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Auvray C, Perez-Martin S, Schuffenecker I, Pitoiset C, Tarris G, Ambert-Balay K, Martin L, Dullier-Taillefumier N, Bour JB, Manoha C. Sudden Infant Death Associated with Rhinovirus Infection. Viruses 2024; 16:518. [PMID: 38675861 PMCID: PMC11054477 DOI: 10.3390/v16040518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
A less than one-month-old infant with symptoms of rhinitis died unexpectedly in his sleep. He was not born prematurely and had no known underlying disease. Cerebrospinal fluid, nasopharyngeal and lung samples, and rectal swab were found to be positive for subgroup A rhinovirus, while the blood was negative. This case highlights the important finding that the rhinovirus, a common pathogen associated with upper respiratory tract infections, can sometimes, as the only pathogen, lead to complications such as a cerebrospinal infection and be involved in the sudden infant death syndrome (SIDS). Vigilance is necessary in case of viral infections in the infant's environment, and measures of hygiene and protection must be encouraged in order to reduce the risk of the SIDS.
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Affiliation(s)
- Christelle Auvray
- Department of Microbiology, Virology Laboratory, Dijon University Hospital, 21070 Dijon, France; (C.A.); (C.P.)
| | | | - Isabelle Schuffenecker
- French National Enterovirus/Parechovirus Reference Centre, Hospices Civils de Lyon, 69317 Lyon, France;
| | - Cécile Pitoiset
- Department of Microbiology, Virology Laboratory, Dijon University Hospital, 21070 Dijon, France; (C.A.); (C.P.)
| | - Georges Tarris
- Department of Pathology, Dijon University Hospital, 21070 Dijon, France; (G.T.); (L.M.); (N.D.-T.)
| | - Katia Ambert-Balay
- French National Reference Centre for Gastroenteritis Viruses, Virology Laboratory, University Hospital of Dijon, 21070 Dijon, France;
| | - Laurent Martin
- Department of Pathology, Dijon University Hospital, 21070 Dijon, France; (G.T.); (L.M.); (N.D.-T.)
| | | | - Jean-Baptiste Bour
- Department of Microbiology, Virology Laboratory, Dijon University Hospital, 21070 Dijon, France; (C.A.); (C.P.)
| | - Catherine Manoha
- Department of Microbiology, Virology Laboratory, Dijon University Hospital, 21070 Dijon, France; (C.A.); (C.P.)
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2
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Child HT, Airey G, Maloney DM, Parker A, Wild J, McGinley S, Evens N, Porter J, Templeton K, Paterson S, van Aerle R, Wade MJ, Jeffries AR, Bassano I. Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater. mBio 2023; 14:e0146823. [PMID: 37877702 PMCID: PMC10746264 DOI: 10.1128/mbio.01468-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - George Airey
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Daniel M. Maloney
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Abby Parker
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jonathan Wild
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Suzie McGinley
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Nicholas Evens
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Jonathan Porter
- Environment Agency, National Monitoring, Starcross, Exeter, United Kingdom
| | - Kate Templeton
- Viral Genotyping Reference Laboratory Edinburgh, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Cefas, Weymouth, United Kingdom
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Matthew J. Wade
- Centre for Sustainable Aquaculture Futures, University of Exeter, Exeter, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
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3
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Li CX, Burrell R, Dale RC, Kesson A, Blyth CC, Clark JE, Crawford N, Jones CA, Britton PN, Holmes EC. Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing. J Gen Virol 2022; 103. [PMID: 35486523 DOI: 10.1099/jgv.0.001736] [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
Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.
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Affiliation(s)
- Ci-Xiu Li
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
| | - Rebecca Burrell
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, Children's Hospital at Westmead Clinical School, Faculty of Medicine, University of Sydney, NSW, Australia
| | - Alison Kesson
- Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Christopher C Blyth
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute and School of Medicine, University of Western Australia, Nedlands, WA, Australia.,Department of Infectious Diseases, Perth Children's Hospital, Nedlands, WA, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, QEII Medical Centre, Nedlands, WA, Australia
| | - Julia E Clark
- Infection Management, Queensland Children's Hospital, Brisbane, QLD, Australia.,School of Clinical Medicine, Childrens Health Queensland Clinical Unit, University of Queensland, QLD, Australia
| | - Nigel Crawford
- Murdoch Children's Research Institute, Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia
| | - Cheryl A Jones
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Philip N Britton
- Kids Research, Sydney Children's Hospitals Network (Westmead), Westmead, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia.,The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, NSW, Australia.,Sydney Institute for Infectious Diseases, Sydney Medical School, The University of Sydney, NSW, Australia
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4
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Moresco V, Oliver DM, Weidmann M, Matallana-Surget S, Quilliam RS. Survival of human enteric and respiratory viruses on plastics in soil, freshwater, and marine environments. ENVIRONMENTAL RESEARCH 2021; 199:111367. [PMID: 34029551 DOI: 10.1016/j.envres.2021.111367] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 05/24/2023]
Abstract
The public health significance of plastics and microplastics in different environmental matrices has mainly focused on the toxicological effects of human ingestion. But these pollutants can also harbour pathogenic bacteria as the surfaces of plastics in the environment quickly become colonised by microbial biofilm. This novel microbial habitat has been termed the 'plastisphere' and could facilitate the survival and dissemination of important bacterial and fungal pathogens. Importantly, however, the role of plastic pollution as a secondary pathway for the transmission of human pathogenic viruses has never been addressed. Due to the high prevalence of both enteric and respiratory viruses in the population and in the environment, there is significant potential for human viruses to become associated with the plastisphere. In this review we critically evaluate current knowledge on the interaction of human enteric and respiratory viruses with plastic surfaces and identify the main environmental conditions and plastic characteristics that could affect virus survival and persistence in the environment. Our hypothesis is that the plastisphere can enhance the adhesion, survival and dissemination of human pathogenic viruses and potentially lead to more effective transfer and transmission of viral diseases within the environment. We identify key research questions needed to more fully assess the potential human health risks associated with viruses on plastic surfaces. These include understanding, (1) the mechanisms of viral attachment to either naked or biofilm-colonised plastic (2) how the structural characteristics of viruses (e.g., enveloped, or non-enveloped), affect their persistence in the plastisphere, (3) whether the plastisphere offers protection and increases the persistence of infectious viruses in soil, freshwater, and marine environments.
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Affiliation(s)
- Vanessa Moresco
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - David M Oliver
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, Senftenberg, D-01968, Germany
| | - Sabine Matallana-Surget
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
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5
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Clinically Mild Encephalitis/Encephalopathy with a Reversible Splenial Lesion Associated with Rhinovirus. Pediatr Infect Dis J 2021; 40:e122-e125. [PMID: 33464018 DOI: 10.1097/inf.0000000000002995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A 2-year-old girl with fever and seizures was diagnosed as having clinically mild encephalitis/encephalopathy with a reversible splenial lesion, as indicated by magnetic resonance imaging. Virologic analysis identified human rhinovirus A49 in her serum. Although human rhinovirus rarely involves the central nervous system, such involvement could result in mild encephalitis/encephalopathy with a reversible splenial lesion.
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6
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Bizot E, Bousquet A, Charpié M, Coquelin F, Lefevre S, Le Lorier J, Patin M, Sée P, Sarfati E, Walle S, Visseaux B, Basmaci R. Rhinovirus: A Narrative Review on Its Genetic Characteristics, Pediatric Clinical Presentations, and Pathogenesis. Front Pediatr 2021; 9:643219. [PMID: 33829004 PMCID: PMC8019700 DOI: 10.3389/fped.2021.643219] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Human rhinoviruses (HRVs) are the leading cause of common colds. With the development of new molecular methods since the 2000s, HRVs have been increasingly involved among severe clinical infections. Recent knowledge of the HRV genetic characteristics has also improved the understanding of their pathogenesis. This narrative review aims to provide a current comprehensive knowledge about this virus in the pediatric community. HRVs represent a main cause of upper and lower respiratory tract infections in children. HRV is the second virus involved in bronchiolitis and pneumonia in children, and HRV bronchiolitis has a higher risk of recurrent wheezing episode or asthma. Some recent findings described HRVs in stools, blood, or cerebrospinal fluid, thanks to new molecular techniques such as polymerase chain reaction (PCR) by detecting HRVs with high sensibility. However, the high rate of asymptomatic carriage and the prolonged excretion in postsymptomatic patients complicate interpretation. No sufficient data exist to avoid antibiotic therapy in pediatric high-risk population with HRV detection. Severe clinical presentations due to HRVs can be more frequent in specific population with chronic pathology or genetic particularity. Inflammatory response is mediated by the nuclear factor (NF)-kappa B pathway and production of interferon (IFN)-beta and IFN-gamma, interleukin 8 (IL8), and IL1b. No specific treatment or antiviral therapy exists, although research is still ongoing. Nowadays, in addition to benign diseases, HRVs are recognized to be involved in some severe clinical presentations. Recent advances in genetic knowledge or specific inflammatory response may lead to specific treatment.
