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Lema C, Torres C, Van der Sanden S, Cisterna D, Freire MC, Gómez RM. Global phylodynamics of Echovirus 30 revealed differential behavior among viral lineages. Virology 2019; 531:79-92. [PMID: 30856485 DOI: 10.1016/j.virol.2019.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/16/2019] [Accepted: 02/16/2019] [Indexed: 01/03/2023]
Abstract
Echovirus 30 (E30) is an important causative agent of aseptic meningitis worldwide. Despite this, the global and regional dispersion patterns, especially in South America, are still largely unknown. We performed an in-depth analysis of global E30 population dynamics, by using the VP1 sequences of 79 strains isolated in Argentina, between 1998 and 2012, and 856 sequences from GenBank. Furthermore, the 3Dpol regions of 329 sequences were analyzed to study potential recombination events. E30 evolution was characterized by co-circulation and continuous replacement of lineages over time, where four lineages appear to circulate at present and another four lineages appear to have stopped circulating. Five lineages showed a global distribution, whereas three other lineages had a more restricted circulation pattern. Strains isolated in South America belong to lineages E and F. Analysis of the 3Dpol region of Argentinean strains indicated that recombination events occurred in both lineages.
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Affiliation(s)
- Cristina Lema
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina.
| | - Carolina Torres
- Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Argentina
| | | | - Daniel Cisterna
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina
| | - María Cecilia Freire
- Neurovirosis Service at Virology Department, INEI-ANLIS, Dr. Carlos G. Malbran Institute, Argentina
| | - Ricardo M Gómez
- Institute of Biotechnology and Molecular Biology, CONICET-UNLP, 1900 La Plata, Argentina.
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2
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Laassri M, Zagorodnyaya T, Hassin-Baer S, Handsher R, Sofer D, Weil M, Karagiannis K, Simonyan V, Chumakov K, Shulman L. Evolution of echovirus 11 in a chronically infected immunodeficient patient. PLoS Pathog 2018; 14:e1006943. [PMID: 29554133 PMCID: PMC5875893 DOI: 10.1371/journal.ppat.1006943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/29/2018] [Accepted: 02/16/2018] [Indexed: 01/20/2023] Open
Abstract
Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of 1990s. Genomic regions coding for individual viral proteins did not appear to be under strong selective pressure except for protease 3C that was remarkably conserved. This may suggest its important role in maintaining persistent infection. We describe evolution of Echovirus 11 genome in chronically infected immunodeficient patient over a period of several years and compare it with the evolution of circulating echoviruses from which it originated. Ratio of silent to missense mutations in protein coding regions suggests that chronic virus was under lower selective pressure than circulating viruses, except for a region coding for viral protease that may participate in neutralizing host cell anti-viral defense mechanisms. This suggests that adaptation to persistence in immunodeficient host may require maintaining functional viral counter-defense mechanisms.
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Affiliation(s)
- Majid Laassri
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Tatiana Zagorodnyaya
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Sharon Hassin-Baer
- Movement Disorders Institute and Department of Neurology, Sheba Medical Center, Tel Hashomer; and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Handsher
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Merav Weil
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Konstantinos Karagiannis
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Vahan Simonyan
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Konstantin Chumakov
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
- * E-mail:
| | - Lester Shulman
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
- Dept. of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Abstract
Infections with enteroviruses and human parechoviruses are highly prevalent, particularly in neonates, where they may cause substantial morbidity and mortality. Individuals with B-cell-related immunodeficiencies are at risk for severe enteroviral infections, usually a chronic and fatal meningoencephalitis. In transplant recipients and patients with malignancy, enterovirus infections typically involve the respiratory tract, but cases of severe, disseminated infection have been described. The mainstay of diagnosis for enterovirus and human parechovirus infections involves the use of molecular diagnostic techniques. However, routine nucleic acid-detection methods for enteroviruses will not detect human parechoviruses. Laboratory diagnosis of these viral infections is important in determining a patient's prognosis and guiding clinical management.
