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Chang X, Zhang Z, Cui X, Zhang Q, Lin Q, Hu J, Guo Y, Wang X. Genetic diversity and recombination of bovine enterovirus strains in China. Microbiol Spectr 2024; 12:e0280023. [PMID: 38315051 PMCID: PMC10913430 DOI: 10.1128/spectrum.02800-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Bovine enterovirus (BEV) consisting of enterovirus species E (EV-E) and F (EV-F) is the causative agent associated with respiratory and gastrointestinal diseases in cattle. Here, we reported the characterization, genetic diversity, and recombination of novel BEV strains isolated from the major cattle-raising regions in China during 2012-2018. Twenty-seven BEV strains were successfully isolated and characterized. Molecular characterization demonstrated that the majority of these novel BEV strains (24/27) were EV-E, while only few strains (3/27) were EV-F. Sequence analysis revealed the diversity of the circulating BEV strains such as species and subtypes where different species or subtype coinfections were detected in the same regions and even in the same cattle herds. For the EV-E, two novel subtypes, designated as EV-E6 and EV-E7, were revealed in addition to the currently reported EV-E1-EV-E5. Comparative genomic analysis revealed the intraspecies and interspecies genetic exchanges among BEV isolates. The representative strain HeN-B62 was probably from AN12 (EV-F7) and PS-87-Belfast (EV-F3) strains. The interspecies recombination between EV-E and EV-F was also discovered, where the EV-F7-AN12 might be from EV-E5 and EV-F1, and EV-E5-MexKSU/5 may be recombined from EV-F7 and EV-E1. The aforementioned results revealed the genetic diversity and recombination of novel BEV strains and unveiled the different BEV species or subtype infections in the same cattle herd, which will broaden the understanding of enterovirus genetic diversity, recombination, pathogenesis, and prevention of disease outbreaks. IMPORTANCE Bovine enterovirus (BEV) infection is an emerging disease in China that is characterized by digestive, respiratory, and reproductive disorders. In this study, we first reported two novel EV-E subtypes detected in cattle herds in China, unveiled the coinfection of two enterovirus species (EV-E/EV-F) and different subtypes (EV-E2/EV-E7, EV-E1/EV-E7, and EV-E3/EV-E6) in the same cattle herds, and revealed the enterovirus genetic exchange in intraspecies and interspecies recombination. These results provide an important update of enterovirus prevalence and epidemiological aspects and contribute to a better understanding of enterovirus genetic diversity, evolution, and pathogenesis.
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Affiliation(s)
- Xiaoran Chang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhiyuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuyuan Cui
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Qun Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Qian Lin
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Junying Hu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yidi Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xinping Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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Georgieva I, Stoyanova A, Stoitsova S, Nikolaeva-Glomb L. Echovirus 30 in Bulgaria during the European Upsurge of the Virus, 2017-2018. Pathogens 2024; 13:143. [PMID: 38392881 PMCID: PMC10893257 DOI: 10.3390/pathogens13020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In 2018, an increase in echovirus 30 (E30) detections was reported in some European countries. To assess the circulation and phylogenetic relationships of E30 in Bulgaria, E30 samples identified at the National Reference Laboratory for Enteroviruses, National Centre of Infectious and Parasitic Diseases, Bulgaria (NRL for Enteroviruses) in 2017 and 2018 were subjected to sequencing and phylogenetic analysis. The present study revealed that sample positivity did not significantly increase in Bulgaria during the European upsurge. E30 was identified in six patients, two of whom were epidemiologically linked. The maximum-likelihood phylogenetic tree showed that sequences from five patients belonged to the G1 lineage (clades G1a and G1b). The sequence from one patient belonged to the G2 lineage and was grouped closer to sequences from the last E30 outbreak in Bulgaria in 2012. No recombination events were detected. The European E30 upsurge in 2018 was caused by two clades, and one of them was G1. The fact that the majority of the Bulgarian samples belonged to G1 indicated that the virus was present in the country but did not cause a local upsurge. Phylogenetic and epidemiological data indicated sporadic E30 cases and a possible shift towards G1 lineage in 2017 and 2018.
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Affiliation(s)
- Irina Georgieva
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
| | - Asya Stoyanova
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
| | - Savina Stoitsova
- Department of Epidemiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria
| | - Lubomira Nikolaeva-Glomb
- National Reference Laboratory for Enteroviruses, Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria (L.N.-G.)
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Patterns and Temporal Dynamics of Natural Recombination in Noroviruses. Viruses 2023; 15:v15020372. [PMID: 36851586 PMCID: PMC9961210 DOI: 10.3390/v15020372] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Noroviruses infect a wide range of mammals and are the major cause of gastroenteritis in humans. Recombination at the junction of ORF1 encoding nonstructural proteins and ORF2 encoding major capsid protein VP1 is a well-known feature of noroviruses. Using all available complete norovirus sequences, we systematically analyzed patterns of natural recombination in the genus Norovirus both throughout the genome and across the genogroups. Recombination events between nonstructural (ORF1) and structural genomic regions (ORF2 and ORF3) were found in all analyzed genogroups of noroviruses, although recombination was most prominent between members of GII, the most common genogroup that infects humans. The half-life times of recombinant forms (clades without evidence of recombination) of human GI and GII noroviruses were 10.4 and 8.4-11.3 years, respectively. There was evidence of many recent recombination events, and most noroviruses that differed by more than 18% of nucleotide sequence were recombinant relative to each other. However, there were no distinct recombination events between viruses that differed by over 42% in ORF2/3, consistent with the absence of systematic recombination between different genogroups. The few inter-genogroup recombination events most likely occurred between ancient viruses before they diverged into contemporary genogroups. The recombination events within ORF1 or between ORF2/3 were generally rare. Thus, noroviruses routinely exchange full structural and nonstructural blocks of the genome, providing a modular evolution.
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Genomic Epidemiology and Phylodynamic Analysis of Enterovirus A71 Reveal Its Transmission Dynamics in Asia. Microbiol Spectr 2022; 10:e0195822. [PMID: 36200890 PMCID: PMC9603238 DOI: 10.1128/spectrum.01958-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Enterovirus A71 (EV-A71) is one of the main pathogens causing hand, foot, and mouth disease (HFMD) outbreaks in Asian children under 5 years of age. In severe cases, it can cause neurological complications and be life-threatening. In this study, 200 newly sequenced EV-A71 whole-genome sequences were combined with 772 EV-A71 sequences from GenBank for large-scale analysis to investigate global EV-A71 epidemiology, phylogeny, and Bayesian phylodynamic characteristics. Based on the phylogenetic analysis of the EV-A71 3Dpol region, six new evolutionary lineages (lineages B, J, K, O, P, and Q) were found in this study, and the number of evolutionary lineages was expanded from 11 to 17. Temporal dynamics and recombination breakpoint analyses based on genotype C revealed that recombination of nonstructural protein-coding regions, including 3Dpol, is an important reason for the emergence of new lineages. The EV-A71 epidemic in the Asia-Pacific region is complex, and phylogeographic analysis found that Vietnam played a key role in the spread of subgenotypes B5 and C4. The origin of EV-A71 subgenotype C4 in China is East China, which is closely related to the prevalence of subgenotype C4 in the south and throughout China. Selection pressure analysis revealed that, in addition to VP1 amino acid residues VP1-98 and VP1-145, which are associated with EV-A71 pathogenicity, amino acid residues VP1-184 and VP1-249 were also positively selected, and their functions still need to be determined by biology and immunology. This study aimed to provide a solid theoretical basis for EV-A71-related disease surveillance and prevention, antiviral research, and vaccine development through a comprehensive analysis. IMPORTANCE EV-A71 is one of the most important pathogens causing HFMD outbreaks; however, large-scale studies of EV-A71 genomic epidemiology are currently lacking. In this study, 200 new EV-A71 whole-genome sequences were determined. Combining these with 772 EV-A71 whole-genome sequences in the GenBank database, the evolutionary and transmission characteristics of global and Asian EV-A71 were analyzed. Six new evolutionary lineages were identified in this study. We also found that recombination in nonstructural protein-coding regions, including 3Dpol, is an important cause for the emergence of new lineages. The results provided a solid theoretical basis for EV-A71-related disease surveillance and prevention, antiviral research, and vaccine development.
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Sun Q, Li J, Zhang B, Wang R, Wang C, Li X, Liu Y, Zhang Y. Transcriptome sequencing analysis of echovirus 30 infection reveals its potential pathogenesis. Front Microbiol 2022; 13:958385. [PMID: 36147849 PMCID: PMC9486006 DOI: 10.3389/fmicb.2022.958385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/15/2022] [Indexed: 12/02/2022] Open
Abstract
Echovirus 30 (E30) causes various diseases, such as viral encephalitis; aseptic meningitis; hand, foot, and mouth diseases; and acute flaccid paralysis. Related neurological infections are most concerning. However, the molecular mechanisms of E30 pathogenesis are not fully understood. There is a growing research interest in E30 as a cause of neurological disease. The aim of this study was to describe E30 infection, especially the changes in differential factor expressions after infection, in human glioma (U251) cells and mice brains using transcriptome sequencing analysis. Clear changes in the gene expression of factors associated with the defense response to viruses, inflammation-related signaling pathways, and neurological complication-related pathways were observed. Our results suggest that after E30 infection, the genes related to immune response were induced in the human glioma cells and mice brains, whereas genes functioning in the development and function of neural tissue were inhibited. Overall, this study successfully established E30 infection of U251 and mouse brain tissue, profiled the infection-induced changes in cellular and organizational transcriptomes, and revealed the molecular level changes during E30 infection.
