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Mogotsi MT, Ogunbayo AE, O’Neill HG, Nyaga MM. High Detection Frequency of Vaccine-Associated Polioviruses and Non-Polio Enteroviruses in the Stools of Asymptomatic Infants from the Free State Province, South Africa. Microorganisms 2024; 12:920. [PMID: 38792747 PMCID: PMC11124149 DOI: 10.3390/microorganisms12050920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Enterovirus (EV) infections are widespread and associated with a range of clinical conditions, from encephalitis to meningitis, gastroenteritis, and acute flaccid paralysis. Knowledge about the circulation of EVs in neonatal age and early infancy is scarce, especially in Africa. This study aimed to unveil the frequency and diversity of EVs circulating in apparently healthy newborns from the Free State Province, South Africa (SA). For this purpose, longitudinally collected faecal specimens (May 2021-February 2022) from a cohort of 17 asymptomatic infants were analysed using metagenomic next-generation sequencing. Overall, seven different non-polio EV (NPEV) subtypes belonging to EV-B and EV-C species were identified, while viruses classified under EV-A and EV-D species could not be characterised at the sub-species level. Additionally, under EV-C species, two vaccine-related poliovirus subtypes (PV1 and PV3) were identified. The most prevalent NPEV species was EV-B (16/17, 94.1%), followed by EV-A (3/17, 17.6%), and EV-D (4/17, 23.5%). Within EV-B, the commonly identified NPEV types included echoviruses 6, 13, 15, and 19 (E6, E13, E15, and E19), and coxsackievirus B2 (CVB2), whereas enterovirus C99 (EV-C99) and coxsackievirus A19 (CVA19) were the only two NPEVs identified under EV-C species. Sabin PV1 and PV3 strains were predominantly detected during the first week of birth and 6-8 week time points, respectively, corresponding with the OPV vaccination schedule in South Africa. A total of 11 complete/near-complete genomes were identified from seven NPEV subtypes, and phylogenetic analysis of the three EV-C99 identified revealed that our strains were closely related to other strains from Cameroon and Brazil, suggesting global distribution of these strains. This study provides an insight into the frequency and diversity of EVs circulating in asymptomatic infants from the Free State Province, with the predominance of subtypes from EV-B and EV-C species. This data will be helpful to researchers looking into strategies for the control and treatment of EV infection.
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Affiliation(s)
- Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
| | - Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
| | - Hester G. O’Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa;
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa; (M.T.M.); (A.E.O.)
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Cong R, Xiao J, Ji T, Sun Q, Lu H, Yan D, Zhu S, Li X, Wang D, Liu Y, Li J, Wang X, Yang T, Xu X, Zhang Y. Genetic characterization and molecular epidemiological analysis of enterovirus C99 in China. J Med Virol 2024; 96:e29449. [PMID: 38314919 DOI: 10.1002/jmv.29449] [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: 11/07/2023] [Revised: 01/01/2024] [Accepted: 01/24/2024] [Indexed: 02/07/2024]
Abstract
Enterovirus C99 (EV-C99) is a newly identified EV serotype within the species Enterovirus C. Few studies on EV-C99 have been conducted globally. More information and research on EV-C99 are needed to assess its genetic characteristics, phylogenetic relationships, and associations with enteroviral diseases. Here, the phylogenetic characteristics of 11 Chinese EV-C99 strains have been reported. The full-length genomic sequences of these 11 strains show 79.4-80.5% nucleotide identity and 91.7-94.3% amino acid (aa) identity with the prototype EV-C99. A maximum likelihood phylogenetic tree constructed based on the entire VP1 coding region identified 13 genotypes (A-M), revealing a high degree of variation among the EV-C99 strains. Phylogeographic analysis showed that the Xinjiang Uygur Autonomous Region is an important source of EV-C99 epidemics in various regions of China. Recombination analysis revealed inter-serotype recombination events of 16 Chinese EV-C99 strains in 5' untranslated regions and 3D regions, resulting in the formation of a single recombination form. Additionally, the Chinese strain of genotype J showed rich aa diversity in the P1 region, indicating that the genotype J of EV-C99 is still going through variable dynamic changes. This study contributes to the global understanding of the EV-C99 genome sequence and holds substantial implications for the surveillance of EV-C99.