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Zhou F, Wang Q, Sintchenko V, Gilbert GL, O'Sullivan MVN, Iredell JR, Dwyer DE. Use of the 5' untranslated region and VP1 region to examine the molecular diversity in enterovirus B species. J Med Microbiol 2014; 63:1339-1355. [PMID: 25038138 DOI: 10.1099/jmm.0.074682-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human enteroviruses evolve quickly. The 5' untranslated region (UTR) is fundamentally important for efficient viral replication and for virulence; the VP1 region correlates well with antigenic typing by neutralization, and can be used for virus identification and evolutionary studies. In order to investigate the molecular diversity in EV-B species, the 5' UTR and VP1 regions were analysed for 208 clinical isolates from a single public-health laboratory (serving New South Wales, Australia), representing 28 EV-B types. Sequences were compared with the 5' UTR and VP1 regions of 98 strains available in GenBank, representing the same 28 types. The genetic relationships were analysed using two types of software (mega and BioNumerics). The sequence analyses of the 5' UTR and VP1 regions of 306 EV-B strains demonstrated that: (i) comparing the two regions gives strong evidence of epidemiological linkage of strains in some serotypes; (ii) the intraserotypic genetic variation within each gene reveals that they evolve distinctly largely due to their different functions; and (iii) mutation and possible recombination in the two regions play significant roles in the molecular diversity of EV-B. Understanding the tempo and pattern of molecular diversity and evolution is of great importance in the pathogenesis of EV-B enteroviruses, information which will assist in disease prevention and control.
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Affiliation(s)
- Fei Zhou
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Gwendolyn L Gilbert
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Matthew V N O'Sullivan
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
| | - Dominic E Dwyer
- Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, University of Sydney, Westmead, New South Wales, Australia
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High susceptibility for enterovirus infection and virus excretion features in Tunisian patients with primary immunodeficiencies. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2012; 19:1684-9. [PMID: 22914367 DOI: 10.1128/cvi.00293-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To estimate the susceptibility to enterovirus infection and the frequency of long-term poliovirus excreters in Tunisian patients with primary immunodeficiencies (PIDs), enteroviruses were assessed in stool specimens of 82 patients with humoral, combined, and other PIDs. Isolated viruses were typed and intratyped by standard molecular techniques, and the whole VP1 region of poliovirus isolates was sequenced. Polioviruses were detected in 6 patients; all isolates were vaccine related. Five patients rapidly stopped excretion; one excreted a poliovirus type 1 isolate for several months, and the isolate accumulated up to 14 mutations in the VP1 region. Nonpolio enteroviruses were identified in 6 patients; 4 of them kept excreting the same strain for more than 6 months. The rate of enterovirus infection was 13.4% of the PID patients and 20.7% of those with an IgG defect; it greatly exceeded the rates generally found in Tunisian supposed-immunocompetent individuals (4.1% during the study period; P = 0.001 and P < 0.0001, respectively). Interestingly, patients with combined immunodeficiencies were at a higher risk for enterovirus infection than those with an exclusively B cell defect. A major histocompatibility complex (MHC) class II antigen expression defect was found in 54% of enterovirus-positive patients and in the unique long-term poliovirus excreter. The study results also suggest that substitutive immunoglobulin therapy may help clearance of a poliovirus infection and that most PID patients have the ability to stop poliovirus excretion within a limited period. However, the high susceptibility of these patients to enterovirus infection reinforces the need for enhanced surveillance of these patients until the use of oral poliovirus vaccine (OPV) is stopped.
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van de Ven AAJM, Hoytema van Konijnenburg DP, Wensing AMJ, van Montfrans JM. The role of prolonged viral gastrointestinal infections in the development of immunodeficiency-related enteropathy. Clin Rev Allergy Immunol 2012; 42:79-91. [PMID: 22116710 DOI: 10.1007/s12016-011-8292-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Patients with primary immunodeficiencies are prone to develop enteropathy of unknown pathogenesis. We hypothesize that ineffective clearance of gastrointestinal pathogens, particularly viruses, in combination with defective immune regulation may cause inflammatory enteropathy in certain immunodeficient hosts. We reviewed publications related to prolonged enteric viral infection, immunodeficiency, and the subsequent development of inflammatory enteropathy. Prolonged infection with especially enteroviral infections was reported more often in immunocompromised hosts than in healthy individuals. Protracted enteric viral shedding was not always associated with the presence or duration of gastrointestinal symptoms. The development of immunodeficiency-associated enteropathy after prolonged viral infections was described in sporadic cases. Clinical consequences of viral gut infections in immunocompromised hosts comprise isolation issues and supportive care. Prospective studies in cohorts of immunodeficient patients are required to study the impact of prolonged enteric viral replication with respect to the pathogenesis of non-infectious enteropathy.
