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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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2
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Fang C, Fu W, Liu N, Zhao H, Zhao C, Yu K, Liu C, Yin Z, Xu L, Xia N, Wang W, Cheng T. Investigating the virulence of coxsackievirus B6 strains and antiviral treatments in a neonatal murine model. Antiviral Res 2024; 221:105781. [PMID: 38097049 DOI: 10.1016/j.antiviral.2023.105781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
Coxsackievirus B6 (CVB6), a member of the human enterovirus family, is associated with severe diseases such as myocarditis in children. However, to date, only a limited number of CVB6 strains have been identified, and their characterization in animal models has been lacking. To address this gap, in this study, a neonatal murine model of CVB6 infection was established to compare the replication and virulence of three infectious-clone-derived CVB6 strains in vivo. The results showed that following challenge with a lethal dose of CVB6 strains, the neonatal mice rapidly exhibited a series of clinical signs, such as weight loss, limb paralysis, and death. For the two high-virulence CVB6 strains, histological examination revealed myocyte necrosis in skeletal and cardiac muscle, and immunohistochemistry confirmed the expression of CVB6 viral protein in these tissues. Real-time PCR assay also revealed higher viral loads in the skeletal and cardiac muscle than in other tissues at different time points post infection. Furthermore, the protective effect of passive immunization with antisera and a neutralizing monoclonal antibody against CVB6 infection was evaluated in the neonatal mouse model. This study should provide insights into the pathogenesis of CVB6 and facilitate further research in the development of vaccines and antivirals against CVBs.
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Affiliation(s)
- Changjian Fang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wenkun Fu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Nanyi Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Huan Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Canyang Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Kang Yu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Che Liu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Zhichao Yin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Longfa Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China
| | - Wei Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen, 361102, PR China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Collaborative Innovation Center of Biologic Products, National Innovation Platform for Industry-Education Integration in Vaccine Research, Xiamen University, Xiamen, 361102, PR China.
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Alsayed AR, Abed A, Abu-Samak M, Alshammari F, Alshammari B. Etiologies of Acute Bronchiolitis in Children at Risk for Asthma, with Emphasis on the Human Rhinovirus Genotyping Protocol. J Clin Med 2023; 12:3909. [PMID: 37373604 DOI: 10.3390/jcm12123909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
This research aims to determine acute bronchiolitis' causative virus(es) and establish a viable protocol to classify the Human Rhinovirus (HRV) species. During 2021-2022, we included children 1-24 months of age with acute bronchiolitis at risk for asthma. The nasopharyngeal samples were taken and subjected to a quantitative polymerase chain reaction (qPCR) in a viral panel. For HRV-positive samples, a high-throughput assay was applied, directing the VP4/VP2 and VP3/VP1 regions to confirm species. BLAST searching, phylogenetic analysis, and sequence divergence took place to identify the degree to which these regions were appropriate for identifying and differentiating HRV. HRV ranked second, following RSV, as the etiology of acute bronchiolitis in children. The conclusion of the investigation of all available data in this study distributed sequences into 7 HRV-A, 1 HRV-B, and 7 HRV-C types based on the VP4/VP2 and VP3/VP1 sequences. The nucleotide divergence between the clinical samples and the corresponding reference strains was lower in the VP4/VP2 region than in the VP3/VP1 region. The results demonstrated the potential utility of the VP4/VP2 region and the VP3/VP1 region for differentiating HRV genotypes. Confirmatory outcomes were yielded, indicating how nested and semi-nested PCR can establish practical ways to facilitate HRV sequencing and genotyping.
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Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Mahmoud Abu-Samak
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2440, Saudi Arabia
| | - Bushra Alshammari
- Department of Medical Surgical Nursing, College of Nursing, University of Hail, Hail 2440, Saudi Arabia
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Guo Q, Zhao H, Zhang Y, Wang X, Yu Q, Tan Z, Lu H, Xiao J, Ji T, Zhu S, Wang D, Yang Q, Han Z, Xu W, Yan D. Genetic characterization and molecular epidemiology of Coxsackievirus A12 from mainland China during 2010-2019. Front Microbiol 2022; 13:988538. [PMID: 36620057 PMCID: PMC9811122 DOI: 10.3389/fmicb.2022.988538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Coxsackievirus A12 (CVA12) is an enterovirus that has been isolated in many countries in recent years. However, studies on CVA12 are limited, and its effective population size, evolutionary dynamics and recombination patterns have not been clarified now. In this study, we described the phylogenetic characteristics of 16 CVA12 strains isolated from pediatric HFMD patients in mainland China from 2010 to 2019. Comparison of the nucleotide sequences and amino acid sequences with the CVA12 prototype strain revealed that the 16 CVA12 strains are identical in 78.8-79% and 94-94.2%, respectively. A phylodynamic analysis based on the 16 full-length VP1 sequences from this study and 21 sequences obtained from GenBank revealed a mean substitution rate of 6.61 × 10-3 substitutions/site/year (95% HPD: 5.16-8.20 × 10-3), dating the time to most recent common ancestor (tMRCA) of CVA12 back to 1946 (95% HPD: 1942-1947). The Bayesian skyline plot showed that the effective population size has experienced twice dynamic fluctuations since 2007. Phylogeographic analysis identified two significant migration pathways, indicating the existence of cross-provincial transmission of CVA12 in mainland China. Recombination analysis revealed two recombination patterns between 16 CVA12 strains and other EV-A, suggesting that there may be extensive genetic exchange between CVA12 and other enteroviruses. In summary, a total of 16 full-length CVA12 strains were reported in this study, providing valuable references for further studies of CVA12 worldwide.
