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Yang T, Sun Q, Yan D, Zhu S, Ji T, Xiao J, Lu H, Liu Y, He Y, Wang W, Cong R, Wang X, Yang Q, Xing W, Zhang Y. Characterizing enterovirus C96 genome and phylodynamics analysis. J Med Virol 2023; 95:e29289. [PMID: 38050821 DOI: 10.1002/jmv.29289] [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: 09/14/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/07/2023]
Abstract
Enterovirus C96 (EV-C96) is a recently discovered serotype belonging to enterovirus C species. It had been isolated from patients with acute flaccid paralysis, hand, foot, and mouth disease, diarrhea, healthy people, or environmental specimens. Despite increasing reports of the virus, the small number of full-length genomes available for EV-C96 has limited molecular epidemiological studies. In this study, newly collected rare EV-C96 strains in China from 1997 to 2020 were combined with sequences available in GenBank for comprehensive analyses. Sequence analysis revealed that the nucleotide sequence similarity of EV-C96 and the prototype strain (BAN00-10488) was 75%-81.8% and the amino acid sequence similarity was 85%-94.9%. EV-C96 had a high degree of genetic variation and could be divided into 15 genogroups. The mean evolutionary rate was 5.16 × 10-3 substitution/site/year, and the most recent common ancestor was dated to 1925. A recombination analysis revealed that EV-C96 may be a recombinant derived from other serotypes in the EV-C group in the nonstructural protein coding region. This comprehensive and integrated analysis of the whole genome sequence of EV-C96 provides valuable data for further studies on the molecular epidemiology of EV-C96 worldwide.
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Affiliation(s)
- Tingting Yang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiang Sun
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Tianjiao Ji
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinbo Xiao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huanhuan Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yun He
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenhui Wang
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruyi Cong
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoyi Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Medical School, Anhui University of Science and Technology, Huainan, China
| | - Qian Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Weijia Xing
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Yong Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID), National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [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: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
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Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
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Ivanova OE, Shakaryan AK, Morozova NS, Vakulenko YA, Eremeeva TP, Kozlovskaya LI, Baykova OY, Shustova EY, Mikhailova YM, Romanenkova NI, Rozaeva NR, Dzhaparidze NI, Novikova NA, Zverev VV, Golitsyna LN, Lukashev AN. Cases of Acute Flaccid Paralysis Associated with Coxsackievirus A2: Findings of a 20-Year Surveillance in the Russian Federation. Microorganisms 2022; 10:microorganisms10010112. [PMID: 35056561 PMCID: PMC8780984 DOI: 10.3390/microorganisms10010112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Surveillance for acute flaccid paralysis syndrome (AFP) in children under 15 is the backbone of the Global Polio Eradication Initiative. Laboratory examination of stool samples from AFP cases allows the detection of, along with polioviruses, a variety of non-polio enteroviruses (NPEV). The etiological significance of these viruses in the occurrence of AFP cases has been definitively established only for enteroviruses A71 and D68. Enterovirus Coxsackie A2 (CVA2) is most often associated with vesicular pharyngitis and hand, foot and mouth disease. Among 7280 AFP cases registered in Russia over 20 years (2001–2020), CVA2 was isolated only from five cases. However, these included three children aged 3 to 4 years, without overt immune deficiency, immunized with 4–5 doses of poliovirus vaccine in accordance with the National Vaccination Schedule. The disease resulted in persistent residual paralysis. Clinical and laboratory data corresponded to poliomyelitis developing during poliovirus infection. These findings are compatible with CVA2 being the cause of AFP. Molecular analysis of CVA2 from these patients and a number of AFP cases in other countries did not reveal association with a specific phylogenetic group, suggesting that virus genetics is unlikely to explain the pathogenic profile. The overall results highlight the value of AFP surveillance not just for polio control but for studies of uncommon AFP agents.