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Affiliation(s)
- Ruyi Cong
- School of Public Health, Shandong First Medical University & 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Xiaolei Li
- 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
| | - Dongyan 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
| | - 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
| | - Jichen Li
- 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
| | - Tingting Yang
- School of Public Health, Shandong First Medical University & 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
| | - Xizhu Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- The Second Affiliated Hospital of Shandong First Medical University, Taian, 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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Zhang M, Zhang Y, Hong M, Xiao J, Han Z, Song Y, Zhu S, Yan D, Yang Q, Xu W, Liu Z. Molecular typing and characterization of a novel genotype of EV-B93 isolated from Tibet, China. PLoS One 2020; 15:e0237652. [PMID: 32841272 PMCID: PMC7447049 DOI: 10.1371/journal.pone.0237652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/30/2020] [Indexed: 11/18/2022] Open
Abstract
EV-B93 is a novel serotype within the Enterovirus B species and is uncommon worldwide. Currently, only one full-length genomic sequence (the prototype strain) has been deposited in the GenBank database. In this study, three EV-B93 were identified, including one from an acute flaccid paralysis (AFP) patient (named 99052/XZ/CHN/1999, hereafter XZ99052) and two from healthy children (named 99096/XZ/CHN/1999 and 99167/XZ/CHN/1999, hereafter XZ99096 and XZ99167, respectively) from Tibet in 1999 during the polio eradication program. The identity between the nucleotide and amino acid sequences of the Tibet EV-B93 strain and the EV-B93 prototype strain is 83.2%–83.4% and 96.8%–96.9%, respectively. The Tibet EV-B93 strain was found to have greater nucleotide sequence identity in the P3 region to another enterovirus EV-B107 as per a phylogenetic tree analysis, which revealed that recombination occurred. Seroepidemiology data showed that EV-B93 has not produced an epidemic in Tibet and there may be susceptible individuals. The three Tibet EV-B93 strains are temperature-resistant with prognosticative virulence, suggesting the possibility of a potential large-scale outbreak of EV-B93. The analyzed EV-B93 strains enrich our knowledge about this serotype and provide valuable information on global EV-B93 molecular epidemiology. What is more, they permit the appraisal of the serotype's potential public health impact and aid in understanding the role of recombination events in the evolution of enteroviruses.
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Affiliation(s)
- Man Zhang
- Department of Medical Microbiology, Weifang Medical University, Weifang, People’s Republic of China
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail: (YZ); (ZL)
| | - Mei Hong
- Tibet Center for Disease Control and Prevention, Lhasa City, Tibet Autonomous Region, People’s Republic of China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Song
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, 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 Biosafety, 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 Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory and National Health Commission Key Laboratory for Biosafety, 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 Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Zhijun Liu
- Department of Medical Microbiology, Weifang Medical University, Weifang, People’s Republic of China
- * E-mail: (YZ); (ZL)
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Luchs A, Leal E, Tardy K, Milagres FADP, Komninakis SV, Brustulin R, Teles MDAR, Lobato MCABS, das Chagas RT, Abrão MDFNDS, Soares CVDDA, Deng X, Delwart E, Sabino EC, da Costa AC. The rare enterovirus c99 and echovirus 29 strains in Brazil: potential risks associated to silent circulation. Mem Inst Oswaldo Cruz 2019; 114:e190160. [PMID: 31411312 PMCID: PMC6690645 DOI: 10.1590/0074-02760190160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/17/2019] [Indexed: 01/10/2023] Open
Abstract
Human enteroviruses (EVs) are associated with a wide spectrum of human diseases.
Here we report the complete genome sequences of one EV-C99 strain and one E29
strain obtained from children suffering from acute gastroenteritis, without
symptoms of enteroviral syndromes. This is the first report of EV-C99 in South
America, and the second E29 genome described worldwide. Continuous surveillance
on EVs is vital to provide further understanding of the circulation of new or
rare EV serotypes in the country. The present study also highlights the capacity
of EVs to remain in silent circulation in populations.