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Affiliation(s)
- Qin Guo
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Da Zhou Vocational College of Chinese Medicine, Dazhou, China
| | - Hehe Zhao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yong Zhang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong, China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, China
| | - Zhaolin Tan
- Tianjin Center for Disease Control and Prevention, Tianjin, China
| | - Huanhuan Lu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Jinbo Xiao
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Tianjiao Ji
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Shuangli Zhu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongyan Wang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Qian Yang
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Zhenzhi Han
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dongmei Yan
- National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosecurity, National Health Commission Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention Beijing, National Institute for Viral Disease Control and Prevention, Beijing, China,*Correspondence: Dongmei Yan,
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5
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Molecular Characteristics and Genetic Evolution of Echovirus 33 in Mainland of China. Pathogens 2022; 11:pathogens11111379. [PMID: 36422630 PMCID: PMC9697921 DOI: 10.3390/pathogens11111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/22/2022] Open
Abstract
Echovirus, a member of the Enterovirus B (EV-B) family, has led to numerous outbreaks and pandemics, causing a broad spectrum of diseases. Based on the national hand, foot, and mouth disease (HFMD) surveillance system, seven strains of echovirus 33 (E33) were isolated from Mainland of China between 2010 and 2018. The whole genomes of these strains were isolated and sequenced, and phylogenetic trees were constructed based on the gene sequences in different regions of the EV-B prototype strains. It was found that E33 may be recombined in the P2 and P3 regions. Five genotypes (A–E) were defined based on the entire VP1 region of E33, of which the C gene subtype was the dominant gene subtype at present. Recombinant analysis showed that genotype C strains likely recombined with EV-B80, EV-B85, E13, and CVA9 in the P2 and P3 regions, while genotype E had the possibility of recombination with CVB3, E3, E6, and E4. Results of Bayesian analysis indicated that E33 may have appeared around 1955 (95% confidence interval: 1945–1959), with a high evolutionary rate of 1.11 × 10−2 substitution/site/year (95% highest posterior density (HPD): 8.17 × 10−3 to 1.4 × 10−2 substitution/site/year). According to spatial transmission route analysis, two significant transmission routes were identified: from Australia to India and from Oman to Thailand, which the E33 strain in Mainland of China likely introduced from Mexico and India. In conclusion, our study fills the gaps in the evolutionary analysis of E33 and can provide important data for enterovirus surveillance.
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Song Y, Wang D, Zhang Y, Han Z, Xiao J, Lu H, Yan D, Ji T, Yang Q, Zhu S, Xu W. Genetic Diversity Analysis of Coxsackievirus A8 Circulating in China and Worldwide Reveals a Highly Divergent Genotype. Viruses 2020; 12:E1061. [PMID: 32977444 PMCID: PMC7598191 DOI: 10.3390/v12101061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Coxsackievirus A8 (CV-A8) is one of the pathogens associated with hand, foot and mouth disease (HFMD) and herpangina (HA), occasionally leading to severe neurological disorders such as acute flaccid paralysis (AFP). Only one study aimed at CV-A8 has been published to date, and only 12 whole-genome sequences are publicly available. In this study, complete genome sequences from 11 CV-A8 strains isolated from HFMD patients in extensive regions from China between 2013 and 2018 were determined, and all sequences from GenBank were retrieved. A phylogenetic analysis based on a total of 34 complete VP1 sequences of CV-A8 revealed five genotypes: A, B, C, D and E. The newly emerging genotype E presented a highly phylogenetic divergence compared with the other genotypes and was composed of the majority of the strains sequenced in this study. Markov chain Monte Carlo (MCMC) analysis revealed that genotype E has been evolving for nearly a century and somehow arose in approximately 2010. The Bayesian skyline plot showed that the population size of CV-A8 has experienced three dynamic fluctuations since 2001. Amino acid residues of VP1100N, 103Y, 240T and 241V, which were embedded in the potential capsid loops of genotype E, might enhance genotype E adaption to the human hosts. The CV-A8 whole genomes displayed significant intra-genotypic genetic diversity in the non-capsid region, and a total of six recombinant lineages were detected. The Chinese viruses from genotype E might have emerged recently from recombining with European CV-A6 strains. CV-A8 is a less important HFMD pathogen, and the capsid gene diversity and non-capsid recombination variety observed in CV-A8 strains indicated that the constant generation of deleterious genomes and a constant selection pressure against these deleterious mutations is still ongoing within CV-A8 quasispecies. It is possible that CV-A8 could become an important pathogen in the HFMD spectrum in the future. Further surveillance of CV-A8 is greatly needed.
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Affiliation(s)
- Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Dongyan Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing 102206, China; (Y.S.); (D.W.); (Z.H.); (J.X.); (H.L.); (D.Y.); (T.J.); (Q.Y.); (S.Z.)
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
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Multiple genotypes of enterovirus G carrying a papain-like cysteine protease (PL-CP) sequence circulating on two pig farms in Japan: first identification of enterovirus G10 carrying a PL-CP sequence. Arch Virol 2020; 165:2909-2914. [PMID: 32951133 DOI: 10.1007/s00705-020-04816-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/18/2020] [Indexed: 10/23/2022]
Abstract
Two and three genotypes of enterovirus G (EV-G) carrying a papain-like cysteine protease (PL-CP) sequence were detected on two pig farms and classified into genotypes G1 and G10, and G1, G8, and G17, respectively, based on VP1 sequences. A G10 EV-G virus bearing a PL-CP sequence was detected for the first time. Phylogenetic analysis of the P2 and P3 regions grouped the viruses by farm with high sequence similarity. Furthermore, clear recombination break points were detected in the 2A region, suggesting that PL-CP EV-G-containing strains gained sequence diversity through recombination events among the multiple circulating EV-G genotypes on the farms.
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Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, Wang J, Yang J, Yu Q, Yu D, Chen J, Huang W, Li J, Xie T, Lu H, Ji T, Yang Q, Yan D, Zhu S, Xu W. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol 2020; 6:veaa048. [PMID: 34804589 PMCID: PMC8597624 DOI: 10.1093/ve/veaa048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Hand, foot, and mouth disease (HFMD) is a common global epidemic. From 2008
onwards, many HFMD outbreaks caused by coxsackievirus A6 (CV-A6) have been
reported worldwide. Since 2013, with a dramatically increasing number of
CV-A6-related HFMD cases, CV-A6 has become the predominant HFMD pathogen in
mainland China. Phylogenetic analysis based on the VP1 capsid
gene revealed that subtype D3 dominated the CV-A6 outbreaks. Here, we performed
a large-scale (near) full-length genetic analysis of global and Chinese CV-A6
variants, including 158 newly sequenced samples collected extensively in
mainland China between 2010 and 2018. During the global transmission of subtype
D3 of CV-A6, the noncapsid gene continued recombining, giving rise to a series
of viable recombinant hybrids designated evolutionary lineages, and each lineage
displayed internal consistency in both genetic and epidemiological features. The
emergence of lineage –A since 2005 has triggered CV-A6 outbreaks
worldwide, with a rate of evolution estimated at
4.17 × 10−3 substitutions
site-1 year−1 based on a
large number of monophyletic open reading frame sequences, and created a series
of lineages chronologically through varied noncapsid recombination events. In
mainland China, lineage –A has generated another two novel widespread
lineages (–J and –L) through recombination within the
enterovirus A gene pool, with robust estimates of occurrence time. Lineage
–A, –J, and –L infections presented dissimilar clinical
manifestations, indicating that the conservation of the CV-A6 capsid gene
resulted in high transmissibility, but the lineage-specific noncapsid gene might
influence pathogenicity. Potentially important amino acid substitutions were
further predicted among CV-A6 variants. The evolutionary phenomenon of noncapsid
polymorphism within the same subtype observed in CV-A6 was uncommon in other
leading HFMD pathogens; such frequent recombination happened in fast-spreading
CV-A6, indicating that the recovery of deleterious genomes may still be ongoing
within CV-A6 quasispecies. CV-A6-related HFMD outbreaks have caused a
significant public health burden and pose a great threat to children’s
health; therefore, further surveillance is greatly needed to understand the full
genetic diversity of CV-A6 in mainland China.
