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Sanjay RE, Josmi J, Sasidharanpillai S, Shahin S, Michael CJ, Sabeena S, Aswathyraj S, Kavitha K, Shilpa C, Prasada SV, Anup J, Arunkumar G. Molecular epidemiology of enteroviruses associated with hand, foot, and mouth disease in South India from 2015 to 2017. Arch Virol 2022; 167:2229-2238. [PMID: 35970888 PMCID: PMC9377658 DOI: 10.1007/s00705-022-05561-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022]
Abstract
Hand, foot, and mouth disease (HFMD) is a common childhood infection caused by human enteroviruses and is clinically characterised by fever with vesicular rash on the hands, feet, and mouth. While enterovirus A71 (EV-A71) and coxsackievirus A16 (CVA16) were the major etiological agents of HFMD in India earlier, the data on recently circulating enteroviruses associated with HFMD are sparse. Here, we describe the molecular epidemiology of enteroviruses associated with HFMD in South India from 2015 to 2017. We used archived enterovirus real-time reverse transcription (RT) PCR-positive vesicle swab and/or throat swab specimens from clinically suspected HFMD cases collected from four secondary-care hospitals in South India between July 2015 and December 2017. PCR amplification and sequencing were done based on the 5’VP1, 3’VP1, VP2, or 5´NCR regions to identify enterovirus types. Genetic diversity among enteroviruses was inferred by phylogenetic analysis. Of the 107 enterovirus RNA real-time RT-PCR-positive HFMD cases, 69 (64%) were typed as CVA6, 16 (15%) were CVA16, and one (1%) was CVA10, whereas in 21 (20%) cases, the virus was not typeable by any of the methods used in the study. The majority of HFMD cases (89, 83%) were in children less than five years old, while 11 (10.3%) were in adults. 5’VP1 yielded the maximum number of enteroviruses genotyped, and phylogenetic analysis showed that the CVA6 strains belonged to subclade D3, while the subclades of CVA16 and CVA10 were B1c and D, respectively. The predominant etiological agent of HFMD in South India during 2015-2017 was CVA6, followed by CVA16 and CVA10.
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Affiliation(s)
- Ramachandran Erathodi Sanjay
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - Joseph Josmi
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - Sarita Sasidharanpillai
- Department of Dermatology and Venereology, Government Medical College, Kozhikode, Kerala, 673008, India
| | - Sheik Shahin
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - C J Michael
- Department of ENT, Government General Hospital, Kozhikode, Kerala, 673032, India
| | - Sasidharanpillai Sabeena
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India.,, Allure Residency, Near The British School, Jhamsikhel Lalitpur, Kathmandu, 44600, Nepal
| | - S Aswathyraj
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India.,Institute of Advanced Virology (IAV) (Autonomous Institute under Science and Technology Dept Govt of Kerala), Bio360 Life Sciences Park, Thonnakkal, Trivandrum, Kerala, 695317, India
| | - Karunakaran Kavitha
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - Cheerngod Shilpa
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - S Varamballi Prasada
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - Jayaram Anup
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India
| | - Govindakarnavar Arunkumar
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, 576104, India. .,, 2-49, Vaikathu, Marotithota Road, Mooduathrady, Athrady Post, Udupi, Karnataka, 576107, India.
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Sanjay RE, Sabeena S, Robin S, Shaji JT, Jayakrishnan MP, Suresh EKK, Michael CJ, Aswathyraj S, Josmi J, Shahin S, Anup J, Arunkumar G. Genetic analysis of Enterovirus D68 associated with pneumonia in children from South India. J Med Microbiol 2021; 70. [PMID: 33999799 DOI: 10.1099/jmm.0.001356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
EV-D68 is an emerging enterovirus infection associated with severe acute respiratory illness (SARI), acute flaccid myelitis (AFM) and acute flaccid paralysis (AFP). While EV-D68 outbreaks and sporadic cases are reported globally, a single case has been reported from India. The present study aims to investigate the molecular epidemiology and clinical characteristics of EV-D68-associated SARI cases from South India. We screened influenza-negative archived throat swab specimens from Influenza-Like Illness (ILI) and SARI cases (n=959; 2016 to 2018 period) for enteroviruses by pan-enterovirus real-time RT-PCR. Thirteen samples positive for enteroviruses were typed by PCR and sequencing based on VPI, VP2 and/or 5'NCR regions. One EV-D68 RNA sample was subjected to next-generation sequencing for whole genome characterisation. Among 13 enterovirus cases, four were ECHO-11, three EV-D68, two CV-A16 and one each EV-71, CV-B1, CV-B2 and CV-A9. All three cases of EV-D68 infection were reported in children below 2 years of age from Kerala state of South India during June and July 2017. The patients developed pneumonia without any neurological complications. Sequencing based on VPI and 5'NCR regions showed that EV-D68 strains belong to the novel subclade B3. The EV-D68 complete genome identified with two unique amino acid substitutions in VP1 (T-246-I) and 3D (K-344-R) regions. This study reiterates the EV-D68 novel subclade B3 circulation in India and indicates the urgent need for structured EV-D68 surveillance in the country to describe the epidemiology.
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Affiliation(s)
- Ramachandran Erathodi Sanjay
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sasidharanpillai Sabeena
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sudandiradas Robin
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - John T Shaji
- Department of Paediatrics & Neonatology, Baby Memorial Hospital, Kozhikode, Kerala, India
| | - M P Jayakrishnan
- Department of Paediatrics, Government Medical College, Kozhikode, Kerala, India
| | - E K Kumar Suresh
- Department of Paediatrics, Aster MIMS Hospital, Kozhikode, Kerala, India
| | - C J Michael
- Department of ENT, Government General Hospital, Kozhikode, Kerala, India
| | - S Aswathyraj
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Joseph Josmi
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Sheik Shahin
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Jayaram Anup
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
| | - Govindakarnavar Arunkumar
- Present address: Consultant at World Health Organisation- country office for Nepal, Nepal, India.,Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, Karnataka, India
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Zhang H, Liu D, Zhang Z, Hewitt J, Li X, Hou P, Wang D, Wu Q. Surveillance of human norovirus in oysters collected from production area in Shandong Province, China during 2017–2018. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107649] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Howson-Wells HC, Winckles S, Aliker C, Tarr AW, Irving WL, Clark G, McClure CP. Enterovirus subtyping in a routine UK laboratory setting between 2013 and 2017. J Clin Virol 2020; 132:104646. [PMID: 32979770 DOI: 10.1016/j.jcv.2020.104646] [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: 06/12/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Human enteroviruses (EV) are the leading cause of viral meningitis. EV genotyping is predominantly performed through amplification and sequencing of viral capsid protein-1 (VP1), frequently by national reference laboratories (NRLs). OBJECTIVE To determine the frequency of genotyping failure in our NRL-submitted samples and apply a superior alternative assay to resolve untyped specimens. STUDY DESIGN We initially audited genotyping data received for a cohort of patients in the East Midlands, UK by the NRL between 2013 and 2017, then identified an alternative RT-PCR typing method by literature review and evaluated primers from both assays in silico against comprehensive publicly available genomic data. The alternative assay was further optimised and applied to archived nucleic acids from previously untypable samples. RESULTS Genotyping data showed a significant increase in untypable EV strains through the study period (p = 0.0073). Typing failure appeared unrelated to sample type or viral load. In silico analyses of 2,201 EV genomes showed high levels of mismatch between reference assay primers and clinically significant EV-species, in contrast to a selected alternative semi-nested RT-PCR VP1-typing assay. This alternative assay, with minor modifications, successfully genotyped 23 of 24 previously untypable yet viable archived specimens (EV-A, n = 4; EV-B, n = 19). Phylogenetic analyses identified no predominant strain within NRL untypable isolates, suggesting sub-optimal reference assay sensitivity across EV species, in agreement with in silico analyses. CONCLUSION This modified highly sensitive RT-PCR assay presents a suitable alternative to the current English national reference VP1-typing assay and is recommended in other settings experiencing typing failure.
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Affiliation(s)
- Hannah C Howson-Wells
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
| | - Stephen Winckles
- Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Camille Aliker
- Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Alexander W Tarr
- Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, United Kingdom
| | - William L Irving
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom; Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, United Kingdom
| | - Gemma Clark
- Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, NG7 2UH, United Kingdom
| | - C Patrick McClure
- Life Sciences, University of Nottingham, Nottingham, NG7 2UH, United Kingdom; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, United Kingdom.