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Affiliation(s)
- Adriana Luchs
- Instituto Adolfo Lutz, Centro de Virologia, Núcleo de Doenças Entéricas, São Paulo, SP, Brasil
| | - Elcio Leal
- Universidade Federal do Pará, Instituto de Ciências Biológicas, Belém, PA, Brasil
| | - Kaelan Tardy
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Flavio Augusto de Pádua Milagres
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | - Shirley Vasconcelos Komninakis
- Faculdade de Medicina do ABC, Programa de Pós-Graduação em Ciências da Saúde, Santo André, SP, Brasil.,Universidade Federal de São Paulo, Laboratório de Retrovirologia, São Paulo, SP, Brasil
| | - Rafael Brustulin
- Universidade Federal de Tocantins, Palmas, TO, Brasil.,Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | | | | | - Rogério Togisaki das Chagas
- Laboratório de Saúde Pública do Estado de Tocantins, Palmas, TO, Brasil.,Secretaria de Saúde de Tocantins, Palmas, TO, Brasil
| | | | | | - Xutao Deng
- Blood Systems Research Institute, San Francisco, USA.,University of California San Francisco, Department Laboratory Medicine, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, USA.,University of California San Francisco, Department Laboratory Medicine, San Francisco, CA, USA
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
| | - Antonio Charlys da Costa
- Universidade de São Paulo, Instituto de Medicina Tropical, São Paulo, SP, Brasil.,Universidade de São Paulo, Faculdade de Medicina, LIM/46, São Paulo, SP, Brasil
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Complete Genome Sequence of a Human Enterovirus C99 Strain Isolated from a Healthy Child in Yunnan, China, in 2013. Microbiol Resour Announc 2019; 8:8/16/e01489-18. [PMID: 31000560 PMCID: PMC6473154 DOI: 10.1128/mra.01489-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of a human enterovirus C99 strain isolated from a healthy child in Yunnan, China, in 2013 was determined. The isolate belonged to genotype C, according to phylogenetic and homogeneity analyses. The complete genome sequence of a human enterovirus C99 strain isolated from a healthy child in Yunnan, China, in 2013 was determined. The isolate belonged to genotype C, according to phylogenetic and homogeneity analyses.
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Hu L, Zhang Y, Hong M, Fan Q, Yan D, Zhu S, Wang D, Xu W. Phylogenetic analysis and phenotypic characterisatics of two Tibet EV-C96 strains. Virol J 2019; 16:40. [PMID: 30922336 PMCID: PMC6439968 DOI: 10.1186/s12985-019-1151-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/22/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Enterovirus C96 (EV-C96) is a newly named type of enterovirus belonging to species C, and the prototype strain (BAN00-10488) was firstly isolated in 2000 from a stool specimen of a patient with acute flaccid paralysis in Bangladesh. In this study, we report the genomic and phenotypic characteristics of two EV-C96 strains isolated from individuals from the Tibet Autonomous Region of China. METHODS Human rhabdomyosarcoma (RD), human laryngeal epidermoid carcinoma (HEp-2), and human cervical cancer (Hela) cells were infected with the Tibet EV-C96 strains, and enterovirus RNA in the cell culture was detected with a real time RT-PCR-based enterovirus screening method. The temperature sensitivity of Tibet EV-C96 strains were assayed on a monolayer of RD cells in 24-well plates. Full-length genome sequencing was performed by a 'primer-walking' strategy, and the evolutionary history of EV-C96 was studied by maximum likelihood analysis. RESULTS Strain 2005-T49 grew in all three kinds of cells, and it was not temperature sensitive. In contrast, none of the three cells produced CPE for strain 2012-94H. Phylogenetic analysis of the two Tibetan viruses, other EV-C96 strains, and EV-C prototypes showed that EV-C96 strains were grouped into three clusters (Cluster1-3) based on their VP1 sequences, which may represent three genotypes. Phylogenetic trees based on the P2 and P3 regions highlighted the difference between Chinese EV-C96 strains and the EV-C96 prototype strain BAN-10488. All Chinese strains formed a cluster separate from BAN-10488, which clustered with CV-A1/CV-A22/CV-A19. CONCLUSIONS There is genetic variability between EV-C96 strains which suggest that at least few genetic lineages co-exist and there has been some degree of circulation in different geographical regions for some time. Some recombination events must have occurred during EV-C96 evolution as EV-C96 isolates cluster with different EV-C prototype strains in phylogenetic trees in different genomic regions. However, recombination does not seem to have occurred frequently as EV-C96 isolates from different years and locations appear to cluster together in all genomic regions analysed. These findings expand the understanding of the characterization of EV-C96 and are meaningful for the surveillance of the virus.