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Affiliation(s)
- Olga E. Ivanova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
| | - Armen K. Shakaryan
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Pirogov Russian National Research Medical University, 119121 Moscow, Russia
| | - Nadezhda S. Morozova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Tatyana P. Eremeeva
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Liubov I. Kozlovskaya
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
- Department of Organization and Technology of Production of Immunobiological Preparations, Institute for Translational Medicine and Biotechnology, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Olga Y. Baykova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Elena Y. Shustova
- Federal State Autonomous Scientific Institution “Chumakov Federal Center for Research and Development of Immune-and-Biological Products of the Russian Academy of Sciences” (Institute of Poliomyelitis) (FSASI “Chumakov FSC R&D IBP RAS”), 108819 Moscow, Russia; (A.K.S.); (T.P.E.); (L.I.K.); (O.Y.B.); (E.Y.S.)
| | - Yulia M. Mikhailova
- Federal Budget Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in Moscow”, 129626 Moscow, Russia; (N.S.M.); (Y.M.M.)
| | | | - Nadezhda R. Rozaeva
- Saint-Petersburg Pasteur Institute, 197101 Saint-Petersburg, Russia; (N.I.R.); (N.R.R.)
| | - Natela I. Dzhaparidze
- Federal Budgetary Institution of Healthcare of Rospotrebnadzor “Center for Hygiene and Epidemiology in the Vladimir Region”, 600005 Vladimir, Russia;
| | - Nadezhda A. Novikova
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Vladimir V. Zverev
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Lyudmila N. Golitsyna
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology, 603950 Nizhny Novgorod, Russia; (N.A.N.); (V.V.Z.); (L.N.G.)
| | - Alexander N. Lukashev
- Martsinovsky Institute of Meidcal Parasitology, Tropical and Vector-Borne Diseases, First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
- Correspondence: (O.E.I.); (A.N.L.); Tel.: +7-916-677-2403 (O.E.I.); +7-915-160-7489 (A.N.L.)
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Ji W, Zhu P, Liang R, Zhang L, Zhang Y, Wang Y, Zhang W, Tao L, Chen S, Yang H, Jin Y, Duan G. Coxsackievirus A2 Leads to Heart Injury in a Neonatal Mouse Model. Viruses 2021; 13:v13081588. [PMID: 34452454 PMCID: PMC8402683 DOI: 10.3390/v13081588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Coxsackievirus A2 (CVA2) has emerged as an active pathogen that has been implicated in hand, foot, and mouth disease (HFMD) and herpangina outbreaks worldwide. It has been reported that severe cases with CVA2 infection develop into heart injury, which may be one of the causes of death. However, the mechanisms of CVA2-induced heart injury have not been well understood. In this study, we used a neonatal mouse model of CVA2 to investigate the possible mechanisms of heart injury. We detected CVA2 replication and apoptosis in heart tissues from infected mice. The activity of total aspartate transaminase (AST) and lactate dehydrogenase (LDH) was notably increased in heart tissues from infected mice. CVA2 infection also led to the disruption of cell-matrix interactions in heart tissues, including the increases of matrix metalloproteinase (MMP)3, MMP8, MMP9, connective tissue growth factor (CTGF) and tissue inhibitors of metalloproteinases (TIMP)4. Infiltrating leukocytes (CD45+ and CD11b+ cells) were observed in heart tissues of infected mice. Correspondingly, the expression levels of inflammatory cytokines in tissue lysates of hearts, including tumor necrosis factor alpha (TNF-α), interleukin-1beta (IL-1β), IL6 and monocyte chemoattractant protein-1 (MCP-1) were significantly elevated in CVA2 infected mice. Inflammatory signal pathways in heart tissues, including phosphatidylinositol 3-kinase (PI3K)-AKT, mitogen-activated protein kinases (MAPK) and nuclear factor kappa B (NF-κB), were also activated after infection. In summary, CVA2 infection leads to heart injury in a neonatal mouse model, which might be related to viral replication, increased expression levels of MMP-related enzymes and excessive inflammatory responses.
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Affiliation(s)
- Wangquan Ji
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Peiyu Zhu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Ruonan Liang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Liang Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Yu Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Yuexia Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Weiguo Zhang
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Ling Tao
- School of Public Health, Xinxiang Medical University, Xinxiang 453003, China;
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
- Correspondence: (Y.J.); (G.D.)
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, China; (W.J.); (P.Z.); (R.L.); (L.Z.); (Y.Z.); (Y.W.); (S.C.); (H.Y.)
- Henan Key Laboratory of Molecular Medicine, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (Y.J.); (G.D.)
