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Cheng D, Chiu YW, Huang SW, Lien YY, Chang CL, Tsai HP, Wang YF, Wang JR. Genetic and Cross Neutralization Analyses of Coxsackievirus A16 Circulating in Taiwan from 1998 to 2021 Suggest Dominant Genotype B1 can Serve as Vaccine Candidate. Viruses 2022; 14:2306. [PMID: 36298861 PMCID: PMC9608817 DOI: 10.3390/v14102306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 07/30/2023] Open
Abstract
Coxsackievirus A16 (CVA16) is well known for causing hand-foot-and-mouth disease (HFMD) and outbreaks were frequently reported in Taiwan in the past twenty years. The epidemiology and genetic variations of CVA16 in Taiwan from 1998 to 2021 were analyzed in this study. CVA16 infections usually occurred in early summer and early winter, and showed increased incidence in 1998, 2000-2003, 2005, 2007-2008, and 2010 in Taiwan. Little or no CVA16 was detected from 2017 to 2021. CVA16 infection was prevalent in patients between 1 to 3 years old. A total of 69 isolates were sequenced. Phylogenetic analysis based on the VP1 region showed that CVA16 subgenotype B1 was dominantly isolated in Taiwan from 1998 to 2019, and B2 was identified only from isolates collected in 1999 and 2000. There was a high frequency of synonymous mutations in the amino acid sequences of the VP1 region among CVA16 isolates, with the exception of position 145 which showed positive selection. The recombination analysis of the whole genome of CVA16 isolates indicated that the 5'-untranslated region and the non-structural protein region of CVA16 subgenotype B1 were recombined with Coxsackievirus A4 (CVA4) and enterovirus A71 (EVA71) genotype A, respectively. The recombination pattern of subgenotype B2 was similar to B1, however, the 3D region was similar to EVA71 genotype B. Cross-neutralization among CVA16 showed that mouse antisera from various subgenotypes viruses can cross-neutralize different genotype with high neutralizing antibody titers. These results suggest that the dominant CVA16 genotype B1 can serve as a vaccine candidate for CVA16.
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Affiliation(s)
- Dayna Cheng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yo-Wei Chiu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
| | - Yun-Yin Lien
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Chia-Lun Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ya-Fang Wang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Jen-Ren Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan 70101, Taiwan
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China. Sci Rep 2022; 12:593. [PMID: 35022489 PMCID: PMC8755819 DOI: 10.1038/s41598-021-04604-x] [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: 08/17/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.
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Yu Y, Luo Z, Jin W, Mai J, Qian S, Lu J, Wei Z, Meng S, Wang Z, Guan X, Tong Y, Shen S. Emergence of a novel recombinant of CV-A5 in HFMD epidemics in Xiangyang, China. BMC Med Genomics 2021; 14:279. [PMID: 34819054 PMCID: PMC8611921 DOI: 10.1186/s12920-021-01107-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Background Hand, foot and mouth disease (HFMD) is caused by a variety of enterovirus serotypes and the etiological spectrum worldwide has changed since a large scale of outbreaks occurred in 1997. Methods A large number of clinical specimens of HFMD patients were collected in Xiangyang and genotyping was performed by qRT-PCR, conventional PCR amplification and sequencing. Among the 146 CV-A5 detected cases, the complete genome sequences of representative strains were determined for genotyping and for recombination analysis. Results It was found that CV-A5 was one of the six major serotypes that caused the epidemic from October 2016 to December 2017. Phylogenetic analyses based on the VP1 sequences showed that these CV-A5 belonged to the genotype D which dominantly circulated in China. Recombination occurred between the CV-A5 and CV-A2 strains with a breakpoint in the 2A region at the nucleotide 3791. Conclusions The result may explain the emergence of CV-A5 as one of the major pathogens of HFMD. A multivalent vaccine against HFMD is urgently needed to control the disease and to prevent emerging and spreading of new recombinants.