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Affiliation(s)
- Yang Song
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Zhenzhi Han
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Wen Xu
- Yunnan Center for Disease Control and Prevention, Kunming, Yunnan Province, China
| | - Jinbo Xiao
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong Province, China
| | - Jianfang Yang
- Shanxi Center for Disease Control and Prevention, Taiyuan, Shanxi Province, China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Deshan Yu
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Jianhua Chen
- Gansu Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Wei Huang
- Chongqing Center for Disease Control and Prevention, Chongqing City, China
| | - Jie Li
- Beijing Center for Disease Control and Prevention, Beijing City, China
| | - Tong Xie
- Tianjin Center for Disease Control and Prevention, Tianjin City, China
| | - Huanhuan Lu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Tianjiao Ji
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Qian Yang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Dongmei Yan
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Shuangli Zhu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China
| | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, 102206, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei Province, China.,Anhui University of Science and Technology, Anhui Province, China
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9
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The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019; 11:v11111032. [PMID: 31698764 PMCID: PMC6893659 DOI: 10.3390/v11111032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/05/2022] Open
Abstract
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters.
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10
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Ji T, Guo Y, Lv L, Wang J, Shi Y, Yu Q, Zhang F, Tong W, Ma J, Zeng H, Zhao H, Zhang Y, Han T, Song Y, Yan D, Yang Q, Zhu S, Zhang Y, Xu W. Emerging recombination of the C2 sub-genotype of HFMD-associated CV-A4 is persistently and extensively circulating in China. Sci Rep 2019; 9:13668. [PMID: 31541120 PMCID: PMC6754396 DOI: 10.1038/s41598-019-49859-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Sporadic outbreaks caused by coxsackievirus A4 (CV-A4) have been reported worldwide. To further elucidate the detailed genetic characteristics and evolutionary recombination events of CV-A4, virus samples from nationwide hand, foot and mouth disease (HFMD) surveillance, encompassing 27 out of the 31 provinces in China, were investigated. Comprehensive and systematic phylogenetic analyses were performed by using 29 complete genomes, 142 complete CV-A4 VP1 sequences. Four genotypes (A, B, C and D) and five sub-genotypes (C1-C5) were re-identified based on the complete VP1 sequences. C2 is the predominant sub-genotype of CV-A4 associated with HFMD and has evolved into 3 clusters. Cluster 1 is a major cluster that has been persistently and extensively circulating in China since 2006 and has been associated with all severe cases. All the sequences showed high homology with the CV-A4 prototype in the P1 region, while higher identities with CV-A5, CV-14 and CV-16 in the P2 and P3 regions. Recombination analysis revealed that C2 had two specific genetic recombination patterns with other EV-A prototypes in the 5'-UTR and 3D region compared with C5. These recombination patterns might be associated with the increased transmissibility of C2 viruses, which were obtained due to their persistent and extensive circulation in populations.
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Affiliation(s)
- Tianjiao Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Yue Guo
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Likun Lv
- Tianjin Municipal Center for Disease Control and Prevention, Tianjin Municipal, People's Republic of China
| | - Jianxing Wang
- Shandong Center for Disease Control and Prevention, Shandong Province, People's Republic of China
| | - Yong Shi
- Jiangxi Center for Disease Control and Prevention, Nanchang, Jiangxi Province, People's Republic of China
| | - Qiuli Yu
- Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, People's Republic of China
| | - Fan Zhang
- Hunan Center for Disease Control and Prevention, Changsha, Hunan Province, People's Republic of China
| | - Wenbin Tong
- Sichuan Center for Disease Control and Prevention, Chengdu, Sichuan Province, People's Republic of China
| | - Jiangtao Ma
- Ningxia Center for Disease Control and Prevention, Yinchuan, Ningxia Province, People's Republic of China
| | - Hanri Zeng
- Guangdong Center for Disease Control and Prevention, Guangzhou, Guangdong Province, People's Republic of China
| | - Hua Zhao
- Chongqing Center for Disease Control and Prevention, Chongqing Municipal, People's Republic of China
| | - Yong Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Taoli Han
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Yang Song
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Dongmei Yan
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Qian Yang
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Shuangli Zhu
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China
| | - Yan Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China.
| | - Wenbo Xu
- NHC Key Laboratory of Medical Virology and Viral Diseases (National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention), Beijing, People's Republic of China.