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Sousa IP, Oliveira MDLA, Burlandy FM, Machado RS, Oliveira SS, Tavares FN, Gomes-Neto F, da Costa EV, da Silva EE. Molecular characterization and epidemiological aspects of non-polio enteroviruses isolated from acute flaccid paralysis in Brazil: a historical series (2005-2017). Emerg Microbes Infect 2021; 9:2536-2546. [PMID: 33179584 PMCID: PMC7717866 DOI: 10.1080/22221751.2020.1850181] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Due to the advanced stage of polio eradication, the possible role of non-polio enteroviruses (NPEVs) associated to acute flaccid paralysis (AFP) cases has been highlighted. In this study, we described epidemiological aspects of NPEVs infections associated to AFP and explore the viral genetic diversity, information still scarce in Brazil. From 2005 to 2017, 6707 stool samples were collected in the scope of the Brazilian Poliomyelitis Surveillance Program. NPEVs were isolated in 359 samples (5.3%) and 341 (94.9%) were genotyped. About 46 different NPEV types were identified with the following detection pattern EV-B > EV-A > EV-C. The major EV-types were CVA2, CV4, EV-A71, CVB3, CVB5, E6, E7, E11, CVA13 and EV-C99, which corresponds to 51.6% of the total. Uncommon types, such as CVA12, EV-90 and CVA11, were also identified. Different E6 genogroups were observed, prevailing the GenIII, despite periods of co-circulation, and replacement of genogroups along time. CVA2 sequences were classified as genotype C and data suggested its dispersion in South-American countries. CVA13 viruses belonged to cluster B and Venezuelan viruses composed a new putative cluster. This study provides extensive information on enterovirus diversity associated with AFP, reinforcing the need of tailoring current surveillance strategies to timely monitor emergence/re-emergence of NPEVs.
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Affiliation(s)
- Ivanildo P Sousa
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Fernanda M Burlandy
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Raiana S Machado
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Silas S Oliveira
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fernando N Tavares
- Laboratório de Referência Regional em Enteroviroses, Seção de Virologia, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Francisco Gomes-Neto
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Eliane V da Costa
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson E da Silva
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Xiao J, Wang J, Zhang Y, Sun D, Lu H, Han Z, Song Y, Yan D, Zhu S, Pei Y, Xu W, Wang X. Coxsackievirus B4: an underestimated pathogen associated with a hand, foot, and mouth disease outbreak. Arch Virol 2021; 166:2225-2234. [PMID: 34091782 DOI: 10.1007/s00705-021-05128-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/17/2021] [Indexed: 02/02/2023]
Abstract
In order to discover the causes of a coxsackievirus B4 (CV-B4)-associated hand, foot, and mouth disease (HFMD) outbreak and to study the evolutionary characteristics of the virus, we sequenced isolates obtained during an outbreak for comparative analysis with previously sequenced strains. Phylogenetic and evolutionary dynamics analysis was performed to examine the genetic characteristics of CV-B4 in China and worldwide. Phylogenetic analysis showed that CV-B4 originated from a common ancestor in Shandong. CV-B4 strains isolated worldwide could be classified into genotypes A-E based on the sequence of the VP1 region. All CV-B4 strains in China belonged to genotype E. The global population diversity of CV-B4 fluctuated substantially over time, and CV-B4 isolated in China accounted for a significant increase in the diversity of CV-B4. The average nucleotide substitution rate in VP1 of Chinese CV-B4 (5.20 × 10-3 substitutions/site/year) was slightly higher than that of global CV-B4 (4.82 × 10-3 substitutions/site/year). This study is the first to investigate the evolutionary dynamics of CV-B4 and its association with an HFMD outbreak. These findings explain both the 2011 outbreak and the global increase in CV-B4 diversity. In addition to improving our understanding of a major outbreak, these findings provide a basis for the development of surveillance strategies.
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Affiliation(s)
- Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | - Dapeng Sun
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China
| | - Yaowen Pei
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Laboratory for Poliomyelitis, National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping District, Beijing, People's Republic of China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, People's Republic of China.
