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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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102
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Garcia J, Espejo V, Nelson M, Sovero M, Villaran MV, Gomez J, Barrantes M, Sanchez F, Comach G, Arango AE, Aguayo N, de Rivera IL, Chicaiza W, Jimenez M, Aleman W, Rodriguez F, Gonzales MS, Kochel TJ, Halsey ES. Human rhinoviruses and enteroviruses in influenza-like illness in Latin America. Virol J 2013; 10:305. [PMID: 24119298 PMCID: PMC3854537 DOI: 10.1186/1743-422x-10-305] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 07/31/2013] [Indexed: 11/10/2022] Open
Abstract
Background Human rhinoviruses (HRVs) belong to the Picornaviridae family with high similarity to human enteroviruses (HEVs). Limited data is available from Latin America regarding the clinical presentation and strains of these viruses in respiratory disease. Methods We collected nasopharyngeal swabs at clinics located in eight Latin American countries from 3,375 subjects aged 25 years or younger who presented with influenza-like illness. Results Our subjects had a median age of 3 years and a 1.2:1.0 male:female ratio. HRV was identified in 16% and HEV was identified in 3%. HRVs accounted for a higher frequency of isolates in those of younger age, in particular children < 1 years old. HRV-C accounted for 38% of all HRVs detected. Phylogenetic analysis revealed a high proportion of recombinant strains between HRV-A/HRV-C and between HEV-A/HEV-B. In addition, both EV-D68 and EV-A71 were identified. Conclusions In Latin America as in other regions, HRVs and HEVs account for a substantial proportion of respiratory viruses identified in young people with ILI, a finding that provides additional support for the development of pharmaceuticals and vaccines targeting these pathogens.
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103
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Tsukagoshi H, Ishioka T, Noda M, Kozawa K, Kimura H. Molecular epidemiology of respiratory viruses in virus-induced asthma. Front Microbiol 2013; 4:278. [PMID: 24062735 PMCID: PMC3771312 DOI: 10.3389/fmicb.2013.00278] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 08/27/2013] [Indexed: 11/22/2022] Open
Abstract
Acute respiratory illness (ARI) due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma.
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Affiliation(s)
- Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences Gunma, Japan
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104
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Etemadi MR, Othman N, Savolainen-Kopra C, Sekawi Z, Wahab N, Sann LM. Biodiversity and clinico-demographic characteristics of human rhinoviruses from hospitalized children with acute lower respiratory tract infections in Malaysia. J Clin Virol 2013; 58:671-7. [PMID: 23932333 PMCID: PMC7172529 DOI: 10.1016/j.jcv.2013.05.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/10/2013] [Accepted: 05/23/2013] [Indexed: 11/25/2022]
Abstract
Background There is accumulating evidence that human rhinovirus (HRV) causes acute lower respiratory tract infections (ALRTI). Recently, HRV-C was identified as a new species of HRV, but its spectrum of clinical disease is not well understood. Objectives We investigated the molecular epidemiology, demographic and clinical characteristics of HRVs among hospitalized children with ALRIs. Study design One hundred and sixty-five nasopharangeal aspirates taken from children <5 years hospitalized with ALRTIs in Serdang Hospital, Malaysia, were subject to reverse transcriptase-PCR for HRV. Phylogenetic analysis on VP4/VP2 and 5′-NCR regions was used to further characterize HRV. Other respiratory viruses were also investigated using semi-nested multiplex RT-PCR assay. Clinical parameters were analyzed between HRV, RSV and IFV-A mono-infections and between HRV species. Results HRV was detected in 54 (33%) patients for both single (36 samples) and multiple (18 samples) infections, 61.1% (22/36) represents HRV-A strains while the remaining 14 HRV-C. Strain P51was the first reported representative of HRV98. The majority of the single HRV cases were in the second half of infancy; HRV-C occurred among older children compared with HRV-A. HRV children were admitted significantly earlier and less febrile than RSV and IFV-A infection. HRV-C infected children were more likely to have rhonchi and vomiting as compared to HRV-A. Pneumonia was the most common discharge diagnosis followed by bronchiolitis and post-viral wheeze in HRV patients. Conclusion Our study showed high prevalence of HRVs and detection of HRV-C among hospitalized children with ALRTIs in Malaysia. Analysis of clinical parameters suggested specific features associated with HRVs infections and specific HRV groups.
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Affiliation(s)
- Mohammad Reza Etemadi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Malaysia
| | - Norlijah Othman
- Department of Pediatrics, Faculty of Medicine and Health Sciences, University Putra Malaysia, Malaysia
- Corresponding author at: Department of Pediatrics, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. Tel.: +60 389472602; fax: +60 389472805.
| | - Carita Savolainen-Kopra
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Malaysia
| | - NoraAbd Wahab
- Department of Paediatrics, Hospital Serdang, Malaysia
| | - Lye Munn Sann
- Department of Community Health, Faculty of Medicine and Health Sciences, University Putra Malaysia, Malaysia
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Shen J, Wang F, Li F, Housley R, Carolan H, Yasuda I, Burrows E, Binet R, Sampath R, Zhang J, Allard MW, Meng J. Rapid Identification and Differentiation of Non-O157 Shiga Toxin–ProducingEscherichia coliUsing Polymerase Chain Reaction Coupled to Electrospray Ionization Mass Spectrometry. Foodborne Pathog Dis 2013; 10:737-43. [DOI: 10.1089/fpd.2012.1469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jinling Shen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
- Zhangjiagang Entry-Exit Inspection and Quarantine Bureau, Zhangjiagang, Jiangsu Province, China
| | - Fei Wang
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
| | - Feng Li
- Ibis Biosciences, Abbott, Carlsbad, California
| | | | | | | | - Erik Burrows
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Rachel Binet
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | | | | | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Jianghong Meng
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland
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106
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A prospective study of agents associated with acute respiratory infection among young American Indian children. Pediatr Infect Dis J 2013; 32:e324-33. [PMID: 23470677 PMCID: PMC3753779 DOI: 10.1097/inf.0b013e31828ff4bc] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Native American children have higher rates of morbidity associated with acute respiratory infection than children in the general US population, yet detailed information is lacking regarding their principal clinical presentations and infectious etiologies. METHODS We pursued a comprehensive molecular survey of bacteria and viruses in nasal wash specimens from children with acute respiratory disease collected prospectively over 1 year (January 1 through December 31, 2009) from 915 Navajo and White Mountain Apache children in their second or third year of life who had been enrolled in an efficacy study of a respiratory syncytial virus monoclonal antibody in the first year of life. RESULTS During the surveillance period, 1476 episodes of disease were detected in 669 children. Rates of outpatient and inpatient lower respiratory tract illness were 391 and 79 per 1000 child-years, respectively, and were most commonly diagnosed as pneumonia. Potential pathogens were detected in 88% of specimens. Viruses most commonly detected were respiratory syncytial virus and human rhinovirus; the 2009 pandemic influenza A (H1N1) illnesses primarily occurred in the fall. Streptococcus pneumoniae was detected in 60% of subjects; only human rhinovirus was significantly associated with S. pneumoniae carriage. The presence of influenza virus, human rhinovirus or S. pneumoniae was not associated with increased risk for lower respiratory tract involvement or hospitalization. CONCLUSIONS Acute lower respiratory illnesses occur at disproportionately high rates among young American Indian children and are associated with a range of common pathogens. This study provides critical evidence to support reducing the disproportionate burden of acute respiratory disease among young Native Americans.