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Affiliation(s)
- Etienne Bizot
- Department of Microbiology, Robert Debré Hospital, APHP, Paris, France.,Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Anais Bousquet
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Maelle Charpié
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Florence Coquelin
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Servane Lefevre
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Justin Le Lorier
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Margaux Patin
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Perrine Sée
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Eytan Sarfati
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Servane Walle
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France
| | - Benoit Visseaux
- Department of Virology, Bichat Hospital, APHP, Paris, France.,University of Paris, Inserm, IAME, UMR1137, Paris, France
| | - Romain Basmaci
- Departement of Emergency and Pediatrics, Louis-Mourier Hospital, APHP, Colombes, France.,University of Paris, Inserm, IAME, UMR1137, Paris, France
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7
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Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses. Viruses 2020; 12:v12111260. [PMID: 33167516 PMCID: PMC7694487 DOI: 10.3390/v12111260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/25/2022] Open
Abstract
Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.
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8
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Hellferscee O, Treurnicht FK, Walaza S, Du Plessis M, Von Gottberg A, Wolter N, Moyes J, Dawood H, Variava E, Pretorius M, Venter M, Cohen C, Tempia S. The Fraction of Rhinovirus Detections Attributable to Mild and Severe Respiratory Illness in a Setting of High Human Immunodeficiency Virus Prevalence, South Africa, 2013-2015. J Infect Dis 2020; 219:1697-1704. [PMID: 30590585 DOI: 10.1093/infdis/jiy725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/20/2018] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The association of rhinovirus (RV) detection to illness is poorly understood. METHODS We enrolled case patients hospitalized with severe respiratory illness (SRI) at 2 hospitals and outpatients with influenza-like illness (ILI) and asymptomatic individuals (controls) from 2 affiliated clinics during 2013-2015. We compared the RV prevalence among ILI and SRI cases to those of controls stratified by human immunodeficiency virus (HIV) serostatus using penalized logistic regression. The attributable fraction (AF) was calculated. RESULTS During 2013-2015, RV was detected in 17.4% (368/2120), 26.8% (979/3654), and 23.0% (1003/4360) of controls, ILI cases, and SRI cases, respectively. The RV AF (95% confidence interval) was statistically significant among children aged <5 years (ILI: 44.6% [30.7%-55.7%] and SRI: 50.3% [38.6%-59.9%]; P < .001) and individuals aged ≥5 years (ILI: 62.9% [54.4%-69.8%] and SRI: 51.3% [38.7%-61.3%]; P < .001) as well as among HIV-infected (ILI: 59.9% [45.8%-70.3%] and SRI: 39.8% [22.3%-53.3%]; P < .001) and HIV-uninfected (ILI: 53.6% [44.7%-61.1%] and SRI: 55.3% [45.6%-63.2%]; P < .001) individuals. CONCLUSIONS Although RV detection was common among controls, it was also associated with a substantial proportion of clinical illness across age groups, irrespective of HIV status.
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Affiliation(s)
- Orienka Hellferscee
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Florette K Treurnicht
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg
| | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Mignon Du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg
| | - Anne Von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Halima Dawood
- Department of Medicine, Pietermaritzburg Metropolitan Hospital.,Department of Medicine, University of KwaZulu-Natal, Pietermaritzburg
| | - Ebrahim Variava
- Department of Medicine, Klerksdorp-Tshepong Hospital Complex, Klerksdorp.,Department of Medicine, Faculty of Health Sciences, Johannesburg, South Africa.,Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Marthi Pretorius
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,Technical Research and Development, Novartis Pharma AG, Basel, Switzerland
| | - Marietjie Venter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,Center for Viral Zoonoses, Department of Medical Virology, University of Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg.,Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia.,Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
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9
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Tokarz R, Hyams JS, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Shah S, Markowitz J, Baker SS, Rosh J, Baldassano RN, Kugathasan S, Walters T, Tagliafierro T, Sameroff S, Lee B, Che X, Oleynik A, Denson LA, Lipkin WI. Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:1656-1662. [PMID: 31112614 PMCID: PMC7108593 DOI: 10.1093/ibd/izz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC). METHODS We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome. RESULTS Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence. CONCLUSION Presence of virus in stool was not associated with the onset of pediatric UC.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA,Address correspondence to: Rafal Tokarz, Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, New York, NY 10032, USA. E-mail:
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Sapana Shah
- Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - James Markowitz
- Cohen Children’s Medical Center of New York, New Hyde Park, NY, USA
| | - Susan S Baker
- Women & Children’s Hospital of Buffalo WCHOB, Buffalo, NY, USA
| | - Joel Rosh
- Goryeb Children’s Hospital, Atlantic Health, Morristown, NJ, USA
| | | | | | | | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Bohyun Lee
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | | | - W Ian Lipkin
- Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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10
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Rhinovirus-associated acute encephalitis/encephalopathy and cerebellitis. Brain Dev 2019; 41:551-554. [PMID: 30850156 DOI: 10.1016/j.braindev.2019.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 11/21/2022]
Abstract
BACKGROUND Rhinovirus is a common respiratory pathogen for children throughout the year; nevertheless, its central nervous system involvement is extremely rare, and only two cases have been reported to date: meningitis and sepsis-like illness. PATIENT A previously healthy 2-year-old Japanese boy developed fever, followed by seizures and lethargy. His cerebrospinal fluid cell count and protein level were slightly increased; brain magnetic resonance imaging showed abnormal intensities in the bilateral cerebellar dentate nuclei, which were prominent in diffusion-weighted images. After his consciousness disturbance improved, cerebellar dysfunction became apparent. He was treated symptomatically, without steroids or any other immunosuppressants. He almost recovered within a few months; however, cerebellar atrophy became evident on brain magnetic resonance imaging. Using acute specimens, human rhinovirus A was detected in his throat swab and cerebrospinal fluid. DISCUSSION Acute cerebellitis, in which cerebellar inflammation is predominant, is occasionally accompanied by cerebral symptoms, such as consciousness disturbance and seizures. As a causative pathogen, rotavirus is the most common; however, rhinovirus-associated acute encephalitis/encephalopathy and concurrent cerebellitis have not been reported before. Further research, using recent molecular techniques to detect various central nervous system pathogens, including rhinovirus, is needed to delineate the underlying pathophysiology.
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11
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Korhonen L, Oikarinen S, Lehtonen J, Mustonen N, Tyni I, Niemelä O, Honkanen H, Huhtala H, Ilonen J, Hämäläinen AM, Peet A, Tillmann V, Siljander H, Knip M, Lönnrot M, Hyöty H. Rhinoviruses in infancy and risk of immunoglobulin E sensitization. J Med Virol 2019; 91:1470-1478. [PMID: 30866076 DOI: 10.1002/jmv.25455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/20/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
Previous data about the role of viruses in the development of allergic immunoglobulin E (IgE) sensitization are contradictory. The aim of this study was to determine the possible associations between exposure to different viruses (rhinovirus, enterovirus, norovirus, and parechovirus) during the first year of life and IgE sensitization. Viruses were analyzed from stool samples collected monthly from infants participating in a prospective birth cohort study. From that study, 244 IgE sensitized case children and 244 nonsensitized control children were identified based on their allergen-specific IgE antibody levels at the age of 6, 18, and 36 months. Stool samples (n = 4576) from the case and control children were screened for the presence of rhinovirus, enterovirus, norovirus, and parechovirus RNA by reverse transcription quantitative polymerase chain reaction. The study showed that rhinovirus was the most prevalent virus detected, present in 921 (20%) samples. None of the viruses were associated with IgE sensitization in the full cohort but after stratifying by sex, the number of rhinovirus positive samples was inversely associated with IgE sensitization in boys (odds ratio [OR]: 0.81; 95% confidence interval [CI]: 0.69-0.94; P = 0.006). There was also a temporal relation between rhinoviruses and IgE sensitization, as rhinovirus exposure during the first 6 months of life was associated with a reduced risk of subsequent IgE sensitization in boys (OR: 0.76; 95% CI: 0.6-0.94; P = 0.016). In conclusion, early exposure to rhinoviruses was inversely associated with IgE sensitization but this protective association was restricted to boys.