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7
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Ai Y, Zhang W, Wu J, Zhang J, Shen M, Yao S, Deng C, Li X, Wu D, Tian P, Cheng X, Zha H, Wu K. Molecular Epidemiology and Clinical Features of Enteroviruses-Associated Hand, Foot, and Mouth Disease and Herpangina Outbreak in Zunyi, China, 2019. Front Med (Lausanne) 2021; 8:656699. [PMID: 33981716 PMCID: PMC8109248 DOI: 10.3389/fmed.2021.656699] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/31/2021] [Indexed: 11/25/2022] Open
Abstract
Background: Hand, foot and mouth disease (HFMD) and herpangina (HA), two of the most common childhood infectious diseases, are associated with enteroviruses (EVs) infection. The aim of this study was to identify the molecular epidemiology of enterovirus causing HFMD/HA in Zunyi, China, during 2019, and to describe the clinical features of the cases. Methods: We collected the information on demographic and clinical characteristics, laboratory data of laboratory-confirmed EVs associated HFMD/HA cases in Zunyi Medical University Third Affiliated Hospital between March 1 and July 31, 2019. EV types were determined by either one-step real time RT-PCR or partial VP1 gene sequencing and sequence alignment. Phylogenetic analysis of CVA6, CVA2, and CVA5 were established based on the partial VP1 gene sequences by neighbor-joining method. Differences in clinical characteristics and laboratory results of the cases were compared among patients infected with the most prevalent EV types. Results: From 1 March to 31 July 2019, 1,377 EVs associated HFMD/HA inpatients were confirmed. Of them, 4 (0.3%, 4/1,377) were EV-A71-associated cases, 84 (6.1%, 84/1,377) were CVA16-associated cases, and 1,289 (93.6%, 1,289/1,377) were non-EV-A71/CVA16-associated cases. Of the randomly selected 372 non-EV-A71/CVA16 cases, EV types have been successfully determined in 273 cases including 166 HFMD and 107 HA cases. For HFMD cases, the three most common types were CVA6 (80.7%, 134/166), CVA2 (5.4%, 9/166) and CVA5 (3.0%, 5/166); similarly, for HA cases, the three most prevalent serotypes were CVA6 (36.5%, 39/107), CVA2 (21.5%, 23/107) and CVA5 (18.7%, 20/107). Phylogenetic analysis showed that subclade D of CVA5, and subclade E of CVA6 and CVA2 were predominant in Zunyi during the outbreak in 2019. Compared with the cases caused by CVA16, the incidence of high fever and severe infection associated with CVA2, CVA5, and CVA6 was higher. Conclusions: The recent HFMD/HA outbreak in Zunyi is due to a larger incidence of CVA6, CVA2, and CVA5. Novel diagnostic reagents and vaccines against these types would be important to monitor and control EV infections.
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Affiliation(s)
- Yuanhang Ai
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Weiwei Zhang
- Department of Pediatrics and Child Health, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Jie Wu
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Jingzhi Zhang
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Meijing Shen
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Shifei Yao
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Chengmin Deng
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Xiaoqian Li
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Dejing Wu
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Peng Tian
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Xiaoju Cheng
- Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - He Zha
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
| | - Kaifeng Wu
- Department of Clinical Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China.,Department of Scientific Research Laboratory, Zunyi Medical University Third Affiliated Hospital, Zunyi, China
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8
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Epidemical and etiological study on hand, foot and mouth disease following EV-A71 vaccination in Xiangyang, China. Sci Rep 2020; 10:20909. [PMID: 33262488 PMCID: PMC7708472 DOI: 10.1038/s41598-020-77768-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/12/2020] [Indexed: 12/29/2022] Open
Abstract
Coxsackievirus A6 (CV-A6) and Coxsackievirus A10 (CV-A10) have been emerging as the prevailing serotypes and overtaking Enterovirus A71 (EV-A71) and Coxsackievirus A16 (CV-A16) in most areas as main pathogens of hand, foot and mouth disease (HFMD) in China since 2013. To investigate whole etiological spectrum following EV-A71 vaccination of approximate 40,000 infants and young children in Xiangyang, enteroviruses were serotyped in 4415 HFMD cases from October 2016 to December 2017 using Real Time and conventional PCR and cell cultures. Of the typeable 3201 specimen, CV-A6 was the predominant serotype followed by CV-A16, CV-A10, CV-A5, CV-A2 and EV-A71 with proportions of 59.54%, 15.31%, 11.56%, 4.56%, 3.78% and 3.03%, respectively. Other 12 minor serotypes were also detected. The results demonstrated that six major serotypes of enteroviruses were co-circulating, including newly emerged CV-A2 and CV-A5. A dramatic decrease of EV-A71 cases was observed, whereas the total cases remained high. Multivalent vaccines against major serotypes are urgently needed for control of HFMD.