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107
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Jacobs SE, Soave R, Shore TB, Satlin MJ, Schuetz AN, Magro C, Jenkins SG, Walsh TJ. Human rhinovirus infections of the lower respiratory tract in hematopoietic stem cell transplant recipients. Transpl Infect Dis 2013; 15:474-86. [PMID: 23890179 PMCID: PMC3962254 DOI: 10.1111/tid.12111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/19/2012] [Accepted: 01/16/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND Human rhinoviruses (HRVs) are a common cause of upper respiratory infection (URI) in hematopoietic stem cell transplant (HSCT) recipients; yet, their role in lower respiratory illness is not well understood. METHODS We performed a retrospective chart review of HSCT recipients with HRV infection from the time molecular detection methods were implemented at our institution in 2008. Factors associated with proven or possible HRV pneumonia at the first HRV detection were evaluated by univariate and multivariate analysis. We then characterized all episodes of proven and possible HRV pneumonia from the initial HRV infection through a 1-year follow-up period. RESULTS Between 2008 and 2011, 63 HSCT recipients had ≥1 documented HRV infections. At first HRV detection, 36 (57%) patients had HRV URI and 27 (43%) had proven or possible HRV pneumonia; in multivariate analysis, hypoalbuminemia (odds ratio [OR] 9.5, 95% confidence interval [CI] 1.3-71.7; P = 0.03) and isolation of respiratory co-pathogen(s) (OR 24.2, 95% CI 2.0-288.4; P = 0.01) were independently associated with pneumonia. During the study period, 22 patients had 25 episodes of proven HRV pneumonia. Fever (60%), cough (92%), sputum production (61%), and dyspnea (60%) were common symptoms. Fifteen (60%) episodes demonstrated bacterial (n = 7), fungal (n = 5), or viral (n = 3) co-infection. Among the remaining 10 (40%) cases of HRV monoinfection, patients' oxygen saturations ranged from 80% to 97% on ambient air, and computed tomography scans showed peribronchiolar, patchy, ground glass infiltrates. CONCLUSIONS HRV pneumonia is relatively common after HSCT and frequently accompanied by bacterial co-infection. As use of molecular assays for respiratory viral diagnosis becomes widespread, HRV will be increasingly recognized as a significant cause of pneumonia in immunocompromised hosts.
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Affiliation(s)
- S E Jacobs
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Weill Cornell Medical College, New York, New York, USA
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108
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Identification of Recombinant Human Rhinovirus A and C in Circulating Strains from Upper and Lower Respiratory Infections. PLoS One 2013; 8:e68081. [PMID: 23826363 PMCID: PMC3695095 DOI: 10.1371/journal.pone.0068081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/24/2013] [Indexed: 01/15/2023] Open
Abstract
Human rhinoviruses (HRVs), in the Enterovirus genus within the family Picornaviridae, are a highly prevalent cause of acute respiratory infection (ARI). Enteroviruses are genetically highly variable, and recombination between serotypes is known to be a major contribution to their diversity. Recently it was reported that recombination events in HRVs cause the diversity of HRV-C. This study analyzed parts of the viral genes spanning the 5′ non- coding region (NCR) through to the viral protein (VP) encoding sequences of 105 HRV field isolates from 51 outpatient cases of Acute Respiratory Infectious Network (ARINET) and 54 inpatient cases of severe lower respiratory infection (SLRI) surveillance, in order to identify recombination in field samples. When analyzing parts of the 5′NCR and VP4/VP2 encoding sequences, we found intra- and interspecies recombinants in field strains of HRV-A and -C. Nineteen cases of recombination events (18.1%) were found among 105 field strains. For HRV-A, there were five cases (4.8%) of intraspecies recombination events and three cases (2.8%) of interspecies recombination events. For HRV-C, there were four cases (3.8%) of intraspecies recombination events and seven cases (6.7%) of interspecies recombination events. Recombination events were significantly more frequently observed in the ARINET samples (18 cases) than in the SLRI samples (1 case; P< 0.0001). The recombination breakpoints were located in nucleotides (nt) 472–554, which comprise stem-loop 5 in the internal ribosomal entry site (IRES), based on the HRV-B 35 sequence (accession no. FJ445187). Our findings regarding genomic recombination in circulating HRV-A and -C strains suggest that recombination might play a role in HRV fitness and could be a possible determinant of disease severity caused by various HRV infections in patients with ARI.
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Espínola EE, Russomando G, Aquino C, Basualdo W. Phylogeny-based classification of human rhinoviruses detected in hospitalized children with acute lower respiratory infection in Paraguay, 2010-2011. J Med Virol 2013; 85:1645-51. [PMID: 23780670 DOI: 10.1002/jmv.23638] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 11/06/2022]
Abstract
Human rhinovirus (HRV), a single-stranded, positive-sense RNA virus, is associated with mild upper respiratory tract infections in children. The aim of this study was to carry out a molecular characterization and phylogeny-based classification of the circulating genotypes of HRV in hospitalized children with clinical manifestations of acute lower respiratory infection in Paraguay. Nasopharyngeal aspirates were collected from 101 children under 5 years of age, hospitalized with symptoms of acute lower respiratory infection, between May 2010 and December 2011, at the largest public pediatric hospital in the Central Department of Paraguay. Detection was performed by a real-time polymerase chain reaction, followed by conventional amplification of the VP4/VP2 genomic region, sequencing, and phylogenetic analysis. Rhinovirus was detected in 33.7% of the samples. Amplification of 18 samples showed the presence of all three species (HRV-A, -B, and -C). Different genotypes were found for each species: 11 for HRV-A (-9, -12, -22, -30, -36, -43, -59, -61, -68, -88, and -89), one for HRV-B (-4), and four for HRV-C (-C2, -C3, -C6, and -C9). In South America, information about HRV diversity is scarce. This is the first report on HRV genotype diversity in South America.
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Affiliation(s)
- Emilio E Espínola
- Departamento de Biología Molecular y Genética, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Paraguay.
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110
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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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111
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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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112
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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: 172] [Impact Index Per Article: 15.6] [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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113
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Pierangeli A, Ciccozzi M, Chiavelli S, Concato C, Giovanetti M, Cella E, Spano L, Scagnolari C, Moretti C, Papoff P, Muraca M, Midulla F, Antonelli G. Molecular epidemiology and genetic diversity of human rhinovirus affecting hospitalized children in Rome. Med Microbiol Immunol 2013; 202:303-11. [PMID: 23625169 DOI: 10.1007/s00430-013-0296-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
Human rhinoviruses (HRV) have been re-classified into three species (A-C), but the recently discovered HRV-C strains are not fully characterized yet. This study aimed to undertake a molecular and epidemiological characterization of HRV strains infecting children hospitalized over one year in two large research hospitals in Rome. Nasal washings from single HRV infections were retrospectively subjected to phylogenetic analysis on two genomic regions: the central part of the 5'Untranslated Region (5'UTR) and the Viral Protein (VP) 4 gene with the 5' portion of the VP2 gene (VP4/2). Forty-five different strains were identified in 73 HRV-positive children: 55 % of the cases were HRV-A, 38 % HRV-C and only 7 % HRV-B. HRV-C cases were less frequent than HRV-A during summer months and more frequent in cases presenting wheezing with respect to HRV-A. Species distribution was similar with respect to patient age, and seasonality differed during summer months with fewer HRV-C than HRV-A cases. On admission, a significantly higher number of HRV-C cases presented with wheezing with respect to HRV-A. The inter- and intra-genotype variability in VP4/2 was higher than in 5'UTR; in particular, HRV-A patient VP4/2 sequences were highly divergent (8-14 %) at the nucleotide level from those of their reference strains, but VP4 amino acid sequence was highly conserved. In HRV-C isolates, the region preceding the initiator AUG, the amino acids involved in VP4 myristoylation, the VP4-VP2 cleavage site and the cis-acting replication element were highly conserved. Differently, VP4 amino acid conservation was significantly lower in HRV-C than in HRV-A strains, especially in the transiently exposed VP4 N-terminus. This study confirmed the high number of different HRV genotypes infecting hospitalized children over one year and reveals a greater than expected variability in HRV-C VP4 protein, potentially suggestive of differences in replication.