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Affiliation(s)
- Yuting Yu
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Zhiyu Luo
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Weiping Jin
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Jianyi Mai
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Shasha Qian
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Jia Lu
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Zhenni Wei
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Shengli Meng
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Zejun Wang
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China
| | - Xuhua Guan
- Xiangyang Center for Disease Control and Prevention, Hubei, People's Republic of China.
| | - Yeqing Tong
- Xiangyang Center for Disease Control and Prevention, Hubei, People's Republic of China.
| | - Shuo Shen
- Wuhan Institute of Biological Products, Co. Ltd, Wuhan, 430207, People's Republic of China.
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Virulence of Enterovirus A71 Fluctuates Depending on the Phylogenetic Clade Formed in the Epidemic Year and Epidemic Region. J Virol 2021; 95:e0151521. [PMID: 34523967 DOI: 10.1128/jvi.01515-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although epidemics of hand, foot, and mouth disease (HFMD) caused by enterovirus A71 (EV-A71) have occurred worldwide, the Asia-Pacific region has seen large sporadic outbreaks with many severe neurological cases. This suggests that the virulence of the circulating viruses fluctuates in each epidemic and that HFMD outbreaks with many severe cases occur when highly virulent viruses are circulating predominantly, which has not been experimentally verified. Here, we analyzed 32 clinically isolated strains obtained in Japan from 2002 to 2013, along with 27 Vietnamese strains obtained from 2015 to 2016 that we characterized previously using human SCARB2 transgenic mice. Phylogenetic analysis of the P1 region classified them into five clades belonging to subgenogroup B5 (B5-I to B5-V) and five clades belonging to subgenogroup C4 (C4-I to C4-V) according to the epidemic year and region. Interestingly, clades B5-I and B5-II were very virulent, while clades B5-III, B5-IV, and B5-V were less virulent. Clades C4-II, C4-III, C4-IV, and C4-V were virulent, while clade C4-I was not. The result experimentally showed for the first time that several clades with different virulence levels emerged one after another. The experimental virulence evaluation of circulating viruses using SCARB2 transgenic mice is helpful to assess potential risks of circulating viruses. These results also suggest that a minor nucleotide or amino acid substitution in the EV-A71 genome during circulation causes fluctuations in virulence. The data presented here may increase our understanding of the dynamics of viral virulence during epidemics. IMPORTANCE Outbreaks of hand, foot, and mouth disease (HFMD) with severe enterovirus A71 (EV-A71) cases have occurred repeatedly, mainly in Asia. In severe cases, central nervous system complications can lead to death, making it an infectious disease of importance to public health. An unanswered question about this disease is why outbreaks of HFMD with many severe cases sometimes occur. Here, we collected EV-A71 strains that were prevalent in Japan and Vietnam over the past 20 years and evaluated their virulence in a mouse model of EV-A71 infection. This method clearly revealed that viruses belonging to different clades have different virulence, indicating that the method is powerful to assess the potential risks of the circulating viruses. The results also suggested that factors in the virus genome cause an outbreak with many severe cases and that further studies facilitate the prediction of large epidemics of EV-A71 in the future.
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Janissen R, Woodman A, Shengjuler D, Vallet T, Lee KM, Kuijpers L, Moustafa IM, Fitzgerald F, Huang PN, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih SR, Vignuzzi M, Cameron CE, Dekker NH. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 2021; 81:4467-4480.e7. [PMID: 34687604 PMCID: PMC8628313 DOI: 10.1016/j.molcel.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022]
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Louis Kuijpers
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Fiona Fitzgerald
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Angela L Perkins
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands.