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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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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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7
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Oshiki M, Miura T, Kazama S, Segawa T, Ishii S, Hatamoto M, Yamaguchi T, Kubota K, Iguchi A, Tagawa T, Okubo T, Uemura S, Harada H, Kobayashi N, Araki N, Sano D. Microfluidic PCR Amplification and MiSeq Amplicon Sequencing Techniques for High-Throughput Detection and Genotyping of Human Pathogenic RNA Viruses in Human Feces, Sewage, and Oysters. Front Microbiol 2018; 9:830. [PMID: 29755444 PMCID: PMC5934477 DOI: 10.3389/fmicb.2018.00830] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/11/2018] [Indexed: 01/31/2023] Open
Abstract
Detection and genotyping of pathogenic RNA viruses in human and environmental samples are useful for monitoring the circulation and prevalence of these pathogens, whereas a conventional PCR assay followed by Sanger sequencing is time-consuming and laborious. The present study aimed to develop a high-throughput detection-and-genotyping tool for 11 human RNA viruses [Aichi virus; astrovirus; enterovirus; norovirus genogroup I (GI), GII, and GIV; hepatitis A virus; hepatitis E virus; rotavirus; sapovirus; and human parechovirus] using a microfluidic device and next-generation sequencer. Microfluidic nested PCR was carried out on a 48.48 Access Array chip, and the amplicons were recovered and used for MiSeq sequencing (Illumina, Tokyo, Japan); genotyping was conducted by homology searching and phylogenetic analysis of the obtained sequence reads. The detection limit of the 11 tested viruses ranged from 100 to 103 copies/μL in cDNA sample, corresponding to 101–104 copies/mL-sewage, 105–108 copies/g-human feces, and 102–105 copies/g-digestive tissues of oyster. The developed assay was successfully applied for simultaneous detection and genotyping of RNA viruses to samples of human feces, sewage, and artificially contaminated oysters. Microfluidic nested PCR followed by MiSeq sequencing enables efficient tracking of the fate of multiple RNA viruses in various environments, which is essential for a better understanding of the circulation of human pathogenic RNA viruses in the human population.
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Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Shinobu Kazama
- Center for Simulation Sciences and Informational Biology, Ochanomizu University, Bunkyô, Japan
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Kofu, Japan
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, Minneapolis, MN, United States
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
| | - Akinori Iguchi
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Tadashi Tagawa
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Tsutomu Okubo
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Shigeki Uemura
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
| | - Naohiro Kobayashi
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Japan
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Harvala H, Broberg E, Benschop K, Berginc N, Ladhani S, Susi P, Christiansen C, McKenna J, Allen D, Makiello P, McAllister G, Carmen M, Zakikhany K, Dyrdak R, Nielsen X, Madsen T, Paul J, Moore C, von Eije K, Piralla A, Carlier M, Vanoverschelde L, Poelman R, Anton A, López-Labrador FX, Pellegrinelli L, Keeren K, Maier M, Cassidy H, Derdas S, Savolainen-Kopra C, Diedrich S, Nordbø S, Buesa J, Bailly JL, Baldanti F, MacAdam A, Mirand A, Dudman S, Schuffenecker I, Kadambari S, Neyts J, Griffiths MJ, Richter J, Margaretto C, Govind S, Morley U, Adams O, Krokstad S, Dean J, Pons-Salort M, Prochazka B, Cabrerizo M, Majumdar M, Nebbia G, Wiewel M, Cottrell S, Coyle P, Martin J, Moore C, Midgley S, Horby P, Wolthers K, Simmonds P, Niesters H, Fischer TK. Recommendations for enterovirus diagnostics and characterisation within and beyond Europe. J Clin Virol 2018; 101:11-17. [DOI: 10.1016/j.jcv.2018.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 12/18/2022]
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Bouin A, Nguyen Y, Wehbe M, Renois F, Fornes P, Bani-Sadr F, Metz D, Andreoletti L. Major Persistent 5' Terminally Deleted Coxsackievirus B3 Populations in Human Endomyocardial Tissues. Emerg Infect Dis 2018; 22:1488-90. [PMID: 27434549 PMCID: PMC4982168 DOI: 10.3201/eid2208.160186] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We performed deep sequencing analysis of the enterovirus 5′ noncoding region in cardiac biopsies from a patient with dilated cardiomyopathy. Results displayed a mix of deleted and full-length coxsackievirus B3, characterized by a low viral RNA load (8.102 copies/μg of nucleic acids) and a low viral RNA positive-sense to RNA negative-sense ratio of 4.8.
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Midgley SE, Nielsen AG, Trebbien R, Poulsen MW, Andersen PH, Fischer TK. Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016. ACTA ACUST UNITED AC 2017; 22:30565. [PMID: 28681718 PMCID: PMC6518347 DOI: 10.2807/1560-7917.es.2017.22.26.30565] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/29/2017] [Indexed: 12/14/2022]
Abstract
In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and characterisation of these new emerging EV variants is challenging as standard EV assays may not be adequate, necessitating the use of whole genome analysis.
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Affiliation(s)
- Sofie E Midgley
- Section for Virus Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Astrid G Nielsen
- Section for Virus Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Ramona Trebbien
- Section for Virus Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mille W Poulsen
- Section for Virus Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Peter H Andersen
- Infectious Disease Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Section for Virus Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark.,Center for Global Health, Department of Infectious Diseases, University of Southern Denmark, Odense, Denmark
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11
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Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life. PLoS One 2017; 12:e0185569. [PMID: 28968427 PMCID: PMC5624699 DOI: 10.1371/journal.pone.0185569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/14/2017] [Indexed: 12/13/2022] Open
Abstract
Few studies have analyzed the gut microbiota of child in unindustrialized countries, but none during the first month of life. Stool samples were collected from healthy newborns in hospitals of Gabon (n = 6) and Republic of the Congo (n = 9) at different time points during the first month of life: meconium, day 2 (D02), day 7 (D07) and day 28 (D28). In addition, one fecal sample was collected from each mother after delivery. Metagenomic sequencing was performed to determine the bacterial communities, and multiplex real-time PCR was used to detect the presence of seven enteric viruses (rotavirus a, adenovirus, norovirus I and II, sapovirus, astrovirus, enterovirus) in these samples. Bacterial diversity was high in the first days of life, and was dominated by the genus Prevotella. Then, it rapidly decreased and remained low up to D28 when the gut flora was composed almost exclusively of strictly anaerobic bacteria. Each infant’s fecal bacterial microbiota composition was significantly closer to that of their mother than to that of any other woman in the mothers’ group, suggesting an intrauterine, placental or amniotic fluid origin of such bacteria. Moreover, bacterial communities differed according to the delivery mode. Overall, the bacterial microbiota communities displayed a similar diversification and expansion in newborns within and between countries during the first four weeks of life. Moreover, six of the fifteen infants of this study harbored enteric viruses (rotavirus, enterovirus and adenovirus) in fecal samples, but never in the meconium. A maternal source for the viruses detected at D02 and D07 can be excluded because none of them was found also in the child’s mother. These findings improve our knowledge on the gut bacterial and viral communities of infants from two Sub-Saharan countries during their first month of life.
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12
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Barnadas C, Midgley SE, Skov MN, Jensen L, Poulsen MW, Fischer TK. An enhanced Enterovirus surveillance system allows identification and characterization of rare and emerging respiratory enteroviruses in Denmark, 2015-16. J Clin Virol 2017; 93:40-44. [PMID: 28618288 DOI: 10.1016/j.jcv.2017.05.017] [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] [Received: 02/13/2017] [Revised: 05/09/2017] [Accepted: 05/19/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND The potential for outbreaks due to Enteroviruses (EV) with respiratory tropism, such as EV-D68, and the detection of new and rare EV species C is a concern. These EVs are typically not detected in stool specimens and may therefore be missed by standard EV surveillance systems. Following the North American outbreak of EV-D68 in 2014, Denmark piloted an enhanced EV surveillance system that included the screening of respiratory samples. OBJECTIVES We aim to report clinical manifestations and phylogenetic descriptions from the rare and emerging EVs identified thereby demonstrating the usefulness of this system. STUDY DESIGN Positive EV samples received through the enhanced non-polio EV pilot surveillance system were characterized by sequencing fragments of VP1, VP2 and VP4 capsid proteins and clinical observations were compiled. RESULTS Between January 2015 and October 2016, six cases of rare genotypes EV-C104, C105 and C109 and nine cases of EV-D68 were identified. Patients presented with mild to moderately severe respiratory illness; no paralysis occurred. Distinct EV-C104, EV-C109 and EV-D68 sequences argue against a common source of introduction of these genotypes in the Danish population. CONCLUSIONS The enhanced EV surveillance system enabled detection and characterization of rare EVs in Denmark. In order to improve our knowledge of and our preparedness against emerging EVs, public health laboratories should consider expanding their EV surveillance system to include respiratory specimens.
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Affiliation(s)
- Céline Barnadas
- European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden; Statens Serum Institut, Copenhagen, Denmark.
| | | | | | | | | | - Thea Kølsen Fischer
- Statens Serum Institut, Copenhagen, Denmark; University of Southern Denmark, Denmark.