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Affiliation(s)
- Laura Korhonen
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland.,Department of Dermatology, Tampere University Hospital, Tampere, Finland.,Allergy Centre, Tampere University Hospital, Tampere, Finland
| | - Sami Oikarinen
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland.,Department of Clinical Microbiology, Fimlab Laboratories Ltd, Tampere, Finland
| | - Jussi Lehtonen
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland
| | - Neea Mustonen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Iiris Tyni
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland
| | - Onni Niemelä
- Department of Laboratory Medicine and Medical Research Unit, Seinäjoki Central Hospital and University of Tampere, Seinäjoki, Finland
| | - Hanna Honkanen
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Anu-Maaria Hämäläinen
- Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, Espoo, Finland
| | - Aleksandr Peet
- Department of Pediatrics, University of Tartu, Tartu, Estonia.,Children's Clinic of Tartu University Hospital, Tartu, Estonia
| | - Vallo Tillmann
- Department of Pediatrics, University of Tartu, Tartu, Estonia.,Children's Clinic of Tartu University Hospital, Tartu, Estonia
| | - Heli Siljander
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
| | - Maria Lönnrot
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland.,Department of Dermatology, Tampere University Hospital, Tampere, Finland.,Allergy Centre, Tampere University Hospital, Tampere, Finland
| | - Heikki Hyöty
- Department of Virology, Faculty of Medical Sciences and Biotechnology, Tampere University, Tampere, Finland.,Department of Clinical Microbiology, Fimlab Laboratories Ltd, Tampere, Finland
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12
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Affiliation(s)
- Jennifer E Schuster
- Department of Pediatrics, Children's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA.
| | - John V Williams
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, 9122 Rangos Research Building, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
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13
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Turi KN, Romick-Rosendale L, Ryckman KK, Hartert TV. A review of metabolomics approaches and their application in identifying causal pathways of childhood asthma. J Allergy Clin Immunol 2018; 141:1191-1201. [PMID: 28479327 PMCID: PMC5671382 DOI: 10.1016/j.jaci.2017.04.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 12/20/2022]
Abstract
Because asthma is a disease that results from host-environment interactions, an approach that allows assessment of the effect of the environment on the host is needed to understand the disease. Metabolomics has appealing potential as an application to study pathways to childhood asthma development. The objective of this review is to provide an overview of metabolomics methods and their application to understanding host-environment pathways in asthma development. We reviewed recent literature on advances in metabolomics and their application to study pathways to childhood asthma development. We highlight the (1) potential of metabolomics in understanding the pathogenesis of disease and the discovery of biomarkers; (2) choice of metabolomics techniques, biospecimen handling, and data analysis; (3) application to studying the role of the environment on asthma development; (4) review of metabolomics applied to the outcome of asthma; (5) recommendations for application of metabolomics-based -omics data integration in understanding disease pathogenesis; and (6) limitations. In conclusion, metabolomics allows use of biospecimens to identify useful biomarkers and pathways involved in disease development and subsequently to inform a greater understanding of disease pathogenesis and endotypes and prediction of the clinical course of childhood asthma phenotypes.
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Affiliation(s)
- Kedir N Turi
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn
| | - Lindsey Romick-Rosendale
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kelli K Ryckman
- Departments of Epidemiology and Pediatrics, College of Public Health and Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Tina V Hartert
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tenn.
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14
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Chansaenroj J, Tuanthap S, Thanusuwannasak T, Duang-in A, Klinfueng S, Thaneskongtong N, Vutithanachot V, Vongpunsawad S, Poovorawan Y. Human enteroviruses associated with and without diarrhea in Thailand between 2010 and 2016. PLoS One 2017; 12:e0182078. [PMID: 28750058 PMCID: PMC5531555 DOI: 10.1371/journal.pone.0182078] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/12/2017] [Indexed: 11/23/2022] Open
Abstract
Non-bacterial acute gastroenteritis (AGE) associated with virus infection affects individuals living in developing countries, especially children. To investigate whether shedding of certain human enterovirus (EV) is more frequently detected in the stool of individuals with AGE of unknown etiology than individuals without AGE symptoms, we tested fecal samples collected from 2,692 individuals with diarrhea between January 2010 and December 2016. Samples were tested for rotavirus, norovirus, and EV by reverse-transcription polymerase chain reaction (RT-PCR) and adenovirus by PCR. EV-positive samples were subjected to sequencing and phylogenetic analysis to identify EV species and types. Findings were compared to EV found in 1,310 fecal samples from individuals without AGE who were diagnosed with hand, foot, and mouth disease (HFMD). While the majority of viruses identified in AGE consisted of human rotavirus (22.7%), norovirus (11.4%) and adenovirus (9.3%), we identified EV (6.2%) belonging mainly to species B, C, and rhinovirus. In contrast, >92% of EV found without AGE symptoms belonged to species A. Although AGE symptoms are not often attributed to EV infection, EV was associated with diarrhea of unknown etiology at least in 3.4% of AGE cases. While CV-A6 was most likely to be found in stools of HFMD patients, rhinovirus A and C were the two most common EV species associated with AGE. Elucidating group-specific EV infection in diseases with and without AGE will be useful in assisting identification, clinical management, and the surveillance of EV infection in the community.
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Affiliation(s)
- Jira Chansaenroj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supansa Tuanthap
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thanundorn Thanusuwannasak
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ausanee Duang-in
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirapa Klinfueng
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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15
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Abstract
Enteroviruses are RNA viruses that are responsible for both mild gastroenteritis and mild respiratory illnesses as well as debilitating diseases such as meningitis and myocarditis. The disease burden of enteroviruses in the United States is difficult to assess because most infections are not recorded. Since infected individuals shed enterovirus in feces and urine, surveillance of municipal wastewater can reveal the diversity of enteroviruses circulating in human populations. Therefore, monthly municipal wastewater samples were collected for 1 year and enteroviruses were quantified by reverse transcriptase quantitative PCR and identified by next-generation, high-throughput sequencing. Enterovirus concentrations ranged from 3.8 to 5.9 log10 equivalent copies/liter in monthly samples. From the mean monthly concentration, it can be estimated that 2.8% of the contributing population was shedding enterovirus daily. Sequence analysis showed that Enterovirus A and Enterovirus B alternate in predominance, with Enterovirus B comprising over 80% of the reads during the summer and fall months and Enterovirus A accounting for >45% of the reads in spring. Enterovirus C was observed throughout the year, while Enterovirus D was present intermittently. Principal-component analysis further supported the date corresponding to enterovirus seasonal trends as CVA6 (Enterovirus A) was predominant in the spring months; CVB3, CVB5, and E9 (Enterovirus B) were predominant in the summer and fall months; and CVA1, CVA19, and CVA22 (Enterovirus C) and EV97 (Enterovirus B) were predominant in winter. Rhinoviruses were also observed. Wastewater monitoring of human enterovirus provided improved insight into the seasonal patterns of enteroviruses circulating in communities and can contribute to understanding of enterovirus disease burden. IMPORTANCE Enterovirus infections are often not tracked or reported to health officials. This makes it hard to know how many people in a community are infected with these viruses at any given time. Here, we explored enterovirus in municipal wastewater to look at this issue. We show that enteroviruses are present year-round in municipal wastewater at levels of up to 800,000 genomic copies per liter. We estimate that, on average, 2.8% of the people contributing to the wastewater shed enterovirus daily. Sequence analysis of the viral capsid protein 4 gene shows that 8 enterovirus types are key drivers of seasonal trends. Populations of Enterovirus A members peak in the spring, while Enterovirus B types are most prevalent during the summer and fall months and Enterovirus C members influence the winter months. Enterovirus D was observed sporadically and did not influence seasonal trends.