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Affiliation(s)
- Lan Hu
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Department of the Laboratory, Guanghua Hospital of Traditional and Western Medicine, Changning District, Shanghai, People's Republic of China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Mei Hong
- Tibet Center for Disease Control and Prevention, Lhasa City, Tibet Autonomous Region, People's Republic of China
| | - Qin Fan
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Zhejiang Center for Disease Control and Prevention, Hangzhou city, Zhejiang Province, People's Republic of China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory of Biosafety, 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 NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongyan Wang
- WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory of Biosafety, 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 NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China. .,Anhui University of Science and Technology, Hefei city, Anhui Province, People's Republic of China.
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7
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Circulation of multiple serotypes of highly divergent enterovirus C in the Xinjiang Uighur Autonomous Region of China. Sci Rep 2016; 6:33595. [PMID: 27642136 PMCID: PMC5027535 DOI: 10.1038/srep33595] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 08/30/2016] [Indexed: 12/29/2022] Open
Abstract
Poliomyelitis associated with circulating vaccine-derived polioviruses (cVDPVs) is a serious public health issue in the post-eradication era, and the occurrence of recombinant cVDPVs emphasizes the need to elucidate enterovirus C (EV-C) epidemiology. Stool samples were collected from 826 healthy children in Southern Xinjiang in 2011 to investigate EV-C circulation and epidemiology. Thirty-six EV-Cs were isolated and assigned to eight EV-C serotypes by molecular serotyping, suggesting the circulation of diverse EV-Cs in Xinjiang. Phylogenetic analysis showed that the Xinjiang EV-C strains had larger variation compared to the prototype and other modern strains. Additionally, the results showed unique characteristics of Xinjiang EV-Cs, such as the cytopathicity of CV-A1 strains to RD cells; the high divergence in CV-A11, CV-A13, CV-A17, and CV-A20 strains; the divergence of Xinjiang CV-A24 from AHC-related CV-A24 variant stains distributed worldwide; and the circulation of two novel EV-C serotypes (EV-C96 and EV-C99). Evaluations of this dense and diverse EV-C ecosystem will help elucidate the processes shaping enteroviral biodiversity. This study will improve our understanding of the evolution of enteroviruses and the recombination potential between polioviruses and other EV-Cs.
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8
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Isolation and Characterization of a Highly Mutated Chinese Isolate of Enterovirus B84 from a Patient with Acute Flaccid Paralysis. Sci Rep 2016; 6:31059. [PMID: 27499334 PMCID: PMC4976325 DOI: 10.1038/srep31059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/13/2016] [Indexed: 12/03/2022] Open
Abstract
Enterovirus B84 (EV-B84) is a newly identified serotype within the species Enterovirus B (EV-B). To date, only ten nucleotide sequences of EV-B84 are published and only one full-length genome sequence (the prototype strain) is available in the GenBank database. Here, a highly mutated EV-B84 (strain AFP452/GD/CHN/2004) was recovered from a patient with acute flaccid paralysis in the Guangdong province of China in 2004 making this the first report of EV-B84 in China. Sequence comparison and phylogenetic dendrogram analysis revealed high variation from the global EV-B84 strains (African and Indian strains) and frequent intertypic recombination in the non-structural protein region, suggesting high genetic diversity in EV-B84. The Chinese EV-B84 strain, apparently evolving independently of the other ten strains, strongly suggests that the EV-B84 strain has been circulating for many years. However, the extremely low isolation rate suggests that it is not a prevalent EV serotype in China or worldwide. This study provides valuable information about the molecular epidemiology of EV-B84 in China, and will be helpful in future studies to understand the association of EV-B84 with neurological disorders; it also helps expand the number of whole virus genome sequences of EV-B84 in the GenBank database.