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13
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Condell O, Midgley S, Christiansen CB, Chen M, Chen Nielsen X, Ellermann-Eriksen S, Mølvadgaard M, Schønning K, Vermedal Hoegh S, Andersen PH, Voldstedlund M, Fischer TK. Evaluation of the enterovirus laboratory surveillance system in Denmark, 2010 to 2013. ACTA ACUST UNITED AC 2017; 21:30218. [PMID: 27173593 DOI: 10.2807/1560-7917.es.2016.21.18.30218] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/20/2016] [Indexed: 11/20/2022]
Abstract
The primary aim of the Danish enterovirus (EV) surveillance system is to document absence of poliovirus infection. The conflict in Syria has left many children unvaccinated and movement from areas with polio cases to Europe calls for increased awareness to detect and respond to virus-transmission in a timely manner. We evaluate the national EV laboratory surveillance, to generate recommendations for system strengthening. The system was analysed for completeness of viral typing analysis and clinical information and timeliness of specimen collection, laboratory results and reporting of clinical information. Of 23,720 specimens screened, 2,202 (9.3%) were EV-positive. Submission of cerebrospinal fluid and faecal specimens from primary diagnostic laboratories was 79.5% complete (845/1,063), and varied by laboratory and patient age. EV genotypes were determined in 68.5% (979/1,430) of laboratory-confirmed cases, clinical information was available for 63.1% (903/1,430). Primary diagnostic results were available after a median of 1.4 days, typing results after 17 days, detailed clinical information after 33 days. The large number of samples typed demonstrated continued monitoring of EV-circulation in Denmark. The system could be strengthened by increasing the collection of supplementary faecal specimens, improving communication with primary diagnostic laboratories, adapting the laboratory typing methodology and collecting clinical information with electronic forms.
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Affiliation(s)
- Orla Condell
- Department of Microbiological Diagnostics and Virology, Statens Serum Insitut, Copenhagen S, Denmark
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14
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Abstract
Enteroviruses (EVs) belong to the family Picornaviridae and are responsible for mild to severe diseases in mammals including humans and non-human primates (NHP). Simian EVs were first discovered in the 1950s in the Old World Monkeys and recently in wild chimpanzee, gorilla and mandrill in Cameroon. In the present study, we screened by PCR EVs in 600 fecal samples of wild apes and monkeys that were collected at four sites in Gabon. A total of 32 samples were positive for EVs (25 from mandrills, 7 from chimpanzees, none from gorillas). The phylogenetic analysis of VP1 and VP2 genes showed that EVs identified in chimpanzees were members of two human EV species, EV-A and EV-B, and those identified in mandrills were members of the human species EV-B and the simian species EV-J. The identification of two novel enterovirus types, EV-B112 in a chimpanzee and EV-B113 in a mandrill, suggests these NHPs could be potential sources of new EV types. The identification of EV-B107 and EV90 that were previously found in humans indicates cross-species transfers. Also the identification of chimpanzee-derived EV110 in a mandrill demonstrated a wide host range of this EV. Further research of EVs in NHPs would help understanding emergence of new types or variants, and evaluating the real risk of cross-species transmission for humans as well for NHPs populations.
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15
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Opanda SM, Wamunyokoli F, Khamadi S, Coldren R, Bulimo WD. Genotyping of enteroviruses isolated in Kenya from pediatric patients using partial VP1 region. SPRINGERPLUS 2016; 5:158. [PMID: 27026855 PMCID: PMC4766141 DOI: 10.1186/s40064-016-1834-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/15/2016] [Indexed: 01/12/2023]
Abstract
Enteroviruses (EV) are responsible for a wide range of clinical diseases in humans. Though studied broadly in several regions of the world, the genetic diversity of human enteroviruses (HEV) circulating in the sub-Saharan Africa remains under-documented. In the current study, we molecularly typed 61 HEV strains isolated in Kenya between 2008 and 2011 targeting the 3′-end of the VP1 gene. Viral RNA was extracted from the archived isolates and part of the VP1 gene amplified by RT-PCR, followed by sequence analysis. Twenty-two different EV types were detected. Majority (72.0 %) of these belonged to Enterovirus B species followed by Enterovirus D (21.3 %) and Enterovirus A (6.5 %). The most frequently detected types were Enterovirus-D68 (EV-D68), followed by Coxsackievirus B2 (CV-B2), CV-B1, CV-B4 and CV-B3. Phylogenetic analyses of these viruses revealed that Kenyan CV-B1 isolates were segregated among sequences of global CV-B1 strains. Conversely, the Kenyan CV-B2, CV-B3, CV-B4 and EV-D68 strains generally grouped together with those detected from other countries. Notably, the Kenyan EV-D68 strains largely clustered with sequences of global strains obtained between 2008 and 2010 than those circulating in recent years. Overall, our results indicate that HEV strains belonging to Enterovirus D and Enterovirus B species pre-dominantly circulated and played a significant role in pediatric respiratory infection in Kenya, during the study period. The Kenyan CV-B1 strains were genetically divergent from those circulating in other countries. Phylogenetic clustering of Kenyan EV-D68 strains with sequences of global strains circulating between 2008 and 2010 than those obtained in recent years suggests a high genomic variability associated with the surface protein encoding VP1 gene in these enteroviruses.
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Affiliation(s)
- Silvanos M Opanda
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya, P.O. Box 606-00621, Nairobi, Kenya ; College of Health Sciences (COHES), Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Fred Wamunyokoli
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Samoel Khamadi
- The Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Rodney Coldren
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya, P.O. Box 606-00621, Nairobi, Kenya
| | - Wallace D Bulimo
- Department of Emerging Infectious Diseases (DEID), United States Army Medical Research Directorate-Kenya, P.O. Box 606-00621, Nairobi, Kenya ; Department of Biochemistry, School of Medicine, University of Nairobi, Nairobi, Kenya
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16
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Lin CH, Wang YB, Chen SH, Hsiung CA, Lin CY. Precise genotyping and recombination detection of Enterovirus. BMC Genomics 2015; 16 Suppl 12:S8. [PMID: 26678286 PMCID: PMC4682392 DOI: 10.1186/1471-2164-16-s12-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Enteroviruses (EV) with different genotypes cause diverse infectious diseases in humans and mammals. A correct EV typing result is crucial for effective medical treatment and disease control; however, the emergence of novel viral strains has impaired the performance of available diagnostic tools. Here, we present a web-based tool, named EVIDENCE (EnteroVirus In DEep conception, http://symbiont.iis.sinica.edu.tw/evidence), for EV genotyping and recombination detection. We introduce the idea of using mixed-ranking scores to evaluate the fitness of prototypes based on relatedness and on the genome regions of interest. Using phylogenetic methods, the most possible genotype is determined based on the closest neighbor among the selected references. To detect possible recombination events, EVIDENCE calculates the sequence distance and phylogenetic relationship among sequences of all sliding windows scanning over the whole genome. Detected recombination events are plotted in an interactive figure for viewing of fine details. In addition, all EV sequences available in GenBank were collected and revised using the latest classification and nomenclature of EV in EVIDENCE. These sequences are built into the database and are retrieved in an indexed catalog, or can be searched for by keywords or by sequence similarity. EVIDENCE is the first web-based tool containing pipelines for genotyping and recombination detection, with updated, built-in, and complete reference sequences to improve sensitivity and specificity. The use of EVIDENCE can accelerate genotype identification, aiding clinical diagnosis and enhancing our understanding of EV evolution.
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Vollbach S, Müller A, Drexler JF, Simon A, Drosten C, Eis-Hübinger AM, Panning M. Prevalence, type and concentration of human enterovirus and parechovirus in cerebrospinal fluid samples of pediatric patients over a 10-year period: a retrospective study. Virol J 2015; 12:199. [PMID: 26607060 PMCID: PMC4660665 DOI: 10.1186/s12985-015-0427-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/16/2015] [Indexed: 11/14/2022] Open
Abstract
Background Human enterovirus (EV) and parechovirus (HPeV) are significant causes of encephalitis and meningitis in children. The aim of this study was to determine the prevalence, type and viral RNA concentration of EV and HPeV in cerebrospinal fluid (CSF) samples in an unselected cohort of patients <18 years admitted to Bonn university hospital from 1998 to 2008. Methods A total of 327 CSF samples from 327 patients were retrospectively tested by real-time reverse-transcriptase PCR (RT-PCR) for EV and HPeV, and by real-time PCR for cytomegalovirus (CMV), herpes simplex virus 1/2 (HSV), and varizella zoster-virus (VZV). Samples had been submitted for routine virological work-up due to suspected meningitis or encephalitis and had been stored at −20 °C hereafter. Positive samples for EV and HPeV were sequenced within the gene encoding the VP1 region (EV), the VP2 and the VP3/VP1 junction region (HPeV). Results The overall prevalence was 4.3 % (14/327) for EV, 0.6 % (2/327) for HPeV, and 0.3 % (1/327) for HSV and VZV, respectively. CMV was not detected in this cohort. In children less than 3 months of age the prevalence was 7.7 % (2/26) for EV and 7.7 % (2/26) for HPeV, respectively. Frequency of EV detection ranged from 0 to 12 % per year and highest rates were observed from June to September. All typed EV belonged to species B. Both HPeV infections were detected in the fall of 2008 and were typed as HPeV genotype 3. Viral RNA concentrations were highest in patients with HPeV infection, followed by echovirus 30 and other EV. In total, 86 % (12/14) of EV infections presented as aseptic meningitis, whereas both HPeV infections presented as severe sepsis-like illness. Conclusions EV and HPeV were equally prevalent in children <3 months of age. Beyond the detection of EV and HPeV, the determination of viral RNA concentration and typing of EV and HPeV might prove beneficial for patient management and public health.