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Affiliation(s)
- Qiang Sun
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jichen Li
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bo Zhang
- Teaching Department of Basic Medicine, Taishan Vocational College of Nursing, Tai’a, China
| | - Rui Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Congcong Wang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoliang Li
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Zhang
- WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Yong Zhang,
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Abstract
Echovirus 30 (E30), a member of species B enterovirus, is associated with outbreaks of aseptic meningitis and has become a global health emergency. However, the pathogenesis of E30 remains poorly understood due to the lack of appropriate animal models. In this study, we established a mouse infection model to explore the pathogenicity of E30. The 2-day-old IFNAR-/- mice infected with E30 strain WZ16 showed lethargy and paralysis, and some died. Obvious pathological changes were observed in the skeletal muscle, brain tissue, and other tissues, with the highest viral load in the skeletal muscles. Transcriptome analysis of brain and skeletal muscle tissues from infected mice showed that significant differentially expressed genes were enriched in complement response and neuropathy-related pathways. Using immunofluorescence assay, we found that the viral double-stranded RNA (dsRNA) was detected in the mouse brain region and could infect human glioma (U251) cells. These results indicated that E30 affects the nervous system, and they provide a theoretical basis for understanding its pathogenesis. IMPORTANCE Echovirus 30 (E30) infection causes a wide spectrum of diseases with mild symptoms, such as hand, foot, and mouth disease (HFMD), acute flaccid paralysis, and aseptic meningitis and other diseases, especially one of the most common pathogens causing aseptic meningitis outbreaks. We established a novel mouse model of E30 infection by inoculating neonatal mice with clinical isolates of E30 and observed the pathological changes induced by E30. Using the E30 infection model, we found complement responses and neuropathy-related genes in the mice tissues at the transcriptome level. Moreover, we found that the viral dsRNA localized in the mouse brain and could replicate in human glioma cell line U251 rather than in the neuroblastoma cell line, SK-N-SH.
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Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand. Viruses 2022; 14:v14040658. [PMID: 35458388 PMCID: PMC9030895 DOI: 10.3390/v14040658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/16/2022] [Accepted: 03/19/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we describe a small enterovirus outbreak including nine cases of aseptic meningitis in a New Zealand hospital in 2017. Most patients had a lymphocytic predominance in the CSF, their length of stay was short, and there were no paediatric cases or ICU admissions. VP1 genotyping revealed that the outbreak was caused by an echovirus E30 strain closely related to strains reported from the US, UK, Brazil, and Denmark. They all form a separate cluster within lineage “h”, which leads to the proposal of establishing a new lineage tentatively named “j” for this group of echovirus E30 strains. However, whole genome sequencing and reference mapping to echovirus E30 sequences showed very poor mapping of reads to the 3′ half of the genome. Further bioinformatic analysis indicated that the causative agent of this outbreak might be a mosaic triple-recombinant enterovirus composed of echovirus E6, echovirus E11, and echovirus E30 genome segments.
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Cassidy H, Schuele L, Lizarazo-Forero E, Couto N, Rossen JWA, Friedrich AW, van Leer-Buter C, Niesters HGM. OUP accepted manuscript. Virus Evol 2022; 8:veab109. [PMID: 35317350 PMCID: PMC8932292 DOI: 10.1093/ve/veab109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/16/2021] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10−3 substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient.
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Affiliation(s)
| | | | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Salt Lake City, UT 84112, USA
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Coretta van Leer-Buter
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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Genomic surveillance of enterovirus associated with aseptic meningitis cases in southern Spain, 2015-2018. Sci Rep 2021; 11:21523. [PMID: 34728763 PMCID: PMC8564535 DOI: 10.1038/s41598-021-01053-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
New circulating Enterovirus (EV) strains often emerge through recombination. Upsurges of recombinant non-polio enteroviruses (NPEVs) associated with neurologic manifestations such as EVA71 or Echovirus 30 (E30) are a growing public health concern in Europe. Only a few complete genomes of EVs circulating in Spain are available in public databases, making it difficult to address the emergence of recombinant EVs, understand their evolutionary relatedness and the possible implication in human disease. We have used metagenomic (untargeted) NGS to generate full-length EV genomes from CSF samples of EV-positive aseptic meningitis cases in Southern Spain between 2015 and 2018. Our analyses reveal the co-circulation of multiple Enterovirus B (EV-B) types (E6, E11, E13 and E30), including a novel E13 recombinant form. We observed a genetic turnover where emergent lineages (C1 for E6 and I [tentatively proposed in this study] for E30) replaced previous lineages circulating in Spain, some concomitant with outbreaks in other parts of Europe. Metagenomic sequencing provides an effective approach for the analysis of EV genomes directly from PCR-positive CSF samples. The detection of a novel, disease-associated, recombinant form emphasizes the importance of genomic surveillance to monitor spread and evolution of EVs.
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First evidence of enterovirus A71 and echovirus 30 in Uruguay and genetic relationship with strains circulating in the South American region. PLoS One 2021; 16:e0255846. [PMID: 34383835 PMCID: PMC8360592 DOI: 10.1371/journal.pone.0255846] [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: 04/12/2021] [Accepted: 07/24/2021] [Indexed: 11/19/2022] Open
Abstract
Human enteroviruses (EVs) comprise more than 100 types of coxsackievirus, echovirus, poliovirus and numbered enteroviruses, which are mainly transmitted by the faecal-oral route leading to diverse diseases such as aseptic meningitis, encephalitis, and acute flaccid paralysis, among others. Since enteroviruses are excreted in faeces, wastewater-based epidemiology approaches are useful to describe EV diversity in a community. In Uruguay, knowledge about enteroviruses is extremely limited. This study assessed the diversity of enteroviruses through Illumina next-generation sequencing of VP1-amplicons obtained by RT-PCR directly applied to viral concentrates of 84 wastewater samples collected in Uruguay during 2011-2012 and 2017-2018. Fifty out of the 84 samples were positive for enteroviruses. There were detected 27 different types belonging to Enterovirus A species (CVA2-A6, A10, A16, EV-A71, A90), Enterovirus B species (CVA9, B1-B5, E1, E6, E11, E14, E21, E30) and Enterovirus C species (CVA1, A13, A19, A22, A24, EV-C99). Enterovirus A71 (EV-A71) and echovirus 30 (E30) strains were studied more in depth through phylogenetic analysis, together with some strains previously detected by us in Argentina. Results unveiled that EV-A71 sub-genogroup C2 circulates in both countries at least since 2011-2012, and that the C1-like emerging variant recently entered in Argentina. We also confirmed the circulation of echovirus 30 genotypes E and F in Argentina, and reported the detection of genotype E in Uruguay. To the best of our knowledge this is the first report of the EV-A71 C1-like emerging variant in South-America, and the first report of EV-A71 and E30 in Uruguay.
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Benschop KSM, Broberg EK, Hodcroft E, Schmitz D, Albert J, Baicus A, Bailly JL, Baldvinsdottir G, Berginc N, Blomqvist S, Böttcher S, Brytting M, Bujaki E, Cabrerizo M, Celma C, Cinek O, Claas ECJ, Cremer J, Dean J, Dembinski JL, Demchyshyna I, Diedrich S, Dudman S, Dunning J, Dyrdak R, Emmanouil M, Farkas A, De Gascun C, Fournier G, Georgieva I, Gonzalez-Sanz R, van Hooydonk-Elving J, Jääskeläinen AJ, Jancauskaite R, Keeren K, Fischer TK, Krokstad S, Nikolaeva-Glomb L, Novakova L, Midgley SE, Mirand A, Molenkamp R, Morley U, Mossong J, Muralyte S, Murk JL, Nguyen T, Nordbø SA, Österback R, Pas S, Pellegrinelli L, Pogka V, Prochazka B, Rainetova P, Van Ranst M, Roorda L, Schuffenecker I, Schuurman R, Stoyanova A, Templeton K, Verweij JJ, Voulgari-Kokota A, Vuorinen T, Wollants E, Wolthers KC, Zakikhany K, Neher R, Harvala H, Simmonds P. Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe. Emerg Infect Dis 2021; 27:1616-1626. [PMID: 34013874 PMCID: PMC8153861 DOI: 10.3201/eid2706.203096] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In 2018, an upsurge in echovirus 30 (E30) infections was reported in Europe. We conducted a large-scale epidemiologic and evolutionary study of 1,329 E30 strains collected in 22 countries in Europe during 2016-2018. Most E30 cases affected persons 0-4 years of age (29%) and 25-34 years of age (27%). Sequences were divided into 6 genetic clades (G1-G6). Most (53%) sequences belonged to G1, followed by G6 (23%), G2 (17%), G4 (4%), G3 (0.3%), and G5 (0.2%). Each clade encompassed unique individual recombinant forms; G1 and G4 displayed >2 unique recombinant forms. Rapid turnover of new clades and recombinant forms occurred over time. Clades G1 and G6 dominated in 2018, suggesting the E30 upsurge was caused by emergence of 2 distinct clades circulating in Europe. Investigation into the mechanisms behind the rapid turnover of E30 is crucial for clarifying the epidemiology and evolution of these enterovirus infections.
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Modular Evolution of Coronavirus Genomes. Viruses 2021; 13:v13071270. [PMID: 34209881 PMCID: PMC8310335 DOI: 10.3390/v13071270] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.
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Molecular Epidemiology of Enterovirus in Children with Central Nervous System Infections. Viruses 2021; 13:v13010100. [PMID: 33450832 PMCID: PMC7828273 DOI: 10.3390/v13010100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023] Open
Abstract
Limited recent molecular epidemiology data are available for pediatric Central Nervous System (CNS) infections in Europe. The aim of this study was to investigate the molecular epidemiology of enterovirus (EV) involved in CNS infections in children. Cerebrospinal fluid (CSF) from children (0–16 years) with suspected meningitis–encephalitis (ME) who were hospitalized in the largest pediatric hospital of Greece from October 2017 to September 2020 was initially tested for 14 common pathogens using the multiplex PCR FilmArray® ME Panel (FA-ME). CSF samples positive for EV, as well as pharyngeal swabs and stools of the same children, were further genotyped employing Sanger sequencing. Of the 330 children tested with FA-ME, 75 (22.7%) were positive for EV and 50 different CSF samples were available for genotyping. The median age of children with EV CNS infection was 2 months (IQR: 1–60) and 44/75 (58.7%) of them were male. There was a seasonal distribution of EV CNS infections, with most cases detected between June and September (38/75, 50.7%). EV genotyping was successfully processed in 84/104 samples: CSF (n = 45/50), pharyngeal swabs (n = 15/29) and stools (n = 24/25). Predominant EV genotypes were CV-B5 (16/45, 35.6%), E30 (10/45, 22.2%), E16 (6/45, 13.3%) and E11 (5/45, 11.1%). However, significant phylogenetic differences from previous described isolates were detected. No unusual neurologic manifestations were observed, and all children recovered without obvious acute sequelae. Specific EV circulating genotypes are causing a significant number of pediatric CNS infections. Phylogenetic analysis of these predominant genotypes found genetic differences from already described EV isolates.