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16
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Seppälä E, Sillanpää S, Nurminen N, Huhtala H, Toppari J, Ilonen J, Veijola R, Knip M, Sipilä M, Laranne J, Oikarinen S, Hyöty H. Human enterovirus and rhinovirus infections are associated with otitis media in a prospective birth cohort study. J Clin Virol 2016; 85:1-6. [PMID: 27780081 DOI: 10.1016/j.jcv.2016.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/16/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Human enteroviruses (HEVs) and rhinoviruses (HRVs) have been linked to acute otitis media (AOM). OBJECTIVES The present study evaluates the aforementioned association in a birth cohort setting. STUDY DESIGN The cohort included 286 healthy infants (191 boys) followed from birth up to the age of 2 years in the Type 1 Diabetes Prediction and Prevention study in Finland. Stool samples were collected monthly and analyzed for the presence of HRV and HEV RNA using RT-PCR. Clinical symptoms were recorded by a questionnaire every 3-6 months. RESULTS Altogether 610 AOM episodes were reported during the follow-up. 9.8% of the stool samples were positive for HRV and 6.8% for HEV. HRV positivity peaked at the age of 3-6 months declining gradually after this age, whereas HEV positivity peaked later, at the age of 12-24 months. The risk of AOM was increased in children who were HEV positive at least once at the age of 6-12 months (OR 2.2 [95%CI 1.1-4.2], P=0.023) or who were HRV positive at least once at the age of 18-24 months (OR 2.3 [95%CI 1.0-5.2], P=0.042). Having an older sibling, short breast-feeding and maternal smoking during pregnancy were also significantly associated with AOM. CONCLUSIONS HRV and HEV infections are frequent during the first months of life. The observed trend for increased risk of AOM in HRV and HEV positive children is in line with the results from hospital series suggesting that these viruses may play an independent role in the pathogenesis of AOM.
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Affiliation(s)
- Elina Seppälä
- School of Medicine, University of Tampere, Lääkärinkatu 1, FIN-33520, Tampere, Finland.
| | - Saara Sillanpää
- Department of Anatomy, School of Medicine, University of Tampere, Finland; Department of Otorhinolaryngology, Head and Neck Surgery, Tampere University Hospital and School of Medicine, University of Tampere, Finland
| | - Noora Nurminen
- School of Medicine, University of Tampere, Lääkärinkatu 1, FIN-33520, Tampere, Finland
| | - Heini Huhtala
- School of Health Sciences, University of Tampere, Tampere, Finland
| | - Jorma Toppari
- Department of Physiology, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku and Turku University Hospital, Turku, Finland
| | - Riitta Veijola
- Department of Pediatrics, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Markku Sipilä
- Department of Otorhinolaryngology, Head and Neck Surgery, Tampere University Hospital and School of Medicine, University of Tampere, Finland
| | - Jussi Laranne
- Department of Otorhinolaryngology, Head and Neck Surgery, Tampere University Hospital and School of Medicine, University of Tampere, Finland
| | - Sami Oikarinen
- School of Medicine, University of Tampere, Lääkärinkatu 1, FIN-33520, Tampere, Finland
| | - Heikki Hyöty
- School of Medicine, University of Tampere, Lääkärinkatu 1, FIN-33520, Tampere, Finland; Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
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17
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Prevalence and molecular characterization of human rhinovirus in stool samples of individuals with and without acute gastroenteritis. J Med Virol 2016; 89:801-808. [DOI: 10.1002/jmv.24698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2016] [Indexed: 11/07/2022]
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18
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Oude Munnink BB, van der Hoek L. Viruses Causing Gastroenteritis: The Known, The New and Those Beyond. Viruses 2016; 8:E42. [PMID: 26867198 PMCID: PMC4776197 DOI: 10.3390/v8020042] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/15/2016] [Accepted: 01/23/2016] [Indexed: 02/07/2023] Open
Abstract
The list of recently discovered gastrointestinal viruses is expanding rapidly. Whether these agents are actually involved in a disease such as diarrhea is the essential question, yet difficult to answer. In this review a summary of all viruses found in diarrhea is presented, together with the current knowledge about their connection to disease.
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Affiliation(s)
- Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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19
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Royston L, Tapparel C. Rhinoviruses and Respiratory Enteroviruses: Not as Simple as ABC. Viruses 2016; 8:E16. [PMID: 26761027 PMCID: PMC4728576 DOI: 10.3390/v8010016] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/09/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022] Open
Abstract
Rhinoviruses (RVs) and respiratory enteroviruses (EVs) are leading causes of upper respiratory tract infections and among the most frequent infectious agents in humans worldwide. Both are classified in the Enterovirus genus within the Picornaviridae family and they have been assigned to seven distinct species, RV-A, B, C and EV-A, B, C, D. As viral infections of public health significance, they represent an important financial burden on health systems worldwide. However, the lack of efficient antiviral treatment or vaccines against these highly prevalent pathogens prevents an effective management of RV-related diseases. Current advances in molecular diagnostic techniques have revealed the presence of RV in the lower respiratory tract and its role in lower airway diseases is increasingly reported. In addition to an established etiological role in the common cold, these viruses demonstrate an unexpected capacity to spread to other body sites under certain conditions. Some of these viruses have received particular attention recently, such as EV-D68 that caused a large outbreak of respiratory illness in 2014, respiratory EVs from species C, or viruses within the newly-discovered RV-C species. This review provides an update of the latest findings on clinical and fundamental aspects of RV and respiratory EV, including a summary of basic knowledge of their biology.
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Affiliation(s)
- Léna Royston
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Caroline Tapparel
- University of Geneva Faculty of Medicine, 1 Rue Michel-Servet, 1205 Geneva, Switzerland.
- Laboratory of Virology, Division of Infectious Diseases, University of Geneva Hospitals, 4 Rue Gabrielle Perret-Gentil, 1211 Geneva 14, Switzerland.
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20
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Jin D, Heo TH, Byeon JH, Kim GH, Kim MK, Eun SH, Eun BL. Analysis of clinical information and reverse transcriptase-polymerase chain reaction for early diagnosis of enteroviral meningitis. KOREAN JOURNAL OF PEDIATRICS 2015; 58:446-50. [PMID: 26692881 PMCID: PMC4675926 DOI: 10.3345/kjp.2015.58.11.446] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 11/27/2022]
Abstract
Purpose Meningitis is among the most common infections affecting the central nervous system. It can be difficult to determine the exact pathogen responsible for the infection and patients are often treated with empiric antibiotics. This study was conducted to identify the most common clinical characteristics of enteroviral meningitis in children and evaluate the diagnostic efficacy of reverse transcriptase-polymerase chain reaction (RT-PCR) for early detection of an enterovirus. Methods We analyzed the medical records of children admitted to Korea University Medical Center and diagnosed with meningitis on the basis of cerebrospinal fluid (CSF) analysis and RT-PCR from CSF and other samples from January 2010 to August 2013. Results A total of 333 patients were enrolled and classified into four groups based on diagnosis: enteroviral meningitis (n=110), bacterial meningitis (n=23), other viral meningitis (n=36), and unknown etiology (n=164). Patients with bacterial meningitis were younger than those in the other groups (P<0.001). Pleocytosis in CSF was similar across all groups. Of patients in the enteroviral meningitis group, 92.7% were diagnosed based on RT-PCR findings. Mean length of hospital stay for patients with enteroviral meningitis was 6.08 days, which was significantly shorter than that for patients with meningitis of bacterial etiology (19.73 days, P<0.001). Conclusion Diagnosis of enteroviral meningitis before viral culture results are available is possible using RT-PCR. Accurate diagnosis reduces the length of hospital stay and helps to avoid unnecessary empiric antibiotic treatment.