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Affiliation(s)
- Silke Vollbach
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany.
| | - Andreas Müller
- Department of Paediatrics, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany.
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany.
| | - Arne Simon
- Department of Paediatrics, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany. .,Present address: Paediatric Oncology and Haematology, University of the Saarland, Homburg, Germany.
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany.
| | - Anna Maria Eis-Hübinger
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany.
| | - Marcus Panning
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud Str. 25, 53105, Bonn, Germany. .,Institute of Virology, Medical Center - University of Freiburg, Hermann-Herder Str. 11, 79104, Freiburg, Germany.
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18
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Abstract
Hepatitis A virus (HAV) is an ancient and ubiquitous human pathogen recovered previously only from primates. The sole species of the genus Hepatovirus, existing in both enveloped and nonenveloped forms, and with a capsid structure intermediate between that of insect viruses and mammalian picornaviruses, HAV is enigmatic in its origins. We conducted a targeted search for hepatoviruses in 15,987 specimens collected from 209 small mammal species globally and discovered highly diversified viruses in bats, rodents, hedgehogs, and shrews, which by pairwise sequence distance comprise 13 novel Hepatovirus species. Near-complete genomes from nine of these species show conservation of unique hepatovirus features, including predicted internal ribosome entry site structure, a truncated VP4 capsid protein lacking N-terminal myristoylation, a carboxyl-terminal pX extension of VP1, VP2 late domains involved in membrane envelopment, and a cis-acting replication element within the 3D(pol) sequence. Antibodies in some bat sera immunoprecipitated and neutralized human HAV, suggesting conservation of critical antigenic determinants. Limited phylogenetic cosegregation among hepatoviruses and their hosts and recombination patterns are indicative of major hepatovirus host shifts in the past. Ancestral state reconstructions suggest a Hepatovirus origin in small insectivorous mammals and a rodent origin of human HAV. Patterns of infection in small mammals mimicked those of human HAV in hepatotropism, fecal shedding, acute nature, and extinction of the virus in a closed host population. The evolutionary conservation of hepatovirus structure and pathogenesis provide novel insight into the origins of HAV and highlight the utility of analyzing animal reservoirs for risk assessment of emerging viruses.
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Midgley SE, Christiansen CB, Poulsen MW, Hansen CH, Fischer TK. Emergence of enterovirus D68 in Denmark, June 2014 to February 2015. ACTA ACUST UNITED AC 2015; 20. [PMID: 25955773 DOI: 10.2807/1560-7917.es2015.20.17.21105] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
From June 2014 through February 2015, respiratory samples from 130 Danish patients were screened for enterovirus D68 (EV-D68). Fourteen EV-D68 cases were detected, of which 12 presented with respiratory symptoms, and eight had known underlying disease. The median age of EV-D68 cases was three years (interquartile range: 0–30 years). Acute flaccid paralysis (AFP) was not detected although Danish EV-D68 strains showed > 98% nt identity with EV-D68-strains from AFP cases from the United States and France.
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Affiliation(s)
- S E Midgley
- Section for Virus Surveillance and Research, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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20
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Droplet digital PCR as a useful tool for the quantitative detection of Enterovirus 71. J Virol Methods 2014; 207:200-3. [DOI: 10.1016/j.jviromet.2014.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 12/15/2022]
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21
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Fischer TK, Nielsen AY, Sydenham TV, Andersen PH, Andersen B, Midgley SE. Emergence of enterovirus 71 C4a in Denmark, 2009 to 2013. ACTA ACUST UNITED AC 2014; 19. [PMID: 25306878 DOI: 10.2807/1560-7917.es2014.19.38.20911] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enterovirus (EV) 71 has emerged as a primary cause of severe neurologic enterovirus infection in the aftermath of the global polio eradication effort. Eleven subgenotypes of EV71 exist, the C4 subgenotype being associated with large outbreaks in Asia with high mortality rates. This subgenotype has rarely been reported in Europe. In the period between 1 January 2009 and 31 December 2013 a total of 1,447 EV positive samples from 1,143 individuals were sent to the Statens Serum Institute (SSI), and 938 samples from 913 patients were genotyped at the Danish National World Health Organization Reference laboratory for Poliovirus at SSI. Echovirus 6 (E06) (n=141 patients), echovirus 30 (E30) (n=114), coxsackievirus A6 (CA06) (n=96) and EV71 (n=63) were the most prevalent genotypes. We observed a shift in circulating EV71 subgenotypes during the study period, with subgenotype C4 dominating in 2012. A total of 34 EV71 patients were found to be infected with strains of the C4 subgenotype, and phylogenetic analysis revealed that they belonged to the C4a lineage. In our study, the proportions of cases with cerebral and/or sepsis-like symptoms were similar in those affected by C4a (19/34) and those with C1 and C2 (15/35). The majority (n=30) of the 34 EV71 C4 cases were children≤5 years of age, and males (n=22) were over-represented. Continued EV surveillance is required to monitor the spread of EV71 C4 in Denmark and the rest of Europe.
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Affiliation(s)
- T K Fischer
- Virus Surveillance and Research Section, Statens Serum Institute, Denmark
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22
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Ibrahim W, Ouerdani I, Pillet S, Aouni M, Pozzetto B, Harrath R. Direct typing of human enteroviruses from wastewater samples. J Virol Methods 2014; 207:215-9. [PMID: 25066280 DOI: 10.1016/j.jviromet.2014.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 07/08/2014] [Accepted: 07/15/2014] [Indexed: 12/15/2022]
Abstract
A RT-PCR approach for the direct detection and typing of human enteroviruses in the environment is described in this study. A semi-nested RT-PCR using COnsensus-DEgenerated Hybrid Oligonucleotide Primers (CODEHOP) designed from the VP2 genome region has been developed for the direct typing of enteroviruses in clinical samples (Ibrahim et al., 2013). This CODEHOP/VP2 PCR strategy as well as the CODEHOP/VP1 technique described by Nix et al. (2006), were tested for the detection and typing of enteroviruses in wastewater samples. Virus particles were first extracted and concentrated from wastewater samples by using respectively beef extract and polyethylene glycol 6000, and the presence of enteroviruses was screened by a RT-PCR method using primers from the 5'-end non-coding region (5'NCR). Fifty-two of 172 samples (30.2%) were revealed positive by the 5'NCR method. From these 52 samples, only 19 samples (36.5%) were found positive by at least one of the two CODEHOP techniques, with the following distribution: VP1(+)/VP2(+)=4 (7.7%), VP1(-)/VP2(+)=13 (25%) and VP1(+)/VP2(-)=2 (3.8%). These results illustrate that the direct typing of enteroviruses in environmental samples is insensitive, possibly due to the presence of large amounts of amplification inhibitors; however, the VP2 method was found able to allow the direct detection and typing of c. one-third of the positive environmental samples.
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Affiliation(s)
- Wafa Ibrahim
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia; Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Imène Ouerdani
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
| | - Sylvie Pillet
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
| | - Bruno Pozzetto
- Laboratory of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France.
| | - Rafik Harrath
- Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
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Riabi S, Harrath R, Gaaloul I, Bouslama L, Nasri D, Aouni M, Pillet S, Pozzetto B. Study of Coxsackie B viruses interactions with Coxsackie Adenovirus receptor and Decay-Accelerating Factor using Human CaCo-2 cell line. J Biomed Sci 2014; 21:50. [PMID: 24885774 PMCID: PMC4035751 DOI: 10.1186/1423-0127-21-50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/06/2014] [Indexed: 01/20/2023] Open
Abstract
Background Decay Accelerating Factor (DAF) and Coxsackievirus-Adenovirus Receptor (CAR) have been identified as cellular receptors for Coxsackie B viruses (CV-B). The aim of this study is to elucidate the different binding properties of CV-B serotypes and to find out if there are any amino acid changes that could be associated to the different phenotypes. Twenty clinical CV-B isolates were tested on CaCo-2 cell line using anti-DAF (BRIC216) and anti-CAR (RmcB) antibodies. CV-B3 Nancy prototype strain and a recombinant strain (Rec, CV-B3/B4) were tested in parallel. The P1 genomic region of 12 CV-B isolates from different serotypes was sequenced and the Trans-Epithelial Electrical Resistance (TEER) along with the virus growth cycle was measured. Results Infectivity assays revealed clear differences between CV-B isolates with regard to their interactions with DAF and CAR. All tested CV-B isolates showed an absolute requirement for CAR but varied in their binding to DAF. We also reported that for some isolates of CV-B, DAF attachment was not adapted. Genetic analysis of the P1 region detected multiple differences in the deduced amino acid sequences. Conclusion Within a given serotype, variations exist in the capacity of virus isolates to bind to specific receptors, and variants with different additional ligands may arise during infection in humans as well as in tissue culture.