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Affiliation(s)
- Alessandra Pierangeli
- Istituto Pasteur-Fondazione Cenci Bolognetti, Laboratory of Virology, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
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114
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Abstract
Efficient responses to viral threats require a integrated multidisciplinary approach. Several relatively newly formed initiatives focus on effective response management.
Recent advances in the metagenomics field have had huge effects on the identification and characterization of newly emerging viral pathogens. To allow timely and efficient responses to future viral threats, an integrated multidisciplinary approach utilizing expertises in several areas, including clinical assessment, virus surveillance, virus discovery, pathogenesis, and the molecular basis of the host response to infection, is required. It requires the scientific community involved in virus discovery to go one step beyond.
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Affiliation(s)
- Saskia L Smits
- ViroClinics Biosciences B.V., Marconistraat 16, 3029 AK Rotterdam, The Netherlands; Department of Virology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Albert Dme Osterhaus
- ViroClinics Biosciences B.V., Marconistraat 16, 3029 AK Rotterdam, The Netherlands; Department of Virology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
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115
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Kiyota N, Kushibuchi I, Kobayashi M, Tsukagoshi H, Ryo A, Nishimura K, Hirata-Saito A, Harada S, Arakawa M, Kozawa K, Noda M, Kimura H. Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan. J Med Microbiol 2013; 62:610-617. [DOI: 10.1099/jmm.0.049072-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Izumi Kushibuchi
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Asumi Hirata-Saito
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
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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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117
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Ferguson PE, Gilroy NM, Faux CE, Mackay IM, Sloots TP, Nissen MD, Dwyer DE, Sorrell TC. Human rhinovirus C in adult haematopoietic stem cell transplant recipients with respiratory illness. J Clin Virol 2013; 56:255-9. [PMID: 23290385 PMCID: PMC7172717 DOI: 10.1016/j.jcv.2012.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/03/2012] [Accepted: 11/13/2012] [Indexed: 11/26/2022]
Abstract
Background A previously unidentified species of human rhinovirus, HRV-C, was described in 2006 in association with lower respiratory tract infection (LRTI). Features of infection in immunosuppressed adults are poorly characterised. Objectives This study aims to determine the epidemiology of HRV-C in haematopoietic stem cell transplant (HSCT) recipients in a single centre. Study design A prospective cohort study of all HSCT recipients admitted to Westmead Hospital, Westmead, Australia from 1 July 2005 to 30 September 2007 was undertaken. Nose/throat samples were collected from all patients at the time of admission and patients developing pre-defined symptoms and/or signs of respiratory infection during the admission. Samples were processed and tested for rhinoviruses and 14 other respiratory viruses using nucleic acid-based methods, immunofluorescence and culture. HRV genotyping was performed by sequencing a region of the rhinovirus 5′ untranslated region (UTR). Clinical data on each episode were collected prospectively. Results HRVs were identified in 24 episodes: 8% of 299 episodes of clinically- defined respiratory infections and 39% of 61 episodes in which respiratory viruses were detected. HRV-C was most frequent (HRV-C: nine, HRV-A: eight and HRV-B: two). Seven episodes of HRV-C, five with pneumonia, occurred within 100 days of HSCT. Co-pathogens were frequent. Conclusions The newly described HRV-C was the most common rhinovirus group detected in HSCT recipients with respiratory infection, with co-pathogens being frequent. Further research is required to understand the activity and pathogenicity of this virus in HSCT recipients.
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Affiliation(s)
- Patricia E Ferguson
- Centre for Infectious Diseases and Microbiology, Westmead Hospital, Westmead, NSW, Australia.
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118
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Zlateva KT, Coenjaerts FEJ, Crusio KM, Lammens C, Leus F, Viveen M, Ieven M, Spaan WJM, Claas ECJ, Gorbalenya AE. No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers. Arch Virol 2013; 158:251-5. [PMID: 23053517 PMCID: PMC7087030 DOI: 10.1007/s00705-012-1487-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/16/2012] [Indexed: 11/26/2022]
Abstract
Novel viruses might be responsible for numerous disease cases with unknown etiology. In this study, we screened 1800 nasopharyngeal samples from adult outpatients with respiratory disease symptoms and healthy individuals. We employed a reverse transcription (RT)-PCR assay and CODEHOP-based primers (CT12-mCODEHOP) previously developed to recognize known and unknown corona- and toroviruses. The CT12-mCODEHOP assay detected 42.0 % (29/69) of samples positive for human coronaviruses (HCoV), including HCoV-229 (1/16), HCoV-NL63 (9/17), and HCoV-OC43 (19/36), and additionally HCoV-HKU1 (3), which was not targeted by the diagnostic real-time PCR assays. No other coronaviruses were identified in the analyzed samples.
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Affiliation(s)
- Kalina T. Zlateva
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Frank E. J. Coenjaerts
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kelly M. Crusio
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Christine Lammens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, University Hospital Antwerp, Antwerp, Belgium
| | - Frank Leus
- Department of Data Management, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marco Viveen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, Universiteit Antwerpen, University Hospital Antwerp, Antwerp, Belgium
| | - Willy J. M. Spaan
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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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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121
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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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122
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Human rhinovirus C: Age, season, and lower respiratory illness over the past 3 decades. J Allergy Clin Immunol 2012; 131:69-77.e1-6. [PMID: 23146382 PMCID: PMC3748586 DOI: 10.1016/j.jaci.2012.09.033] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Human rhinoviruses (HRVs) cause common colds, and the recently discovered HRV-C is increasingly associated with lower respiratory illness among populations such as children and asthmatic patients. OBJECTIVE To determine how HRV-C is associated with respiratory illness and to evaluate changes in prevalence and species over 2 decades. METHODS A prospective study of children younger than 5 years was performed at the Vanderbilt Vaccine Clinic over a 21-year period. Nasal-wash specimens from children presenting with upper or lower respiratory illness at acute care visits were tested for HRV and HRV-positives genotyped. Demographic and clinical features were compared between children with or without HRV, and with different HRV species. RESULTS HRV was detected in 190 of 527 (36%) specimens from a population of 2009 children from 1982 through 2003. Of these, 36% were HRV-C. Age (P = .039) and month of illness (P < .001) were associated with HRV infection and HRV species. HRV-C was significantly associated with lower respiratory illness, compared with HRV-A (P = .014). HRV-A and HRV-C prevalence fluctuated throughout the 21-year period; HRV-C was more prevalent during winter (P = .058). CONCLUSIONS HRV-C is not a new virus but has been significantly associated with childhood lower respiratory illness in this population for several decades. Temporal changes in virus prevalence occur, and season may predict virus species. Our findings have implications for diagnostic, preventive, and treatment strategies due to the variation in disease season and severity based on species of HRV infection.
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123
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Debiaggi M, Canducci F, Ceresola ER, Clementi M. The role of infections and coinfections with newly identified and emerging respiratory viruses in children. Virol J 2012; 9:247. [PMID: 23102237 PMCID: PMC3573994 DOI: 10.1186/1743-422x-9-247] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 10/18/2012] [Indexed: 02/03/2023] Open
Abstract
Acute respiratory infections are a major cause of morbidity in children both in developed and developing countries. A wide range of respiratory viruses, including respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza viruses (PIVs), adenovirus, rhinovirus (HRV), have repeatedly been detected in acute lower respiratory tract infections (LRTI) in children in the past decades. However, in the last ten years thanks to progress in molecular technologies, newly discovered viruses have been identified including human Metapneumovirus (hMPV), coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus. These discoveries have heavily modified previous knowledge on respiratory infections mainly highlighting that pediatric population is exposed to a variety of viruses with similar seasonal patterns. In this context establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present an overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.