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Brown DM, Zhang Y, Scheuermann RH. Epidemiology and Sequence-Based Evolutionary Analysis of Circulating Non-Polio Enteroviruses. Microorganisms 2020; 8:microorganisms8121856. [PMID: 33255654 PMCID: PMC7759938 DOI: 10.3390/microorganisms8121856] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Enteroviruses (EVs) are positive-sense RNA viruses, with over 50,000 nucleotide sequences publicly available. While most human infections are typically associated with mild respiratory symptoms, several different EV types have also been associated with severe human disease, especially acute flaccid paralysis (AFP), particularly with endemic members of the EV-B species and two pandemic types—EV-A71 and EV-D68—that appear to be responsible for recent widespread outbreaks. Here we review the recent literature on the prevalence, characteristics, and circulation dynamics of different enterovirus types and combine this with an analysis of the sequence coverage of different EV types in public databases (e.g., the Virus Pathogen Resource). This evaluation reveals temporal and geographic differences in EV circulation and sequence distribution, highlighting recent EV outbreaks and revealing gaps in sequence coverage. Phylogenetic analysis of the EV genus shows the relatedness of different EV types. Recombination analysis of the EV-A species provides evidence for recombination as a mechanism of genomic diversification. The absence of broadly protective vaccines and effective antivirals makes human enteroviruses important pathogens of public health concern.
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Affiliation(s)
- David M Brown
- Department of Synthetic Biology, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
- La Jolla Institute for Immunology, La Jolla, CA 92065, USA
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Sub-genotype change and recombination of coxsackievirus A6s may be the cause of it being the predominant pathogen for HFMD in children in Beijing, as revealed by analysis of complete genome sequences. Int J Infect Dis 2020; 99:156-162. [PMID: 32663604 DOI: 10.1016/j.ijid.2020.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES To investigate why coxsackievirus A6 (CVA6) has replaced enterovirus A71 (EV71) and coxsackievirus A16 (CVA16), which used to be the most predominant etiological agents, for hand, foot and mouth disease (HFMD) in children in Beijing, China. METHODS Sixty-four CVA6-positive samples were identified from 2010 to 2016 and selected for whole genome sequence amplification and analysis. RESULTS It was demonstrated that the whole genome sequences of CVA6s in this study were 7432-7435 nucleotides in length, and the different lengths were only in the 5'UTR region. The phylogenetic tree analysis of the full-length VP1 region of CVA6s indicated that the prevalent CVA6s in Beijing changed from the previous D2 sub-genotype to the D3 sub-genotype in 2013. In this study, two recombinant forms (RFs)- RF-C and RF-D - of CVA6 mainly appeared in 2010 and 2011. Since 2013, three recombinant CVA6 variants - RF-A, J and L - have been prevalent in children with HFMD in Beijing. The recombination region of RF-J was located at the 2C region, while RF-L had a new recombination point in the 3D region. The recombination of prevalent CVA6s in Beijing from 2013 to 2016 occurred within non-capsid regions of the genome, especially the P2 and P3 regions. CONCLUSIONS The sub-genotype change and recombination of CVA6s indicated from this study may explain why CVA6 has become the predominant pathogen causing HFMD since 2013.
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16
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Smura T, Blomqvist S, Kolehmainen P, Schuffenecker I, Lina B, Böttcher S, Diedrich S, Löve A, Brytting M, Hauzenberger E, Dudman S, Ivanova O, Lukasev A, Fischer TK, Midgley S, Susi P, Savolainen-Kopra C, Lappalainen M, Jääskeläinen AJ. Aseptic meningitis outbreak associated with echovirus 4 in Northern Europe in 2013-2014. J Clin Virol 2020; 129:104535. [PMID: 32652478 DOI: 10.1016/j.jcv.2020.104535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 01/23/2023]
Abstract
Picornaviruses (family Picornaviridae) are small, nonenveloped, positive-sense, single-stranded RNA viruses. The members of this family are currently classified into 47 genera and 110 species. Of picornaviruses, entero- and parechoviruses are associated with aseptic meningitis. They are transmitted via fecal-oral and respiratory routes, and occasionally, these viruses may cause a brief viremia and gain access to central nervous system (CNS). During the diagnostic screening of entero- and parechovirus types in Finland in year 2013-14, we detected a cluster of echovirus 4 (E4) infections in young adults and adolescents. As E4 is infrequently detected in Finland, we contacted several Northern and Central European laboratories that conduct routine surveillance for enteroviruses and, for those who have had E4 cases, we send a query for E4 sequences and data. Here we report CNS infections caused by E4 in Finland, Sweden, Norway, Denmark, Iceland and Germany in 2013 and 2014, and show that the E4 detected in these countries form a single lineage. In contrast, E4 strains circulating in these countries preceding the year 2013, and those circulating elsewhere in Europe during 2013-2014, formed several independent clusters.
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Affiliation(s)
- Teemu Smura
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland
| | - Soile Blomqvist
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | | | - Isabelle Schuffenecker
- Institut des Agents infectieux des HCL, CNR des enterovirus, Hôpital de la Croix-Rousse & Université de Lyon, CIRI INSERM U1111, UCBL, Lyon, France
| | - Bruno Lina
- Institut des Agents infectieux des HCL, CNR des enterovirus, Hôpital de la Croix-Rousse & Université de Lyon, CIRI INSERM U1111, UCBL, Lyon, France
| | | | | | - Arthur Löve
- Landspitali, National University Hospital, Reykjavik, Iceland
| | - Mia Brytting
- Folkhälsomyndigheten, Public Health Agency of Sweden, Solna, Sweden
| | | | | | - Olga Ivanova
- Chumakov Federal Scientific Center for Research and Development, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alexander Lukasev
- Chumakov Federal Scientific Center for Research and Development, Moscow, Russia; Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | | | - Petri Susi
- University of Turku, Institute of Biomedicine, Turku, Finland
| | - Carita Savolainen-Kopra
- National Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Maija Lappalainen
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland
| | - Anne J Jääskeläinen
- University of Helsinki and Helsinki University Hospital, Virology and Immunology, Helsinki, Finland.
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17
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Brouwer L, Benschop KS, Nguyen D, Kamau E, Pajkrt D, Simmonds P, Wolthers KC. Recombination Analysis of Non-Poliovirus Members of the Enterovirus C Species; Restriction of Recombination Events to Members of the Same 3DPol Cluster. Viruses 2020; 12:v12070706. [PMID: 32629843 PMCID: PMC7412211 DOI: 10.3390/v12070706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Enteroviruses (EVs) are highly prevalent viruses worldwide. Recombination is known to occur frequently in EVs belonging to species Enterovirus A, Enterovirus B, and Enterovirus C. Although many recombinant vaccine-derived poliovirus (VDPV) strains have been reported, our knowledge on recombination in non-polio EVs in the species Enterovirus C is limited. Here, we combined a dataset consisting of 11 newly generated full-length Enterovirus C sequences and 180 publicly available sequences to study recombination dynamics in non-polio EVs. To identify recombination patterns, maximum likelihood phylogenetic trees of different genomic regions were constructed, and segregation analyses were performed. Recombination was observed between members of the same 3DPol cluster, but was rarely observed between members of different clusters. We hypothesize that this restriction may have arisen through their different compartmentalization in respiratory and enteric tracts related to differences in cellular tropisms so that the opportunity to recombine may not be available.
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Affiliation(s)
- Lieke Brouwer
- Department of Medical Microbiology, Academic Medical Center (AMC), Amsterdam University Medical Centers (Amsterdam UMC), 1105AZ Amsterdam, The Netherlands;
- Correspondence:
| | - Kimberley S.M. Benschop
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3721MA Bilthoven, The Netherlands;
| | - Dung Nguyen
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (D.N.); (E.K.); (P.S.)
| | - Everlyn Kamau
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (D.N.); (E.K.); (P.S.)
| | - Dasja Pajkrt
- Department of Pediatric Infectious Diseases, Academic Medical Center (AMC), Amsterdam University Medical Centers (Amsterdam UMC), 1105AZ Amsterdam, The Netherlands;
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (D.N.); (E.K.); (P.S.)