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Affiliation(s)
- Samira Riabi
- Laboratory of Transmissible Diseases LR99-ES27, Faculty of Pharmacy, Avenue Avicenne 5000, Monastir, Tunisia.
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Ahmad S, Dalwai A, Al-Nakib W. Frequency of enterovirus detection in blood samples of neonates admitted to hospital with sepsis-like illness in Kuwait. J Med Virol 2014; 85:1280-5. [PMID: 23918545 DOI: 10.1002/jmv.23604] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2013] [Indexed: 11/09/2022]
Abstract
This study investigated the role of enteroviruses in sepsis-like illness among neonates in Kuwait. Serum samples from 139 consecutive neonates presenting with sepsis-like illness during a three and a half-year-period whose blood cultures were negative for bacterial pathogens were tested. Enterovirus RNA was detected by single-step reverse-transcription PCR (RT-PCR). Specific genotypes were identified by direct DNA sequencing of enteroviral genome. Serotype-specific antibodies in serum samples from some selected patients were detected by virus neutralization test using coxsackievirus B types (CBVs). All 139 neonates presented with sepsis-like illness and blood samples were uniformly negative for aerobic/anaerobic bacterial cultures. Fifty-six (40%) neonates had further complications of sepsis including carditis (n = 34) and multi-organ involvement (n = 22). Enterovirus RNA was detected by RT-PCR in 34 of 139 (24%) serum samples which is among the highest frequency reported so far in non-epidemic settings. Genotyping identified CBVs as most common enteroviruses, causing 19 of 34 (56%) enteroviral sepsis episodes in neonates. Of 34 carditis cases, 18 were positive for CBVs by serotyping including all 10 enterovirus RNA-positive samples. Only one fatality was observed due to liver failure in a neonate with hepatitis. Our data showed that enteroviruses are responsible for 24% of neonatal sepsis cases due to non-bacterial causes in Kuwait. The data indicate that enteroviruses should be considered in the differential diagnosis of sepsis-like illness among neonates, particularly those with negative blood cultures for bacterial pathogens.
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Affiliation(s)
- Suhail Ahmad
- Faculty of Medicine, Department of Microbiology, Kuwait University, Safat, Kuwait
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25
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Ibrahim W, Boukhadra N, Nasri-Zoghlami D, Berthelot P, Omar S, Bourlet T, Pozzetto B, Pillet S. Partial sequencing of the VP2 capsid gene for direct enterovirus genotyping in clinical specimens. Clin Microbiol Infect 2014; 20:O558-65. [PMID: 24372815 DOI: 10.1111/1469-0691.12520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 11/02/2013] [Accepted: 12/19/2013] [Indexed: 11/26/2022]
Abstract
Typing of human enterovirus (EV) remains a major goal for diagnostic and epidemiological purposes. Whereas sequencing of the VP1 coding region is the reference standard for EV typing, a method relying on sequencing of the VP2 coding region has been proposed as an alternative; however, this has been validated only on cell culture supernatants. To avoid the selection of cultivable strains and to quicken the identification step, a new semi-nested PCR method targeting the VP2 region was developed by use of the CODEHOP strategy. After validation of the method on reference and clinical strains, a total of 352 clinical specimens found to be positive for EV RNA (138 with the GeneXpert EV kit and 214 with the Enterovirus R-gene kit) during a 3-year period (2010-2012) were analysed prospectively for VP2 genotyping. Overall, 204 (58%) specimens were typeable. A higher proportion of throat swab/stool specimens than of cerebrospinal fluid (CSF) specimens was found to be typeable (94 of 142 (66.2%) vs. 83 of 169 (49.1%), respectively, p <0.01 by the chi-square test). Moreover, the median Ct value obtained was lower for typeable specimens than for untypeable specimens (32.20 vs. 33.01, p <0.05, and 25.96 vs. 31.74, p <0.001, for the GeneXpert and R-gene tests, respectively, by the Mann-Whitney-Wilcoxon test). These results suggest that, in cases of EV meningitis, a peripheral specimen (i.e. throat swab or stool) that is susceptible to exhibiting a higher viral load should be used in preference to CSF for identifying the causative EV genotype by use of the VP2 typing method without cell culture isolation.
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Affiliation(s)
- W Ibrahim
- EA-3064, Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP), Faculty of Medicine of Saint-Etienne, University of Lyon, Saint-Etienne, France; Laboratory of Transmissible Diseases and Biologically Active Substances, Faculty of Pharmacy, Monastir, Tunisia
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26
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Ganesh A, Lin J. Waterborne human pathogenic viruses of public health concern. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2013; 23:544-64. [PMID: 23432800 DOI: 10.1080/09603123.2013.769205] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In recent years, the impending impact of waterborne pathogens on human health has become a growing concern. Drinking water and recreational exposure to polluted water have shown to be linked to viral infections, since viruses are shed in extremely high numbers in the faeces and vomit of infected individuals and are routinely introduced into the water environment. All of the identified pathogenic viruses that pose a significant public health threat in the water environment are transmitted via the faecal-oral route. This group, are collectively known as enteric viruses, and their possible health effects include gastroenteritis, paralysis, meningitis, hepatitis, respiratory illness and diarrhoea. This review addresses both past and recent investigations into viral contamination of surface waters, with emphasis on six types of potential waterborne human pathogenic viruses. In addition, the viral associated illnesses are outlined with reference to their pathogenesis and routes of transmission.
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Affiliation(s)
- Atheesha Ganesh
- a Discipline of Microbiology, School of Life Sciences , University of KwaZulu-Natal (Westville) , Durban , South Africa
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27
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Nielsen ACY, Böttiger B, Midgley SE, Nielsen LP. A novel enterovirus and parechovirus multiplex one-step real-time PCR-validation and clinical experience. J Virol Methods 2013; 193:359-63. [PMID: 23845901 PMCID: PMC7119552 DOI: 10.1016/j.jviromet.2013.06.038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 06/24/2013] [Accepted: 06/30/2013] [Indexed: 11/30/2022]
Abstract
As the number of new enteroviruses and human parechoviruses seems ever growing, the necessity for updated diagnostics is relevant. We have updated an enterovirus assay and combined it with a previously published assay for human parechovirus resulting in a multiplex one-step RT-PCR assay. The multiplex assay was validated by analysing the sensitivity and specificity of the assay compared to the respective monoplex assays, and a good concordance was found. Furthermore, the enterovirus assay was able to detect 42 reference strains from all 4 species, and an additional 9 genotypes during panel testing and routine usage. During 15 months of routine use, from October 2008 to December 2009, we received and analysed 2187 samples (stool samples, cerebrospinal fluids, blood samples, respiratory samples and autopsy samples) were tested, from 1546 patients and detected enteroviruses and parechoviruses in 171 (8%) and 66 (3%) of the samples, respectively. 180 of the positive samples could be genotyped by PCR and sequencing and the most common genotypes found were human parechovirus type 3, echovirus 9, enterovirus 71, Coxsackievirus A16, and echovirus 25. During 2009 in Denmark, both enterovirus and human parechovirus type 3 had a similar seasonal pattern with a peak during the summer and autumn. Human parechovirus type 3 was almost invariably found in children less than 4 months of age. In conclusion, a multiplex assay was developed allowing simultaneous detection of 2 viruses, which can cause similar clinical symptoms.
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Affiliation(s)
- Alex Christian Yde Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark; Department of Infectious Diseases, University Hospital Odense, Odense, Denmark.