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Affiliation(s)
- Annick A J M van de Ven
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht/Wilhelmina Children's Hospital, Utrecht, the Netherlands
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dos Santos GPL, da Costa EV, Tavares FN, da Costa LJ, da Silva EE. Genetic diversity of Echovirus 30 involved in aseptic meningitis cases in Brazil (1998-2008). J Med Virol 2012; 83:2164-71. [PMID: 22012725 DOI: 10.1002/jmv.22235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Aseptic meningitis is one of the most common neurological disorders caused by enteroviruses. Among them, Echovirus 30 (E30) is described as the main etiological agent of many outbreaks and sporadic cases. This study investigated the genomic variability of E30 isolated from the cerebrospinal fluid (CSF) of aseptic meningitis cases that occurred from 1998 to 2008 in Brazil. Over a 10-year period (1998-2008), 302 non-polio enteroviruses were isolated, of which 177 were identified as E30 (58.6%). Phylogenetic analysis of the complete VP1 gene (876 nt) of 48 E30 isolates was performed and compared with additional Brazilian and foreign strains. E30 VP1 sequences segregated into three distinct major groups and seven subgroups, which were linked to the isolation year. In general, sequence divergence among E30 strains ranged from 0.2% to 13.8%. A common direct ancestor for this set of E30 strains was not defined. Brazilian isolates from Group I were related genetically to a 1997 USA isolate and both may have a common origin. Group III representatives showed close relationship to the 2007 Argentinean isolates. The present results complement existing data on the molecular characterization and genetic variability of E30 and may contribute to the understanding of the epidemiology of aseptic meningitis in the region.
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Fares W, Rezig D, Seghier M, Ben Yahia A, Touzi H, Triki H. Phylogenetic analysis of complete VP1 sequences of echoviruses 11 and 6: high genetic diversity and circulation of genotypes with a wide geographical and temporal range. J Med Microbiol 2011; 60:1017-1025. [DOI: 10.1099/jmm.0.028795-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Wasfi Fares
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunisia
| | - Dorra Rezig
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunisia
| | - Mohamed Seghier
- Laboratory of Enteroviruses, National Laboratory for Poliomyelitis, Institut Pasteur d’Algérie, Algeria
| | - Ahlem Ben Yahia
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunisia
| | - Henda Touzi
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunisia
| | - Henda Triki
- Laboratory of Clinical Virology, WHO Regional Reference Laboratory on Poliomyelitis and Measles, Institut Pasteur de Tunis, Tunisia
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9
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Rhinovirus genome variation during chronic upper and lower respiratory tract infections. PLoS One 2011; 6:e21163. [PMID: 21713005 PMCID: PMC3119694 DOI: 10.1371/journal.pone.0021163] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/21/2011] [Indexed: 02/02/2023] Open
Abstract
Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5′UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.
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Petitjean-Lecherbonnier J, Dina J, Nguyen E, Gouarin S, Lebigot E, Vabret A. [Molecular diagnosis of respiratory enterovirus infections: Use of PCR and molecular identification for a best approach of the main circulating strains during 2008]. PATHOLOGIE-BIOLOGIE 2011; 59:113-21. [PMID: 20828940 PMCID: PMC7126958 DOI: 10.1016/j.patbio.2010.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 07/29/2010] [Indexed: 11/26/2022]
Abstract
UNLABELLED The PCR assays are currently used in diagnosis of enterovirus (EV) meningitis. Nevertheless, the use of molecular diagnosis of EV should be investigated in respiratory tract infections (RTI). OBJECTIVES To perform enterovirus molecular diagnostic tools, PCR and genotyping, in nasal samples for diagnostic and epidemiologic purposes. METHODS During 2008, 3612 nasal specimen (NS) were studied by IFD and MRC5 culture. Next, we realised successively viral isolation on HuH7 culture (for NS negative by IFD assay) and a duplex PCR enterovirus-rhinovirus for the 816 HuH7 positive supernatants. Furthermore, 327 NS collected from neonates were systematically tested by a real-time RT-PCR. This assay was used in routine for EV diagnosis setting in cerebrospinal fluid. Enterovirus genotyping was then performed for the 68 positive supernatants. RESULTS Thirty-five NS (0.97%) were positive for EV by culture (MRC5). A combination of both PCR assays, PEVRV and PEV, allowed an additional identification of 41 EV, eight EV-RV and 12 RV, increasing the number of positive to 96 NS (2.6%). Among the neonates, 32 NS (11.3%) were positive for EV by PEV. Of the 98 NS tested by the two PCR assays (PEV and PEVRV), 27 were positive and we detected 10 EV, five EV-RV and 12 RV. From January to December 2008, the circulation of EV showed the usual peak in June-July when a small outbreak of aseptic meningitis occurred and an additional autumnal peak corresponding to respiratory tract infections. Five main serotypes were isolated: 19 EV68 (29.7%), 12 CB3 (18.7%), nine E3 (14,1%), six CA9 (9.4%) and six CB1 (9.4%); the 19 EV68 were isolated in October-November and 17/19 (89.5%) of positive patients were hospitalised for severe respiratory diseases. CONCLUSION The use of molecular screening techniques (PCR assays and genotyping) on nasal samples collected from patients with respiratory infections allowed a prospective, effective and precise identification of circulating strains.