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Affiliation(s)
- Dahee Jin
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Tae Hoon Heo
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Jung Hye Byeon
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Gun-Ha Kim
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Mi Kyung Kim
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - So-Hee Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Baik-Lin Eun
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
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21
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Linsuwanon P, Poovorawan Y, Li L, Deng X, Vongpunsawad S, Delwart E. The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses. PLoS One 2015; 10:e0135573. [PMID: 26288145 PMCID: PMC4545796 DOI: 10.1371/journal.pone.0135573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 07/24/2015] [Indexed: 01/21/2023] Open
Abstract
Hand, foot, and mouth disease (HFMD) affects infant and young children. A viral metagenomic approach was used to identify the eukaryotic viruses in fecal samples from 29 Thai children with clinical diagnosis of HFMD collected during the 2012 outbreak. These children had previously tested negative by PCR for enterovirus 71 and coxsackievirus A16 and A6. Deep sequencing revealed nine virus families: Picornaviridae, Astroviridae, Parvoviridae, Caliciviridae, Paramyxoviridae, Adenoviridae, Reoviridae, Picobirnaviridae, and Polyomaviridae. The highest number of viral sequences belonged to human rhinovirus C, astrovirus-MLB2, and coxsackievirus A21. Our study provides an overview of virus community and highlights a broad diversity of viruses found in feces from children with HFMD.
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Affiliation(s)
- Piyada Linsuwanon
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
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22
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Tomusange K, Yu W, Suhrbier A, Wijesundara D, Grubor-Bauk B, Gowans EJ. Engineering human rhinovirus serotype-A1 as a vaccine vector. Virus Res 2015; 203:72-6. [PMID: 25869880 DOI: 10.1016/j.virusres.2015.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/28/2015] [Accepted: 04/01/2015] [Indexed: 01/30/2023]
Abstract
Herein we describe the construction of recombinant human rhinoviruses (rHRVs) encoding HIV Gag or Tat by inserting the full length tat gene or regions of the gag gene flanked by sequences encoding the HRV 2A protease cleavage site into the junction between HRV genes encoding structural (P1) and non-structural (P2) proteins. Most recombinants were unstable, but this was corrected by mutation of the flanking cleavage sites. Thereafter, all rHRV constructs retained the inserts throughout six passages. Such constructs may find utility as vaccine vectors to generate mucosal immunity.
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Affiliation(s)
- Khamis Tomusange
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Wenbo Yu
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Danushka Wijesundara
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Branka Grubor-Bauk
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Eric J Gowans
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia.
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23
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Disseminated rhinovirus C8 infection with infectious virus in blood and fatal outcome in a child with repeated episodes of bronchiolitis. J Clin Microbiol 2015; 53:1775-7. [PMID: 25694520 DOI: 10.1128/jcm.03484-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/14/2015] [Indexed: 01/23/2023] Open
Abstract
We report a fatal case of acute lower respiratory tract disease with human rhinovirus C (HRV-C) as the unique cause in a 19-month-old girl with a history of repeated episodes of bronchiolitis. HRV-C type 8 nucleic acids were observed in respiratory, stool, and cerebrospinal fluid samples, and infectious virions were isolated from patient serum after inoculation onto reconstituted airway epithelia.
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24
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Abstract
Human rhinoviruses (HRVs) are widespread respiratory pathogens and a major cause of acute respiratory tract infections. The aim of this study was to investigate the molecular epidemiology of rhinovirus infections in children in Cyprus over three consecutive winter seasons. From a total of 116 rhinovirus-positive samples, 68 were sequenced in the 5'-UTR and VP4/VP2 regions. Thirty-six (52.9%) samples were identified as HRV-A and 27 (39.7%) as HRV-C, with only five (7.4%) samples belonging to the HRV-B species. Of these, a total of 46 different genotypes were identified. In the VP2/VP4 phylogenetic tree all strains clustered in three different well-defined clades, whereas the 5'-UTR tree exhibited clades with a mixed clustering of HRV-A and HRV-C strains reflecting the evolutionary history of recombination between HRV-A and HRV-C that has been observed previously. In summary, a high intra- and inter-season diversity of HRV types was observed. Despite its geographical isolation the frequency of HRV species in Cyprus is comparable to that reported in other regions of the world supporting the concept of an unrestricted global circulation. This study assesses, for the first time, the epidemiology of rhinovirus infections in Cypriot children and will be helpful to clinicians and researchers interested in the treatment and control of viral respiratory tract infections.
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Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 2014; 11:146. [PMID: 25112200 PMCID: PMC4254409 DOI: 10.1186/1743-422x-11-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Methods VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. Results Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. Conclusion Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan.
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Parker LC, Stokes CA, Sabroe I. Rhinoviral infection and asthma: the detection and management of rhinoviruses by airway epithelial cells. Clin Exp Allergy 2014; 44:20-8. [PMID: 24355017 DOI: 10.1111/cea.12182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 07/02/2013] [Accepted: 07/22/2013] [Indexed: 11/28/2022]
Abstract
Human rhinoviruses (HRV) have been linked to the development of childhood asthma and recurrent acute asthma exacerbations throughout life, and contribute considerably to the healthcare and economic burden of this disease. However, the ability of HRV infections to trigger exacerbations, and the link between allergic status and HRV responsiveness, remains incompletely understood. Whilst the receptors on human airway cells that detect and are utilized by most HRV group A and B, but not C serotypes are known, how endosomal pattern recognition receptors (PRRs) detect HRV replication products that are generated within the cytoplasm remains somewhat of an enigma. In this article, we explore a role for autophagy, a cellular homeostatic process that allows the cell to encapsulate its own cytosolic constituents, as the crucial mechanism controlling this process and regulating the innate immune response of airway epithelial cells to viral infection. We will also briefly describe some of the recent insights into the immune responses of the airway to HRV, focusing on neutrophilic inflammation that is a potentially unwanted feature of the acute response to viral infection, and the roles of IL-1 and Pellinos in the regulation of responses to HRV.
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Affiliation(s)
- L C Parker
- Academic Unit of Respiratory Medicine, Department of Infection and Immunity, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, UK
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27
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Abstract
Non-influenza respiratory virus infections are common worldwide and contribute to morbidity and mortality in all age groups. The recently identified Middle East respiratory syndrome coronavirus has been associated with rapidly progressive pneumonia and high mortality rate. Adenovirus 14 has been increasingly recognized in severe acute respiratory illness in both military and civilian individuals. Rhinovirus C and human bocavirus type 1 have been commonly detected in infants and young children with respiratory tract infection and studies have shown a positive correlation between respiratory illness and high viral loads, mono-infection, viremia, and/or serologically-confirmed primary infection.
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Affiliation(s)
- James J Dunn
- Department of Pathology and Laboratory Medicine, Cook Children's Medical Center, 801 Seventh Avenue, Fort Worth, TX 76104, USA.
| | - Melissa B Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Campus Box 7525, Chapel Hill, NC 27599-7525, USA
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Harvala H, Calvert J, Van Nguyen D, Clasper L, Gadsby N, Molyneaux P, Templeton K, McWilliams Leitch C, Simmonds P. Comparison of diagnostic clinical samples and environmental sampling for enterovirus and parechovirus surveillance in Scotland, 2010 to 2012. ACTA ACUST UNITED AC 2014; 19. [PMID: 24762664 DOI: 10.2807/1560-7917.es2014.19.15.20772] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human enteroviruses (EV) and parechoviruses (HPeV) within the family Picornaviridae are the most common causes of viral central nervous system (CNS)-associated infections including meningitis and neonatal sepsis-like disease. The frequencies of EV and HPeV types identified in clinical specimens collected in Scotland over an eight-year period were compared to those identified in sewage surveillance established in Edinburgh. Of the 35 different EV types belonging to four EV species (A to D) and the four HPeV types detected in this study, HPeV3 was identified as the most prevalent picornavirus in cerebrospinal fluid samples, followed by species B EV. Interestingly, over half of EV and all HPeV CNS-associated infections were observed in young infants (younger than three months). Detection of species A EV including coxsackievirus A6 and EV71 in clinical samples and sewage indicates that these viruses are already widely circulating in Scotland. Furthermore, species C EV were frequently identified EV in sewage screening but they were not present in any of 606 EV-positive clinical samples studied, indicating their likely lower pathogenicity. Picornavirus surveillance is important not only for monitoring the changing epidemiology of these infections but also for the rapid identification of spread of emerging EV and/or HPeV types.