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6
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Genetic diversity and evolution of enterovirus A71 subgenogroup C1 from children with hand, foot, and mouth disease in Thailand. Arch Virol 2021; 166:2209-2216. [PMID: 34086143 DOI: 10.1007/s00705-021-05130-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/17/2021] [Indexed: 10/21/2022]
Abstract
Enterovirus A71 (EV-A71) can cause hand, foot, and mouth disease (HFMD) in children and may be associated with severe neurological complications. There have been numerous reports of increased incidence of EV-A71 subgenogroup C1 (EV-A71 C1) infections associated with neurological diseases since the first occurrence in Germany in 2015. Here, we describe 11 full-length genome sequences of 2019 EV-A71 C1 strains isolated from HFMD patients in Thailand from 2019 to early 2020. The genetic evolution of 2019 EV-A71 C1 was traced in the outbreaks, and the emergence of multiple lineages was detected. Our results demonstrated that 2019 EV-A71 C1 from Thailand emerged through recombination between its nonstructural protein gene and those of other EV-A genotypes. Bayesian-based phylogenetic analysis showed that the 2019 EV-A71 C1 Thai strains share a common ancestor with variants in Europe (Denmark and France). The substitution rate for the 2019 EV-A71 C1 genome was estimated to be 4.38 × 10-3 substitutions/(site∙year-1) (95% highest posterior density interval: 3.84-4.94 × 10-3 substitutions/[site∙year-1]), approximating that observed between previous EV-A71 C1 outbreaks. These data are essential for understanding the evolution of EV-A C1 during the ongoing HFMD outbreak and may be relevant to disease outcomes in children worldwide.
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7
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Chang CS, Liao CC, Liou AT, Chou YC, Yu YY, Lin CY, Lin JS, Suen CS, Hwang MJ, Shih C. Novel Naturally Occurring Mutations of Enterovirus 71 Associated With Disease Severity. Front Microbiol 2021; 11:610568. [PMID: 33519765 PMCID: PMC7838335 DOI: 10.3389/fmicb.2020.610568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/21/2020] [Indexed: 02/02/2023] Open
Abstract
Infection with the re-emerging enterovirus 71 (EV-A71) is associated with a wide range of disease severity, including herpangina, encephalitis, and cardiopulmonary failure. At present, there is no FDA-approved therapeutics for EV-A71. Early diagnosis for the high-risk children is the key to successful patient care. We examined viral genome sequences at the 5′ untranslated region (UTR) and the capsid protein VP1 from 36 mild and 27 severe cases. We identified five EV-A71 mutations associated with severe diseases, including (1) the 5′ UTR mutations C580U, A707G, C709U; (2) a VP1 alanine-to-threonine mutation at position 280 (280T), and (3) a VP1 glutamic acid-to-(non-glutamic acid) at position 145 [145(non-E)]. SCARB2 is a known entry receptor for EV-A71. Based on a recent cryoEM structure of the EV-A71-SCARB2 binding complex, VP1-280T is near the binding interface between the VP1-VP2 complex and its entry receptor SCARB2. A de novo created hydrogen bonding between the mutant VP1-280T and the VP2-139T, could help strengthen a web-like interaction structure of the VP1-VP2 complex. A stabilized loop turn of VP2, once in contact with SCARB2, can enhance interaction with the host SCARB2 receptor for viral entry. Our findings here could facilitate early detection of severe cases infected with EV-A71 in clinical medicine. In addition, it opens up the opportunity of functional studies via infectious cDNA cloning, site-directed mutagenesis, and animal models in the future.
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Affiliation(s)
- Chih-Shin Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - An-Ting Liou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Chun Chou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Yen Yu
- Section of Clinical Virology and Molecular Diagnosis, Department of Laboratory Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Chi-Yung Lin
- Section of Clinical Virology and Molecular Diagnosis, Department of Laboratory Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Jen-Shiou Lin
- Section of Clinical Virology and Molecular Diagnosis, Department of Laboratory Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Shu Suen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chiaho Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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8
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Huang KYA, Huang PN, Huang YC, Yang SL, Tsao KC, Chiu CH, Shih SR, Lin TY. Emergence of genotype C1 Enterovirus A71 and its link with antigenic variation of virus in Taiwan. PLoS Pathog 2020; 16:e1008857. [PMID: 32936838 PMCID: PMC7521691 DOI: 10.1371/journal.ppat.1008857] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/28/2020] [Accepted: 08/04/2020] [Indexed: 12/16/2022] Open
Abstract