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Affiliation(s)
- Maurizia Debiaggi
- Dipartimento di Scienze Clinico-Chirurgiche, Diagnostiche e Pediatriche, Sezione di Microbiologia, 20132 Milan, Italy
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Suzuki A, Lupisan S, Furuse Y, Fuji N, Saito M, Tamaki R, Galang H, Sombrero L, Mondoy M, Aniceto R, Olveda R, Oshitani H. Respiratory viruses from hospitalized children with severe pneumonia in the Philippines. BMC Infect Dis 2012; 12:267. [PMID: 23092190 PMCID: PMC3519714 DOI: 10.1186/1471-2334-12-267] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pneumonia remains a leading cause of child death in developing countries. The viruses in severe pneumonia remain poorly defined. METHODS The study was conducted at the Eastern Visayas Regional Medical Center in Tacloban City, Philippines from May 2008 to May 2009. Patients aged 8 days to 13 years old who were admitted to the Department of Pediatrics with severe pneumonia were enrolled for the study. Upon admission, polymerase chain reaction was performed using nasopharyngeal swabs and blood cultures to detect respiratory viruses and bacteria, respectively. RESULT Among the 819 patients enrolled, at least one virus was detected in 501 cases (61.2%). In addition, 423 cases were positive for a single virus while bacteria were detected in the blood culture sample of 31 cases. The most commonly detected viruses were human rhinoviruses (n = 189), including types A (n = 103), B (n = 17), and C (n = 69), and respiratory syncytial virus (RSV) (n = 165). Novel viruses such as human metapneumovirus, human coronavirus NL63, human bocavirus, and human polyomaviruses WU and KI were also detected. There were 70 deaths, and one or more viruses were detected in 35 (50%) of these cases. Positivity only for influenza A virus (OR = 4.3, 95% CI = 1.3-14.6) was significantly associated with fatal outcome. From the blood culture, Burkholderia cepacia group (n = 9), Streptococcus pneumoniae (n = 4), Staphylococcus aureus (n = 4), Haemophilus influenzae (n = 1), and Salmonella C1 (n = 1) were also isolated. CONCLUSION Viruses were commonly detected in children with severe pneumonia in the Philippines. Hence, viral etiologies should be considered while developing better effective strategies to reduce child pneumonia-related deaths in developing countries.
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Affiliation(s)
- Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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125
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Evolutionary pattern of 5'-UTR of enteroviruses and primer update for the detection of enteroviral RNA in environmental samples. ASIAN PAC J TROP MED 2012; 5:703-8. [PMID: 22805721 DOI: 10.1016/s1995-7645(12)60110-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 02/25/2012] [Accepted: 05/20/2012] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE To study the recombination events among enterovirus strains and the development of specific primers for the detection of enteroviruses in environmental samples. METHODS Nucleotide sequence analysis of enteroviruses deposited in the international database GenBank (www.ncbi.nlm.nih.gov/Genbank) was conducted to develop specific primers for the detection of these viruses. The specificity and sensitivity of the method were tested using coxackievirus B3 strain Nancy, environmental isolate of human hepatitis A virus and human rotavirus strain WA. Seventy sewage samples were analyzed. RESULTS Enterovirus genome was detected in all positive samples. The genome of enterovirus was not detected in negative samples. The level of detection of these viruses was 10(2) TCID(50)/mL. CONCLUSIONS The development of new primers is an important issue for the detection of enteroviruses in the environment and the assessment of risk factors to human health.
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126
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Detection and Identification of Salmonella enterica, Escherichia coli, and Shigella spp. via PCR-electrospray ionization mass spectrometry: isolate testing and analysis of food samples. Appl Environ Microbiol 2012; 78:8403-11. [PMID: 23001674 DOI: 10.1128/aem.02272-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An assay to identify the common food-borne pathogens Salmonella, Escherichia coli, Shigella, and Listeria monocytogenes was developed in collaboration with Ibis Biosciences (a division of Abbott Molecular) for the Plex-ID biosensor system, a platform that uses electrospray ionization mass spectroscopy (ESI-MS) to detect the base composition of short PCR amplicons. The new food-borne pathogen (FBP) plate has been experimentally designed using four gene segments for a total of eight amplicon targets. Initial work built a DNA base count database that contains more than 140 Salmonella enterica, 139 E. coli, 11 Shigella, and 36 Listeria patterns and 18 other Enterobacteriaceae organisms. This assay was tested to determine the scope of the assay's ability to detect and differentiate the enteric pathogens and to improve the reference database associated with the assay. More than 800 bacterial isolates of S. enterica, E. coli, and Shigella species were analyzed. Overall, 100% of S. enterica, 99% of E. coli, and 73% of Shigella spp. were detected using this assay. The assay was also able to identify 30% of the S. enterica serovars to the serovar level. To further characterize the assay, spiked food matrices and food samples collected during regulatory field work were also studied. While analysis of preenrichment media was inconsistent, identification of S. enterica from selective enrichment media resulted in serovar-level identifications for 8 of 10 regulatory samples. The results of this study suggest that this high-throughput method may be useful in clinical and regulatory laboratories testing for these pathogens.
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Gandhi A, Walsh EE, Formica MA, Hennessey PA, Criddle MM, Peterson DR, Baran A, Falsey AR. Factors associated with symptomatic rhinovirus infection in patients with COPD. J Clin Virol 2012; 55:343-7. [PMID: 22999488 DOI: 10.1016/j.jcv.2012.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/22/2012] [Accepted: 08/25/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Human rhinoviruses (HRV) can be detected by RT-PCR in a large proportion of acute exacerbations of chronic obstructive pulmonary disease (AECOPD) but can also be detected in COPD patients without symptoms. OBJECTIVES The purpose of this study was to compare host, virologic and environmental factors associated with symptomatic and asymptomatic HRV infection. STUDY DESIGN One hundred twenty-seven patients with COPD were evaluated every 2 months routinely and for all respiratory illnesses during a one year period. RT-PCR testing for HRV was performed on nasal and sputum samples. Amplification products were sequenced to assign species HRV-A, B or C. Clinical, virologic and environmental factors were compared for those infected with HRV compared to those without HRV infection as well as symptomatic HRV infection and asymptomatic HRV infection. RESULTS HRVs were detected in 29 participants during 20 illnesses and 11 routine visits. HRV was detected in nasal samples from 15/102 (14.7%) illnesses compared to 2/685 (0.4%) routine visits (p<.0001). Sputum samples were also more frequently positive from illnesses than routine visits [14/72 (19.4%) vs. 16/310 (5.2%) p<.0001]. Contact with school age children was the only factor that was significantly associated with HRV infection and symptomatic HRV illness. Severity of underlying lung disease and virologic factors were not associated with symptomatic illness. CONCLUSIONS Contact with school aged children is a risk factor for both infection and symptomatic HRV illness. Attention to good hand hygiene and avoidance of direct contact with ill children may help patients with COPD avoid HRV related illness.