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9
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Zhou Y, Van Tan L, Luo K, Liao Q, Wang L, Qiu Q, Zou G, Liu P, Anh NT, Hong NTT, He M, Wei X, Yu S, Lam TTY, Cui J, van Doorn HR, Yu H. Genetic Variation of Multiple Serotypes of Enteroviruses Associated with Hand, Foot and Mouth Disease in Southern China. Virol Sin 2020; 36:61-74. [PMID: 32725479 PMCID: PMC7385209 DOI: 10.1007/s12250-020-00266-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/06/2020] [Indexed: 12/04/2022] Open
Abstract
Enteroviruses (EVs) species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand, foot and mouth disease (HFMD) in China. Mild infections are common in children; however, HFMD can also cause severe illness that affects the central nervous system. To molecularly characterize EVs, a prospective HFMD virological surveillance program was performed in China between 2013 and 2016. Throat swabs, rectal swabs and stool samples were collected from suspected HFMD patients at participating hospitals. EVs were detected using generic real-time and nested reverse transcription-polymerase chain reactions (RT-PCRs). Then, the complete VP1 regions of enterovirus A71 (EV-A71), coxsackievirus A16 (CVA16) and CVA6 were sequenced to analyze amino acid changes and construct a viral molecular phylogeny. Of the 2836 enrolled HFMD patients, 2,517 (89%) were EV positive. The most frequently detected EVs were CVA16 (32.5%, 819), CVA6 (31.2%, 785), and EV-A71 (20.4%, 514). The subgenogroups CVA16_B1b, CVA6_D3a and EV-A71_C4a were predominant in China and recombination was not observed in the VP1 region. Sequence analysis revealed amino acid variations at the 30, 29 and 44 positions in the VP1 region of EV-A71, CVA16 and CVA6 (compared to the respective prototype strains BrCr, G10 and Gdula), respectively. Furthermore, in 21 of 24 (87.5%) identified EV-A71 samples, a known amino acid substitution (D31N) that may enhance neurovirulence was detected. Our study provides insights about the genetic characteristics of common HFMD-associated EVs. However, the emergence and virulence of the described mutations require further investigation.
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Affiliation(s)
- Yonghong Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam
| | - Kaiwei Luo
- Hunan Provincial Center for Disease Control and Prevention, Changsha, 410005, China
| | - Qiaohong Liao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China.,Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - Lili Wang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China
| | - Gang Zou
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ping Liu
- Anhua County Center for Disease Control and Prevention, Anhua, 413000, China
| | - Nguyen To Anh
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam
| | | | - Min He
- Anhua County Center for Disease Control and Prevention, Anhua, 413000, China
| | - Xiaoman Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shuanbao Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, 102206, China
| | - Tommy Tsan-Yuk Lam
- Centre of Influenza Research & State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200032, China
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Ho Chi Minh City, 700000, Vietnam.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, 200032, China.
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10
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Genetic characterization of VP1 of coxsackieviruses A2, A4, and A10 associated with hand, foot, and mouth disease in Vietnam in 2012-2017: endemic circulation and emergence of new HFMD-causing lineages. Arch Virol 2020; 165:823-834. [PMID: 32008121 DOI: 10.1007/s00705-020-04536-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
While conducting sentinel surveillance of hand, foot, and mouth disease (HFMD) in Vietnam, we found a sudden increase in the prevalence of coxsackievirus A10 (CV-A10) in 2016 and CV-A2 and CV-A4 in 2017, the emergence of which has been reported recently to be associated with various clinical manifestations in other countries. However, there have been only a limited number of molecular studies on those serotypes, with none being conducted in Vietnam. Therefore, we sequenced the entire VP1 genes of CV-A10, CV-A4, and CV-A2 strains associated with HFMD in Vietnam between 2012 and 2017. Phylogenetic analysis revealed a trend of endemic circulation of Vietnamese CV-A10, CV-A4, and CV-A2 strains and the emergence of thus-far undescribed HFMD-causing lineages of CV-A4 and CV-A2. The Vietnamese CV-A10 strains belonged to a genotype comprising isolates from patients with HFMD from several other countries; however, most of the Vietnamese strains were grouped into a local lineage. Recently, emerging CV-A4 strains in Vietnam were grouped into a unique lineage within a genotype comprising strains isolated from patients with acute flaccid paralysis from various countries. New substitutions were detected in the putative BC and HI loops in the Vietnamese CV-A4 strains. Except for one strain, Vietnamese CV-A2 isolates were grouped into a unique lineage of a genotype that includes strains from various countries that are associated with other clinical manifestations. Enhanced surveillance is required to monitor their spread and to specify their roles as etiological agents of HFMD or "HFMD-like" diseases, especially for CV-A4 and CV-A2. Further studies including whole-genome sequencing should be conducted to fully understand the evolutionary changes occurring in these newly emerging strains.