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Affiliation(s)
- J Petitjean-Lecherbonnier
- Laboratoire de virologie humaine et moléculaire, CHU de Caen, avenue Georges-Clémenceau, 14033 Caen, France.
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Ke GM, Lin KH, Lu PL, Tung YC, Wang CF, Ke LY, Lee MS, Lin PC, Su HJ, Lin YY, Huang TP, Wang JR, Wang SY, Hsu LC, Chu PY. Molecular epidemiology of Echovirus 30 in Taiwan, 1988-2008. Virus Genes 2011; 42:178-88. [PMID: 21369829 DOI: 10.1007/s11262-010-0565-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 12/24/2010] [Indexed: 11/29/2022]
Abstract
To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).
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Affiliation(s)
- Guan-Ming Ke
- Department of Clinical Laboratory, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Mirand A, Bailly JL, Henquell C, Peigue-Lafeuille H. [Rapid enterovirus genotyping in cerebrospinal fluids: a two-year prospective study in a virology laboratory setting]. ACTA ACUST UNITED AC 2008; 56:471-81. [PMID: 18835107 DOI: 10.1016/j.patbio.2008.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 08/06/2008] [Indexed: 11/28/2022]
Abstract
UNLABELLED Enterovirus (EV - 68 serotypes) infections comprise a wide spectrum of clinical presentations including infections of the central nervous system. In severe clinical presentation or epidemics, the precise identification of the involved serotype is necessary. OBJECTIVES To perform enterovirus genotyping directly in cerebrospinal fluid (CSF) samples, and to assess its feasibility in a laboratory setting. METHODS Enterovirus genotyping was carried out directly with CSF specimens tested for the diagnostic procedure by amplifying the complete 1D gene encoding the VP1 protein of the HEV-B serotypes (the most frequent) - providing results in two days. Secondly, sequences 1A/1B encoding the VP4/VP2 capsid proteins, respectively, were analysed (results in five days). RESULTS Direct enterovirus genotyping allowed the identification of enterovirus involved in 77 out of 81 (95%) meningitis cases between January 2006 and December 2007. In combination with the indirect genotyping of enterovirus isolates, identification of the type was achieved in 94 out of 97 (96.9%) patients included in the study. The most frequent serotypes were echovirus 6 (E6) and 13 in 2006, coxsackievirus B2 and E30 in 2007. Four children presented an EV71 associated meningitis. CONCLUSION When prospectively applied in a laboratory setting, direct enterovirus genotyping in CSF samples allows the identification of the involved enterovirus in two to five days. This time frame is relevant for an optimal patient management, the rapid identification of a new enterovirus variant or in the context of an epidemic alert.
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Affiliation(s)
- A Mirand
- Laboratoire de virologie, centre de biologie, CHU de Clermont-Ferrand, 58, rue Montalembert, 63003 Clermont-Ferrand, France.
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Bosch A, Guix S, Sano D, Pintó RM. New tools for the study and direct surveillance of viral pathogens in water. Curr Opin Biotechnol 2008; 19:295-301. [PMID: 18508257 PMCID: PMC7126527 DOI: 10.1016/j.copbio.2008.04.006] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 04/14/2008] [Accepted: 04/17/2008] [Indexed: 12/05/2022]
Abstract
Half a century ago scientists attempted the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. However, most viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets in water. The inclusion of virus analysis in regulatory standards for viruses in water samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. However, new tools are nowadays available for the study and direct surveillance of viral pathogens in water that may contribute to fulfil these requirements.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Laboratory, Department of Microbiology, University of Barcelona, Spain.