An outbreak of the hand-foot-mouth disease with severe neurological cases, mainly caused by the genotype C1 enterovirus A71 (EV-A71), occurred in Taiwan between 2018 and early 2019. In the recent decade, the most dominant EV-A71 genotypes in Taiwan were B5 and C4 but changed to C1 in 2018. Antibody-mediated immunity plays a key role in limiting the EV-A71 illness in humans. However, the level of neutralizing activities against genotype C1 virus by human polyclonal and monoclonal antibodies (MAbs) remains largely unclear. In the study, we demonstrated that that 39% (9 in 23) of post-infection sera from the genotype B5- or C4-infected patients in 2014–2017 exhibit reduced titers with the 2018–2019 genotype C1 viruses than with the earlier B5 and C4 viruses tested. This finding with polyclonal sera is confirmed with human MAbs derived from genotype B5 virus-infected individuals. The 2018–2019 genotype C1 virus is resistant to the majority of canyon-targeting human MAbs, which may be associated with the residue change near or at the bottom of the canyon region on the viral capsid. The remaining three antibodies (16-2-11B, 16-3-4D, and 17-1-12A), which target VP1 S241 on the 5-fold vertex, VP3 E81 on the 3-fold plateau and VP2 D84 on the 2-fold plateau of genotype C1 viral capsid, respectively, retained neutralizing activities with variable potencies. These neutralizing antibodies were also found to be protective against a lethal challenge of the 2018–2019 genotype C1 virus in an hSCARB2-transgenic mice model. These results indicate that the EV-A71-specific antibody response may consist of a fraction of poorly neutralizing antibodies against 2018–2019 genotype C1 viruses among a subset of previously infected individuals. Epitope mapping of protective antibodies that recognize the emerging genotype C1 virus has implications for anti-EV-A71 MAbs and the vaccine field. EV-A71 is a cause of hand-foot-mouth disease, epidemics of which still regularly occur around the globe. Given that EV-A71 immune protection from the disease correlates with neutralizing antibody responses, but the responses in humans prior to an outbreak are still poorly understood. An outbreak of hand-foot-mouth disease among children emerged in Taiwan from 2018 to 2019, and genotype C1 EV-A71 caused most of the cases. Here, we characterized EV-A71-neutralizing antibody profiles in details at both the serological and monoclonal levels and showed that antibodies generated by humans prior to the emergence of genotype C1 EV-A71 less effectively neutralize C1 compared to the prior circulating genotypes, which implies the presence of antigenic variation in the EV-A71 genotypes. We further identified and mapped critical neutralizing epitopes of 2018–2019 genotype C1 EV-A71 on the top and margin of the viral capsid pentamer and demonstrated the in vivo protective effect of human monoclonal antibodies, which highlight the properties of human antibody-neutralizing sites on EV-A71 and the potential of human antibodies as antiviral agents.
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MESH Headings
- Animals
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Child
- Child, Preschool
- Enterovirus A, Human/genetics
- Enterovirus A, Human/immunology
- Enterovirus A, Human/isolation & purification
- Female
- Genetic Variation
- Genome, Viral
- Genotype
- Hand, Foot and Mouth Disease/epidemiology
- Hand, Foot and Mouth Disease/genetics
- Hand, Foot and Mouth Disease/immunology
- Humans
- Male
- Mice
- Mice, Transgenic
- Taiwan
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Affiliation(s)
- Kuan-Ying A. Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- * E-mail: (KYAH); (TYL)
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yhu-Chering Huang
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shu-Li Yang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuo-Chien Tsao
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tzou-Yien Lin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- * E-mail: (KYAH); (TYL)
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Lee KM, Wu CC, Wu SE, Lin YH, Wang LT, Chang CR, Huang PN, Shih SR, Kuo RL. The RNA-dependent RNA polymerase of enterovirus A71 associates with ribosomal proteins and positively regulates protein translation. RNA Biol 2020; 17:608-622. [PMID: 32009553 DOI: 10.1080/15476286.2020.1722448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Enteroviruses, which may cause neurological complications, have become a public health threat worldwide in recent years. Interactions between cellular proteins and enteroviral proteins could interfere with cellular biological processes to facilitate viral replication in infected cells. Enteroviral RNA-dependent RNA polymerase (RdRP), known as 3D protein, mainly functions as a replicase for viral RNA synthesis in infected cells. However, the 3D protein encoded by enterovirus A71 (EV-A71) could also interact with several cellular proteins to regulate cellular events and responses during infection. To globally investigate the functions of the EV-A71 3D protein in regulating biological processes in host cells, we performed immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify host proteins that may associate with the 3D protein. We found that the 3D protein interacts with factors involved in translation-related biological processes, including ribosomal proteins. In addition, polysome profiling analysis showed that the 3D protein cosediments with small and large subunits of ribosomes. We further discovered that the EV-A71 3D protein could enhance EV-A71 internal ribosome entry site (IRES)-dependent translation as well as cap-dependent translation. Collectively, this research demonstrated that the RNA polymerase encoded by EV-A71 could join a functional ribosomal complex and positively regulate viral and host translation.
