9:e93737. [PMID: 24695547 PMCID: PMC3973639 DOI: 10.1371/journal.pone.0093737] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/07/2014] [Indexed: 12/17/2022] Open
Abstract
Genus Enterovirus (Family Picornaviridae,) consists of twelve species divided into genetically diverse types by their capsid protein VP1 coding sequences. Each enterovirus type can further be divided into intra-typic sub-clusters (genotypes). The aim of this study was to elucidate what leads to the emergence of novel enterovirus clades (types and genotypes). An evolutionary analysis was conducted for a sub-group of Enterovirus C species that contains types Coxsackievirus A21 (CVA-21), CVA-24, Enterovirus C95 (EV-C95), EV-C96 and EV-C99. VP1 gene datasets were collected and analysed to infer the phylogeny, rate of evolution, nucleotide and amino acid substitution patterns and signs of selection. In VP1 coding gene, high intra-typic sequence diversities and robust grouping into distinct genotypes within each type were detected. Within each type the majority of nucleotide substitutions were synonymous and the non-synonymous substitutions tended to cluster in distinct highly polymorphic sites. Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. Despite robust clustering to intra-typic genotypes, only few genotype-specific ‘signature’ amino acids were detected. In contrast, when different enterovirus types were compared, there was a clear tendency towards fixation of type-specific ‘signature’ amino acids. The results suggest that permanent fixation of type-specific amino acids is a hallmark associated with evolution of different enterovirus types, whereas neutral evolution and/or (frequency-dependent) positive selection in few highly polymorphic amino acid sites are the dominant forms of evolution when strains within an enterovirus type are compared.
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Huang YP, Lin TL, Chen YJ, Hsu CC, Lin TH, Wu HS. Phylogenetic analysis and development of an immunofluorescence assay for untypeable strains of coxsackievirus B3. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2013; 47:447-54. [PMID: 23993765 DOI: 10.1016/j.jmii.2013.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/22/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND/PURPOSE In recent years, coxsackievirus B3 (CV-B3) has been determined as a dominant enterovirus serotype that may cause severe complications in patients. Since 2008 in Taiwan, some enterovirus isolates have been regarded as untypeable [by employing commercial immunofluorescence assay (IFA) kits]. In 2012, the number of isolates increased. Genetic sequence analysis further confirmed that CV-B3 was present in most of the untypeable viruses. METHODS Isolates of CV-B3 were collected for basic local alignment search tool (BLAST) analysis and for phylogenetic analyses, based on VP1 gene sequences. In addition, the Taiwan Centers for Disease Control (Taiwan CDC) developed an in-house indirect IFA using polyclonal antibodies (e.g., rabbit antisera) for diagnosis. The sensitivity and specificity were both evaluated by testing 61 reference enteroviruses and 307 local enteroviruses that were isolated between 1998 and 2010. RESULTS Based on the results of the BLAST and phylogenetic analyses, five main genogroups (i.e., GI-GV) were classified and the reference strains in Taiwan in previous years were primarily clustered in the GV-A subgenogroup. However, the 15 CV-B3 isolates recently analyzed in this study were classified in four different groups: GIII, GIV, GV-A, and GV-B. Among these 15 isolates, all 10 isolates in the GV-B group were initially reported as untypeable nonpolio enteroviruses when using commercial kits. The conditions of the in-house indirect IFA were optimized by checkerboard titration, thereby resulting in a sensitivity of 100% and a specificity of 98.5%. CONCLUSION This is the first report describing the phylogenetic relatedness of recent CV-B3 strains in Taiwan. An indirect IFA kit was developed by the Taiwan CDC for detecting CV-B3 viruses that are untypeable by commercial IFA kits.
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Affiliation(s)
- Yuan-Pin Huang
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC
| | - Tsuey-Li Lin
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC
| | - Yu-Ju Chen
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC
| | - Chiu-Chu Hsu
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC
| | - Ting-Han Lin
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC
| | - Ho-Sheng Wu
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, ROC; School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan, ROC.
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Smura T, Kakkola L, Blomqvist S, Klemola P, Parsons A, Kallio-Kokko H, Savolainen-Kopra C, Kainov DE, Roivainen M. Molecular evolution and epidemiology of echovirus 6 in Finland. INFECTION GENETICS AND EVOLUTION 2013; 16:234-47. [DOI: 10.1016/j.meegid.2013.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/10/2013] [Accepted: 02/05/2013] [Indexed: 12/30/2022]
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14
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Combined 5′ UTR RFLP analysis and VP1 sequencing for epidemic investigation of enteroviruses. Arch Virol 2012; 158:103-11. [DOI: 10.1007/s00705-012-1472-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
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Chu PY, Lu PL, Tsai YL, Hsi E, Yao CY, Chen YH, Hsu LC, Wang SY, Wu HS, Lin YY, Su HJ, Lin KH. Spatiotemporal phylogenetic analysis and molecular characterization of coxsackievirus A4. INFECTION GENETICS AND EVOLUTION 2011; 11:1426-35. [PMID: 21635970 DOI: 10.1016/j.meegid.2011.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 04/03/2011] [Accepted: 05/16/2011] [Indexed: 01/02/2023]
Abstract
Coxsackievirus A4 outbreaks occurred in Taiwan in 2004 and 2006. The spatiotemporal transmission of this error-prone RNA virus involves a continuous interaction between rapid sequence variation and natural selection. To elucidate the molecular characteristics of CV-A4 and the spatiotemporal dynamic changes in CV-A4 transmission, worldwide sequences of the 3' VP1 region (420 nt) obtained from GenBank were analyzed together with sequences isolated in Taiwan from 2002 to 2009. Sequences were characterized in terms of recombination, variability, and selection. Phylogenetic trees were constructed using neighbor-joining, maximum likelihood and Monte Carlo Markov Chain methods. Spatiotemporal dynamics of CV-A4 transmission were further estimated by a Bayesian statistical inference framework. No recombination was detected in the 420 nt region. The estimated evolution rate of CV-A4 was 8.65 × 10(-3) substitutions/site/year, and a purifying selection (d(N)/d(S)=0.032) was noted over the 3' VP1 region. All trees had similar topology: two genotypes (GI and GII), each including two subgenotypes (A and B), with the prototype and a Kenyan strain in separate branches. The results revealed that the virus first appeared in USA in 1950. Since 1998, it has evolved into the Kenya, GI-A (Asia) and GII-A (Asia and Europe) strains. Since 2004, GI-B and GII-B have evolved continuously and have remained prevalent. The co-existence of several positive selection lineages of GI-B in 2006 indicates that the subgenotype might have survived lineage extinction. This study revealed rapid lineage turnover of CV-A4 and the replacement of previously circulating strains by a new dominant variant. Therefore, continuous surveillance for further CV-A4 transmission is essential.
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Affiliation(s)
- Pei-Yu Chu
- Department of Medical Laboratory Science and Biotechnology, College of Health Science, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Ke GM, Lin KH, Lu PL, Tung YC, Wang CF, Ke LY, Lee MS, Lin PC, Su HJ, Lin YY, Huang TP, Wang JR, Wang SY, Hsu LC, Chu PY. Molecular epidemiology of Echovirus 30 in Taiwan, 1988-2008. Virus Genes 2011; 42:178-88. [PMID: 21369829 DOI: 10.1007/s11262-010-0565-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 12/24/2010] [Indexed: 11/29/2022]
Abstract
To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).
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Affiliation(s)
- Guan-Ming Ke
- Department of Clinical Laboratory, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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