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Affiliation(s)
- H Harvala
- Infection and Immunity, Roslin Institute, University of Edinburgh, Edinburgh United Kingdom
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29
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High rates of infection with novel enterovirus variants in wild populations of mandrills and other old world monkey species. J Virol 2014; 88:5967-76. [PMID: 24623420 DOI: 10.1128/jvi.00088-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Enteroviruses (EVs) are a genetically and antigenically diverse group of viruses infecting humans. A mostly distinct set of EV variants have additionally been documented to infect wild apes and several, primarily captive, Old World monkey (OWM) species. To investigate the prevalence and genetic characteristics of EVs infecting OWMs in the wild, fecal samples from mandrills (Mandrillus sphinx) and other species collected in remote regions of southern Cameroon were screened for EV RNA. Remarkably high rates of EV positivity were detected in M. sphinx (100 of 102 screened), Cercocebus torquatus (7/7), and Cercopithecus cephus (2/4), with high viral loads indicative of active infection. Genetic characterization in VP4/VP2 and VP1 regions allowed EV variants to be assigned to simian species H (EV-H) and EV-J (including one or more new types), while seven matched simian EV-B variants, SA5 and EV110 (chimpanzee). Sequences from the remaining 70 formed a new genetic group distinct in VP4/2 and VP1 region from all currently recognized human or simian EV species. Complete genome sequences were obtained from three to determine their species assignment. In common with EV-J and the EV-A A13 isolate, new group sequences were chimeric, being most closely related to EV-A in capsid genes and to EV-B in the nonstructural gene region. Further recombination events created different groupings in 5' and 3' untranslated regions. While clearly a distinct EV group, the hybrid nature of new variants prevented their unambiguous classification as either members of a new species or as divergent members of EV-A using current International Committee on Taxonomy of Viruses (ICTV) assignment criteria. IMPORTANCE This study is the first large-scale investigation of the frequency of infection and diversity of enteroviruses (EVs) infecting monkeys (primarily mandrills) in the wild. Our findings demonstrate extremely high frequencies of active infection (95%) among mandrills and other Old World monkey species inhabiting remote regions of Cameroon without human contact. EV variants detected were distinct from those infecting human populations, comprising members of enterovirus species B, J, and H and a large novel group of viruses most closely related to species A in the P1 region. The viral sequences obtained contribute substantially to our growing understanding of the genetic diversity of EVs and the existence of interspecies chimerism that characterizes the novel variants in the current study, as well as in previously characterized species A and J viruses infecting monkeys. The latter findings will contribute to future development of consensus criteria for species assignments in enteroviruses and other picornavirus genera.
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Principi N, Daleno C, Esposito S. Human rhinoviruses and severe respiratory infections: is it possible to identify at-risk patients early? Expert Rev Anti Infect Ther 2014; 12:423-30. [PMID: 24559383 DOI: 10.1586/14787210.2014.890048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular methods of viral screening have demonstrated that human rhinoviruses (HRVs) are associated with lower respiratory tract infections (LRTIs, including bronchiolitis and pneumonia), exacerbations of chronic pulmonary disease and the development of asthma. Patients with severe chronic diseases are at greater risk of developing major clinical problems when infected by HRVs, particularly if they are immunocompromised or have a chronic lung disease. Analysing the characteristics of HRVs does not provide any certainty concerning the risk of a poor prognosis and, although viremia seems to be associated with an increased risk of severe HRV infection, the available data are too scanty to be considered conclusive. However, a chest x-ray showing alveolar involvement suggests the potentially negative evolution of a bacterial superinfection. There is therefore an urgent need for more effective diagnostic, preventive and therapeutic measures in order to prevent HRV infection, and identify and treat the patients at highest risk.
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Affiliation(s)
- Nicola Principi
- Department of Pathophysiology and Transplantation, Pediatric High Intensity Care Unit, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
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31
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Chen J, Fu Y, Ju L, Miao X, Shen Y, He L, Wang W, Jin J, Shao L, Sampath R, Ecker DJ, Zhang Y, Li M, Cheng X, Zhang W. Detection and identification of viral pathogens in patients with hand, foot, and mouth disease by multilocus PCR, reverse-transcription PCR and electrospray ionization mass spectrometry. J Clin Virol 2014; 59:115-9. [DOI: 10.1016/j.jcv.2013.11.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/11/2013] [Accepted: 11/18/2013] [Indexed: 11/25/2022]
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Rhinoviruses. VIRAL INFECTIONS OF HUMANS 2014. [PMCID: PMC7120790 DOI: 10.1007/978-1-4899-7448-8_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tapparel C, Sobo K, Constant S, Huang S, Van Belle S, Kaiser L. Growth and characterization of different human rhinovirus C types in three-dimensional human airway epithelia reconstituted in vitro. Virology 2013; 446:1-8. [DOI: 10.1016/j.virol.2013.06.031] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/10/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Rovida F, Campanini G, Piralla A, Adzasehoun KMG, Sarasini A, Baldanti F. Molecular detection of gastrointestinal viral infections in hospitalized patients. Diagn Microbiol Infect Dis 2013; 77:231-5. [PMID: 24035383 PMCID: PMC7125882 DOI: 10.1016/j.diagmicrobio.2013.07.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/10/2013] [Accepted: 07/31/2013] [Indexed: 11/19/2022]
Abstract
Gastrointestinal viral syndromes are a common cause of morbidity and mortality in humans worldwide. Etiological agents include a large number of viruses encompassing several orders, families, and genera. During the period April 2011 to April 2012, 689 stool samples from as many patients hospitalized at the Fondazione IRCCS Policlinico San Matteo of Pavia exhibiting gastrointestinal syndromes were examined for the presence of rotavirus, norovirus, astrovirus, adenovirus, rhinovirus, enterovirus, parechovirus, bocavirus, coronavirus, sapovirus, cosavirus, and aichi virus using polymerase chain reaction assays. Gastrointestinal viral agents were detected in 246 (36%) patients of the 689 analyzed. Adenovirus and norovirus were the most common viruses in this cohort, while aichi virus was the only gastrointestinal agent not detected. Surprisingly, rhinovirus was one of the most frequently detected viruses. However, a potential association with gastroenteritis remains to be confirmed.
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Affiliation(s)
| | | | | | | | | | - Fausto Baldanti
- Corresponding author. Tel.: +39-0382-502420; fax: +39-0382-502599.
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35
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Esposito S, Daleno C, Scala A, Castellazzi L, Terranova L, Sferrazza Papa S, Longo MR, Pelucchi C, Principi N. Impact of rhinovirus nasopharyngeal viral load and viremia on severity of respiratory infections in children. Eur J Clin Microbiol Infect Dis 2013; 33:41-8. [PMID: 23893065 PMCID: PMC7088146 DOI: 10.1007/s10096-013-1926-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/05/2013] [Indexed: 11/26/2022]
Abstract
There are few and partially discordant data regarding nasopharyngeal rhinovirus (RV) load and viremia, and none of the published studies evaluated the two variables together. The aim of this study was to provide new information concerning the clinical relevance of determining nasopharyngeal viral load and viremia when characterising RV infection. Nasopharyngeal swabs were obtained from 251 children upon their admission to hospital because of fever and signs and symptoms of acute respiratory infection in order to identify the virus and determine its nasopharyngeal load, and a venous blood sample was taken in order to evaluate viremia. Fifty children (19.9 %) had RV-positive nasopharyngeal swabs, six (12 %) of whom also had RV viremia: RV-C in four cases (66.6 %), and RV-A and RV-B in one case each. The RV nasopharyngeal load was significantly higher in the children with RV viremia (p < 0.001), who also had a higher respiratory rate (p = 0.02), white blood cell counts (p = 0.008) and C-reactive protein levels (p = 0.006), lower blood O2 saturation levels (P = 0.005), and more often required O2 therapy (p = 0.009). The presence of RV viremia is associated with a significantly higher nasopharyngeal viral load and more severe disease, which suggests that a high nasopharyngeal viral load is a prerequisite for viremia, and that viremia is associated with considerable clinical involvement.