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Affiliation(s)
- Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Shang-En Wu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Han Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li-Ting Wang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Ru Chang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Virology Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Rei-Lin Kuo
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
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Lee JT, Yen TY, Shih WL, Lu CY, Liu DP, Huang YC, Chang LY, Huang LM, Lin TY. Enterovirus 71 seroepidemiology in Taiwan in 2017 and comparison of those rates in 1997, 1999 and 2007. PLoS One 2019; 14:e0224110. [PMID: 31622436 PMCID: PMC6797108 DOI: 10.1371/journal.pone.0224110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/04/2019] [Indexed: 01/31/2023] Open
Abstract
Background During recent 20 years, enterovirus 71 (EV71) has emerged as a major concern among children, particularly in the Asia-Pacific region. To understand current EV71 serostatus, to find risk factors associated with EV71 infection and to establish future EV71 vaccine policy, we performed a seroepidemiology study in Taiwan in 2017. Methods After informed consent was obtained, we enrolled preschool children, 6–15-year-old students, 16–50-year-old people. They received a questionnaire and a blood sample was collected to measure the EV71 neutralization antibody. Results Altogether, 920 subjects were enrolled with a male-to-female ratio of 1.03. The EV71 seropositive rate was 10% (8/82) in infants, 4% (6/153) in 1-year-old children, 8% (7/83) in 2-year-old children, 8% (13/156) in 3–5-year-old children, 31% (38/122) in 6–11-year-old primary school students, 45% (54/121) in 12–15-year-old high school students and 75% (152/203) in 16-50-year-old people. Risk factors associated with EV71 seropositivity in preschool children were female gender, having siblings, more siblings, and contact with herpangina or hand-foot-and-mouth disease. The risk factor with EV71 seropositivity in 16–50-year-old people was having children in their families in addition to older age (p<0.001). Compared with the rates in 1997, 1999 and 2007, the rates in children were significantly lower in 2017. Conclusion EV71 seropositive rates were very low, at 4% to 10%, in preschool children and not high, at 31%, in primary school students. Preschool children are highly susceptible and need EV71 vaccine most.
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Affiliation(s)
- Jian-Te Lee
- Department of Pediatrics, National Taiwan University Hospital, Yun-Lin Branch, Yunlin, Taiwan
| | - Ting-Yu Yen
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Wei-Liang Shih
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University and Infectious Diseases Research and Education Center, Ministry of Health and Welfare and National Taiwan University, Taipei, Taiwan
| | - Chun-Yi Lu
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Ding-Ping Liu
- Epidemic Intelligence Center, Centers for Disease Control, Taipei, Taiwan
- National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Yi-Chuan Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Luan-Yin Chang
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
- * E-mail:
| | - Li-Min Huang
- Department of Pediatrics, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Tzou-Yien Lin
- Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
- The National Health Research Institutes, Miaoli, Taiwan
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High Permissiveness for Genetic Exchanges between Enteroviruses of Species A, including Enterovirus 71, Favors Evolution through Intertypic Recombination in Madagascar. J Virol 2019; 93:JVI.01667-18. [PMID: 30602612 DOI: 10.1128/jvi.01667-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
Human enteroviruses of species A (EV-A) are the leading cause of hand-foot-and-mouth disease (HFMD). EV-A71 is frequently implicated in HFMD outbreaks and can also cause severe neurological manifestations. We investigated the molecular epidemiological processes at work and the contribution of genetic recombination to the evolutionary history of EV-A in Madagascar, focusing on the recently described EV-A71 genogroup F in particular. Twenty-three EV-A isolates, collected mostly in 2011 from healthy children living in various districts of Madagascar, were characterized by whole-genome sequencing. Eight different types were identified, highlighting the local circulation and diversity of EV-A. Comparative genome analysis revealed evidence of frequent recent intra- and intertypic genetic exchanges between the noncapsid sequences of Madagascan EV-A isolates. The three EV-A71 isolates had