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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: 53] [Impact Index Per Article: 10.6] [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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Nikolaidis M, Mimouli K, Kyriakopoulou Z, Tsimpidis M, Tsakogiannis D, Markoulatos P, Amoutzias GD. Large-scale genomic analysis reveals recurrent patterns of intertypic recombination in human enteroviruses. Virology 2019; 526:72-80. [DOI: 10.1016/j.virol.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
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13
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Pu X, Qian Y, Yu Y, Shen H. Echovirus plays a major role in natural recombination in the coxsackievirus B group. Arch Virol 2019; 164:853-860. [DOI: 10.1007/s00705-018-4114-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/12/2018] [Indexed: 11/29/2022]
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14
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Kyriakopoulou Z, Amoutzias GD, Dimitriou TG, Tsakogiannis D, Mossialos D, Markoulatos P. Intra- and inter-serotypic recombinations in the 5΄ UTR-VP4 region of Echovirus 30 strains. Arch Virol 2017; 163:365-375. [DOI: 10.1007/s00705-017-3600-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
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15
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Recombination among human non-polio enteroviruses: implications for epidemiology and evolution. Virus Genes 2014; 50:177-88. [PMID: 25537948 DOI: 10.1007/s11262-014-1152-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022]
Abstract
Human enteroviruses (EV) belong to the Picornaviridae family and are among the most common viruses infecting humans. They consist of up to 100 immunologically and genetically distinct types: polioviruses, coxsackieviruses A and B, echoviruses, and the more recently characterized 43 EV types. Frequent recombinations and mutations in enteroviruses have been recognized as the main mechanisms for the observed high rate of evolution, thus enabling them to rapidly respond and adapt to new environmental challenges. The first signs of genetic exchanges between enteroviruses came from polioviruses many years ago, and since then recombination has been recognized, along with mutations, as the main cause for reversion of vaccine strains to neurovirulence. More recently, non-polio enteroviruses became the focus of many studies, where recombination was recognized as a frequent event and was correlated with the appearance of new enterovirus lineages and types. The accumulation of multiple inter- and intra-typic recombination events could also explain the series of successive emergences and disappearances of specific enterovirus types that could in turn explain the epidemic profile of circulation of several types. This review focuses on recombination among human non-polio enteroviruses from all four species (EV-A, EV-B, EV-C, and EV-D) and discusses the recombination effects on enterovirus epidemiology and evolution.
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16
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Ibrahim W, Ouerdani I, Pillet S, Aouni M, Pozzetto B, Harrath R. Direct typing of human enteroviruses from wastewater samples. J Virol Methods 2014; 207:215-9. [PMID: 25066280 DOI: 10.1016/j.jviromet.2014.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 07/08/2014] [Accepted: 07/15/2014] [Indexed: 12/15/2022]
Abstract
A RT-PCR approach for the direct detection and typing of human enteroviruses in the environment is described in this study. A semi-nested RT-PCR using COnsensus-DEgenerated Hybrid Oligonucleotide Primers (CODEHOP) designed from the VP2 genome region has been developed for the direct typing of enteroviruses in clinical samples (Ibrahim et al., 2013). This CODEHOP/VP2 PCR strategy as well as the CODEHOP/VP1 technique described by Nix et al. (2006), were tested for the detection and typing of enteroviruses in wastewater samples. Virus particles were first extracted and concentrated from wastewater samples by using respectively beef extract and polyethylene glycol 6000, and the presence of enteroviruses was screened by a RT-PCR method using primers from the 5'-end non-coding region (5'NCR). Fifty-two of 172 samples (30.2%) were revealed positive by the 5'NCR method. From these 52 samples, only 19 samples (36.5%) were found positive by at least one of the two CODEHOP techniques, with the following distribution: VP1(+)/VP2(+)=4 (7.7%), VP1(-)/VP2(+)=13 (25%) and VP1(+)/VP2(-)=2 (3.8%). These results illustrate that the direct typing of enteroviruses in environmental samples is insensitive, possibly due to the presence of large amounts of amplification inhibitors; however, the VP2 method was found able to allow the direct detection and typing of c. one-third of the positive environmental samples.
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Affiliation(s)
- Wafa Ibrahim
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia; Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Imène Ouerdani
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
| | - Sylvie Pillet
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
| | - Bruno Pozzetto
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France.
| | - Rafik Harrath
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
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17
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Riabi S, Harrath R, Gaaloul I, Bouslama L, Nasri D, Aouni M, Pillet S, Pozzetto B. Study of Coxsackie B viruses interactions with Coxsackie Adenovirus receptor and Decay-Accelerating Factor using Human CaCo-2 cell line. J Biomed Sci 2014; 21:50. [PMID: 24885774 PMCID: PMC4035751 DOI: 10.1186/1423-0127-21-50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/06/2014] [Indexed: 01/20/2023] Open
Abstract
Background Decay Accelerating Factor (DAF) and Coxsackievirus-Adenovirus Receptor (CAR) have been identified as cellular receptors for Coxsackie B viruses (CV-B). The aim of this study is to elucidate the different binding properties of CV-B serotypes and to find out if there are any amino acid changes that could be associated to the different phenotypes. Twenty clinical CV-B isolates were tested on CaCo-2 cell line using anti-DAF (BRIC216) and anti-CAR (RmcB) antibodies. CV-B3 Nancy prototype strain and a recombinant strain (Rec, CV-B3/B4) were tested in parallel. The P1 genomic region of 12 CV-B isolates from different serotypes was sequenced and the Trans-Epithelial Electrical Resistance (TEER) along with the virus growth cycle was measured. Results Infectivity assays revealed clear differences between CV-B isolates with regard to their interactions with DAF and CAR. All tested CV-B isolates showed an absolute requirement for CAR but varied in their binding to DAF. We also reported that for some isolates of CV-B, DAF attachment was not adapted. Genetic analysis of the P1 region detected multiple differences in the deduced amino acid sequences. Conclusion Within a given serotype, variations exist in the capacity of virus isolates to bind to specific receptors, and variants with different additional ligands may arise during infection in humans as well as in tissue culture.
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Affiliation(s)
- Samira Riabi
- Laboratory of Transmissible Diseases LR99-ES27, Faculty of Pharmacy, Avenue Avicenne 5000, Monastir, Tunisia.
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18
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Smura T, Blomqvist S, Vuorinen T, Ivanova O, Samoilovich E, Al-Hello H, Savolainen-Kopra C, Hovi T, Roivainen M. Recombination in the evolution of enterovirus C species sub-group that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99. PLoS One 2014; 9:e94579. [PMID: 24722726 PMCID: PMC3983234 DOI: 10.1371/journal.pone.0094579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/17/2014] [Indexed: 01/16/2023] Open
Abstract
Genetic recombination is considered to be a very frequent phenomenon among enteroviruses (Family Picornaviridae, Genus Enterovirus). However, the recombination patterns may differ between enterovirus species and between types within species. Enterovirus C (EV-C) species contains 21 types. In the capsid coding P1 region, the types of EV-C species cluster further into three sub-groups (designated here as A–C). In this study, the recombination pattern of EV-C species sub-group B that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99 was determined using partial 5′UTR and VP1 sequences of enterovirus strains isolated during poliovirus surveillance and previously published complete genome sequences. Several inter-typic recombination events were detected. Furthermore, the analyses suggested that inter-typic recombination events have occurred mainly within the distinct sub-groups of EV-C species. Only sporadic recombination events between EV-C species sub-group B and other EV-C sub-groups were detected. In addition, strict recombination barriers were inferred for CVA-21 genotype C and CVA-24 variant strains. These results suggest that the frequency of inter-typic recombinations, even within species, may depend on the phylogenetic position of the given viruses.