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Lui YLE, Lin Z, Lee JJ, Chow VTK, Poh CL, Tan EL. Beta-actin variant is necessary for Enterovirus 71 replication. Biochem Biophys Res Commun 2013; 433:607-10. [DOI: 10.1016/j.bbrc.2013.03.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 03/17/2013] [Indexed: 11/16/2022]
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Shaukat S, Angez M, Alam MM, Sharif S, Khurshid A, Mahmood T, Zaidi SSZ. Characterization of non-polio enterovirus isolates from acute flaccid paralysis children in Pakistan reflects a new genotype of EV-107. Virus Res 2012; 170:164-8. [DOI: 10.1016/j.virusres.2012.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 09/09/2012] [Accepted: 09/24/2012] [Indexed: 11/28/2022]
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El Hiar R, Haddad S, Jaïdane H, Hober D, Ben M'hadheb-Gharbi M, Gullberg M, Neji-Guediche M, Lindberg AM, Gharbi J, Aouni M. Enteroviral central nervous system infections in children of the region of monastir, Tunisia: diagnosis, laboratory findings of cerebrospinal fluid and clinical manifestations. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:294-302. [PMID: 24293816 DOI: 10.1007/s13337-012-0104-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022]
Abstract
Human enteroviruses (HEV) are one of the major causes of central nervous system (CNS) infections in pediatrics. A prospective study was conducted to assess the epidemiological, clinical, and laboratory characteristics of enterovirus (EV) infections of the CNS in children under 15-years-old, suspected of having viral CNS infections and admitted to the Pediatric Department of Monastir University Hospital, Tunisia. Enteroviral RNA was detected by 5' NCR nested RT-PCR assay in 33 % (20 out of 60) of cerebrospinal fluid specimens, whereas only six samples (10 %) were EV positive in cell culture. EV-positive patients were clustered according to their clinical manifestations, predominantly diagnosed as aseptic meningitis (65 %) and meningoencephalitis (20 %). Fever, headache, vomiting, and neck stiffness were the most pronounced symptoms. Pleocytosis with the predominance of lymphocytes was observed in 60 % of EV positive specimens. Although patients suffering from EV infections were encountered throughout the year, most occurred during spring and summer months. Using VP1-2A nested RT-PCR and sequence analysis, three of the 20 positive HEV were identified as Echovirus (E)-9. This is the first report of a cluster of aseptic meningitis cases caused by E-9 in Monastir.
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Affiliation(s)
- Raida El Hiar
- Laboratory of Infectious Diseases and Biological Agents LR99-ES27, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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Linsuwanon P, Puenpa J, Suwannakarn K, Auksornkitti V, Vichiwattana P, Korkong S, Theamboonlers A, Poovorawan Y. Molecular epidemiology and evolution of human enterovirus serotype 68 in Thailand, 2006-2011. PLoS One 2012; 7:e35190. [PMID: 22586446 PMCID: PMC3346751 DOI: 10.1371/journal.pone.0035190] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 03/09/2012] [Indexed: 11/29/2022] Open
Abstract
Background Publications worldwide have reported on the re-occurrence of human enterovirus 68 (EV68), a rarely detected pathogen usually causing respiratory illness. However, epidemiological data regarding this virus in particular on the Asian continent has so far been limited. Methodology/Findings We investigated the epidemiology and genetic variability of EV68 infection among Thai children with respiratory illnesses from 2006–2011 (n = 1810). Semi-nested PCR using primer sets for amplification of the 5′-untranslated region through VP2 was performed for rhino-enterovirus detection. Altogether, 25 cases were confirmed as EV68 infection indicating a prevalence of 1.4% in the entire study population. Interestingly, the majority of samples were children aged >5 years (64%). Also, co-infection with other viruses was found in 28%, while pandemic H1N1 influenza/2009 virus was the most common co-infection. Of EV68-positive patients, 36% required hospitalizations with the common clinical presentations of fever, cough, dyspnea, and wheezing. The present study has shown that EV68 was extremely rare until 2009 (0.9%). An increasing annual prevalence was found in 2010 (1.6%) with the highest detection frequency in 2011 (4.3%). Based on analysis of the VP1 gene, the evolutionary rate of EV68 was estimated at 4.93×10−3 substitutions/site/year. Major bifurcation of the currently circulating EV68 strains occurred 66 years ago (1945.31 with (1925.95–1960.46)95% HPD). Among the current lineages, 3 clusters of EV68 were categorized based on the different molecular signatures in the BC and DE loops of VP1 combined with high posterior probability values. Each cluster has branched off from their common ancestor at least 36 years ago (1975.78 with (1946.13–1984.97)95% HPD). Conclusion Differences in epidemiological characteristic and seasonal profile of EV68 have been found in this study. Results from Bayesian phylogenetic investigations also revealed that EV68 should be recognized as a genetically diverse virus with a substitution rate identical to that of enterovirus 71 genotype B (4.2×10−3 s/s/y).
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Molecular characterization of human enteroviruses in the Central African Republic: uncovering wide diversity and identification of a new human enterovirus A71 genogroup. J Clin Microbiol 2012; 50:1650-8. [PMID: 22337981 DOI: 10.1128/jcm.06657-11] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human enteroviruses (HEV) are among the most common viruses infecting humans. Their circulation has been widely studied in most parts of the world but not in sub-Saharan Africa, where poliomyelitis remains prevalent. We report here the molecular characterization of 98 nonpoliovirus (non-PV) HEV strains isolated from 93 randomly selected cell culture-positive supernatants from stool samples collected from 1997 through 2006 from children with acute flaccid paralysis living in the Central African Republic (CAR). The isolates were typed by sequencing the VP1 coding region and sequenced further in the VP2 coding region, and phylogenetic studies were carried out. Among the 98 VP1 sequences, 3, 74, 18, and 3 were found to belong to the HEV-A, -B, -C, and -D species, respectively. Overall, 42 types were detected. In most cases, the VP2 type was correlated with that of the VP1 region. Some of the isolates belonged to lineages that also contain viruses isolated in distant countries, while others belonged to lineages containing viruses isolated only in Africa. In particular, one isolate (type EV-A71) did not fall into any of the genogroups already described, indicating the existence of a previously unknown genogroup for this type. These results illustrate the considerable diversity of HEV isolates from the stools of paralyzed children in the CAR. The presence of diverse HEV-C types makes recombination between poliovirus and other HEV-C species possible and could promote the emergence of recombinant vaccine-derived polioviruses similar to those that have been implicated in repeated poliomyelitis outbreaks in several developing countries.
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Riabi S, Gaaloul I, Harrath R, Aouni M. Persistent infection of human intestinal Caco-2 cell line by Coxsackieviruses B. ACTA ACUST UNITED AC 2011; 60:347-51. [PMID: 22178701 DOI: 10.1016/j.patbio.2011.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 11/15/2011] [Indexed: 10/14/2022]
Abstract
Coxsackieviruses B (CV-B, Picornaviridae family, genus Enterovirus) are characterized by their ability to cause cytopathic effects in tissue culture. These viruses are considered highly cytolytic, but can establish persistence/latency in susceptible cells, indicating that a regulatory mechanism may exist to shut off viral protein synthesis and replication under certain situations. The persistence of coxsackieviral B RNA is of great interest because of its implication in the pathogenesis of several chronic human diseases. However, a few studies have dealt with the persistence of these viruses at the intestinal level. The aim of this study is to test the capacity of the six CV-B serotypes to establish persistent infection in human intestinal Caco-2 cell line. Ten CV-B isolates, including CV-B3 prototype strain (Nancy) and a recombinant isolate (B3-B4), were tested. Six CV-B isolates were found to establish persistent infections in Caco-2 cell line. Persistent replication was proved by the detection of viral RNA from cell cultures, VP1 capsid protein detection by immunofluorescence (IF) staining, and the release of infectious particles up to two months and a half after infection without any obvious cytolysis. In addition, our results suggest that the establishment of a persistent infection is serotype-independent.
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Affiliation(s)
- S Riabi
- Laboratory of Transmissible Diseases, Faculty of Pharmacy, Monastir, Tunisia.
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Wei C, Wang G, Chen X, Huang H, Liu B, Xu Y, Li F. Identification and typing of human enterovirus: a genomic barcode approach. PLoS One 2011; 6:e26296. [PMID: 22022592 PMCID: PMC3194813 DOI: 10.1371/journal.pone.0026296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
Identification and typing of human enterovirus (HEVs) are important to pathogen detection and therapy. Previous phylogeny-based typing methods are mainly based on multiple sequence alignments of specific genes in the HEVs, but the results are not stable with respect to different choices of genes. Here we report a novel method for identification and typing of HEVs based on information derived from their whole genomes. Specifically, we calculate the k-mer based barcode image for each genome, HEV or other human viruses, for a fixed k, 1<k<7, where a genome barcode is defined in terms of the k-mer frequency distribution across the whole genome for all combinations of k-mers. A phylogenetic tree is constructed using a barcode-based distance and a neighbor-joining method among a set of 443 representative non-HEV human viruses and 395 HEV sequences. The tree shows a clear separation of the HEV viruses from all the non-HEV viruses with 100% accuracy and a separation of the HEVs into four distinct clads with 93.4% consistency with a multiple sequence alignment-based phylogeny. Our detailed analyses of the HEVs having different typing results by the two methods indicate that our results are in better agreement with known information about the HEVs.