different evolutionary histories in terms of recombination, with one isolate displaying a mosaic genome resulting from recent genetic exchanges with Madagascan coxsackieviruses A7 and possibly A5 and A10 or common ancestors. The engineering and characterization of recombinants generated from progenitors belonging to different EV-A types or EV-A71 genogroups with distantly related nonstructural sequences indicated a high level of permissiveness for intertypic genetic exchange in EV-A. This permissiveness suggests that the primary viral functions associated with the nonstructural sequences have been highly conserved through the diversification and evolution of the EV-A species. No outbreak of disease due to EV-A has yet been reported in Madagascar, but the diversity, circulation, and evolution of these viruses justify surveillance of EV-A circulation and HFMD cases to prevent possible outbreaks due to emerging strains.IMPORTANCE Human enteroviruses of species A (EV-A), including EV-A71, are the leading cause of hand-foot-and-mouth disease (HFMD) and may also cause severe neurological manifestations. We investigated the circulation and molecular evolution of EV-A in Madagascar, focusing particularly on the recently described EV-A71 genogroup F. Eight different types, collected mostly in 2011, were identified, highlighting the local circulation and diversity of EV-A. Comparative genome analysis revealed evidence of frequent genetic exchanges between the different types of isolates. The three EV-A71 isolates had different evolutionary histories in terms of recombination. The engineering and characterization of recombinants involving progenitors belonging to different EV-A types indicated a high degree of permissiveness for genetic exchange in EV-A. No outbreak of disease due to EV-A has yet been reported in Madagascar, but the diversity, circulation, and evolution of these viruses justify the surveillance of EV-A circulation to prevent possible HFMD outbreaks due to emerging strains.
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Woodman A, Lee KM, Janissen R, Gong YN, Dekker NH, Shih SR, Cameron CE. Predicting Intraserotypic Recombination in Enterovirus 71. J Virol 2019; 93:e02057-18. [PMID: 30487277 PMCID: PMC6364027 DOI: 10.1128/jvi.02057-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses are well known for their ability to cause neurological damage and paralysis. The model enterovirus is poliovirus (PV), the causative agent of poliomyelitis, a condition characterized by acute flaccid paralysis. A related virus, enterovirus 71 (EV-A71), causes similar clinical outcomes in recurrent outbreaks throughout Asia. Retrospective phylogenetic analysis has shown that recombination between circulating strains of EV-A71 produces the outbreak-associated strains which exhibit increased virulence and/or transmissibility. While studies on the mechanism(s) of recombination in PV are ongoing in several laboratories, little is known about factors that influence recombination in EV-A71. We have developed a cell-based assay to study recombination of EV-A71 based upon previously reported assays for poliovirus recombination. Our results show that (i) EV-A71 strain type and RNA sequence diversity impacts recombination frequency in a predictable manner that mimics the observations found in nature; (ii) recombination is primarily a replicative process mediated by the RNA-dependent RNA polymerase; (iii) a mutation shown to reduce recombination in PV (L420A) similarly reduces EV-A71 recombination, suggesting conservation in mechanism(s); and (iv) sequencing of intraserotypic recombinant genomes indicates that template switching occurs by a mechanism that may require some sequence homology at the recombination junction and that the triggers for template switching may be sequence independent. The development of this recombination assay will permit further investigation on the interplay between replication, recombination and disease.IMPORTANCE Recombination is a mechanism that contributes to genetic diversity. We describe the first assay to study EV-A71 recombination. Results from this assay mimic what is observed in nature and can be used by others to predict future recombination events within the enterovirus species A group. In addition, our results highlight the central role played by the viral RNA-dependent RNA polymerase (RdRp) in the recombination process. Further, our results show that changes to a conserved residue in the RdRp from different species groups have a similar impact on viable recombinant virus yields, which is indicative of conservation in mechanism.
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Affiliation(s)
- Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
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