| | - Katja C. Wolthers
- Department of Medical Microbiology, Academic Medical Center (AMC), Amsterdam University Medical Centers (Amsterdam UMC), 1105AZ Amsterdam, The Netherlands;
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Vandesande H, Laajala M, Kantoluoto T, Ruokolainen V, Lindberg AM, Marjomäki V. Early Entry Events in Echovirus 30 Infection. J Virol 2020; 94:e00592-20. [PMID: 32295914 PMCID: PMC7307138 DOI: 10.1128/jvi.00592-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 11/20/2022] Open
Abstract
Echovirus 30 (E30), a member of the enterovirus B species, is a major cause of viral meningitis, targeting children and adults alike. While it is a frequently isolated enterovirus and the cause of several outbreaks all over the world, surprisingly little is known regarding its entry and replication strategy within cells. In this study, we used E30 strain Bastianni (E30B) generated from an infectious cDNA clone in order to study early entry events during infection in human RD cells. E30B required the newly discovered Fc echovirus receptor (FcRn) for successful infection, but not the coxsackievirus and adenovirus receptor (CAR) or decay-accelerating factor (DAF), although an interaction with DAF was observed. Double-stranded RNA replication intermediate was generated between 2 and 3 h postinfection (p.i.), and viral capsid production was initiated between 4 and 5 h p.i. The drugs affecting Rac1 (NSC 23766) and cholesterol (filipin III) compromised infection, whereas bafilomycin A1, dyngo, U-73122, wortmannin, and nocodazole did not, suggesting the virus follows an enterovirus-triggered macropinocytic pathway rather than the clathrin pathway. Colocalization with early endosomes and increased infection due to constitutively active Rab5 expression suggests some overlap and entry to classical early endosomes. Taken together, these results suggest that E30B induces an enterovirus entry pathway, leading to uncoating in early endosomes.IMPORTANCE Echovirus 30 (E30) is a prevalent enterovirus causing regular outbreaks in both children and adults in different parts of the world. It is therefore surprising that relatively little is known of its infectious entry pathway. We set out to generate a cDNA clone and gradient purified the virus in order to study the early entry events in human cells. We have recently studied other enterovirus B group viruses, like echovirus 1 (EV1) and coxsackievirus A9 (CVA9), and found many similarities between those viruses, allowing us to define a so-called "enterovirus entry pathway." Here, E30 is reminiscent of these viruses, for example, by not relying on acidification for infectious entry. However, despite not using the clathrin entry pathway, E30 accumulates in classical early endosomes.
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Affiliation(s)
- Helena Vandesande
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Mira Laajala
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Tino Kantoluoto
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Visa Ruokolainen
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | - Varpu Marjomäki
- Department of Biological and Environmental Science/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Molecular characterization of enteroviruses among hospitalized patients in Greece, 2013-2015. J Clin Virol 2020; 127:104349. [PMID: 32339946 DOI: 10.1016/j.jcv.2020.104349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/26/2020] [Accepted: 03/29/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND There are only sporadic data for the circulation of Enteroviruses (EVs) in Greece with previous studies reporting mainly the presence of Echoviruses (E) and Coxsackie viruses (CV) B. OBJECTIVES We carried out a surveillance study for the molecular characterization of EVs detected in hospitalized patients throughout Greece as well as a phylogenetic analysis of the most frequently encountered serotypes. STUDY DESIGN Stools, cerebrospinal fluids, throat swabs and blood samples were collected from hospitalized patients with suspicion of EV infection. All samples were tested for EVs by rRT-PCR targeting the 5' untranslated region of EV genome. For positive samples, PCR amplification and sequencing targeting a part of VP1 region was performed. RESULTS We examined 831 samples and 209 were positive for EVs with Enterovirus B species being the most frequently amplified. E30, CVB5 and E9 were the most frequent serotypes of Enterovirus B species, whereas CVA6 and EV-A71 the most frequent serotypes of Enterovirus A species. Evs were significantly detected more frequently in stool samples compared to other types of specimens. Phylogenetic analysis revealed that most EV-A71 strains clustered in the subgenogroups C2 whereas all the CVA6 strains belonged to sub-genotype D3. Additionally, two different lineages of E30 and three different clusters of E9 viruses circulated simultaneously in Greece. Our data indicated that most EV strains from Greece were similar to strains circulating throughout Europe during the same period. CONCLUSIONS We provide a comprehensive picture of EVs circulating in Greece which can be helpful to interpret trends in EV diseases by associating them with circulating serotypes.
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20
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Genetic characterization of a novel recombinant echovirus 30 strain causing a regional epidemic of aseptic meningitis in Hokkaido, Japan, 2017. Arch Virol 2019; 165:433-438. [PMID: 31828510 PMCID: PMC7223842 DOI: 10.1007/s00705-019-04484-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/26/2019] [Indexed: 12/27/2022]
Abstract
A regional epidemic of aseptic meningitis caused by echovirus 30 (E30) occurred in Hokkaido, Japan, during the period of August-December 2017. To investigate their phylogenetic relationship to other human enteroviruses, we determined the complete genomic nucleotide sequences of isolates from this outbreak. Phylogenetic analysis of the viral capsid protein 1 gene showed that the strains were most closely related to E30 strains detected in Germany, France, and Russia in 2013. In contrast, the region encoding the viral protease and the RNA-dependent RNA polymerase had a close phylogenetic relationship to non-E30 enteroviruses detected in the United Kingdom and Switzerland in 2015-2017, suggesting that a recombination event had occurred.
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21
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Wollants E, Beller L, Beuselinck K, Bloemen M, Lagrou K, Reynders M, Van Ranst M. A decade of enterovirus genetic diversity in Belgium. J Clin Virol 2019; 121:104205. [PMID: 31722268 DOI: 10.1016/j.jcv.2019.104205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/15/2019] [Accepted: 10/22/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Enteroviruses are responsible for a wide range of clinical symptoms.Enterovirus D68 was already known to cause mild to severe respiratory infections, but in the last few years, it has also been associated with neurological symptoms and acute flaccid paralysis. OBJECTIVES In this epidemiological surveillance in Belgium, 1521 enteroviruspositive samples were genotyped. STUDY DESIGN Enterovirus-positive patient samples were collected from the University Hospitals Leuven and other hospitals and medical practices in Belgium from 2007 to 2018. Molecular typing was done by RT-PCR using different primers sets. EV-A and EV-B were typed by sequencing part of VP1. For EVC and EV-D, the VP4/VP2 region was used together with the non-coding region. RESULTS In this epidemiological survey with samples collected over 12 years, 35 different EV types were detected in 1521 patient samples. Enterovirus species B was by far the most dominant species in our samples (93%). Echovirus 30 was most frequently found (24%), followed by echovirus 6 (8%) and echovirus 9 (7%). In 2018, there was an outbreak for the first time of enterovirus D68 with severe respiratory infections but no acute flaccid paralysis. Phylogenetic analyses showed that the collected outbreak strains coexist in different clades. CONCLUSIONS For more than a decade, the circulating enterovirus strains were investigated in Belgium. During this time span, echovirus 30 was the most frequently detected and peaked every 3 years. Enterovirus D68 began an upsurge in 2018, but thus far without being clinically associated with acute flaccid paralysis.
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Affiliation(s)
- Elke Wollants
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical & Epidemiological Virology, BE-3000, Leuven, Belgium.
| | - Leen Beller
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Viral Metagenomics, BE-3000, Leuven, Belgium
| | - Kurt Beuselinck
- Department of Laboratory Medicine, University Hospitals Leuven, BE-3000, Leuven, Belgium
| | - Mandy Bloemen
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical & Epidemiological Virology, BE-3000, Leuven, Belgium
| | - Katrien Lagrou
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, BE-3000, Leuven, Belgium; Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens and Enteroviruses, University Hospitals Leuven, BE-3000, Leuven, Belgium
| | - Marijke Reynders
- Unit of Molecular Microbiology, Medical Microbiology, Department of Laboratory Medicine, AZ Sint-Jan Brugge AV, BE-8000 Bruges, Belgium
| | - Marc Van Ranst
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical & Epidemiological Virology, BE-3000, Leuven, Belgium; Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens and Enteroviruses, University Hospitals Leuven, BE-3000, Leuven, Belgium
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Broberg EK, Simone B, Jansa J, The Eu/Eea Member State Contributors. Upsurge in echovirus 30 detections in five EU/EEA countries, April to September, 2018. ACTA ACUST UNITED AC 2019; 23. [PMID: 30401013 PMCID: PMC6337069 DOI: 10.2807/1560-7917.es.2018.23.44.1800537] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An upsurge in Echovirus 30 (E30) infections, associated with meningitis/meningoencephalitis, has been observed in Denmark, Germany, the Netherlands, Norway and Sweden in the period April to September 2018, compared with 2015–2017. In total, 658 E30 infections among 4,537 enterovirus infections were detected in 15 countries between January and September 2018 and affected mainly newborns and 26–45 year-olds. National public health institutes are reminded to remain vigilant and inform clinicians of the ongoing epidemic.
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Affiliation(s)
- Eeva K Broberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Benedetto Simone
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Josep Jansa
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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23
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Vakulenko Y, Deviatkin A, Lukashev A. Using Statistical Phylogenetics for Investigation of Enterovirus 71 Genotype A Reintroduction into Circulation. Viruses 2019; 11:E895. [PMID: 31557961 PMCID: PMC6832606 DOI: 10.3390/v11100895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 02/08/2023] Open
Abstract
Neurovirulent enterovirus 71 (EV-A71) caused a massive epidemic in China in 2008-2011. While subgenotype C4 was the major causative agent, a few isolates were almost identical to the prototype EV-A71 strain and belonged to genotype A. This variant was allegedly extinct since 1970, and its identification in this epidemic suggests reintroduction of the archive virus. Regression analysis of genetic distances (TempEst software) was of moderate utility due to the low resolution of classical phylogenetic methods. Bayesian phylogenetic analysis (BEAST software) suggested artificial introduction event based on highly aberrant phylogenetic tree branch rates that differed by over three standard deviations from the mean substitution rate for EV71. Manual nucleotide-level analysis was used to further explore the virus spread pattern after introduction into circulation. Upon reintroduction, the virus accumulated up to seven substitutions in VP1, most of them non-synonymous and located within the capsid's canyon or at its rims, compatible with readaptation of a lab strain to natural circulation.
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Affiliation(s)
- Yulia Vakulenko
- Sechenov First Moscow State Medical University, Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, 119435 Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Andrei Deviatkin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119048 Moscow, Russia.
| | - Alexander Lukashev
- Sechenov First Moscow State Medical University, Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, 119435 Moscow, Russia.
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, 119048 Moscow, Russia.