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Affiliation(s)
- Teemu Smura
- National Institute for Health and Welfare (THL), Helsinki, Finland
- Department of Virology, Haartman Institute, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Soile Blomqvist
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Tytti Vuorinen
- Department of Virology, University of Turku, Turku, Finland
| | - Olga Ivanova
- M.P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow, Russia
| | - Elena Samoilovich
- Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Republic of Belarus
| | - Haider Al-Hello
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Tapani Hovi
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Merja Roivainen
- National Institute for Health and Welfare (THL), Helsinki, Finland
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19
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Bessaud M, Razafindratsimandresy R, Nougairède A, Joffret ML, Deshpande JM, Dubot-Pérès A, Héraud JM, de Lamballerie X, Delpeyroux F, Bailly JL. Molecular comparison and evolutionary analyses of VP1 nucleotide sequences of new African human enterovirus 71 isolates reveal a wide genetic diversity. PLoS One 2014; 9:e90624. [PMID: 24598878 PMCID: PMC3944068 DOI: 10.1371/journal.pone.0090624] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/01/2014] [Indexed: 01/11/2023] Open
Abstract
Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied.
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Affiliation(s)
- Maël Bessaud
- Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
- * E-mail:
| | | | - Antoine Nougairède
- Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
| | - Marie-Line Joffret
- Institut Pasteur, Unité de biologie des virus entériques, Paris, France
- INSERM U994, Paris, France
| | | | - Audrey Dubot-Pérès
- Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Jean-Michel Héraud
- Institut Pasteur de Madagascar, Unité de Virologie, Antananarivo, Madagascar
| | - Xavier de Lamballerie
- Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health, UMR_D 190 “Emergence des Pathologies Virales”, Marseille, France
| | | | - Jean-Luc Bailly
- Clermont Université, Université d'Auvergne, EPIE EA4843, Clermont-Ferrand, France
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20
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Cabrerizo M, Trallero G, Simmonds P. Recombination and evolutionary dynamics of human echovirus 6. J Med Virol 2013; 86:857-64. [PMID: 24114692 DOI: 10.1002/jmv.23741] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 11/07/2022]
Abstract
Enterovirus (EV) infections are associated with a wide array of often severe disease presentations including aseptic meningitis, encephalitis, and acute flaccid paralysis. Surveillance for polioviruses and other EVs is therefore important as a public health measure both for patient management and epidemiological studies. From 1988 to 2008, echovirus (E) 30 was the predominant genotype in Spain (33.7% of the total typed EVs). E6 was also endemic throughout this period although isolated less frequently (12.5%). In 2009, however, a substantial increase in the incidence of E6 was detected (60%), displacing E30 type (2%). To investigate the evolution and recombination in the epidemiology and transmission of E6 in Spain, a genetic analysis in VP1 and 3Dpol regions of 67 Spanish strains collected during the period 2004-2010 was performed. All VP1 sequences clustered monophyletically in the assigned genogroup C, subgroup 9, currently the predominant circulating strains identified in Europe and elsewhere in the last 10 years. 3Dpol sequences were interspersed with other species B EVs resulting from several recombination events that generated at least 12 different recombinant forms (RFs) among study samples. These showed typically minimal divergence in VP1. The co-circulation of different lineages of E6 in the same geographical area associated with its mainly endemic pattern of transmission may have contributed to the extremely short estimated half-life of E6 RFs (0.87 years). This pattern contrasts markedly with other species B EVs and EV71 where VP1 lineage expansion and extinction occurred in step with defined recombination events and periodic changes in incidence.
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Affiliation(s)
- María Cabrerizo
- Enterovirus Unit, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
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Complete Genome Sequence of a Novel Human Enterovirus 85 (HEV85) Recombinant with an Unknown New Serotype HEV-B Donor Sequence Isolated from a Child with Acute Flaccid Paralysis. GENOME ANNOUNCEMENTS 2013; 1:genomeA00015-12. [PMID: 23405286 PMCID: PMC3556829 DOI: 10.1128/genomea.00015-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/22/2012] [Indexed: 11/20/2022]
Abstract
A Chinese human enterovirus 85 (HEV85) isolate, HTYT-ARL-AFP02F/XJ/CHN/2011, was isolated from a stool specimen of a child with acute flaccid paralysis in Xinjiang, China, in 2011. The complete genome sequence revealed that a natural intertypic recombination event had occurred between HEV85 and a previously undescribed serotype of HEV-B.
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Combined 5′ UTR RFLP analysis and VP1 sequencing for epidemic investigation of enteroviruses. Arch Virol 2012; 158:103-11. [DOI: 10.1007/s00705-012-1472-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
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Singh AK, Chattopadhyay B, Chakraborty S. Biology and interactions of two distinct monopartite begomoviruses and betasatellites associated with radish leaf curl disease in India. Virol J 2012; 9:43. [PMID: 22339942 PMCID: PMC3305473 DOI: 10.1186/1743-422x-9-43] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 02/16/2012] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Emerging whitefly transmitted begomoviruses are major pathogens of vegetable and fibre crops throughout the world, particularly in tropical and sub-tropical regions. Mutation, pseudorecombination and recombination are driving forces for the emergence and evolution of new crop-infecting begomoviruses. Leaf curl disease of field grown radish plants was noticed in Varanasi and Pataudi region of northern India. We have identified and characterized two distinct monopartite begomoviruses and associated beta satellite DNA causing leaf curl disease of radish (Raphanus sativus) in India. RESULTS We demonstrate that RaLCD is caused by a complex of two Old World begomoviruses and their associated betasatellites. Radish leaf curl virus-Varanasi is identified as a new recombinant species, Radish leaf curl virus (RaLCV) sharing maximum nucleotide identity of 87.7% with Tomato leaf curl Bangladesh virus-[Bangladesh:2] (Accession number AF188481) while the virus causing radish leaf curl disease-Pataudi is an isolate of Croton yellow vein mosaic virus-[India] (CYVMV-IN) (Accession number AJ507777) sharing 95.8% nucleotide identity. Further, RDP analysis revealed that the RaLCV has a hybrid genome, a putative recombinant between Euphorbia leaf curl virus and Papaya leaf curl virus. Cloned DNA of either RaLCV or CYVMV induced mild leaf curl symptoms in radish plants. However, when these clones (RaLCV or CYVMV) were individually co-inoculated with their associated cloned DNA betasatellite, symptom severity and viral DNA levels were increased in radish plants and induced typical RaLCD symptoms. To further extend these studies, we carried out an investigation of the interaction of these radish-infecting begomoviruses and their associated satellite, with two tomato infecting begomoviruses (Tomato leaf curl Gujarat virus and Tomato leaf curl New Delhi virus). Both of the tomato-infecting begomoviruses showed a contrasting and differential interaction with DNA satellites, not only in the capacity to interact with these molecules but also in the modulation of symptom phenotypes by the satellites. CONCLUSION This is the first report and experimental demonstration of Koch's postulate for begomoviruses associated with radish leaf curl disease. Further observations also provide direct evidence of lateral movement of weed infecting begomovirus in the cultivated crops and the present study also suggests that the exchange of betasatellites with other begomoviruses would create a new disease complex posing a serious threat to crop production.