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Mirand A, Henquell C, Archimbaud C, Chambon M, Charbonne F, Peigue-Lafeuille H, Bailly JL. Prospective identification of enteroviruses involved in meningitis in 2006 through direct genotyping in cerebrospinal fluid. J Clin Microbiol 2008; 46:87-96. [PMID: 17977989 PMCID: PMC2224282 DOI: 10.1128/jcm.01020-07] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 08/27/2007] [Accepted: 10/24/2007] [Indexed: 11/20/2022] Open
Abstract
Enterovirus infections were investigated with special emphasis on performing rapid molecular identification of enterovirus serotypes responsible for aseptic meningitis directly in cerebrospinal fluid (CSF). Enterovirus genotyping was carried out directly with specimens tested for the diagnostic procedure, using two seminested PCR assays designed to amplify the complete and partial gene sequences encoding the VP1 and VP4/VP2 capsid proteins, respectively. The method was used for identifying the enterovirus serotypes involved in meningitis in 45 patients admitted in 2005. Enterovirus genotyping was achieved in 98% of the patients studied, and we obtained evidence of 10 of the most frequent serotypes identified earlier by genotyping of virus isolates. The method was applied for the prospective investigation of 54 patients with meningitis admitted consecutively in 2006. The enterovirus serotypes involved were identified with the cerebrospinal fluid (CSF) of 52 patients (96%) and comprised 13 serotypes within the human enterovirus B species and 1 within the human enterovirus A species. The three most common serotypes were echovirus 13 (E13; 24%), E6 (23%), and coxsackievirus B5 (11.5%), a pattern different from that observed in 2005. Genotyping of virus isolates was also performed in 35 patients in 2006 (meningitis, n = 31; other diseases, n = 4). By comparison, direct genotyping in CSF yielded a more complete pattern of enterovirus serotypes, thereby allowing the detection of rare serotypes: three less common serotypes (CB2, E21, and E27) were not detected by indirect genotyping alone. The study shows the feasibility of prospective enterovirus genotyping within 1 week in a laboratory setting.
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MESH Headings
- Aged
- Capsid Proteins/genetics
- Cerebrospinal Fluid/virology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Enterovirus A, Human/classification
- Enterovirus A, Human/genetics
- Enterovirus A, Human/isolation & purification
- Enterovirus B, Human/classification
- Enterovirus B, Human/genetics
- Enterovirus B, Human/isolation & purification
- Enterovirus Infections/virology
- Female
- Genotype
- Humans
- Infant
- Male
- Meningitis, Viral/virology
- Molecular Sequence Data
- Polymerase Chain Reaction/methods
- Prospective Studies
- RNA, Viral/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Audrey Mirand
- Centre de Biologie-CHRU Clermont Ferrand, Laboratoire de Virologie, 58, Rue Montalembert, 63003 Clermont-Ferrand, France.
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Lévêque N, Norder H, Zreik Y, Cartet G, Falcon D, Rivat N, Chomel JJ, Hong SS, Lina B. Echovirus 6 strains derived from a clinical isolate show differences in haemagglutination ability and cell entry pathway. Virus Res 2007; 130:1-9. [PMID: 17566587 DOI: 10.1016/j.virusres.2007.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2006] [Revised: 05/02/2007] [Accepted: 05/04/2007] [Indexed: 11/25/2022]
Abstract
Two echovirus 6 (EV6) strains were isolated from a clinical sample after successive sub-cultures in PLC (human hepatocellular carcinoma) and HeLa (human cervical adenocarcinoma) cells. The first strain retained its haemagglutinating capacity (HAEV6) while the second became non-haemagglutinating (NHAEV6). Virus binding assay showed that HAEV6 was capable of binding to DAF-expressing cells but not NHAEV6 confirming the role of DAF in EV6 haemagglutination. The lack of competition between the two viral strains during coinfections suggested that each strain used a different cell entry pathway. We provide evidence showing that HAEV6 used preferentially the lipid raft-dependent caveolae pathway, whereas NHAEV6 followed the clathrin-mediated pathway. Comparison of the sequences of HAEV6 and NHAEV6 revealed five amino acid changes in the VP1, VP2 and VP3 capsid proteins distributed in domains which are known to be highly immunogenic or suggested to be involved in receptor binding, virion stability and pathogenicity.