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24
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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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25
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Cifuente JO, Moratorio G. Evolutionary and Structural Overview of Human Picornavirus Capsid Antibody Evasion. Front Cell Infect Microbiol 2019; 9:283. [PMID: 31482072 PMCID: PMC6710328 DOI: 10.3389/fcimb.2019.00283] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
Picornaviruses constitute one of the most relevant viral groups according to their impact on human and animal health. Etiologic agents of a broad spectrum of illnesses with a clinical presentation that ranges from asymptomatic to fatal disease, they have been the cause of uncountable epidemics throughout history. Picornaviruses are small naked RNA-positive single-stranded viruses that include some of the most important pillars in the development of virology, comprising poliovirus, rhinovirus, and hepatitis A virus. Picornavirus infectious particles use the fecal-oral or respiratory routes as primary modes of transmission. In this regard, successful viral spread relies on the capability of viral capsids to (i) shelter the viral genome, (ii) display molecular determinants for cell receptor recognition, (iii) facilitate efficient genome delivery, and (iv) escape from the immune system. Importantly, picornaviruses display a substantial amount of genetic variability driven by both mutation and recombination. Therefore, the outcome of their replication results in the emergence of a genetically diverse cloud of individuals presenting phenotypic variance. The host humoral response against the capsid protein represents the most active immune pressure and primary weapon to control the infection. Since the preservation of the capsid function is deeply rooted in the virus evolutionary dynamics, here we review the current structural evidence focused on capsid antibody evasion mechanisms from that perspective.
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Affiliation(s)
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
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Richter J, Tryfonos C, Christodoulou C. Molecular epidemiology of enteroviruses in Cyprus 2008-2017. PLoS One 2019; 14:e0220938. [PMID: 31393960 PMCID: PMC6687182 DOI: 10.1371/journal.pone.0220938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 07/26/2019] [Indexed: 12/28/2022] Open
Abstract
Enteroviruses (EVs) are associated with a broad spectrum of disease manifestations, including aseptic meningitis, encephalitis, hand, foot and mouth disease, acute flaccid paralysis and acute flaccid myelitis with outbreaks being reported frequently world-wide. The aim of this study was the molecular characterization of all enteroviruses detected in Cyprus in the ten-year period from January 2008 and December 2017 as well as a description of the circulation patterns associated with the most frequently encountered genotypes. For this purpose, serum, cerebrospinal fluid, nasal swab, skin swab and/or stool samples from 2666 patients with a suspected EV infection were analysed between January 2008 and December 2017. Enteroviruses were detected in 295 (11.1%) patients, which were then investigated further for epidemiological analysis by VP1 genotyping. Overall, 24 different enterovirus types belonging to three different species were identified. The predominant species was EV-B (209/295, 71%), followed by species EV-A (77/295, 26.1%). Only one virus belonged to species EV-D, whereas EV-C enteroviruses were not identified at all. The most frequent genotypes identified were echovirus 30 (26.1%), echovirus 6 (14.2%) and coxsackievirus A6 (10.9%). While Echovirus 30 and echovirus 6 frequency was significantly higher in patients older than 3 years of age, the opposite was observed for CV-A16 and EV-A71, which dominated in young children less than 3 years. Importantly, for the current study period a significant increase of previously only sporadically observed EV-A types, such as EV-A71 and CV-A16 was noted. A phylogenetic analysis of EV-A71 showed that the majority of the EV-A71 strains from Cyprus belonged to sub-genogroup C1 and C2, with the exception of one C4 strain that was observed in 2011. The data presented provide a comprehensive picture of enteroviruses circulating in Cyprus over the last decade and will be helpful to clinicians and researchers involved in the treatment, prevention and control of enteroviral infections by helping interpret trends in enteroviral diseases by associating them with circulating serotypes, for studying the association of enteroviruses with clinical manifestations and develop strategies for designing future EV vaccines.
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Affiliation(s)
- Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
| | - Christina Tryfonos
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Predicting Intraserotypic Recombination in Enterovirus 71. J Virol 2019; 93:JVI.02057-18. [PMID: 30487277 DOI: 10.1128/jvi.02057-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023] Open
Abstract
Enteroviruses are well known for their ability to cause neurological damage and paralysis. The model enterovirus is poliovirus (PV), the causative agent of poliomyelitis, a condition characterized by acute flaccid paralysis. A related virus, enterovirus 71 (EV-A71), causes similar clinical outcomes in recurrent outbreaks throughout Asia. Retrospective phylogenetic analysis has shown that recombination between circulating strains of EV-A71 produces the outbreak-associated strains which exhibit increased virulence and/or transmissibility. While studies on the mechanism(s) of recombination in PV are ongoing in several laboratories, little is known about factors that influence recombination in EV-A71. We have developed a cell-based assay to study recombination of EV-A71 based upon previously reported assays for poliovirus recombination. Our results show that (i) EV-A71 strain type and RNA sequence diversity impacts recombination frequency in a predictable manner that mimics the observations found in nature; (ii) recombination is primarily a replicative process mediated by the RNA-dependent RNA polymerase; (iii) a mutation shown to reduce recombination in PV (L420A) similarly reduces EV-A71 recombination, suggesting conservation in mechanism(s); and (iv) sequencing of intraserotypic recombinant genomes indicates that template switching occurs by a mechanism that may require some sequence homology at the recombination junction and that the triggers for template switching may be sequence independent. The development of this recombination assay will permit further investigation on the interplay between replication, recombination and disease.IMPORTANCE Recombination is a mechanism that contributes to genetic diversity. We describe the first assay to study EV-A71 recombination. Results from this assay mimic what is observed in nature and can be used by others to predict future recombination events within the enterovirus species A group. In addition, our results highlight the central role played by the viral RNA-dependent RNA polymerase (RdRp) in the recombination process. Further, our results show that changes to a conserved residue in the RdRp from different species groups have a similar impact on viable recombinant virus yields, which is indicative of conservation in mechanism.
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Lukashev AN, Vakulenko YA, Turbabina NA, Deviatkin AA, Drexler JF. Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees? Rev Med Virol 2018; 28:e2002. [PMID: 30069956 DOI: 10.1002/rmv.2002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 11/05/2022]
Abstract
Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Preparations, Moscow, Russia
| | - Yulia A Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Virology Department, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Natalia A Turbabina
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | | | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
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29
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Dahm T, Adams O, Boettcher S, Diedrich S, Morozov V, Hansman G, Fallier-Becker P, Schädler S, Burkhardt CJ, Weiss C, Stump-Guthier C, Ishikawa H, Schroten H, Schwerk C, Tenenbaum T, Rudolph H. Strain-dependent effects of clinical echovirus 30 outbreak isolates at the blood-CSF barrier. J Neuroinflammation 2018; 15:50. [PMID: 29463289 PMCID: PMC5819246 DOI: 10.1186/s12974-018-1061-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Echovirus (E) 30 (E-30) meningitis is characterized by neuroinflammation involving immune cell pleocytosis at the protective barriers of the central nervous system (CNS). In this context, infection of the blood-cerebrospinal fluid barrier (BCSFB), which has been demonstrated to be involved in enteroviral CNS pathogenesis, may affect the tight junction (TJ) and adherens junction (AJ) function and morphology. METHODS We used an in vitro human choroid plexus epithelial (HIBCPP) cell model to investigate the effect of three clinical outbreak strains (13-311, 13-759, and 14-397) isolated in Germany in 2013, and compared them to E-30 Bastianni. Conducting transepithelial electrical resistance (TEER), paracellular dextran flux measurement, quantitative real-time polymerase chain reaction (qPCR), western blot, and immunofluorescence analysis, we investigated TJ and AJ function and morphology as well as strain-specific E-30 infection patterns. Additionally, transmission electron and focused ion beam microscopy electron microscopy (FIB-SEM) was used to evaluate the mode of leukocyte transmigration. Genome sequencing and phylogenetic analyses were performed to discriminate potential genetic differences among the outbreak strains. RESULTS We observed a significant strain-dependent decrease in TEER with strains E-30 Bastianni and 13-311, whereas paracellular dextran flux was only affected by E-30 Bastianni. Despite strong similarities among the outbreak strains in replication characteristics and particle distribution, strain 13-311 was the only outbreak isolate revealing comparable disruptive effects on TJ (Zonula Occludens (ZO) 1 and occludin) and AJ (E-cadherin) morphology to E-30 Bastianni. Notwithstanding significant junctional alterations upon E-30 infection, we observed both para- and transcellular leukocyte migration across HIBCPP cells. Complete genome sequencing revealed differences between the strains analyzed, but no explicit correlation with the observed strain-dependent effects on HIBCPP cells was possible. CONCLUSION The findings revealed distinct E-30 strain-specific effects on barrier integrity and junctional morphology. Despite E-30-induced barrier alterations leukocyte trafficking did not exclusively occur via the paracellular route.