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Affiliation(s)
- AK Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - B Chattopadhyay
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
| | - S Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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Molecular characterization of human enteroviruses in the Central African Republic: uncovering wide diversity and identification of a new human enterovirus A71 genogroup. J Clin Microbiol 2012; 50:1650-8. [PMID: 22337981 DOI: 10.1128/jcm.06657-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human enteroviruses (HEV) are among the most common viruses infecting humans. Their circulation has been widely studied in most parts of the world but not in sub-Saharan Africa, where poliomyelitis remains prevalent. We report here the molecular characterization of 98 nonpoliovirus (non-PV) HEV strains isolated from 93 randomly selected cell culture-positive supernatants from stool samples collected from 1997 through 2006 from children with acute flaccid paralysis living in the Central African Republic (CAR). The isolates were typed by sequencing the VP1 coding region and sequenced further in the VP2 coding region, and phylogenetic studies were carried out. Among the 98 VP1 sequences, 3, 74, 18, and 3 were found to belong to the HEV-A, -B, -C, and -D species, respectively. Overall, 42 types were detected. In most cases, the VP2 type was correlated with that of the VP1 region. Some of the isolates belonged to lineages that also contain viruses isolated in distant countries, while others belonged to lineages containing viruses isolated only in Africa. In particular, one isolate (type EV-A71) did not fall into any of the genogroups already described, indicating the existence of a previously unknown genogroup for this type. These results illustrate the considerable diversity of HEV isolates from the stools of paralyzed children in the CAR. The presence of diverse HEV-C types makes recombination between poliovirus and other HEV-C species possible and could promote the emergence of recombinant vaccine-derived polioviruses similar to those that have been implicated in repeated poliomyelitis outbreaks in several developing countries.
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Kyriakopoulou Z, Pliaka V, Tsakogiannis D, Ruether IGA, Komiotis D, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Genome analysis of two type 6 echovirus (E6) strains recovered from sewage specimens in Greece in 2006. Virus Genes 2011; 44:207-16. [DOI: 10.1007/s11262-011-0688-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/31/2011] [Indexed: 11/28/2022]
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Bessaud M, Joffret ML, Holmblat B, Razafindratsimandresy R, Delpeyroux F. Genetic relationship between cocirculating Human enteroviruses species C. PLoS One 2011; 6:e24823. [PMID: 21931857 PMCID: PMC3171481 DOI: 10.1371/journal.pone.0024823] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 08/18/2011] [Indexed: 01/19/2023] Open
Abstract
Recombination events between human enteroviruses (HEV) are known to occur frequently and to participate in the evolution of these viruses. In a previous study, we reported the isolation of a panel of viruses belonging to the Human enterovirus species C (HEV-C) that had been cocirculating in a small geographic area of Madagascar in 2002. This panel included type 2 vaccine-derived polioviruses (PV) that had caused several cases of acute flaccid paralysis in humans. Previous partial sequencing of the genome of these HEV-C isolates revealed considerable genetic diversity, mostly due to recombination. In the work presented herein, we carried out a more detailed characterization of the genomes of viruses from this collection. First, we determined the full VP1 sequence of 41 of these isolates of different types. These sequences were compared with those of HEV-C isolates obtained from other countries or in other contexts. The sequences of the Madagascan isolates of a given type formed specific clusters clearly differentiated from those formed by other strains of the same type isolated elsewhere. Second, we sequenced the entire genome of 10 viruses representing most of the lineages present in this panel. All but one of the genomes appeared to be mosaic assemblies of different genomic fragments generated by intra- and intertypic recombination. The location of the breakpoints suggested potential preferred genomic regions for recombination. Our results also suggest that recombination between type HEV-99 and other HEV-C may be quite rare. This first exhaustive genomic analysis of a panel of non-PV HEV-C cocirculating in a small human population highlights the high frequency of inter and intra-typic genetic recombination, constituting a widespread mechanism of genetic plasticity and continually shifting the HEV-C biodiversity.
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Affiliation(s)
- Maël Bessaud
- Institut Pasteur, Unité Postulante de Biologie des Virus Entériques, Paris, France.
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Kyriakopoulou Z, Dedepsidis E, Pliaka V, Tsakogiannis D, Ruether I, Krikelis A, Markoulatos P. Complete nucleotide sequence analysis of the VP1 genomic region of Echoviruses 6 isolated from sewage in Greece revealed 98% similarity with Echoviruses 6 that were characterized from an aseptic meningitis outbreak 1 year later. Clin Microbiol Infect 2011; 17:1170-3. [DOI: 10.1111/j.1469-0691.2010.03381.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kumari P, Singh AK, Sharma VK, Chattopadhyay B, Chakraborty S. A novel recombinant tomato-infecting begomovirus capable of transcomplementing heterologous DNA-B components. Arch Virol 2011; 156:769-83. [PMID: 21311922 DOI: 10.1007/s00705-011-0915-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Accepted: 01/05/2011] [Indexed: 10/18/2022]
Abstract
The genome of a tomato-infecting begomovirus from Ranchi, India, was cloned, sequenced and analysed. The viral genome shared 88.3% sequence identity with an isolate belonging to the species Tobacco curly shoot virus (TbCSV), and this virus should therefore be considered a member of a new species, tentatively named Tomato leaf curl Ranchi virus (ToLCRnV). The DNA-β molecule, which had 74.5% sequence identity with tomato leaf curl Bangladesh betasatellite (ToLCBDB), is named tomato leaf curl Ranchi betasatellite (ToLCRnB). Phylogenetic analysis revealed that ToLCRnV is related to tomato leaf curl Bangladesh virus (ToLCBDV), tobacco curly shoot virus (TbCSV) and tomato leaf curl Gujarat virus (ToLCGV). An infectivity study with ToLCRnV established the monopartite nature of the viral genome, whereas inoculation with ToLCRnB resulted in increased symptom severity. ToLCRnV could transreplicate DNA-B of tomato leaf curl Gujarat virus (ToLCGV) and tomato leaf curl New Delhi virus (ToLCNDV), both in N. benthamiana and tomato, although DNA-B accumulation of was less than with the wild-type combinations. ToLCRnB could be efficiently replicated by DNA-A of both ToLCNDV and ToLCGV. A leaf disk assay suggests that DNA-A could transreplicate the homologous DNA-B and DNA-β more efficiently than the heterologous one.