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Affiliation(s)
- Nicolas Lévêque
- Centre National de Référence des Entérovirus, Laboratoire de Virologie, Centre de Biologie et de Pathologie Est, Institut de Microbiologie, Hospices Civils de Lyon, 69677 Bron, France.
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16
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Mirand A, Henquell C, Archimbaud C, Peigue-Lafeuille H, Bailly JL. Emergence of recent echovirus 30 lineages is marked by serial genetic recombination events. J Gen Virol 2007; 88:166-176. [PMID: 17170449 DOI: 10.1099/vir.0.82146-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In an earlier report, different variants of echovirus 30 (E-30), an enterovirus serotype, were identified during two outbreaks in 1997 and 2000. Here, the diversity of E-30 was investigated over a longer period (1991–2005) and the variations in four genomic segments were determined in 52 isolates involved in meningitis cases, to characterize the evolutionary processes underlying the emergence of lineages. Phylogenetic analysis of the VP1 sequences showed that five phylogenetic variants succeeded one another. When a partial 3CD segment was examined, the five variants split further into 10 lineages. Phylogenetic groupings observed with both the VP1 and 3CD sequences were clearly related to the calendar time of virus isolation. The rapid turnover of lineages during the study period was not associated with variations in amino acid residues in either the VP1 or the 3CD sequences, indicating major evolutionary contraints in E-30. The variation patterns were examined further along a subgenomic segment of 4878 nt in 13 virus isolates, representative of the 10 lineages. Breakpoints detected in the similarity profiles were investigated by bootscanning and maximum-likelihood phylogenetic analysis of virus genes. Evidence of several past recombination events was observed in the middle of the genome and predicted recombination crossover sites were mapped with precision. The contribution of recombination to the evolution of E-30 is substantial. It is associated tightly with the emergence of new genetic lineages and certain recombinants have undergone epidemic spread.
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Affiliation(s)
- Audrey Mirand
- CHU Clermont-Ferrand, Laboratoire de Virologie, Centre de Biologie, F-63003 Clermont-Ferrand, France
- Université d'Auvergne, Laboratoire de Virologie-EA3843, UFR Médecine, 28 place Henri-Dunant, F-63001 Clermont-Ferrand, France
| | - Cécile Henquell
- CHU Clermont-Ferrand, Laboratoire de Virologie, Centre de Biologie, F-63003 Clermont-Ferrand, France
| | - Christine Archimbaud
- CHU Clermont-Ferrand, Laboratoire de Virologie, Centre de Biologie, F-63003 Clermont-Ferrand, France
- Université d'Auvergne, Laboratoire de Virologie-EA3843, UFR Médecine, 28 place Henri-Dunant, F-63001 Clermont-Ferrand, France
| | - Hélène Peigue-Lafeuille
- CHU Clermont-Ferrand, Laboratoire de Virologie, Centre de Biologie, F-63003 Clermont-Ferrand, France
- Université d'Auvergne, Laboratoire de Virologie-EA3843, UFR Médecine, 28 place Henri-Dunant, F-63001 Clermont-Ferrand, France
| | - Jean-Luc Bailly
- Université d'Auvergne, Laboratoire de Virologie-EA3843, UFR Médecine, 28 place Henri-Dunant, F-63001 Clermont-Ferrand, France
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17
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Minosse C, Zaniratti MS, Calcaterra S, Carletti F, Muscillo M, Pisciotta M, Pillitteri L, Corpolongo A, Lauria FN, Narciso P, Anzidei G, Capobianchi MR. Application of a molecular panel to demonstrate enterotropic virus shedding by healthy and human immunodeficiency virus-infected patients. J Clin Microbiol 2005; 43:1979-81. [PMID: 15815037 PMCID: PMC1081398 DOI: 10.1128/jcm.43.4.1979-1981.2005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used a molecular panel, targeting seven enteric viruses, to explore the advantage of using molecular methods to establish the etiology of enteric diseases and to evaluate the prevalence of enteric viruses in asymptomatic human immunodeficiency virus-infected patients. This approach favors rapidity and sensitivity of laboratory diagnosis of viral enteric syndromes.