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Khot PD, Fisher MA. Mass Spectrometry in the Clinical Microbiology Laboratory, Part I: PCR-MS. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.clinmicnews.2012.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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129
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Lee WM, Lemanske RF, Evans MD, Vang F, Pappas T, Gangnon R, Jackson DJ, Gern JE. Human rhinovirus species and season of infection determine illness severity. Am J Respir Crit Care Med 2012; 186:886-91. [PMID: 22923659 DOI: 10.1164/rccm.201202-0330oc] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Human rhinoviruses (HRVs) consist of approximately 160 types that cause a wide range of clinical outcomes, including asymptomatic infections, common colds, and severe lower respiratory illnesses. OBJECTIVES To identify factors that influence the severity of HRV illnesses. METHODS HRV species and types were determined in 1,445 nasal lavages that were prospectively collected from 209 infants participating in a birth cohort who had at least one HRV infection. Questionnaires were used during each illness to identify moderate to severe illnesses (MSI). MEASUREMENTS AND MAIN RESULTS Altogether, 670 HRV infections were identified, and 519 of them were solitary infections (only one HRV type). These 519 viruses belonged to 93 different types of three species: 49 A, 9 B, and 35 C types. HRV-A (odds ratio, 8.2) and HRV-C (odds ratio, 7.6) were more likely to cause MSI compared with HRV-B. In addition, HRV infections were 5- to 10-fold more likely to cause MSI in the winter months (P < 0.0001) compared with summer, in contrast to peak seasonal prevalence in spring and fall. When significant differences in host susceptibility to MSI (P = 0.004) were considered, strain-specific rates of HRV MSI ranged from less than 1% to more than 20%. CONCLUSIONS Factors related to HRV species and type, season, and host susceptibility determine the risk of more severe HRV illness in infancy. These findings suggest that anti-HRV strategies should focus on HRV-A and -C species and identify the need for additional studies to determine mechanisms for seasonal increases of HRV severity, independent of viral prevalence, in cold weather months.
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Affiliation(s)
- Wai-Ming Lee
- Biological Mimetics Inc., 124 Byte Drive, Frederick, MD 21702, USA.
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Abstract
Viral metagenomics has recently yielded numerous previously uncharacterized viral genomes from human and animal samples. We review some of the metagenomics tools and strategies to determine which orphan viruses are likely pathogens. Disease association studies compare viral prevalence in patients with unexplained symptoms versus healthy individuals but require these case and control groups to be closely matched epidemiologically. The development of an antibody response in convalescent serum can temporarily link symptoms with a recent infection. Neutralizing antibody detection require often difficult cell culture virus amplification. Antibody binding assays require proper antigen synthesis and positive control sera to set assay thresholds. High levels of viral genetic diversity within orphan viral groups, frequent co-infections, low or rare pathogenicity, and chronic virus shedding, can all complicate disease association studies. The limited availability of matched cases and controls sample sets from different age groups and geographic origins is a major block for estimating the pathogenic potential of recently characterized orphan viruses. Current limitations on the practical use of deep sequencing for viral diagnostics are listed.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
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Viral and atypical bacterial etiology of acute respiratory infections in children under 5 years old living in a rural tropical area of Madagascar. PLoS One 2012; 7:e43666. [PMID: 22912897 PMCID: PMC3422262 DOI: 10.1371/journal.pone.0043666] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/23/2012] [Indexed: 11/23/2022] Open
Abstract
Background In Madagascar, very little is known about the etiology and prevalence of acute respiratory infections (ARIs) in a rural tropical area. Recent data are needed to determine the viral and atypical bacterial etiologies in children with defined clinical manifestations of ARIs. Methods During one year, we conducted a prospective study on ARIs in children between 2 to 59 months in the community hospital of Ampasimanjeva, located in the south-east of Madagascar. Respiratory samples were analyzed by multiplex real-time RT-PCR, including 18 viruses and 2 atypical bacteria. The various episodes of ARI were grouped into four clinical manifestations with well-documented diagnosis: “Community Acquired Pneumonia”(CAP, group I), “Other acute lower respiratory infections (Other ALRIs, group II)”, “Upper respiratory tract infections with cough (URTIs with cough, group III)”and “Upper respiratory tract infections without cough (URTIs without cough, group IV)”. Results 295 children were included in the study between February 2010 and February 2011. Viruses and/or atypical bacteria respiratory pathogens were detected in 74.6% of samples, the rate of co-infection was 27.3%. Human rhinovirus (HRV; 20.5%), metapneumovirus (HMPV A/B, 13.8%), coronaviruses (HCoV, 12.5%), parainfluenza virus (HPIV, 11.8%) and respiratory syncytial virus A and B (RSV A/B, 11.8%) were the most detected. HRV was predominantly single detected (23.8%) in all the clinical groups while HMPV A/B (23.9%) was mainly related to CAP (group I), HPIV (17.3%) to the “Other ALRIs” (group II), RSV A/B (19.5%) predominated in the group “URTIs with cough” (group III) and Adenovirus (HAdV, 17.8%) was mainly detected in the “without cough” (group IV). Interpretation This study describes for the first time the etiology of respiratory infections in febrile children under 5 years in a malaria rural area of Madagascar and highlights the role of respiratory viruses in a well clinically defined population of ARIs.
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Dominguez SR, Sims GE, Wentworth DE, Halpin RA, Robinson CC, Town CD, Holmes KV. Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination. J Gen Virol 2012; 93:2387-2398. [PMID: 22837419 DOI: 10.1099/vir.0.044628-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This study compared the complete genome sequences of 16 NL63 strain human coronaviruses (hCoVs) from respiratory specimens of paediatric patients with respiratory disease in Colorado, USA, and characterized the epidemiology and clinical characteristics associated with circulating NL63 viruses over a 3-year period. From 1 January 2009 to 31 December 2011, 92 of 9380 respiratory specimens were found to be positive for NL63 RNA by PCR, an overall prevalence of 1 %. NL63 viruses were circulating during all 3 years, but there was considerable yearly variation in prevalence and the month of peak incidence. Phylogenetic analysis comparing the genome sequences of the 16 Colorado NL63 viruses with those of the prototypical hCoV-NL63 and three other NL63 viruses from the Netherlands demonstrated that there were three genotypes (A, B and C) circulating in Colorado from 2005 to 2010, and evidence of recombination between virus strains was found. Genotypes B and C co-circulated in Colorado in 2005, 2009 and 2010, but genotype A circulated only in 2005 when it was the predominant NL63 strain. Genotype C represents a new lineage that has not been described previously. The greatest variability in the NL63 virus genomes was found in the N-terminal domain (NTD) of the spike gene (nt 1-600, aa 1-200). Ten different amino acid sequences were found in the NTD of the spike protein among these NL63 strains and the 75 partial published sequences of NTDs from strains found at different times throughout the world.
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Affiliation(s)
- Samuel R Dominguez
- Department of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA.,Department of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Gregory E Sims
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - David E Wentworth
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Rebecca A Halpin
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Christine C Robinson
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Christopher D Town
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kathryn V Holmes
- Department of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
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Doellinger J, Schroeder K, Witt N, Heunemann C, Nitsche A. Comparison of real-time PCR and MassTag PCR for the multiplex detection of highly pathogenic agents. Mol Cell Probes 2012; 26:177-81. [PMID: 22819946 DOI: 10.1016/j.mcp.2012.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 06/06/2012] [Accepted: 07/10/2012] [Indexed: 11/30/2022]
Abstract
Multiplex PCR assays are a cost- as well as labour-effective way to analyse one sample for several pathogens simultaneously. Besides the mutual competition of the individual PCR reactions included in a multiplex PCR assay, their specific read-out displays a limiting factor for the total number of PCR reactions that can be multiplexed. In this study, two PCR systems with different read-out approaches are compared, using a pentaplex PCR assay for the detection of highly pathogenic agents. A pentaplex assay was used since five represents the current limit of real-time PCR multiplexing capacity due to the low resolution of fluorescence emission peaks of the current equipment. In contrast, MassTag PCR as a quite new technique offers the possibility to detect up to 20-30 target sequences from one reaction. After extensive and separate optimisation of the PCR protocol for both platforms, a comparative probit analysis showed good sensitivities for MassTag and real-time PCR detection. Nevertheless, the detection limits of MassTag PCR have been undercut by the real-time PCR for each target. We therefore conclude that MassTag PCR is a useful diagnostic technique for the sensitive screening for pathogens by highly multiplexed PCR assays, but cannot reach the sensitivity of real-time PCR for lower multiplexed PCR assays.