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Affiliation(s)
- Tobias Dahm
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ortwin Adams
- Institute of Virology, University Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Sindy Boettcher
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Berlin, Germany
| | - Sabine Diedrich
- National Reference Centre for Poliomyelitis and Enteroviruses, Robert Koch-Institute, Berlin, Germany
| | - Vasily Morozov
- Schaller Research Group, University of Heidelberg and the DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Grant Hansman
- Schaller Research Group, University of Heidelberg and the DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Petra Fallier-Becker
- Institute of Pathology and Neuropathology, University Hospital of Tübingen, Tübingen, Germany
| | | | - Claus J. Burkhardt
- NMI Natural and Medical Sciences Institute, University of Tübingen, Reutlingen, Germany
| | - Christel Weiss
- Institute of Medical Statistics and Biomathematics, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carolin Stump-Guthier
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hiroshi Ishikawa
- Department of NDU Life Sciences, School of life Dentistry, The Nippon Dental University, Tokyo, Japan
| | - Horst Schroten
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Christian Schwerk
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Tobias Tenenbaum
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Henriette Rudolph
- Pediatric Infectious Diseases, University Children’s Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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30
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Lukashev AN, Vakulenko YA. Molecular evolution of types in non-polio enteroviruses. J Gen Virol 2017; 98:2968-2981. [PMID: 29095688 DOI: 10.1099/jgv.0.000966] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-polio enteroviruses are a ubiquitous and divergent group of non-enveloped RNA viruses. Novel types are reported regularly in addition to over 100 known types; however, mechanisms of emergence of novel types remain obscure. Here, the 33 most common types represented by 35-629 non-redundant partial VP1 sequences in GenBank were studied in parallel using Bayesian coalescent molecular clock analysis to investigate common evolutionary trends among enterovirus types. Inferred substitution rates were in the range of 0.41×10-2 to 3.07×10-2 substitutions per site per year. The most recent common ancestors of known isolates of each type presumably existed between 55 and 200 years ago. Phylogenetic analysis results suggested that global type populations underwent bottlenecks that could repeatedly reset the common ancestor dates. Nevertheless, species-level analysis suggested that the contemporary enterovirus types emerged within the last millennium. Analysis of 2657 complete VP1 sequences of the 24 most common types indicated that the type criterion based upon 75 % nucleotide sequence identity remains generally valid, despite exponential growth of the number of known sequences and a high rate of mutation fixation. However, in few types there was evidence that enteroviruses can drift slightly beyond the type threshold, up to 73 % identity, and both amino acid and nucleotide sequences should be considered for type identification. Analysis of sequence distances within types implied that sequence-identity-based identification of genotypes is rational within some, but not all, types and distinct genotype cut-offs (9-20 %) may be useful for different types.
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Affiliation(s)
- Alexander N Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.,Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia
| | - Yulia A Vakulenko
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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31
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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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Siqueira JAM, Bandeira RDS, Oliveira DDS, dos Santos LFP, Gabbay YB. Genotype diversity and molecular evolution of noroviruses: A 30-year (1982-2011) comprehensive study with children from Northern Brazil. PLoS One 2017; 12:e0178909. [PMID: 28604828 PMCID: PMC5467842 DOI: 10.1371/journal.pone.0178909] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/19/2017] [Indexed: 01/19/2023] Open
Abstract
A chronologically comprehensive 30-year study was conducted that involved children living in Belém, in the Amazon region of Northern Brazil, who participated in eight different studies from October 1982 to April 2011. The children were followed either in the community or in health units and hospitals in order to identify the norovirus genotypes involved in infections during this time. A total of 2,520 fecal specimens were obtained and subjected to RT-PCR and nucleotide sequencing for regions A, B, C, D and P2 of the viral genome. An overall positivity of 16.9% (n = 426) was observed, and 49% of the positive samples were genotyped (208/426), evidencing the presence of several genotypes as follows: Polymerase gene (GI.P4, GII.Pa, GII.Pc, GII.Pe, GII.Pg, GII.Pj, GII.P3, GII.P4, GII.P6, GII.P7, GII.P8, GII.P12, GII.P13, GII.P14, GII.P21, GII.P22), and VP1 gene (GI.3, GI.7, GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.8, GII.10, GII.12, GII.14, GII.17, GII.23). The GII.P4/GII.4 genotype determined by both open reading frames (ORFs) (partial polymerase and VP1 genes) was found for 83 samples, and analyses of the subdomain P2 region showed 10 different variants: CHDC (1970s), Tokyo (1980s), Bristol_1993, US_95/96, Kaiso_2003, Asia_2003, Hunter_2004, Yerseke_2006a, Den Haag_2006b (subcluster “O”) and New Orleans_2009. Recombination events were confirmed in 47.6% (n = 20) of the 42 samples with divergent genotyping by ORF1 and ORF2 and with probable different breakpoints within the viral genome. The evolutionary analyses estimated a rate of evolution of 1.02 x 10−2 and 9.05 x 10−3 subs./site/year using regions C and D from the VP1 gene, respectively. The present research shows the broad genetic diversity of the norovirus that infected children for 30 years in Belém. These findings contribute to our understanding of noroviruses molecular epidemiology and viral evolution and provide a baseline for vaccine design.
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Affiliation(s)
- Jones Anderson Monteiro Siqueira
- Laboratório de Norovírus e outros Vírus Gastroentéricos—LNVE, Seção de Virologia—SAVIR, Instituto Evandro Chagas—IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
- * E-mail:
| | - Renato da Silva Bandeira
- Seção de Virologia–SAVIR, Instituto Evandro Chagas—IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Darleise de Souza Oliveira
- Seção de Virologia–SAVIR, Instituto Evandro Chagas—IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Liann Filiphe Pereira dos Santos
- Laboratório de Norovírus e outros Vírus Gastroentéricos—LNVE, Seção de Virologia—SAVIR, Instituto Evandro Chagas—IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
| | - Yvone Benchimol Gabbay
- Laboratório de Norovírus e outros Vírus Gastroentéricos—LNVE, Seção de Virologia—SAVIR, Instituto Evandro Chagas—IEC, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brazil
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Benschop KSM, Rahamat-Langendoen JC, van der Avoort HGAM, Claas ECJ, Pas SD, Schuurman R, Verweij JJ, Wolthers KC, Niesters HGM, Koopmans MPG. VIRO-TypeNed, systematic molecular surveillance of enteroviruses in the Netherlands between 2010 and 2014. ACTA ACUST UNITED AC 2017; 21:30352. [PMID: 27719752 PMCID: PMC5069426 DOI: 10.2807/1560-7917.es.2016.21.39.30352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/23/2016] [Indexed: 12/29/2022]
Abstract
VIRO-TypeNed is a collaborative molecular surveillance platform facilitated through a web-based database. Genetic data in combination with epidemiological, clinical and patient data are shared between clinical and public health laboratories, as part of the surveillance underpinning poliovirus eradication. We analysed the combination of data submitted from 2010 to 2014 to understand circulation patterns of non-polio enteroviruses (NPEV) of public health relevance. Two epidemiological patterns were observed based on VIRO-TypeNed data and classical surveillance data dating back to 1996: (i) endemic cyclic, characterised by predictable upsurges/outbreaks every two to four years, and (ii) epidemic, where rare virus types caused upsurges/outbreaks. Genetic analysis suggests continuous temporal displacement of virus lineages due to the accumulation of (silent) genetic changes. Non-synonymous changes in the antigenic B/C loop suggest antigenic diversification, which may affect population susceptibility. Infections were frequently detected at an age under three months and at an older, parenting age (25–49 years) pointing to a distinct role of immunity in the circulation patterns. Upsurges were detected in the summer and winter which can promote increased transmissibility underlying new (cyclic) upsurges and requires close monitoring. The combination of data provide a better understanding of NPEV circulation required to control and curtail upsurges and outbreaks.
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Affiliation(s)
- Kimberley S M Benschop
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
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Intertypic recombination of human parechovirus 4 isolated from infants with sepsis-like disease. J Clin Virol 2017; 88:1-7. [PMID: 28081453 DOI: 10.1016/j.jcv.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/30/2016] [Accepted: 01/02/2017] [Indexed: 11/24/2022]
Abstract
BACKGROUND Human parechoviruses (HPeVs) (family Picornaviridae), are common pathogens in young children. Despite their high prevalence, research on their genetic identity, diversity and evolution have remained scarce. OBJECTIVES Complete coding regions of three previously reported HPeV-4 isolates from Finnish children with sepsis-like disease were sequenced in order to elucidate the phylogenetic relationships and potential recombination events during the evolution of these isolates. STUDY DESIGN The isolated viruses were sequenced and aligned with all HPeV complete genome sequences available in GenBank. Phylogenetic trees were constructed and similarity plot and bootscanning methods were used for recombination analysis. RESULTS The three HPeV-4 isolates had 99.8% nucleotide sequence similarity. The phylogenetic analysis indicated that capsid-encoding sequences of these HPeV-4 isolates were closely related to other HPeV-4 strains (80.7-94.7% nucleotide similarity), whereas their non-structural region genes 2A to 3C clustered together with several HPeV-1 and HPeV-3 strains, in addition to the HPeV-4 strain K251176-02 (isolated 2002 in the Netherlands), but not with other HPeV-4 strains. However, in 3D-encoding sequence the Finnish HPeV-4 isolates did not cluster with the strain HPeV-4/K251176-02, but instead, formed a distinct group together with several HPeV-1 and HPeV-3 strains. Similarity plot and Bootscan analyses further confirmed intertypic recombination events in the evolution of the Finnish HPeV-4 isolates. CONCLUSION Intertypic recombination event(s) have occurred during the evolution of HPeV-4 isolates from children with sepsis-like disease. However, due to the low number of parechovirus complete genomes available, the precise recombination partners could not be detected. The results suggest frequent intratypic recombination among parechoviruses.
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Puenpa J, Vongpunsawad S, Österback R, Waris M, Eriksson E, Albert J, Midgley S, Fischer TK, Eis-Hübinger AM, Cabrerizo M, Gaunt E, Simmonds P, Poovorawan Y. Molecular epidemiology and the evolution of human coxsackievirus A6. J Gen Virol 2016; 97:3225-3231. [DOI: 10.1099/jgv.0.000619] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Riikka Österback
- Department of Virology, University of Turku, 20520 Turku, Finland
- Department of Clinical Virology, Turku University Hospital, 20520 Turku, Finland
| | - Matti Waris
- Department of Virology, University of Turku, 20520 Turku, Finland
- Department of Clinical Virology, Turku University Hospital, 20520 Turku, Finland
| | - Eva Eriksson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 17177 Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Sofie Midgley
- Department of Microbiological Diagnostics & Virology, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Thea K. Fischer
- Department of Microbiological Diagnostics & Virology, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Anna M. Eis-Hübinger
- Institute for Virology, University of Bonn Medical Center, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - María Cabrerizo
- Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Eleanor Gaunt
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Peter Simmonds
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Krumbholz A, Egerer R, Braun H, Schmidtke M, Rimek D, Kroh C, Hennig B, Groth M, Sauerbrei A, Zell R. Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members. Med Microbiol Immunol 2016; 205:471-83. [PMID: 27369854 DOI: 10.1007/s00430-016-0464-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/20/2016] [Indexed: 11/30/2022]
Abstract
In October and November 2010, six children and one woman were presented with symptoms of aseptic meningitis in Jena, Thuringia, Germany. Enterovirus RNA was detected in the cerebrospinal fluid of all patients by RT-PCR, and preliminary molecular typing revealed echovirus 18 (E-18) as causative agent. Virus isolates were obtained from stool samples of three patients and several contact persons. Again, most isolates were typed as E-18. In addition, coxsackievirus B5 (CV-B5) and echovirus 25 (E-25) were found to co-circulate. As only few complete E-18 sequences are available in GenBank, the entire genomes of these isolates were determined using direct RNA-sequencing technology. We did not find evidence for recombination between E-18, E-25 or CV-B5 during the outbreak. Viral protein 1 gene sequences and the cognate 3D polymerase gene sequences of each isolate and GenBank sequences were analysed in order to define type-specific recombination groups (recogroups).