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Affiliation(s)
- Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases (INMI) L. Spallanzani, Via Portuense, 292-00149 Rome, Italy
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18
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Archimbaud C, Bailly JL, Chambon M, Tournilhac O, Travade P, Peigue-Lafeuille H. Molecular evidence of persistent echovirus 13 meningoencephalitis in a patient with relapsed lymphoma after an outbreak of meningitis in 2000. J Clin Microbiol 2004; 41:4605-10. [PMID: 14532190 PMCID: PMC254333 DOI: 10.1128/jcm.41.10.4605-4610.2003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enteroviral meningoencephalitis was diagnosed in a patient with an immunodeficiency syndrome acquired after treatment with rituximab for a relapsed primary B-cell lymphoma. A second meningoencephalitic episode was diagnosed 6 months later and was successfully treated with a combination of immunoglobulins and pleconaril. The infection was persistent since the enterovirus genome was detected in five sequential specimens of cerebrospinal fluid collected over 9 months. An echovirus 13 isolate was isolated in the first three samples. The viral sequence encoding the VP1 capsid protein of the three isolates was determined and was compared with that of four control viruses. The virus isolates recovered from the patient shared >99% nucleotide sequence similarity with one another. In a phylogenetic tree, they were directly related to a control virus obtained from a patient hospitalized in 2000 during an outbreak of enterovirus meningitis. The epidemiological origin of a chronic echovirus infection in a patient with immune deficiency suggests that the echovirus had been continuously circulating in the general population after the outbreak that had revealed its emergence.
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Affiliation(s)
- Christine Archimbaud
- Laboratoire de Virologie, Faculté de Médecine, 63000 Clermont-Ferrand 1, France.
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19
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Abstract
The development of type 1 diabetes mellitus (T1DM) has been linked to exposure to environmental triggers, with Enteroviruses (EV) historically considered the prime suspects. Early serological studies suggested a link between EV infections and the development of T1DM and, though controversial, have been bolstered by more recent studies using more sensitive techniques such as direct detection of the EV genome by RT-PCR in peripheral blood. In this review, we consider the weight of evidence that EV can be considered a candidate trigger of T1DM, using three major criteria: (1) is EV infection associated with clinical T1DM, (2) can EV trigger the development of autoimmunity and (3) what would explain the putative association?
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Affiliation(s)
- Ruben Varela-Calvino
- Department of Immunology, Guy's, King's and St Thomas' School of Medicine, London, United Kingdom
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20
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Takami T, Nakayama T, Kawashima H, Takei Y, Takekuma K, Hoshika A. Determination of enterovirus serotype inferred from sequence analysis of PCR products. J Clin Virol 2003; 26:355-9. [PMID: 12637085 DOI: 10.1016/s1386-6532(02)00103-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Enterovirus infections are common in neonates. Virus isolation is the only diagnostic method to confirm enterovirus serotype infections, however, is not always successful. OBJECTIVES A new approach for the diagnosis of enterovirus infections was performed, using the reference strain inferred from sequence analysis of PCR products. STUDY DESIGN Virus isolation, enterovirus RT-PCR and sequence analysis were performed from clinical samples or stored sera from two neonates with fever and rash. Neutralizing test (NT) antibodies against prototype reference virus were measured in paired sera. RESULTS Virus isolation was negative in both patients but the enterovirus genome was amplified in the acute phase sera obtained from the two patients. From the results of sequence analysis of 109 nucleotides located in the 5'-noncoding of the conserved region of enteroviruses, a high homology to echovirus types 25 and 30 was found. More than a 4-fold increase in NT antibodies against reference viruses was demonstrated in the acute and convalescent phase sera. They were confirmed as echovirus type 25 and 30 infection, respectively. CONCLUSIONS These virological examinations are practical and useful for clinical settings for a diagnosis of enterovirus infections because of an insufficient positive rate in virus isolation.
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Affiliation(s)
- Takeshi Takami
- Department of Pediatrics, Tokyo Medical University, 6-7-1, Nishi-Shinjuku, Shinjuku-ku, Tokyo, 160-0023, Japan.