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Affiliation(s)
- Joerg Doellinger
- Centre for Biological Security, Robert Koch Institute, Berlin, Germany.
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134
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Comparison of fast-track diagnostics respiratory pathogens multiplex real-time RT-PCR assay with in-house singleplex assays for comprehensive detection of human respiratory viruses. J Virol Methods 2012; 185:259-66. [PMID: 22796035 PMCID: PMC7119496 DOI: 10.1016/j.jviromet.2012.07.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/26/2012] [Accepted: 07/04/2012] [Indexed: 11/21/2022]
Abstract
Fast-track Diagnostics respiratory pathogens (FTDRP) multiplex real-time RT-PCR assay was compared with in-house singleplex real-time RT-PCR assays for detection of 16 common respiratory viruses. The FTDRP assay correctly identified 26 diverse respiratory virus strains, 35 of 41 (85%) external quality assessment samples spiked with cultured virus and 232 of 263 (88%) archived respiratory specimens that tested positive for respiratory viruses by in-house assays. Of 308 prospectively tested respiratory specimens selected from children hospitalized with acute respiratory illness, 270 (87.7%) and 265 (86%) were positive by FTDRP and in-house assays for one or more viruses, respectively, with combined test results showing good concordance (K = 0.812, 95% CI = 0.786–0.838). Individual FTDRP assays for adenovirus, respiratory syncytial virus and rhinovirus showed the lowest comparative sensitivities with in-house assays, with most discrepancies occurring with specimens containing low virus loads and failed to detect some rhinovirus strains, even when abundant. The FTDRP enterovirus and human bocavirus assays appeared to be more sensitive than the in-house assays with some specimens. With the exceptions noted above, most FTDRP assays performed comparably with in-house assays for most viruses while offering enhanced throughput and easy integration by laboratories using conventional real-time PCR instrumentation.
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135
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Prevalence of and risk factors for human rhinovirus infection in healthy aboriginal and non-aboriginal Western Australian children. Pediatr Infect Dis J 2012; 31:673-9. [PMID: 22481423 PMCID: PMC3375341 DOI: 10.1097/inf.0b013e318256ffc6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND Human rhinovirus (HRV) species C (HRV-C) have been associated with frequent and severe acute lower respiratory infections and asthma in hospitalized children. The prevalence of HRV-C among healthy children and whether this varies with ethnicity is unknown. OBJECTIVE To describe the prevalence of HRV species and their associations with demographic, environmental and socioeconomic factors in healthy Aboriginal and non-Aboriginal children. METHODS Respiratory viruses and bacteria were identified in 1006 nasopharyngeal aspirates collected from a cohort of 79 Aboriginal and 88 non-Aboriginal Western Australian children before 2 years of age. HRV-positive nasopharyngeal aspirates were typed for HRV species and genotypes. Longitudinal growth models incorporating generalized estimating equations were used to investigate associations between HRV species and potential risk factors. RESULTS Of the 159 typed specimens, we identified 83 (52.2%) human rhinovirus species A (HRV-A), 26 (16.4%), human rhinovirus species B and 50 (31.4%) HRV-C. HRV-C was associated with upper respiratory symptoms in Aboriginal (odds ratio, 3.77; 95% confidence interval:1.05-13.55) and non-Aboriginal children (odds ratio, 5.85; 95% confidence interval: 2.33-14.66). HRV-A and HRV-C were associated with carriage of respiratory bacteria. In Aboriginal children, HRV-A was more common in the summer and in those whose mothers were employed prior to delivery. In non-Aboriginal children, day-care attendance and exclusive breast-feeding at age 6-8 weeks were associated with detection of HRV-A, and gestational smoking with detection of HRV-C. CONCLUSIONS Factors associated with the presence of HRV differ between Aboriginal and non-Aboriginal children. In contrast to HRV-A, HRV-C is associated with upper respiratory symptoms suggesting that HRV-C is likely to be implicated in respiratory illness.
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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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Tokarz R, Firth C, Madhi SA, Howie SRC, Wu W, Sall AA, Haq S, Briese T, Lipkin WI. Worldwide emergence of multiple clades of enterovirus 68. J Gen Virol 2012; 93:1952-1958. [PMID: 22694903 DOI: 10.1099/vir.0.043935-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human enterovirus 68 (EV-D68) is a historically rarely reported virus linked with respiratory disease. In the past 3 years, a large increase in respiratory disease associated with EV-D68 has been reported, with documented outbreaks in North America, Europe and Asia. In several outbreaks, genetic differences were identified among the circulating strains, indicating the presence of multiple clades. In this report, we analyse archived and novel EV-D68 strains from Africa and the USA, obtained from patients with respiratory illness. Phylogenetic analysis of all EV-D68 sequences indicates that, over the past two decades, multiple clades of the virus have emerged and spread rapidly worldwide. All clades appear to be currently circulating and contributing to respiratory disease.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Shabir A Madhi
- Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa.,National Institute of Communicable Diseases, Division of National Health Laboratory Service, Sandringham, Johannesburg, 2131, South Africa
| | - Stephen R C Howie
- Child Survival Theme, Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | - Winfred Wu
- New York City Department of Health and Mental Hygiene, Gotham Center, 42-09 28th St, New York, NY 11101, USA
| | - Amadou Alpha Sall
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Saddef Haq
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 West 168th Street, Room 1701, NY 10032, USA
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138
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Onyango CO, Welch SR, Munywoki PK, Agoti CN, Bett A, Ngama M, Myers R, Cane PA, Nokes DJ. Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya. J Med Virol 2012; 84:823-31. [PMID: 22431032 PMCID: PMC3500870 DOI: 10.1002/jmv.23251] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2012] [Indexed: 11/17/2022]
Abstract
This study reports pediatric surveillance over 3 years for human rhinovirus (HRV) at the District Hospital of Kilifi, coastal Kenya. Nasopharyngeal samples were collected from children presenting at outpatient clinic with no signs of acute respiratory infection, or with signs of upper respiratory tract infection, and from children admitted to the hospital with lower respiratory tract infection. Samples were screened by real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) and classified further to species by nucleotide sequencing of the VP4/VP2 junction. Of 441 HRV positives by real-time RT-PCR, 332 were classified to species, with 47% (155) being HRV-A, 5% (18) HRV-B, and 48% (159) HRV-C. There was no clear seasonal pattern of occurrence for any species. The species were present in similar proportions in the inpatient and outpatient sample sets, and no significant association between species distribution and the severity of lower respiratory tract infection in the inpatients could be determined. HRV sequence analysis revealed multiple but separate clusters in circulation particularly for HRV-A and HRV-C. Most HRV-C clusters were distinct from reference sequences downloaded from GenBank. In contrast, most HRV-A and HRV-B sequences clustered with either known serotypes or strains from elsewhere within Africa and other regions of the world. This first molecular epidemiological study of HRV in the region defines species distribution in accord with reports from elsewhere in the world, shows considerable strain diversity and does not identify an association between any species and disease severity.