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Affiliation(s)
- S Esposito
- Pediatric Clinic 1, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Commenda 9, 20122, Milano, Italy,
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36
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Savolainen-Kopra C, Simonen-Tikka ML, Klemola P, Blomqvist S, Suomenrinne S, Näntö-Salonen K, Simell O, Roivainen M. Human rhinoviruses in INDIS-study material-evidence for recovery of viable rhinovirus from fecal specimens. J Med Virol 2013; 85:1466-72. [DOI: 10.1002/jmv.23593] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Carita Savolainen-Kopra
- Department of Infectious Disease Surveillance and Control, Virology Unit; National Institute for Health and Welfare (THL); Helsinki Finland
| | - Marja-Leena Simonen-Tikka
- Department of Infectious Disease Surveillance and Control, Virology Unit; National Institute for Health and Welfare (THL); Helsinki Finland
| | - Päivi Klemola
- Department of Infectious Disease Surveillance and Control, Virology Unit; National Institute for Health and Welfare (THL); Helsinki Finland
| | - Soile Blomqvist
- Department of Infectious Disease Surveillance and Control, Virology Unit; National Institute for Health and Welfare (THL); Helsinki Finland
| | | | | | - Olli Simell
- Department of Pediatrics; University of Turku; Turku Finland
| | - Merja Roivainen
- Department of Infectious Disease Surveillance and Control, Virology Unit; National Institute for Health and Welfare (THL); Helsinki Finland
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37
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Tokarz R, Haq S, Sameroff S, Howie SRC, Lipkin WI. Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C. J Gen Virol 2013; 94:1995-2004. [PMID: 23761409 DOI: 10.1099/vir.0.053462-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Saddef Haq
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Stephen R C Howie
- Child Survival Theme, Medical Research Council Unit, Banjul, Fajara, Gambia
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
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Miller EK, Mackay IM. From sneeze to wheeze: what we know about rhinovirus Cs. J Clin Virol 2013; 57:291-9. [PMID: 23714395 DOI: 10.1016/j.jcv.2013.04.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/16/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
While the discovery of HRV-Cs is recent, there are no indications that they are new viruses, or that they are emerging in real-time. Genetically, HRV-Cs are most closely related to the members of HRV-A and HRV-B but even a small genetic difference can impart encompass significant changes to their clinical impact, complicated by a diverse human background of prior virus exposure and underlying host immune and disease variability. It is well known that HRVs are a major trigger of asthma exacerbations and HRV-Cs are now under investigation for their potential involvement in asthma inception. The newly described HRV-Cs account for a large proportion of HRV-related illness, including common colds and wheezing exacerbations. HRV-Cs are genetically diverse and appear to circulate with seasonal variation, exchanging dominance with HRV-A. Whether HRV-Cs are consistently more pathogenic or "asthmagenic" is unproven. Antigenic diversity complicates passive and active prophylactic interventions (i.e. antibodies or vaccines), so further identification and characterisation of individual types (and their neutralising antigens) is likely to inform future preventive strategies. In the meantime, new antivirals should benefit groups at risk of the most severe disease.
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Affiliation(s)
- E Kathryn Miller
- Department of Pediatrics, Division of Allergy, Immunology, and Pulmonary Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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39
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McIntyre CL, Knowles NJ, Simmonds P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol 2013; 94:1791-1806. [PMID: 23677786 PMCID: PMC3749525 DOI: 10.1099/vir.0.053686-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human rhinoviruses (HRVs) frequently cause mild upper respiratory tract infections and more severe disease manifestations such as bronchiolitis and asthma exacerbations. HRV is classified into three species within the genus Enterovirus of the family Picornaviridae. HRV species A and B contain 75 and 25 serotypes identified by cross-neutralization assays, although the use of such assays for routine HRV typing is hampered by the large number of serotypes, replacement of virus isolation by molecular methods in HRV diagnosis and the poor or absent replication of HRV species C in cell culture. To address these problems, we propose an alternative, genotypic classification of HRV-based genetic relatedness analogous to that used for enteroviruses. Nucleotide distances between 384 complete VP1 sequences of currently assigned HRV (sero)types identified divergence thresholds of 13, 12 and 13 % for species A, B and C, respectively, that divided inter- and intra-type comparisons. These were paralleled by 10, 9.5 and 10 % thresholds in the larger dataset of >3800 VP4 region sequences. Assignments based on VP1 sequences led to minor revisions of existing type designations (such as the reclassification of serotype pairs, e.g. A8/A95 and A29/A44, as single serotypes) and the designation of new HRV types A101–106, B101–103 and C34–C51. A protocol for assignment and numbering of new HRV types using VP1 sequences and the restriction of VP4 sequence comparisons to type identification and provisional type assignments is proposed. Genotypic assignment and identification of HRV types will be of considerable value in the future investigation of type-associated differences in disease outcomes, transmission and epidemiology.
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Affiliation(s)
- Chloe L McIntyre
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
| | - Nick J Knowles
- Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Peter Simmonds
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH15 9RG, UK
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McIntyre CL, Savolainen-Kopra C, Hovi T, Simmonds P. Recombination in the evolution of human rhinovirus genomes. Arch Virol 2013; 158:1497-515. [PMID: 23443931 DOI: 10.1007/s00705-013-1634-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Human rhinoviruses (HRV) are highly prevalent human respiratory pathogens that belong to the genus Enterovirus. Although recombination within the coding region is frequent in other picornavirus groups, most evidence of recombination in HRV has been restricted to the 5' untranslated region. We analysed the occurrence of recombination within published complete genome sequences of members of all three HRV species and additionally compared sequences from HRV strains spanning 14 years. HRV-B and HRV-C showed very little evidence of recombination within the coding region. In contrast, HRV-A sequences appeared to have undergone a large number of recombination events, typically involving whole type groups. This suggests that HRV-A may have been subject to extensive recombination during the period of diversification into types. This study demonstrates the rare and sporadic nature of contemporary recombination of HRV strains and contrasts with evidence of extensive recombination within HRV-A and between members of different species during earlier stages in its evolutionary diversification.
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Affiliation(s)
- Chloe L McIntyre
- Infection and Immunity Division, Roslin Institute, University of Edinburgh, Edinburgh, UK.
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41
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Abstract
Human rhinoviruses (HRVs), first discovered in the 1950s, are responsible for more than one-half of cold-like illnesses and cost billions of dollars annually in medical visits and missed days of work. Advances in molecular methods have enhanced our understanding of the genomic structure of HRV and have led to the characterization of three genetically distinct HRV groups, designated groups A, B, and C, within the genus Enterovirus and the family Picornaviridae. HRVs are traditionally associated with upper respiratory tract infection, otitis media, and sinusitis. In recent years, the increasing implementation of PCR assays for respiratory virus detection in clinical laboratories has facilitated the recognition of HRV as a lower respiratory tract pathogen, particularly in patients with asthma, infants, elderly patients, and immunocompromised hosts. Cultured isolates of HRV remain important for studies of viral characteristics and disease pathogenesis. Indeed, whether the clinical manifestations of HRV are related directly to viral pathogenicity or secondary to the host immune response is the subject of ongoing research. There are currently no approved antiviral therapies for HRVs, and treatment remains primarily supportive. This review provides a comprehensive, up-to-date assessment of the basic virology, pathogenesis, clinical epidemiology, and laboratory features of and treatment and prevention strategies for HRVs.