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21
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Siafakas N, Markoulatos P, Vlachos C, Stanway G, Tzanakaki G, Kourea-Kremastinou J. Molecular sub-grouping of enterovirus reference and wild type strains into distinct genetic clusters using a simple RFLP assay. Mol Cell Probes 2003; 17:113-23. [PMID: 12788033 DOI: 10.1016/s0890-8508(03)00029-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
RFLP analysis and sequencing of RT-PCR amplicons in previous studies revealed the existence of intra-serotypic variability in the 5'-UTR of human enteroviruses, complicating the use of this method to serotype isolates. During the present study, the available sequences of many enterovirus reference and wild type strains were analysed in an attempt to discover restriction sites that would rapidly and reliably aid the classification of human enteroviruses into specific sub-groups on the basis of their 5'-UTR for diagnostic and/or epidemiological purposes. Despite intratypic genetic variability in the 5'-UTR, the results of the sequence analysis, as well as data from the RFLP analysis of 61 enterovirus reference strains from 60 different serotypes and 123 clinical isolates showed that one restriction endonuclease, HpaII, may contribute to a reliable sub-classification of CAVs and the rest of enteroviruses, on the basis of 5'-UTR, into five genetic groups, which could be particularly useful in clinical and epidemiological studies. Although more sequence data from enterovirus reference and wild type strains may be required for the elaboration of a precise molecular identification system, the more possible genotypic classification into distinct clusters, as shown with the restriction enzyme HpaII, and the determination of the biological significance of this grouping (pathogenesis, epidemiology) might constitute an alternative means of enterovirus identification against conventional classification into distinct serotypes.
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Affiliation(s)
- Nikolaos Siafakas
- Virology Laboratory, Hellenic Pasteur Institute, 127, Vasilissis Sofias Ave, Athens 115 21, Greece
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Bailly JL, Brosson D, Archimbaud C, Chambon M, Henquell C, Peigue-Lafeuille H. Genetic diversity of echovirus 30 during a meningitis outbreak, demonstrated by direct molecular typing from cerebrospinal fluid. J Med Virol 2002; 68:558-67. [PMID: 12376964 DOI: 10.1002/jmv.10235] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Echovirus 30 is one of the enterovirus serotypes isolated most frequently in meningitis cases. The genetic diversity of echovirus 30 was investigated in patients hospitalised during an outbreak in 2000 in Clermont-Ferrand, France. A nested reverse transcription-PCR (RT-PCR) assay was developed for qualitative analysis of the echovirus 30 VP1 encoding sequence directly from cerebrospinal fluid. The viral sequences obtained for 22 patients were compared with those of virus isolates obtained from nine patients with echovirus 30 meningitis admitted to hospital in 1996-1997 and with echovirus 30 sequences from international databases. In 2000, meningitis cases were caused by two virus variants (C3 and C4) distinct genetically from the other two variants (C1 and C2) identified during the period 1996-1997. A detailed phylogenetic analysis established that the C1, C2, and C3 variants had close relatives among viruses previously identified in other geographical areas. The C4 variant had not been described earlier. The genomic differences observed between the four echovirus 30 variants arose at synonymous sites indicating that the viruses shared similar antigenic sites in the VP1 encoding sequence. Overall, these observations suggest wide circulation of different echovirus 30 variants and periodic importation of new viruses. The apparent displacement observed between virus variants did not result from a selective advantage caused by antigenic variation.
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Affiliation(s)
- Jean-Luc Bailly
- UFR Médecine, Laboratoire de Virologie-EA2148, Clermont-Ferrand, France.
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23
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Bailly JL, Béguet A, Chambon M, Henquell C, Peigue-Lafeuille H. Nosocomial transmission of echovirus 30: molecular evidence by phylogenetic analysis of the VP1 encoding sequence. J Clin Microbiol 2000; 38:2889-92. [PMID: 10921945 PMCID: PMC87138 DOI: 10.1128/jcm.38.8.2889-2892.2000] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated six cases of enterovirus infection in a neonatal unit. The index patient, a 5-day-old boy, was admitted with aseptic meningitis due to echovirus 30 (E30). Secondary infections with E30 occurred in five babies. Comparison of the complete VP1 sequences showed that the isolates recovered from the index patient and his mother were closely related to those recovered from the five babies with secondary infections, demonstrating a nosocomial transmission of the virus. In the phylogenetic tree reconstructed from the VP1 sequences, the isolates formed a monophyletic cluster related to an E30 strain collected in June 1997 during an outbreak of aseptic meningitis.
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Affiliation(s)
- J L Bailly
- UFR Médecine, Laboratoire de Virologie, F-63002, Clermont-Ferrand Cedex 1, France.
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