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Affiliation(s)
- Chengguo Wei
- Department of Pathogeny Biology, Norman Bethune Medical College of Jilin University, Changchun, Jilin, China
| | - Guoqing Wang
- Department of Pathogeny Biology, Norman Bethune Medical College of Jilin University, Changchun, Jilin, China
| | - Xin Chen
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Honglan Huang
- Department of Pathogeny Biology, Norman Bethune Medical College of Jilin University, Changchun, Jilin, China
| | - Bin Liu
- The First Bethune Hospital of Jilin University, Changchun, Jilin, China
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
- * E-mail: (YX); (FL)
| | - Fan Li
- Department of Pathogeny Biology, Norman Bethune Medical College of Jilin University, Changchun, Jilin, China
- * E-mail: (YX); (FL)
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Badran SA, Midgley S, Andersen P, Böttiger B. Clinical and virological features of enterovirus 71 infections in Denmark, 2005 to 2008. ACTA ACUST UNITED AC 2011; 43:642-8. [PMID: 21526904 DOI: 10.3109/00365548.2011.577094] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Since the late 1990s enterovirus 71 (EV71) has caused epidemics of hand, foot and mouth disease with fatal cases especially in the Asian Pacific region. The objective of this study was to describe the clinical and virological features of EV71 infections in Denmark. METHODS All enterovirus-positive samples in Denmark are submitted to the National Poliovirus Laboratory for typing, and the EV71-positive samples are characterized by sequencing and phylogenetic analysis. Clinical information was gathered for the EV71-positive patients. RESULTS During 2005-2008, EV71 was demonstrated in 29 patients. In 2007 EV71 was the second most common enterovirus type detected in Denmark. Twenty-one of the 29 patients were children aged ≤1 y, 24 were hospitalized, and meningitis was the most common diagnosis. Gastroenteritis and hand, foot and mouth disease were other common clinical manifestations, but no fatal cases or cases of pulmonary oedema were seen. A novel subgenotype in Europe, B5, dominated the 2007 outbreak, but co-circulated with subgenotypes C1 and C2. CONCLUSIONS In conclusion EV71 was among the common enterovirus types in Denmark, and in 2007 a novel subgenotype, B5, was observed. EV71 was mainly diagnosed in infants, and the majority of patients were hospitalized with meningitis.
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Affiliation(s)
- Shadia Ali Badran
- Department of Virology, Statens Serum Institut, Copenhagen, Denmark.
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An ex vivo model of coxsackievirus infection using multilayered human conjunctival epithelial cells. Graefes Arch Clin Exp Ophthalmol 2011; 249:1327-32. [DOI: 10.1007/s00417-011-1655-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/18/2011] [Accepted: 02/02/2011] [Indexed: 10/18/2022] Open
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Tan CYQ, Ninove L, Gaudart J, Nougairede A, Zandotti C, Thirion-Perrier L, Charrel RN, de Lamballerie X. A retrospective overview of enterovirus infection diagnosis and molecular epidemiology in the public hospitals of Marseille, France (1985-2005). PLoS One 2011; 6:e18022. [PMID: 21437207 PMCID: PMC3060927 DOI: 10.1371/journal.pone.0018022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 02/22/2011] [Indexed: 12/13/2022] Open
Abstract
Human enteroviruses (HEV) are frequent human pathogens and, associated in particular with large outbreaks of aseptic meningitis. Here, we have compiled a database of clinical HEV isolates from the Public Hospitals of Marseille, from 1985 to 2005. Amongst 654 isolates that could be characterized by complete sequencing of the VP1 gene, 98% belonged to species HEV-B; the most frequently isolated serotypes were Echovirus E30, E11, E7, E6 and E4. The high incidence of E30 and the recent emergence of E13 are consistent with reports worldwide and peak HEV isolation occurred mostly in the late spring and summer months. The proportion of echoviruses has decreased across the years, while that of coxsackieviruses has increased. Stool (the most frequent sample type) allowed detection of all identified serotypes. MRC5 (Human lung fibroblasts) cell line was the most conducive cell line for HEV isolation (84.9% of 10 most common serotype isolates, 96.3% in association with BGM (Buffalo green monkey kidney cells)). Previous seroneutralization-based serotype identification demonstrated 55.4% accuracy when compared with molecular VP1 analysis. Our analysis of a large number of clinical strains over 20 years reinforced the validity of VP1 serotyping and showed that comparative p-distance scores can be coupled with phylogenetic analysis to provide non-ambiguous serotype identification. Phylogenetic analysis in the VP1, 2C and 3D regions also provided evidence for recombination events amongst clinical isolates. In particular, it identified isolates with dissimilar VP1 but almost identical nonstructural regions.
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Affiliation(s)
- Charlene Y Q Tan
- UMR190 Unite des Virus Emergents, Universite de la Méditerranee-Institut de Recherche pour le Développement, Marseille, France.
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Echoviruses are a major cause of aseptic meningitis in infants and young children in Kuwait. Virol J 2010; 7:236. [PMID: 20846386 PMCID: PMC2949838 DOI: 10.1186/1743-422x-7-236] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 09/16/2010] [Indexed: 11/15/2022] Open
Abstract
Background The etiologic agents of aseptic meningitis (AM) often include human enteroviruses. The role of enteroviruses causing AM in young children was investigated during a 3-year period in Kuwait. Results Enteroviral RNA was detected in cerebrospinal fluid (CSF) by reverse transcription-PCR and specific genotypes of enteroviruses were identified by direct DNA sequencing of VP4-VP2 region. Enteroviral RNA was detected in 92 of 387 (24%) suspected AM cases and the results were confirmed by hybridization of amplicons with an internal, enterovirus-specific probe. The CSF samples from 75 of 281 (27%) children < 2 years old but only from 3 of 38 (8%) 4-12 year-old children were positive for enteroviral RNA (p = 0.011). Majority of infections in children < 2 years old (49 of 75, 65%) were due to three echoviruses; echovirus type 9 (E9), E11 and E30. Only three other enteroviruses, namely coxsackievirus type B4, coxsackievirus type B5 and enterovirus 71 were detected among AM cases in Kuwait. Conclusions Our data show that three types of echoviruses (E9, E11 and E30) are associated with the majority of AM cases in Kuwait. To the best of our knowledge, this is the first report to characterize different enterovirus genotypes associated with AM in the Arabian Gulf region.
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Okoh AI, Sibanda T, Gusha SS. Inadequately treated wastewater as a source of human enteric viruses in the environment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2010; 7:2620-37. [PMID: 20644692 PMCID: PMC2905569 DOI: 10.3390/ijerph7062620] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 06/04/2010] [Accepted: 06/04/2010] [Indexed: 12/13/2022]
Abstract
Human enteric viruses are causative agents in both developed and developing countries of many non-bacterial gastrointestinal tract infections, respiratory tract infections, conjunctivitis, hepatitis and other more serious infections with high morbidity and mortality in immunocompromised individuals such as meningitis, encephalitis and paralysis. Human enteric viruses infect and replicate in the gastrointestinal tract of their hosts and are released in large quantities in the stools of infected individuals. The discharge of inadequately treated sewage effluents is the most common source of enteric viral pathogens in aquatic environments. Due to the lack of correlation between the inactivation rates of bacterial indicators and viral pathogens, human adenoviruses have been proposed as a suitable index for the effective indication of viral contaminants in aquatic environments. This paper reviews the major genera of pathogenic human enteric viruses, their pathogenicity and epidemiology, as well as the role of wastewater effluents in their transmission.
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Affiliation(s)
- Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Alice 5700, South Africa; E-Mails: (S.S.G.); (T.S.)
| | - Thulani Sibanda
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Alice 5700, South Africa; E-Mails: (S.S.G.); (T.S.)
| | - Siyabulela S. Gusha
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, P/Bag X1314, Alice 5700, South Africa; E-Mails: (S.S.G.); (T.S.)
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Perera D, Shimizu H, Yoshida H, Tu PV, Ishiko H, McMinn PC, Cardosa MJ. A comparison of the VP1, VP2, and VP4 regions for molecular typing of human enteroviruses. J Med Virol 2010; 82:649-57. [PMID: 20166171 DOI: 10.1002/jmv.21652] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The VP4, VP2, and VP1 gene regions were evaluated for their usefulness in typing human enteroviruses. Three published RT-PCR primers sets targeting separately these three gene regions were used. Initially, from a total of 86 field isolates (36 HEV-A, 40 HEV-B, and 10 HEV-C) tested, 100% concordance in HEV-A was identified from all three gene regions (VP4, VP2, and VP1). However, for HEV-B and HEV-C viruses, only the VP2 and VP1 regions, and not VP4, showed 100% concordance in typing these viruses. To evaluate further the usefulness of VP4 in typing HEV-A enteroviruses, 55 Japanese and 203 published paired VP4 and VP1 nucleotide sequences were also examined. In each case, typing by VP4 was 100% in concordance with typing using VP1. Given these results, it is proposed that for HEV-A enteroviruses, all three gene regions (VP4, VP2, and VP1), would be useful for typing these viruses. These options would enhance the capability of laboratories in identifying these viruses and would greatly help in outbreaks of hand, foot, and mouth disease.