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Affiliation(s)
- Samantha E. Jacobs
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, USA
| | - Daryl M. Lamson
- Laboratory of Viral Diseases, Wadsworth Center, Albany, New York, USA
| | | | - Thomas J. Walsh
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, USA
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Honkanen H, Oikarinen S, Peltonen P, Simell O, Ilonen J, Veijola R, Knip M, Hyöty H. Human rhinoviruses including group C are common in stool samples of young Finnish children. J Clin Virol 2012; 56:250-4. [PMID: 23273491 DOI: 10.1016/j.jcv.2012.11.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 11/08/2012] [Accepted: 11/13/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Human rhinoviruses (HRVs) are common causes of viral respiratory infections. They have been widely studied in respiratory samples in hospital patient series but only a few studies have been performed to assess their occurrence in other sample types and their circulation in healthy children background population. OBJECTIVES To analyze the frequency of HRVs in the background population in Finland by screening HRV RNA from stool samples longitudinally collected in a cohort of young children. STUDY DESIGN Altogether 4184 stool samples were collected regularly from a cohort of children who were observed from birth. Samples were screened for the presence of RNA of HRVs using RT-PCR. HRV specific sequences were identified by sequencing the VP1 or VP4/VP2 coding region. Virus isolation was performed using four different cell lines and the result was confirmed by real time PCR. RESULTS A total of 9% of the stool samples were positive for HRV RNA. Sequence analysis indicated that the most prevalent species was HRV-A, and the most prevalent serotype was HRV61. HRV-B and HRV-C species were also detected. One of the six tested rhinovirus positive samples retained its infectivity and was able to grow in RD and GMK cells. CONCLUSIONS Our study shows that HRVs are frequently detected in the stool samples from the population of young children. We also show that HRV-C, which can cause severe illnesses in children, is commonly circulating in young children in Finland.
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Affiliation(s)
- Hanna Honkanen
- University of Tampere, School of Medicine, Tampere, Finland.
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Tapparel C, Siegrist F, Petty TJ, Kaiser L. Picornavirus and enterovirus diversity with associated human diseases. INFECTION GENETICS AND EVOLUTION 2012. [PMID: 23201849 DOI: 10.1016/j.meegid.2012.10.016] [Citation(s) in RCA: 313] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Members of the Picornaviridae family are non-enveloped, positive-stranded RNA viruses with a 30nm icosahedral capsid. This virus family exhibits a considerable amount of genetic variability driven both by mutation and recombination. Recently, three previously unknown human picornaviruses, namely the human Saffold cardiovirus, cosavirus and salivirus, have been identified in stools or respiratory samples from subjects presenting symptoms ranging from gastroenteritis to acute flaccid paralysis. However, these viruses were also frequently detected in asymptomatic subjects and their clinical relevance remains to be elucidated. The Enterovirus genus is a prototype example of the Picornaviridae heterogeneity at both genetic and phenotypic levels. This genus is divided into 10 species, seven of which contain human viruses, including three Rhinovirus species. Both human rhino- and enteroviruses are also characterized by high levels of genetic variability, as exemplified by the existence of over 250 different serotypes and the recent discovery of new enterovirus genotypes and the Rhinovirus C species. Despite their common genomic features, rhinoviruses are restricted to the respiratory tract, whereas the vast majority of enteroviruses infect the gastrointestinal tract and can spread to other organs, such as the heart or the central nervous system. Understanding the genetic determinants of such phenotypic diversity is an important challenge and a field for future investigation. Better characterization of these ubiquitous human pathogens may help to develop vaccines or antiviral treatments and to monitor the emergence of new strains.
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Affiliation(s)
- Caroline Tapparel
- Laboratory of Virology, Division of Infectious Diseases and Division of Laboratory Medicine, University of Geneva Hospitals, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
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Productive entry pathways of human rhinoviruses. Adv Virol 2012; 2012:826301. [PMID: 23227049 PMCID: PMC3513715 DOI: 10.1155/2012/826301] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 10/18/2012] [Indexed: 12/20/2022] Open
Abstract
Currently, complete or partial genome sequences of more than 150 human rhinovirus (HRV) isolates are known. Twelve species A use members of the low-density lipoprotein receptor family for cell entry, whereas the remaining HRV-A and all HRV-B bind ICAM-1. HRV-Cs exploit an unknown receptor. At least all A and B type viruses depend on receptor-mediated endocytosis for infection. In HeLa cells, they are internalized mainly by a clathrin- and dynamin-dependent mechanism. Upon uptake into acidic compartments, the icosahedral HRV capsid expands by ~4% and holes open at the 2-fold axes, close to the pseudo-3-fold axes and at the base of the star-shaped dome protruding at the vertices. RNA-protein interactions are broken and new ones are established, the small internal myristoylated capsid protein VP4 is expelled, and amphipathic N-terminal sequences of VP1 become exposed. The now hydrophobic subviral particle attaches to the inner surface of endosomes and transfers its genomic (+) ssRNA into the cytosol. The RNA leaves the virus starting with the poly(A) tail at its 3′-end and passes through a membrane pore contiguous with one of the holes in the capsid wall. Alternatively, the endosome is disrupted and the RNA freely diffuses into the cytoplasm.
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Community acquired respiratory and gastrointestinal viral infections: challenges in the immunocompromised host. Curr Opin Infect Dis 2012; 25:423-30. [PMID: 22766648 DOI: 10.1097/qco.0b013e328355660b] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Newer molecular diagnostic techniques have advanced the field of clinical microbiology and infectious diseases, particularly with respect to characterizing the role that community acquired viruses play in the clinical course and outcomes of the immunocompromised host. This review will examine recent studies describing the impact of adenovirus, rhinovirus, hepatitis E and norovirus in the course of solid organ and stem cell transplant recipients, as well as their epidemiology and implications for infection prevention and control. RECENT FINDINGS Adenovirus transmission is poorly understood; recent studies increasingly point to reactivation of latent infection in the immunocompromised host. Rhinovirus shedding can persist for weeks after acute viral infection, complicating hospital infection control policies. Hepatitis E is increasingly recognized as a potential pathogen in the stem cell and solid organ transplant population, and should be considered in the work-up for unexplained liver function test abnormalities. Similar to rhinovirus, norovirus shedding from the gastrointestinal tract may persist for months in the immunocompromised host; infected patients are at a higher risk for transmitting norovirus compared with infected healthcare workers. SUMMARY Additional studies are needed, particularly with respect to transmission, for these community acquired viral infections, which often have devastating consequences in the immunocompromised patient population.
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Wang CYT, Greer RM, Delwart E, Sloots TP, Mackay IM. A newly designed real-time RT-PCR for SAFV detects SAFV-2 and SAFV-3 in the respiratory tracts of ill children during 2011. J Clin Virol 2012; 55:173-6. [PMID: 22832058 PMCID: PMC7108345 DOI: 10.1016/j.jcv.2012.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 01/06/2023]
Affiliation(s)
- C Y T Wang
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Sir Albert Sakzewski Virus Research Centre, Children's Health Services, The University of Queensland, Australia
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Development and assay of RNA transcripts of enterovirus species A to D, rhinovirus species a to C, and human parechovirus: assessment of assay sensitivity and specificity of real-time screening and typing methods. J Clin Microbiol 2012; 50:2910-7. [PMID: 22740708 DOI: 10.1128/jcm.01172-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification methods such as the PCR have had a major impact on the diagnosis of viral infections, often achieving greater sensitivities and shorter turnaround times than conventional assays and an ability to detect viruses refractory to conventional isolation methods. Their effectiveness is, however, significantly influenced by assay target sequence variability due to natural diversity and rapid sequence changes in viruses that prevent effective binding of primers and probes. This was investigated for a diverse range of enteroviruses (EVs; species A to D), human rhinoviruses (HRVs; species A to C), and human parechovirus (HPeV) in a multicenter assay evaluation using a series of full-length prequantified RNA transcripts. RNA concentrations were quantified by absorption (NanoDrop) and fluorescence methods (RiboGreen) prior to dilution in buffer supplemented with RNase inhibitors and carrier RNA. RNA transcripts were extremely stable, showing minimal degradation after prolonged storage at temperatures between ambient and -20°C and after multiple freeze-thaw cycles. Transcript dilutions distributed to six referral laboratories were screened by real-time reverse transcriptase PCR assays using different primers and probes. All of the laboratories reported high assay sensitivities for EV and HPeV transcripts approaching single copies and similar amplification kinetics for all four EV species. HRV detection sensitivities were more variable, often with substantially impaired detection of HRV species C. This could be accounted for in part by the placement of primers and probes to genetically variable target regions. Transcripts developed in this study provide reagents for the ongoing development of effective diagnostics that accommodate increasing knowledge of genetic heterogeneity of diagnostic targets.
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