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11
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Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F. Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process. Viruses 2019; 11:E859. [PMID: 31540135 PMCID: PMC6784155 DOI: 10.3390/v11090859] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 01/15/2023] Open
Abstract
RNA recombination is a major driving force in the evolution and genetic architecture shaping of enteroviruses. In particular, intertypic recombination is implicated in the emergence of most pathogenic circulating vaccine-derived polioviruses, which have caused numerous outbreaks of paralytic poliomyelitis worldwide. Recent experimental studies that relied on recombination cellular systems mimicking natural genetic exchanges between enteroviruses provided new insights into the molecular mechanisms of enterovirus recombination and enabled to define a new model of genetic plasticity for enteroviruses. Homologous intertypic recombinant enteroviruses that were observed in nature would be the final products of a multi-step process, during which precursor nonhomologous recombinant genomes are generated through an initial inter-genomic RNA recombination event and can then evolve into a diversity of fitter homologous recombinant genomes over subsequent intra-genomic rearrangements. Moreover, these experimental studies demonstrated that the enterovirus genome could be defined as a combination of genomic modules that can be preferentially exchanged through recombination, and enabled defining the boundaries of these recombination modules. These results provided the first experimental evidence supporting the theoretical model of enterovirus modular evolution previously elaborated from phylogenetic studies of circulating enterovirus strains. This review summarizes our current knowledge regarding the mechanisms of recombination in enteroviruses and presents a new evolutionary process that may apply to other RNA viruses.
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Affiliation(s)
- Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de las Américas, Quito EC170125, Pichincha, Ecuador.
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, CNRS UMR 3569, 75015 Paris, France.
| | - Bruno Blondel
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
| | - Francis Delpeyroux
- Institut Pasteur, Biology of Enteric Viruses Unit, 75015 Paris, France.
- INSERM U994, Institut National de la Santé et de la Recherche Médicale, 75015 Paris, France.
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12
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Near-Complete Genome Sequences of 12 Coxsackievirus Group A Strains from Hand, Foot, and Mouth Disease and Herpangina Cases with Different Clinical Symptoms. Microbiol Resour Announc 2019; 8:MRA01655-18. [PMID: 30834371 PMCID: PMC6386572 DOI: 10.1128/mra.01655-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022] Open
Abstract
Coxsackievirus group A (CV-A) strains are important pathogens of hand, foot, and mouth disease and herpangina. We report here the near-complete genome sequences of 12 CV-A strains isolated from infants and children with different clinical diseases. The presented data will be very useful for future genome-based epidemiological studies.
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13
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Chiang KL, Wei SH, Fan HC, Chou YK, Yang JY. Outbreak of recombinant coxsackievirus A2 infection and polio-like paralysis of children, Taiwan, 2014. Pediatr Neonatol 2019; 60:95-99. [PMID: 29503223 DOI: 10.1016/j.pedneo.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 10/18/2022] Open
Affiliation(s)
- Kuo-Liang Chiang
- Department of Pediatrics, Kuang-Tien General Hospital, Taichung, Taiwan; Department of Nutrition, Hungkuang University, Taichung, Taiwan
| | - Sung-Hsi Wei
- Department of Pediatrics, China Medical University Children Hospital, Taichung, Taiwan; Department of Public Health, China Medical University, Taichung, Taiwan
| | - Hueng-Chuen Fan
- Department of Pediatrics, Department of Medical Research, Tungs' Taichung Metroharbor Hospital, Taichung, Taiwan
| | - Yu-Kung Chou
- Department of Pediatrics, Kuang-Tien General Hospital, Taichung, Taiwan
| | - Jyh-Yuan Yang
- Research and Diagnosis Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan.