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139
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Piralla A, Lilleri D, Sarasini A, Marchi A, Zecca M, Stronati M, Baldanti F, Gerna G. Human rhinovirus and human respiratory enterovirus (EV68 and EV104) infections in hospitalized patients in Italy, 2008-2009. Diagn Microbiol Infect Dis 2012; 73:162-7. [PMID: 22494556 DOI: 10.1016/j.diagmicrobio.2012.02.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 11/30/2022]
Abstract
The epidemiology of picornavirus infections along with associated risk factors for lower respiratory tract infections (LRTI) and duration of virus shedding were investigated in 985 hospitalized patients in the period October 2008-September 2009. One-third of patients were human rhinovirus (HRV)-positive. Of 336 HRV-associated episodes, 153 (45.5%) were sustained by HRV-A, 31 (9.2%) by HRV-B, and 93 (27.7%) by HRV-C, while 7 episodes showed multiple HRV types and 52 were sustained by undefined HRV species. Independent risk factors for LRTI included high viral load and age less than 5 years. Twenty (2.1%) patients were enterovirus (EV)-positive (12 had EV-68, 7 EV-104, and 1 E-13 infection). Half of the EV-positive patients had a LRTI and were younger with respect to patients with upper RTI (median 18 months versus 37 years; P < 0.001). HRVs are often the cause of LRTI in children less than 5 years, frequently in association with a high viral load.
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Affiliation(s)
- Antonio Piralla
- S.S. Virologia Molecolare, S.C. Virologia e Microbiologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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140
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Lau SKP, Yip CCY, Lung DC, Lee P, Que TL, Lau YL, Chan KH, Woo PCY, Yuen KY. Detection of human rhinovirus C in fecal samples of children with gastroenteritis. J Clin Virol 2012; 53:290-6. [PMID: 22317907 PMCID: PMC7108355 DOI: 10.1016/j.jcv.2012.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 12/31/2022]
Abstract
Background Despite recent discovery of the novel human rhinovirus species, HRV-C, little is known about the association of HRV-C in diseases other than respiratory tract infections. Objectives To investigate the presence of HRV-C in fecal samples of children with gastroenteritis. Study design 734 fecal samples from hospitalized children with gastroenteritis were subject to picornavirus detection by RT-PCR of the conserved 5′-NCR. Positive samples were subject to VP4 and 3Dpol gene analysis for species determination. The clinical and molecular epidemiology of HRV-C and other picornaviruses was analyzed. Results Picornaviruses were detected in 113 (15.4%) of 734 fecal samples from children with gastroenteritis by RT-PCR of 5′-NCR, with 58 containing potential HRVs and 55 containing other enteroviruses. PCR of the VP4 and 3Dpol regions was positive in 21 and 19 samples respectively (both regions positive in 8 samples). Sequencing analysis showed the presence of HRV-C in four samples, and diverse picornaviruses including HRV-A (n = 2), HEV-A (n = 2), HEV-B (n = 2), HEV-C (n = 21) and HPeV (n = 2) in other samples, with co-detection of HRV-C and HPeV in one sample. Of the four children with HRV-C detected in fecal samples, three presented with diarrhea in the absence of respiratory symptoms, while one also had acute bronchiolitis. The four HRV-C strains from fecal samples belonged to the existing clade of diverse HRV-C genotypes, indistinguishable from previous respiratory strains. Conclusions HRV-C can be detected in fecal samples of children with gastroenteritis, in the absence of respiratory symptoms. This study also represented the first to detect HPeV in our population.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong.
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141
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Bochkov YA, Gern JE. Clinical and molecular features of human rhinovirus C. Microbes Infect 2012; 14:485-94. [PMID: 22285901 DOI: 10.1016/j.micinf.2011.12.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/23/2011] [Accepted: 12/26/2011] [Indexed: 02/06/2023]
Abstract
A newly discovered group of human rhinoviruses (HRVs) has been classified as the HRV-C species based on distinct genomic features. HRV-Cs circulate worldwide, and are important causes of upper and lower respiratory illnesses. Methods to culture and produce these viruses have recently been developed, and should enable identification of unique features of HRV-C replication and biology.
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Affiliation(s)
- Yury A Bochkov
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI 53792, USA.
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Wiertsema SP, Chidlow GR, Kirkham LAS, Corscadden KJ, Mowe EN, Vijayasekaran S, Coates HL, Harnett GB, Richmond PC. High detection rates of nucleic acids of a wide range of respiratory viruses in the nasopharynx and the middle ear of children with a history of recurrent acute otitis media. J Med Virol 2012; 83:2008-17. [PMID: 21915878 PMCID: PMC7166877 DOI: 10.1002/jmv.22221] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Both bacteria and viruses play a role in the development of acute otitis media, however, the importance of specific viruses is unclear. In this study molecular methods were used to determine the presence of nucleic acids of human rhinoviruses (HRV; types A, B, and C), respiratory syncytial viruses (RSV; types A and B), bocavirus (HBoV), adenovirus, enterovirus, coronaviruses (229E, HKU1, NL63, and OC43), influenza viruses (types A, B, and C), parainfluenza viruses (types 1, 2, 3, 4A, and 4B), human metapneumovirus, and polyomaviruses (KI and WU) in the nasopharynx of children between 6 and 36 months of age either with (n = 180) or without (n = 66) a history of recurrent acute otitis media and in 238 middle ear effusion samples collected from 143 children with recurrent acute otitis media. The co‐detection of these viruses with Streptococcus pneumoniae, nontypeable Haemophilus influenzae, and Moraxella catarrhalis was analyzed. HRV (58.3% vs. 42.4%), HBoV (52.2% vs. 19.7%), polyomaviruses (36.1% vs. 15.2%), parainfluenza viruses (29.4% vs. 9.1%), adenovirus (25.0% vs. 6.1%), and RSV (27.8% vs. 9.1%) were detected significantly more often in the nasopharynx of children with a history of recurrent acute otitis media compared to healthy children. HRV was predominant in the middle ear and detected in middle ear effusion of 46% of children. Since respiratory viruses were detected frequently in the nasopharynx of both children with and without a history of recurrent acute otitis media, the etiological role of specific viruses in recurrent acute otitis media remains uncertain, however, anti‐viral therapies may be beneficial in future treatment and prevention strategies for acute otitis media. J. Med. Virol. 83:2008–2017, 2011. © 2011 Wiley‐Liss, Inc.
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Affiliation(s)
- Selma P Wiertsema
- School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia.
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143
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Lamson DM, Griesemer S, Fuschino M, St George K. Phylogenetic analysis of human metapneumovirus from New York State patients during February through April 2010. J Clin Virol 2012; 53:256-8. [PMID: 22217900 DOI: 10.1016/j.jcv.2011.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Human metapneumovirus (hMPV) is the second leading cause of lower respiratory infection (LRI) in children around the world and has been linked to LRI in multiple studies. Currently, hMPV is classified into 2 major subtypes (A and B), each with 2 subgroups (1 and 2). OBJECTIVE To determine which hMPV genotypes were present in NYS patients with influenza-like illness (ILI) from February through April 2010, during a period of unusually heightened activity. STUDY DESIGN Specimens were collected from February through April of 2010 from patients presenting with ILI who were previously confirmed as positive for hMPV by real-time RT-PCR. A 700 base pair region of the hMPV fusion (F) gene was amplified, sequenced and resulting sequences aligned. A phylogenic tree was constructed based on prototype strains, and the partial F gene sequences obtained in this study. RESULTS Bi-directional sequence was obtained from 30 patient samples and included in the phylogenic analysis. Specimen sequences grouped into hMPV genotype A2a (16), A2b (9), B2 (4) and B1 (1). No A1 genotypes were found. CONCLUSION Previously, reports have demonstrated that genotypes A1, A2, B1 and B2 circulate every season, usually with one dominant strain. In contrast, late in the 2009-2010 respiratory season, 4 of the 5 recognized genotypes of hMPV were isolated from NYS ILI patients, and by sequencing a larger portion of the fusion gene, we were able to identify the A2a and A2b genotypes.
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Affiliation(s)
- Daryl M Lamson
- Laboratory of Viral Diseases, Wadsworth Center, Albany, NY, USA.