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Affiliation(s)
- Punam Kumari
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Abstract
Several new enterovirus serotypes and a new human rhinovirus species have been characterized in the Enterovirus genus recently, raising a question about the origin of the new viruses. In this article we attempt to outline the general patterns of enterovirus evolution, ultimately leading to the emergence of new serotypes or species. Different evolutionary and epidemiological patterns can be deduced between different enterovirus species, between entero- and rhino-viruses and between different serotypes within a species. This article presents a hypothesis that the divergent evolution leading to a new serotype is likely to involve adaptation to a new ecological niche either within a single host species or due to interspecies transmission. By contrast, evolution within a serotype appears to occur primarily by genetic drift.
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Affiliation(s)
| | - Carita Savolainen-Kopra
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
| | - Merja Roivainen
- National Institute for Health and Welfare (THL), Division of Health Protection, Department of Infectious Disease Surveillance & Control, Intestinal Viruses Unit, P.O. Box 30, FI-00271 Helsinki, Finland; National Institute for Health & Welfare (THL), PO Box 30, FI-00271 Helsinki, Finland
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30
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Huang YP, Lin TL, Hsu LC, Chen YJ, Tseng YH, Hsu CC, Fan WB, Yang JY, Chang FY, Wu HS. Genetic diversity and C2-like subgenogroup strains of enterovirus 71, Taiwan, 2008. Virol J 2010; 7:277. [PMID: 20959020 PMCID: PMC2975644 DOI: 10.1186/1743-422x-7-277] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 10/20/2010] [Indexed: 11/11/2022] Open
Abstract
Background Human enterovirus 71 (EV-71) is known of having caused numerous outbreaks of hand-foot-mouth disease, and other clinical manifestations globally. In 2008, 989 EV-71 strains were isolated in Taiwan. Results In this study, the genetic and antigenic properties of these strains were analyzed and the genetic diversity of EV-71 subgenogroups surfacing in Taiwan was depicted, which includes 3 previously reported subgenogroups of C5, B5, and C4, and one C2-like subgenogroup. Based on the phylogenetic analyses using their complete genome nucleotide sequences and neutralization tests, the C2-like subgenogroup forms a genetically distinct cluster from other subgenogroups, and the antisera show a maximum of 128-fold decrease of neutralization titer against this subgenogroup. In addition, the subgenogroup C4 isolates of 2008 were found quite similar genetically to the Chinese strains that caused outbreaks in recent years and thus they should be carefully watched. Conclusions Other than to be the first report describing the existence of C2-like subgenogroup of EV-71 in Taiwan, this article also foresees a potential of subgenogroup C4 outbreaks in Taiwan in the near future.
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Affiliation(s)
- Yuan-Pin Huang
- Research and Diagnostic Center, Centers for Disease Control, Department of Health, Taipei, Taiwan, R.O.C
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Bailly JL, Mirand A, Henquell C, Archimbaud C, Chambon M, Regagnon C, Charbonné F, Peigue-Lafeuille H. Repeated genomic transfers from echovirus 30 to echovirus 6 lineages indicate co-divergence between co-circulating populations of the two human enterovirus serotypes. INFECTION GENETICS AND EVOLUTION 2010; 11:276-89. [PMID: 20615482 DOI: 10.1016/j.meegid.2010.06.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Revised: 06/07/2010] [Accepted: 06/25/2010] [Indexed: 10/19/2022]
Abstract
Human echovirus types 6 (E-6) and 30 (E-30) cause seasonal epidemics of aseptic meningitis. These two enteroviruses are frequently observed in co-circulation, an epidemiological pattern that is prerequisite for the occurrence of dual infections, which can lead to recombination between co-infecting virus strains. Viral sequences were determined at loci 1D (VP1 capsid protein) and 3CD (non structural proteins) in 49 E-6 strains recovered in a single geographical region in France from 1999 to 2007, during the epidemiological survey of enterovirus infections. They were compared with previously recorded sequences of E-30 strains to investigate their evolutionary histories and possible recombination patterns. Phylogenetic analyses identified two distinct E-6 populations and different subpopulations. Assuming a relaxed molecular clock model and a Bayesian skyline demographic model in coalescent analyses with the BEAST program, the substitution rate in E-6 was estimated at 8.597×10(-3) and 6.252×10(-3) substitution/site/year for loci 1D and 3CD respectively. Consistent estimates of divergence times (t(MRCA)) were obtained for loci 1D and 3CD indicating that two distinct E-6 populations originated in 1997 and 1999. Incongruent phylogenetic patterns inferred for the two loci were indicative of recombination events between the two populations. Phylogenies including the E-30 3CD sequences showed close genetic relationships between E-6 and discrete E-30 subpopulations. Recombination breakpoints were located with statistical significance in E-6 and E-30 genomes. Estimates of t(MRCA) of phylogenetic recombinant clades indicated directional genetic transfers from E-30 to E-6 populations and their co-divergence over the time period studied.
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Affiliation(s)
- J-L Bailly
- Clermont Université, Université d'Auvergne, EA 3843, BP 10448, F-63000 Clermont-Ferrand, France.