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Affiliation(s)
- Andi Krumbholz
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany. .,Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany. .,Institute of Medical Microbiology, Jena University Hospital, Jena, Germany. .,Medical Laboratory Dr. Krause and colleagues MVZ GmbH, Steenbeker Weg 23, 24106, Kiel, Germany.
| | - Renate Egerer
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany.,Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Heike Braun
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Michaela Schmidtke
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Dagmar Rimek
- Thuringian State Authority for Consumer Protection (TLV), Bad Langensalza, Germany
| | - Claudia Kroh
- Public Health Authority, City Council of Jena, Jena, Germany
| | - Bert Hennig
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Andreas Sauerbrei
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
| | - Roland Zell
- Institute of Virology and Antiviral Therapy, Jena University Hospital, Jena, Germany
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Woodman A, Arnold JJ, Cameron CE, Evans DJ. Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination. Nucleic Acids Res 2016; 44:6883-95. [PMID: 27317698 PMCID: PMC5001610 DOI: 10.1093/nar/gkw567] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/14/2016] [Indexed: 11/13/2022] Open
Abstract
Genetic recombination in single-strand, positive-sense RNA viruses is a poorly understand mechanism responsible for generating extensive genetic change and novel phenotypes. By moving a critical cis-acting replication element (CRE) from the polyprotein coding region to the 3′ non-coding region we have further developed a cell-based assay (the 3′CRE-REP assay) to yield recombinants throughout the non-structural coding region of poliovirus from dually transfected cells. We have additionally developed a defined biochemical assay in which the only protein present is the poliovirus RNA dependent RNA polymerase (RdRp), which recapitulates the strand transfer events of the recombination process. We have used both assays to investigate the role of the polymerase fidelity and nucleotide turnover rates in recombination. Our results, of both poliovirus intertypic and intratypic recombination in the CRE-REP assay and using a range of polymerase variants in the biochemical assay, demonstrate that RdRp fidelity is a fundamental determinant of recombination frequency. High fidelity polymerases exhibit reduced recombination and low fidelity polymerases exhibit increased recombination in both assays. These studies provide the basis for the analysis of poliovirus recombination throughout the non-structural region of the virus genome and provide a defined biochemical assay to further dissect this important evolutionary process.
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Affiliation(s)
- Andrew Woodman
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - Jamie J Arnold
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - Craig E Cameron
- Dept. of Biochemistry & Molecular Biology, 201 Althouse Lab, University Park, PA 16802, USA
| | - David J Evans
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, St. Andrews KY16 9ST, UK
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Iwasaki J, Chai LY, Khoo SK, Bizzintino J, Laing IA, Le Souëf PN, Thomas WR, Hales BJ. Lower anti-echovirus antibody responses in children presenting to hospital with asthma exacerbations. Clin Exp Allergy 2016; 45:1523-30. [PMID: 25640320 DOI: 10.1111/cea.12501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/16/2014] [Accepted: 12/02/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Rhinoviruses from the Enterovirus genus cause frequent infections and induce remarkably high titres of anticapsid antigen antibodies in asthmatics, while the prevalence of neutralising antibodies to the gut-trophic echoviruses from the same genus is diminished. OBJECTIVE To assess the absolute and specific antibody titres to VP1 antigens of the gut-trophic enteroviruses, echovirus 30 and Sabin 1 poliovirus, in asthmatic and non-asthmatic children. METHODS Recombinant polypeptides representing the VP1 capsid antigens of echovirus 30 and Sabin poliovirus 1 were produced. Their ability to bind IgG1 antibodies from the plasma of asthmatic (n = 45) and non-asthmatic (n = 29) children were quantitated by immunoassays that incorporated immunoabsorptions to remove cross-reactivity. RESULTS The IgG1 antibody titres and prevalence of antibody binding to echovirus 30 were significantly lower for asthmatic children compared to controls (P < 0.05) and inversely correlated with total IgE levels for the whole study population (r = -0.262; P < 0.05). There was no difference in the prevalence and titre between groups to the VP1 antigen of Sabin poliovirus. Anti-tetanus toxoid titres measured for comparison did not correlate with anti-echovirus or poliovirus, but correlated with anti-rhinovirus titres in controls but not asthmatics, where the titres were higher for the asthmatic group. CONCLUSIONS AND CLINICAL RELEVANCE The associations of lower antibody titres of asthmatic children to echovirus reported here and those of our previous findings of a heightened response to rhinovirus suggest a dichotomy where respiratory enterovirus infection/immunity increases the probability of developing asthma and enteric infections lower the risk. This provides further support for the concept of intestinal infection playing a key role in the development of allergic respiratory disease.
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Affiliation(s)
- J Iwasaki
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - L Y Chai
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - S-K Khoo
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - J Bizzintino
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - I A Laing
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - P N Le Souëf
- School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
| | - W R Thomas
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - B J Hales
- Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, WA, Australia
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Genetic diversity, seasonality and transmission network of human metapneumovirus: identification of a unique sub-lineage of the fusion and attachment genes. Sci Rep 2016; 6:27730. [PMID: 27279080 PMCID: PMC4899729 DOI: 10.1038/srep27730] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important viral respiratory pathogen worldwide. Current knowledge regarding the genetic diversity, seasonality and transmission dynamics of HMPV among adults and children living in tropical climate remains limited. HMPV prevailed at 2.2% (n = 86/3,935) among individuals presented with acute respiratory tract infections in Kuala Lumpur, Malaysia between 2012 and 2014. Seasonal peaks were observed during the northeast monsoon season (November-April) and correlated with higher relative humidity and number of rainy days (P < 0.05). Phylogenetic analysis of the fusion and attachment genes identified the co-circulation of three known HMPV sub-lineages, A2b and B1 (30.2% each, 26/86) and B2 (20.9%, 18/86), with genotype shift from sub-lineage B1 to A2b observed in 2013. Interestingly, a previously unrecognized sub-lineage of A2 was identified in 18.6% (16/86) of the population. Using a custom script for network construction based on the TN93 pairwise genetic distance, we identified up to nine HMPV transmission clusters circulating as multiple sub-epidemics. Although no apparent major outbreak was observed, the increased frequency of transmission clusters (dyads) during seasonal peaks suggests the potential roles of transmission clusters in driving the spread of HMPV. Our findings provide essential information for therapeutic research, prevention strategies, and disease outbreak monitoring of HMPV.
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40
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Molecular characterization of echovirus 30 isolates from Poland, 1995-2015. Virus Genes 2016; 52:400-4. [PMID: 26957092 DOI: 10.1007/s11262-016-1310-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/24/2016] [Indexed: 01/07/2023]
Abstract
Echovirus 30 (E30) is one of the most frequently identified enterovirus and a major cause of meningitis in children and adults. To investigate the genetic variability and relationship of E30 isolated from specimens of aseptic meningitis cases that occurred in Poland over a period of 20 years, sequences of VP1 gene were determined and genetic analysis was performed. From 1995 to 2015, 124 E30 were isolated using RD cells, and 58 isolates were sequenced and characterized by phylogenetic analysis of partial VP1 region (793 nt). In general, nucleotide sequence divergence in pairwise comparisons among Polish E30 isolates ranged from 0.0 to 15.0 %. The phylogenetic analysis revealed that E30 circulating in Poland since 1995 belong to two unique groups: Group I, characterized by high divergence (up to 13.1 %), segregated in four subgroups, and showed strong temporal circulation of E30. Group II, detected in Poland in 2013-2014, was closely correlated with two meningitis outbreaks and formed a separate genetically homogeneous group. Phylogenetic analysis revealed that strains from Poland had the closest genetic relationship with not only the isolates previously identified in Europe (Belarus, France, Germany, Italy, Russia) but also those in other parts of the world (Australia, China). Sequences of outbreak isolates were grouped in group II together with those from Russia and China isolated during 2010-2013. The identification of five distinct viral lineages during 1995-2015 confirmed the high E30 genetic diversity which may be an essential precondition for the emergence of new strains responsible for further potential aseptic meningitis outbreaks.
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41
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Molecular epidemiology of coxsackievirus B3 infection in Spain, 2004-2014. Arch Virol 2016; 161:1365-70. [DOI: 10.1007/s00705-016-2783-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
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42
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43
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Elucidation of echovirus 30's origin and transmission during the 2012 aseptic meningitis outbreak in Guangdong, China, through continuing environmental surveillance. Appl Environ Microbiol 2015; 81:2311-9. [PMID: 25616804 DOI: 10.1128/aem.03200-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An aseptic meningitis outbreak occurred in Luoding City of Guangdong, China, in 2012, and echovirus type 30 (ECHO30) was identified as the major causative pathogen. Environmental surveillance indicated that ECHO30 was detected in the sewage of a neighboring city, Guangzhou, from 2010 to 2012 and also in Luoding City sewage samples (6/43, 14%) collected after the outbreak. In order to track the potential origin of the outbreak viral strains, we sequenced the VP1 genes of 29 viral strains from clinical patients and environmental samples. Sequence alignments and phylogenetic analyses based on VP1 gene sequences revealed that virus strains isolated from the sewage of Guangzhou and Luoding cities matched well the clinical strains from the outbreak, with high nucleotide sequence similarity (98.5% to 100%) and similar cluster distribution. Five ECHO30 clinical strains were clustered with the Guangdong environmental strains but diverged from strains from other regions, suggesting that this subcluster of viruses most likely originated from the circulating virus in Guangdong rather than having been more recently imported from other regions. These findings underscore the importance of long-term, continuous environmental surveillance and genetic analysis to monitor circulating enteroviruses.