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14
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Jin Y, Zhang R, Wu W, Duan G. Innate Immunity Evasion by Enteroviruses Linked to Epidemic Hand-Foot-Mouth Disease. Front Microbiol 2018; 9:2422. [PMID: 30349526 PMCID: PMC6186807 DOI: 10.3389/fmicb.2018.02422] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/21/2018] [Indexed: 11/13/2022] Open
Abstract
Enterovirus (EV) infections are a major threat to global public health, and are responsible for mild respiratory illness, hand, foot, and mouth disease (HFMD), acute hemorrhagic conjunctivitis, aseptic meningitis, myocarditis, severe neonatal sepsis-like disease, and acute flaccid paralysis epidemic. Among them, HFMD is a common pediatric infectious disease caused by EVs of the family Picornaviridae including EV-A71, coxsackieviruses (CV)-A2, CV-A6, CV-A10, and CV-A16. Due to lack of vaccines and specific antiviral therapeutics, millions of children still suffer from HFMD. Innate immune system detects foreign invaders by means of a relatively limited number of sensors, such as pattern recognition receptors (PRRs) [e.g., retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), Toll-like receptors (TLRs), and NOD-like receptors (NLRs)] and even some secreted functional proteins. However, a range of research, highlighted in this review, suggest that EV-associated with HFMD have evolved different strategies to avoid detection by innate immunity via different proteases (e.g., 2A, 3C, 2C, and 3D). Ongoing efforts to better understand virus-host interactions that control innate immunity and then distill how that influences HFMD development promises to have real-world significance. In this review, we address this complex topic in nine sections including multiple proteins associated with PRR and type I interferon (IFN) signaling. Recognizing how EVs linked to HFMD evade host innate immune system, we also describe the interactions between them and, finally, suggest future directions to better inform drug development and public health.
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Affiliation(s)
- Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Rongguang Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Weidong Wu
- Department of Occupational and Environmental Health, School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, China
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15
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Yang Q, Gu X, Zhang Y, Wei H, Li Q, Fan H, Xu Y, Li J, Tan Z, Song Y, Yan D, Ji T, Zhu S, Xu W. Persistent circulation of genotype D coxsackievirus A2 in mainland of China since 2008. PLoS One 2018; 13:e0204359. [PMID: 30235342 PMCID: PMC6147602 DOI: 10.1371/journal.pone.0204359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/06/2018] [Indexed: 11/30/2022] Open
Abstract
Coxsackievirus A2 (CV-A2) has emerged as an important etiological agent in the hand, foot, and mouth disease and herpangina pathogen spectrum because of its high global prevalence. In the present study, we investigated the evolutionary dynamics of CV-A2 circulating in China. We analyzed a total of 163 entire VP1 sequences of CV-A2, including 74 sequences generated from the present study and 89 sequences collected from the GenBank database. Phylogenetic analysis based on the entire VP1 nucleotide sequences confirmed the persistent circulation of the predominant genotype D in mainland of China since 2008. Cluster analysis grouped the sequences into two distinct clusters, clusters 1 and 2, with most grouped under cluster 2. After 2012, cluster 1 was gradually replaced by cluster 2. Results of Bayesian Markov chain Monte Carlo analysis suggested that multiple lineages of genotype D were transmitted in mainland of China at an estimated evolutionary rate of 6.32×10−3 substitutions per site per year, which is consistent with the global evolutionary rate of CV-A2 (5.82×10−3 substitutions per site per year). Continuous transmission and evolution of CV-A2 resulted in the genetic polymorphism.
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Affiliation(s)
- Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Xinrui Gu
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- RCSC National Training Center, Beijing, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Haiyan Wei
- Henan Center for Disease Control and Prevention, Zhengzhou, People's Republic of China
| | - Qi Li
- Hebei Center for Disease Control and Prevention, Shijiazhuang, People's Republic of China
| | - Huan Fan
- Jiangsu Center for Disease Control and Prevention, Nanjing, People's Republic of China
| | - Yi Xu
- Shaanxi Center for Disease Control and Prevention, Xi'an, People's Republic of China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhaolin Tan
- Tianjin Center for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
- Medical School, Anhui University of Science and Technology, Huainan, People’s Republic of China
- * E-mail:
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