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Affiliation(s)
- David Perera
- Institute of Health & Community Medicine, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia.
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She RC, Hymas WC, Taggart EW, Petti CA, Hillyard DR. Performance of enterovirus genotyping targeting the VP1 and VP2 regions on non-typeable isolates and patient specimens. J Virol Methods 2010; 165:46-50. [DOI: 10.1016/j.jviromet.2009.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 10/20/2022]
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Molecular identification and analysis of nonserotypeable human enteroviruses. J Clin Microbiol 2010; 48:1276-82. [PMID: 20164278 DOI: 10.1128/jcm.02384-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Conventional approaches to characterizing human enteroviruses (HEVs) are based on viral isolation and neutralization. Molecular typing methods depend largely on reverse transcription-PCR (RT-PCR) and nucleotide sequencing of the entire or partial VP1 gene. A modified RT-PCR-based reverse line blot (RLB) hybridization assay was developed as a rapid and efficient way to characterize common and nonserotypeable (by neutralization) HEVs. Twenty HEV serotypes accounted for 87.1% of all HEVs isolated at a reference laboratory from 1979 to 2007; these common serotypes were identified using one sense and three antisense primers and a set of 80 serotype-specific probes in VP1 (F. Zhou et al., J. Clin. Microbiol. 47:2737-2743, 2009). In this study, one HEV-specific primer pair, two probes in the 5' untranslated region (UTR), and a new set of 80 serotype-specific probes in VP1 were designed. First, we successfully applied the modified RT-PCR-RLB (using two HEV-specific probes and two sets of serotype-specific probes) to synchronously detect the 5' UTR and VP1 regions of 131/132 isolates previously studied (F. Zhou et al., J. Clin. Microbiol. 47:2737-2743, 2009). Then, this method was used to identify 73/92 nonserotypeable HEV isolates; 19 nonserotypeable isolates were hybridized only with HEV-specific probes. The VP1 region of 92 nonserotypeable HEV isolates was sequenced; 73 sequences corresponded with one or both RLB results and 19 (not belonging to the 20 most common genotypes) were identified only by sequencing. Two sets of serotype-specific probes can capture the majority of strains belonging to the 20 most common serotypes/genotypes simultaneously or complementarily. Synchronous detection of the 5' UTR and VP1 region by RT-PCR-RLB will facilitate the identification of HEVs, especially nonserotypeable isolates.
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Pillet S, Billaud G, Omar S, Lina B, Pozzetto B, Schuffenecker I. Multicenter evaluation of the ENTEROVIRUS R-gene real-time RT-PCR assay for the detection of enteroviruses in clinical specimens. J Clin Virol 2009; 47:54-9. [PMID: 19879186 DOI: 10.1016/j.jcv.2009.09.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 09/25/2009] [Indexed: 11/18/2022]
Abstract
BACKGROUND The rapid molecular diagnosis of enteroviral meningitis has been shown important for an adequate management of the patients. OBJECTIVES A new CE-marked real-time RT-PCR assay (ENTEROVIRUS R-gene, Argene) was evaluated in two university hospital virology laboratories. STUDY DESIGN Reactivity, analytical sensitivity and specificity were evaluated using 54 prototype and 173 clinical human enterovirus (HEV) strains, a 12-sample HEV proficiency panel, and 30 non-HEV microorganisms. The clinical performance of the ENTEROVIRUS R-gene assay was evaluated by testing 197 cerebrospinal fluid (CSF) and 103 respiratory specimens, comparatively to the routinely used diagnostic techniques. RESULTS Sixty-four out of the 65 HEV serotypes tested were detected. The analytical sensitivity ranged between 10(-2.64) and 10(2.39)TCID(50)/50 microl. Cross-reactivity was observed with four human rhinoviruses. On 59 CSF specimens analyzed prospectively, the results of the ENTEROVIRUS R-gene assay showed a 94.8% concordance with those of the Smart enterovirus (EV) assay (Cepheid). On 138 CSF specimens tested retrospectively, the results of the ENTEROVIRUS R-gene assay showed a 97.1% concordance with those of either the GeneXpert EV assay (Cepheid) or the in-house RT-PCR HEV assays used at the time of specimen collection. On 103 respiratory specimens, the concordance between the results of the ENTEROVIRUS R-gene assay and those of the routine RT-PCRs or viral culture was 90.2% and 96.1% before and after retest, respectively. CONCLUSIONS The new test was found able to detect a large panel of enterovirus serotypes; it was sensitive when used on clinical specimens; and, easy and rapid to perform on a routine basis.
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Affiliation(s)
- Sylvie Pillet
- Laboratoire de Bactériologie-Virologie, GIMAP EA 3064 and University Hospital of Saint-Etienne, 42023 Saint-Etienne Cedex 2, France
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Blomqvist S, Paananen A, Savolainen-Kopra C, Hovi T, Roivainen M. Eight years of experience with molecular identification of human enteroviruses. J Clin Microbiol 2008; 46:2410-3. [PMID: 18463218 PMCID: PMC2446933 DOI: 10.1128/jcm.00313-08] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 03/25/2008] [Accepted: 04/24/2008] [Indexed: 11/20/2022] Open
Abstract
We have successfully typed 1,121 human enterovirus (HEV) isolates during the last 8 years by adapting partial VP1 sequencing to routine identification of HEV isolated from diverse clinical and environmental specimens. The isolates include 48 of the 59 traditional nonpoliovirus HEV serotypes and members of 8 newly discovered types, which would have remained untypeable by neutralization using the conventional cross-sectional pools of antisera.
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Affiliation(s)
- Soile Blomqvist
- Department of Viral Diseases and Immunology, Enterovirus Laboratory, National Public Health Institute (KTL), Mannerheimintie 166, 00300 Helsinki, Finland.
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45
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Chapman NM, Kim KS, Drescher KM, Oka K, Tracy S. 5' terminal deletions in the genome of a coxsackievirus B2 strain occurred naturally in human heart. Virology 2008; 375:480-91. [PMID: 18378272 DOI: 10.1016/j.virol.2008.02.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 12/19/2007] [Accepted: 02/21/2008] [Indexed: 01/17/2023]
Abstract
Enteroviruses can induce human myocarditis, which can be modeled in mice inoculated with group B coxsackieviruses (CVB) and in which CVB evolve to produce defective, terminally deleted genomes. The 5' non-translated region (NTR) was enzymatically amplified from heart tissue of a fatal case of enterovirus-associated myocarditis in Japan in 2002. While no intact 5' viral genomic termini were detected, 5' terminal deletions ranged in size from 22 to 36 nucleotides. Sequence of the 5' third of this viral genome is of a modern strain, closely related to CVB2 strains isolated in Japan in 2002. A CVB3 chimera containing the 5' NTR with a 22 nt deletion produced progeny virus upon transfection of HeLa cells. When the 5' 22 nucleotide deletion was repaired, the virus induced myocarditis in mice and replicated like wild type virus in murine heart cells. This is the first report of these naturally-occurring defective enteroviral genomes in human myocarditis.
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Affiliation(s)
- Nora M Chapman
- Enterovirus Research Laboratory, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA.
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46
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Bessaud M, Jegouic S, Joffret ML, Barge C, Balanant J, Gouandjika-Vasilache I, Delpeyroux F. Characterization of the genome of human enteroviruses: design of generic primers for amplification and sequencing of different regions of the viral genome. J Virol Methods 2008; 149:277-84. [PMID: 18329732 DOI: 10.1016/j.jviromet.2008.01.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 01/17/2008] [Accepted: 01/21/2008] [Indexed: 11/26/2022]
Abstract
Human enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Biodiversity and evolution of human enterovirus genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating strains of enteroviruses require partial determination of different genomic regions. The development is described of a simple method allowing amplification and partial sequencing of the P1, P2 and P3 genomic regions of field human enterovirus strains isolated in cell cultures, by performing PCR on cDNAs generated through a single RT reaction. A set of generic primers were designed and tested on a panel of 90 field and prototype viruses belonging to the five species of human enteroviruses. This assay was shown to amplify efficiently the targeted regions of all the 90 genomes tested. The generated amplicons were sequenced successfully without the need for gel purification. This assay could be a valuable tool for laboratories interested in molecular epidemiology and evolution studies implicating a great number of human enterovirus strains isolated from human or environmental samples.
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Affiliation(s)
- Maël Bessaud
- Unité postulante de biologie des virus entériques, Institut Pasteur, 25 rue du Dr Roux, 75 015 Paris, France.
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