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44
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Gaunt E, Harvala H, Österback R, Sreenu VB, Thomson E, Waris M, Simmonds P. Genetic characterization of human coxsackievirus A6 variants associated with atypical hand, foot and mouth disease: a potential role of recombination in emergence and pathogenicity. J Gen Virol 2015; 96:1067-1079. [PMID: 25614593 PMCID: PMC4631059 DOI: 10.1099/vir.0.000062] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/15/2015] [Indexed: 01/21/2023] Open
Abstract
Human coxsackievirus A6 (CVA6) is an enterically transmitted enterovirus. Until recently, CVA6 infections were considered as being of minor clinical significance, and only rarely aetiologically linked with hand, foot and mouth disease (HFMD) associated with other species A enteroviruses (particularly EV71 and CVA16). From 2008 onwards, however, CVA6 infections have been associated with several outbreaks worldwide of atypical HFMD (aHFMD) accompanied by a varicelliform rash. We recently reported CVA6-associated eczema herpeticum occurring predominantly in children and young adults in Edinburgh in January and February 2014. To investigate genetic determinants of novel clinical phenotypes of CVA6, we genetically characterized and analysed CVA6 variants associated with eczema herpeticum in Edinburgh in 2014 and those with aHFMD in CAV isolates collected from 2008. A total of eight recombinant forms (RFs) have circulated worldwide over the past 10 years, with the particularly recent appearance of RF-H associated with eczema herpeticum cases in Edinburgh in 2014. Comparison of phylogenies and divergence of complete genome sequences of CVA6 identified recombination breakpoints in 2A-2C, within VP3, and between 5' untranslated region and VP1. A Bayesian temporal reconstruction of CVA6 evolution since 2004 provided estimates of dates and the actual recombination events that generated more recently appearing recombination groups (RF-E, -F, -G and -H). Associations were observed between recombination groups and clinical presentations of herpangina, aHFMD and eczema herpeticum, but not with VP1 or other structural genes. These observations provided evidence that NS gene regions may potentially contribute to clinical phenotypes and outcomes of CVA6 infection.
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Affiliation(s)
- Eleanor Gaunt
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Heli Harvala
- Specialist Virology Laboratory, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Riikka Österback
- Department of Virology, University of Turku, 20520 Turku, Finland
| | - Vattipally B Sreenu
- MRC University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, UK
| | - Emma Thomson
- MRC University of Glasgow Centre for Virus Research, 8 Church Street, Glasgow G11 5JR, UK
| | - Matti Waris
- Department of Virology, University of Turku, 20520 Turku, Finland
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
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45
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Yarmolskaya MS, Shumilina EY, Ivanova OE, Drexler JF, Lukashev AN. Molecular epidemiology of echoviruses 11 and 30 in Russia: different properties of genotypes within an enterovirus serotype. INFECTION GENETICS AND EVOLUTION 2015; 30:244-248. [PMID: 25562123 DOI: 10.1016/j.meegid.2014.12.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 11/18/2014] [Accepted: 12/26/2014] [Indexed: 11/20/2022]
Abstract
Over 100 known enterovirus serotypes differ in their epidemiological and pathogenic properties. Much less is known about variation of these features on a sub-serotype level, such as genotypes. Echovirus 11 (E11) and E30 are amongst the most frequent causative agents of aseptic meningitis. We studied the molecular epidemiology of these pathogens to evaluate potential epidemiological and pathogenic dissimilarities of their genotypes. The complete VP1 genome region was sequenced for 97 E11 and 62 E30 isolates collected in Russia from 2008 to 2012, and they were studied in comparison with all 140 E11 and 432 E30 sequences available in GenBank. A geographic pattern of genotype prevalence was observed for both types. Russian E11 isolates belonged mainly to A genotype, which is common in Asia, and D5, which is predominant in Europe. For E30, genotype III by classification of Ke et al. (2011), also termed genotype a by Bailly et al. (2009), was endemic in Russia from 2003 to 2012, while it was not detected in Europe and North America during this time. The E30 genotypes VI-B, VI-G, and VI-H (e, f and h) were regularly introduced from different countries, became predominant and vanished after no more than 4years. In addition to geographic patterns, E11 genotypes also differed by isolation source. Genotype A2 viruses were significantly more often found in sewage, compared to genotype D5 that was isolated from both sewage and human samples. In addition, there was evidence of a different capacity for international transfers among E11 GtA subclusters.
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Affiliation(s)
- Maria S Yarmolskaya
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Elena Yu Shumilina
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Olga E Ivanova
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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46
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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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47
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Janes VA, Minnaar R, Koen G, van Eijk H, Dijkman-de Haan K, Pajkrt D, Wolthers KC, Benschop KS. Presence of human non-polio enterovirus and parechovirus genotypes in an Amsterdam hospital in 2007 to 2011 compared to national and international published surveillance data: a comprehensive review. ACTA ACUST UNITED AC 2014; 19. [PMID: 25425513 DOI: 10.2807/1560-7917.es2014.19.46.20964] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Enteroviruses (EV) and human parechoviruses (HPeV) are endemic worldwide. These infections are a constant cause of hospitalisation and severe disease, predominantly in young children and infants. Coordinated monitoring and surveillance are crucial to control these infections. We have monitored EV and HPeV epidemiology in Amsterdam from 2007 to 2011 with real-time RT-PCR and direct genotyping, facilitating highly sensitive surveillance. Moreover, we conducted a literature survey of existing surveillance data for comparison. Only 14 studies were identified. While HPeV1 was most frequently detected in Amsterdam, EV-B viruses dominated nationally and internationally. Furthermore, the top 10 strains detected differed yearly and per study. However, detection and typing methods were too varied to allow direct comparison and comprehension of the worldwide distribution and circulation patterns of the different genotypes. This limited a direct response to anticipate peaks. Uniform European monitoring programmes are essential to aid prediction of outbreaks and disease management.
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Affiliation(s)
- V A Janes
- Emma Children s Hospital, Department of Paediatric Haematology, Immunology and Infectious Diseases, Academic Medical Center, Amsterdam, the Netherlands
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48
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Characteristics of the mosaic genome of a human parechovirus type 1 strain isolated from an infant with pneumonia in China. INFECTION GENETICS AND EVOLUTION 2014; 29:91-8. [PMID: 25461260 DOI: 10.1016/j.meegid.2014.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/02/2014] [Accepted: 11/05/2014] [Indexed: 12/22/2022]
Abstract
Human parechoviruses (HPeVs) belong to the Parechovirus genus of the large and growing family of Picornaviridae with a non-enveloped, single-stranded and positive-sense RNA. An HPeV strain was isolated from the nasopharyngeal aspirate specimen of a 2 months old infant hospitalized with pneumonia in Beijing, China and nominated as BJ-37359 followed the code of the specimen. Strain BJ-37359 was identified as HPeV1 by whole genome sequencing. The full genome of strain BJ-37359 consisted of 7336 nucleotides (nt), excluding a poly (A) tail and contained an ORF of 6537 nt flanked by 5'UTR of 709 nt and 3'UTR of 90 nt. Phylogenetic analyses revealed that strain BJ-37359 were clustered together with HPeV1 strains in the structural capsid protein region, while uncoupling in the non-structural gene regions. Analyses with Simplot and Bootscan indicated that multiple recombination events occurred in the non-structural region and VP0 region of strain BJ-37359 with other HPeV1, and other types might have contributed to the recombination, especially HPeV6 and HPeV7 strains. Recombination analyses indicated that strain BJ-37359 may have a mosaic genome with new genomic recombination breakpoints.
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49
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Nougairede A, Bessaud M, Thiberville SD, Piorkowski G, Ninove L, Zandotti C, Charrel RN, Guilhem N, de Lamballerie X. Widespread circulation of a new echovirus 30 variant causing aseptic meningitis and non-specific viral illness, South-East France, 2013. J Clin Virol 2014; 61:118-24. [DOI: 10.1016/j.jcv.2014.05.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/27/2014] [Accepted: 05/30/2014] [Indexed: 12/21/2022]
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50
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Junttila N, Lévêque N, Magnius L, Kabue J, Muyembe-Tamfum JJ, Maslin J, Lina B, Norder H. Complete coding regions of the prototypes enterovirus B93 and C95: Phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains. J Med Virol 2014; 87:485-97. [DOI: 10.1002/jmv.24062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2014] [Indexed: 01/30/2023]
Affiliation(s)
- N. Junttila
- MTC; Karolinska Institutet; Stockholm Sweden
| | - N. Lévêque
- Clinical and Molecular Virology Unit; University Hospital Faculty of Medicine; Reims France
- Laboratory of Virology, National Enterovirus Laboratory; Hospices Civils de Lyon; France
| | | | - J.P. Kabue
- National Institute of Biomedical Research; Kinshasa, Democratic Republic of the Congo
| | - J. J. Muyembe-Tamfum
- National Institute of Biomedical Research; Kinshasa, Democratic Republic of the Congo
| | - J. Maslin
- Department of Biology; Saint-Anne Military Hospital; Toulon France
| | - B. Lina
- Laboratory of Virology, National Enterovirus Laboratory; Hospices Civils de Lyon; France
| | - H. Norder
- MTC; Karolinska Institutet; Stockholm Sweden
- Department of Infectious Diseases/Section of Clinical Virology; Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
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