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Kumari P, Singh AK, Chattopadhyay B, Chakraborty S. Molecular characterization of a new species of Begomovirus and betasatellite causing leaf curl disease of tomato in India. Virus Res 2010; 152:19-29. [PMID: 20540978 DOI: 10.1016/j.virusres.2010.05.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 04/20/2010] [Accepted: 05/31/2010] [Indexed: 11/29/2022]
Abstract
A new tomato-infecting begomovirus and cognate betasatellite were characterized from the gangetic plain of northern India. Genome organization of this virus was found to be similar to those of other old world begomoviruses. The DNA-A molecule (2752nt) shared maximum (85.8%) identity with Tomato leaf curl Laos virus-[Laos] (ToLCLV-[LA]; AF195782) from Laos and betasatellite molecule (1349nt) shared maximum (75.8%) identity with Tomato leaf curl Joydebpur betasatellite (ToLCJoB-[BD:Gaz:05]; AJ966244) from Bangladesh. Interestingly, both these molecules showed less identity with known tomato-infecting begomoviruses and their satellites from India. The recombination detection program (RDP) revealed that these molecules are not an outcome of direct exchange of sequences between existing begomovirus species. According to International Committee on Taxonomy of viruses (ICTV) species/strains demarcations norms for viruses belonging to the family Geminiviridae, this is a new Begomovirus species and we named this virus as Tomato leaf curl Patna virus (ToLCPaV) and new beta species as Tomato leaf curl Patna betasatellite (ToLCPaB). Partial tandem repeats of ToLCPaV and ToLCPaB could induce typical leaf curl symptom on tomato (Solanum lycopersicum) and Nicotiana benthamiana. Although, DNA-A could alone infect tomato typical to a monopartite Begomovirus, co-inoculation of DNA-A and DNA-beta resulted more stunting and severe symptoms. Interestingly, association of ToLCPaB did not assist in increased ToLCPaV accumulation in systemic leaves. ToLCPaV neither transreplicate DNA-B of Tomato leaf curl New Delhi virus (ToLCNDV) nor of Tomato leaf curl Gujarat virus (ToLCGV), presumably due to difference in rep-binding sequences. However, ToLCPaB formed viable pseudorecombinant with mono-bipartite ToLCGV DNA-A infecting both N. benthamiana and tomato but could not cause systemic infection on natural host tomato when co-inoculated with ToLCNDV DNA-A, which is a bipartite Begomovirus.
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Affiliation(s)
- Punam Kumari
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Chen X, Zhang Q, Li J, Cao W, Zhang JX, Zhang L, Zhang W, Shao ZJ, Yan Y. Analysis of recombination and natural selection in human enterovirus 71. Virology 2010; 398:251-61. [DOI: 10.1016/j.virol.2009.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/13/2009] [Accepted: 12/04/2009] [Indexed: 11/30/2022]
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Weinzierl AO, Rudolf D, Maurer D, Wernet D, Rammensee HG, Stevanović S, Klingel K. Identification of HLA-A*01- and HLA-A*02-restricted CD8+ T-cell epitopes shared among group B enteroviruses. J Gen Virol 2008; 89:2090-2097. [PMID: 18753217 DOI: 10.1099/vir.0.2008/000711-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acute enteroviral infections ranging from meningitis, pancreatitis to myocarditis are common and normally well controlled by the host immune system comprising virus-specific CD8+ cytotoxic T lymphocytes (CTL). However, in some patients enteroviruses and especially coxsackieviruses of group B are capable of inducing severe chronic forms of diseases such as chronic myocarditis. Currently, it is not known whether divergences in the CTL-related immune response may contribute to the different outcome and course of enterovirus myocarditis. A pre-requisite for the study of CTL reactions in patients with acute and chronic myocarditis is the identification of CTL epitopes. In order to define dominant enterovirus CTL epitopes, we have screened, by using gamma interferon (IFN-gamma) ELISPOT, 62 HLA-A*01- and 59 HLA-A*02-positive healthy blood donors for pre-existing CTL reactions against 12 HLA-A*01 and 20 HLA-A*02 predicted CTL epitopes derived from coxsackieviruses of group B. Positive CTL reactions were verified by FACS analysis in a combined major histocompatibility complex-tetramer IFN-gamma staining. A total of 14.8% of all donors reacted against one of the three identified epitopes MLDGHLIAFDY, YGDDVIASY or GIIYIIYKL. The HLA-A*02-restricted epitope ILMNDQEVGV was recognized by 25% of all tested blood donors. For this peptide, we could demonstrate specific granzyme B secretion, a strong cytolytic potential and endogenous processing. All four epitopes were homologous in 36-92% of group B enteroviruses, providing a strong basis for monitoring the divergence of T-cell-based immune responses in enterovirus-induced acute and chronic diseases.
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Affiliation(s)
- Andreas O Weinzierl
- Department of Molecular Pathology, University of Tübingen, Liebermeisterstraße 8, 72076 Tübingen, Germany
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Despina Rudolf
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Dominik Maurer
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Dorothee Wernet
- Institute of Clinical and Experimental Transfusion Medicine, University of Tübingen, Otfried-Müller-Str. 4/1, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Karin Klingel
- Department of Molecular Pathology, University of Tübingen, Liebermeisterstraße 8, 72076 Tübingen, Germany
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Bessaud M, Jegouic S, Joffret ML, Barge C, Balanant J, Gouandjika-Vasilache I, Delpeyroux F. Characterization of the genome of human enteroviruses: design of generic primers for amplification and sequencing of different regions of the viral genome. J Virol Methods 2008; 149:277-84. [PMID: 18329732 DOI: 10.1016/j.jviromet.2008.01.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/17/2008] [Accepted: 01/21/2008] [Indexed: 11/26/2022]
Abstract
Human enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Biodiversity and evolution of human enterovirus genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating strains of enteroviruses require partial determination of different genomic regions. The development is described of a simple method allowing amplification and partial sequencing of the P1, P2 and P3 genomic regions of field human enterovirus strains isolated in cell cultures, by performing PCR on cDNAs generated through a single RT reaction. A set of generic primers were designed and tested on a panel of 90 field and prototype viruses belonging to the five species of human enteroviruses. This assay was shown to amplify efficiently the targeted regions of all the 90 genomes tested. The generated amplicons were sequenced successfully without the need for gel purification. This assay could be a valuable tool for laboratories interested in molecular epidemiology and evolution studies implicating a great number of human enterovirus strains isolated from human or environmental samples.
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Affiliation(s)
- Maël Bessaud
- Unité postulante de biologie des virus entériques, Institut Pasteur, 25 rue du Dr Roux, 75 015 Paris, France.
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