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9
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Tang J, Li Q, Tian B, Zhang J, Li K, Ding Z, Lu L. Complete Genome Analysis of an Enterovirus EV-B83 Isolated in China. Sci Rep 2016; 6:29432. [PMID: 27405393 PMCID: PMC4942604 DOI: 10.1038/srep29432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/16/2016] [Indexed: 11/09/2022] Open
Abstract
Enterovirus B83 (EV-B83) is a recently identified member of enterovirus species B. It is a rarely reported serotype and up to date, only the complete genome sequence of the prototype strain from the United States is available. In this study, we describe the complete genomic characterization of an EV-B83 strain 246/YN/CHN/08HC isolated from a healthy child living in border region of Yunnan Province, China in 2008. Compared with the prototype strain, it had 79.6% similarity in the complete genome and 78.9% similarity in the VP1 coding region, reflecting the great genetic divergence among them. VP1-coding region alignment revealed it had 77.2–91.3% with other EV-B83 sequences available in GenBank. Similarity plot analysis revealed it had higher identity with several other EV-B serotypes than the EV-B83 prototype strain in the P2 and P3 coding region, suggesting multiple recombination events might have occurred. The great genetic divergence with previously isolated strains and the extremely rare isolation suggest this serotype has circulated at a low epidemic strength for many years. This is the first report of complete genome of EV-B83 in China.
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Affiliation(s)
- Jingjing Tang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Qiongfen Li
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Bingjun Tian
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Jie Zhang
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Kai Li
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Zhengrong Ding
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
| | - Lin Lu
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, People's Republic of China
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Tao Z, Yuan Q, Lin X, Wang S, Liu Y, Ji F, Xiong P, Cui N, Song L, Wang M, Xu A. Molecular characterization of enteroviruses including a new type EV-C99 isolated from Xinjiang students in Shandong, China in 2011. Sci Rep 2014; 4:6564. [PMID: 25298041 PMCID: PMC4190507 DOI: 10.1038/srep06564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/15/2014] [Indexed: 12/02/2022] Open
Abstract
The last case of infection with wild-type poliovirus indigenous to China was reported in 1994. In 2011, a poliomyelitis outbreak caused by imported wide-type poliovirus occurred in Xinjiang Uighur Autonomous Region. Here, we report the results of enterovirus (EV) isolation from Xinjiang students that returned to school in Shandong after summer vacation during this outbreak. Stool specimens from 376 students were collected and 10 EV strains were isolated including 4 polioviruses (All Sabin strains), 1 coxsackievirus (CV) A13, 3 CVA17 and 2 EV-C99. VP1 sequence analysis revealed these CVA13, CVA17 and EV-C99 strains had 71.3–81.8%, 76.5–84.6% and 74.2–82.9% nucleotide similarity with strains from other countries within a serotype, respectively. EV-C99 strains had 82.7–92.8% VP1 similarity with two previously reported Xinjiang strains. Complete genome analysis on EV-C99 strains revealed intra-serotypic genetic recombination events. These findings reflect great genetic divergence between Chinese strains and strains from other countries of the three types, and provide valuable information on monitoring EV transmission over long distance.
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Affiliation(s)
- Zexin Tao
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Qun Yuan
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Xiaojuan Lin
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Suting Wang
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Yao Liu
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Feng Ji
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Ping Xiong
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Ning Cui
- Department of Preventive Medicine, College of Basic Medical Sciences, Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Lizhi Song
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Mei Wang
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China
| | - Aiqiang Xu
- 1] Academy of Preventive Medicine, Shandong University, Jinan, People's Republic of China [2] Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, Jinan, People's Republic of China [3] School of Public Health, Shandong University, Jinan, People's Republic of China
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