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144
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Impact of rhinoviruses on pediatric community-acquired pneumonia. Eur J Clin Microbiol Infect Dis 2011; 31:1637-45. [PMID: 22124536 PMCID: PMC7088072 DOI: 10.1007/s10096-011-1487-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/03/2011] [Indexed: 11/11/2022]
Abstract
This study of 592 children seen in our Emergency Department with radiographically confirmed community-acquired pneumonia (CAP) was designed to evaluate the role of rhinoviruses (RVs) in the disease. The respiratory secretions of each child were assayed using RVP Fast in order to detect 17 respiratory viruses, and the RV-positive samples were characterised by means of real-time polymerase chain reaction and sequencing. RVs were identified in 172 cases (29.0%): 48/132 children aged <1 year (36.3%), 80/293 aged 1–3 years (27.3%), and 44/167 aged ≥4 years (26.3%). Sequencing demonstrated that 82 RVs (49.1%) were group A, 17 (10.1%) group B, and 52 (31.1%) group C; 21 (12.2%) were untyped. RVs were found as single agents in 99 cases, and together with two or more other viruses in 73 (40.7%). There were only marginal differences between the different RV groups and between single RV infection and RV co-infections. RV CAP is frequent not only in younger but also in older children, and RV-A is the most common strain associated with it. The clinical relevance of RV CAP seems to be mild to moderate without any major differences between the A and B strains and the recently identified RV C.
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145
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Fuji N, Suzuki A, Lupisan S, Sombrero L, Galang H, Kamigaki T, Tamaki R, Saito M, Aniceto R, Olveda R, Oshitani H. Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines. PLoS One 2011; 6:e27247. [PMID: 22087272 PMCID: PMC3210775 DOI: 10.1371/journal.pone.0027247] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Human rhinovirus (HRV) C was recently identified as the third species of HRV using a molecular technique. Infections caused by previously identified HRVs (A and B) are thought to be limited to the respiratory tract; however, pathogenesis of HRVC is still largely unknown. A total of 816 nasopharyngeal swabs from hospitalized children with severe respiratory infections in the Philippines (May 2008-May 2009) were tested for HRV by reverse transcription polymerase chain reaction (RT-PCR), and 243 samples (29.8%) were positive for HRV. Among these patients, serum samples were also tested to determine whether specific HRV species were associated with viremia. Only 30 serum samples (12.3%) were positive for HRV. However, the HRV positive rates were different among HRV species, 3% (4/135) for HRVA, 0% (0/25) for HRVB, and 31% (26/83) for HRVC, and were the highest on 2 days after the onset of symptoms. These results suggest that HRVC may have a different pathogenicity and can more commonly cause viremia than HRVA and HRVB. Serum positive rates for HRV are affected by age, i.e., higher positive rates for those aged 1 year or more. HRVC that were detected from serum exhibited the same level of sequence diversity as those positive only for nasopharyngeal samples in phylogenetic analysis. However, all HRVA which were detected from serum were clustered in a monophyletic clade based on their 5' non-coding region (NCR) sequences, which is closely related with a certain HRVC genotype (A2) in 5'-NCR. This finding suggests that the 5'NCR region may be associated with viremia.
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Affiliation(s)
- Naoko Fuji
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
| | - Socorro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa, Metro Manila, Philippines
| | - Lydia Sombrero
- Research Institute for Tropical Medicine, Muntinlupa, Metro Manila, Philippines
| | - Hazel Galang
- Research Institute for Tropical Medicine, Muntinlupa, Metro Manila, Philippines
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
| | - Rapunzel Aniceto
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
- Eastern Visayas Regional Medical Center, Leyte, Tacloban, Philippines
| | - Remigio Olveda
- Research Institute for Tropical Medicine, Muntinlupa, Metro Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Tohoku-RITM Collaborating Research Center for Emerging and Reemerging Infectious Diseases, Muntinlupa, Metro Manila, Philippines
- * E-mail:
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146
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Arakawa M, Okamoto-Nakagawa R, Toda S, Tsukagoshi H, Kobayashi M, Ryo A, Mizuta K, Hasegawa S, Hirano R, Wakiguchi H, Kudo K, Tanaka R, Morita Y, Noda M, Kozawa K, Ichiyama T, Shirabe K, Kimura H. Molecular epidemiological study of human rhinovirus species A, B and C from patients with acute respiratory illnesses in Japan. J Med Microbiol 2011; 61:410-419. [PMID: 22016561 DOI: 10.1099/jmm.0.035006-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies suggest that human rhinovirus species A, B and C (HRV-ABCs) may be associated with both the common cold and severe acute respiratory illnesses (ARIs) such as bronchiolitis, wheezy bronchiolitis and pneumonia. However, the state and molecular epidemiology of these viruses in Japan is not fully understood. This study detected the genomes of HRV-ABCs from Japanese patients (92 cases, 0-36 years old, mean±sd 3.5±5.0 years) with various ARIs including upper respiratory infection, bronchiolitis, wheezy bronchiolitis, croup and pneumonia between January and December 2010. HRV-ABCs were provisionally type assigned from the pairwise distances among the strains. On phylogenetic trees based on the nucleotide sequences of the VP4/VP2 coding region, HRV-A, -B and -C were provisionally assigned to 14, 2 and 12 types, respectively. The present HRV-A and -C strains had a wide genetic diversity (>30 % divergence). The interspecies distances were 0.230±0.063 (mean±sd, HRV-A), 0.218±0.048 (HRV-B) and 0.281±0.105 (HRV-C), based on nucleotide sequences, and 0.075±0.036 (HRV-A), 0.049±0.022 (HRV-B) and 0.141±0.064 (HRV-C) at the deduced amino acid level. Furthermore, HRV-A and -C were the predominant species and were detected throughout the seasons. The results suggested that HRV-A and -C strains have a wide genetic divergence and are associated with various ARIs in Japan.
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Affiliation(s)
- Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Reiko Okamoto-Nakagawa
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Shoichi Toda
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata-shi, Yamagata 990-0031, Japan
| | - Shunji Hasegawa
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Reiji Hirano
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Hiroyuki Wakiguchi
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Keiko Kudo
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Ryota Tanaka
- Department of Surgery, Kyorin University, School of Medicine, Mitaka-shi, Tokyo 181-8611, Japan
| | - Yukio Morita
- Department of Nutritional Science, Tokyo Kasei University, Itabashi-ku, Tokyo 173-8602, Japan
| | - Masahiro Noda
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Takashi Ichiyama
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube-shi, Yamaguchi 755-8505, Japan
| | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi-shi, Yamaguchi 753-082, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.,Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
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147
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Watanabe ASA, Carraro E, Candeias JMG, Donalísio MR, Leal E, Granato CFH, Bellei N. Viral etiology among the elderly presenting acute respiratory infection during the influenza season. Rev Soc Bras Med Trop 2011; 44:18-21. [PMID: 21340401 DOI: 10.1590/s0037-86822011000100005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 10/18/2010] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Acute respiratory tract infections are the most common illness in all individuals. Rhinoviruses have been reported as the etiology of more than 50% of respiratory tract infections worldwide. The study prospectively evaluated 47 elderly individuals from a group of 384 randomly assigned for acute respiratory viral infections (cold or flu) and assessed the occurrence of human rhinovirus (HRV), influenza A and B, respiratory syncytial virus and metapneumovirus (hMPV) in Botucatu, State of São Paulo, Brazil. METHODS Forty-nine nasal swabs collected from 47 elderly individuals following inclusion visits from 2002 to 2003 were tested by GenScan RT-PCR. HRV-positive samples were sequenced for phylogenetic analysis. RESULTS No sample was positive for influenza A/B or RSV. HRV was detected in 28.6% (14/47) and hMPV in 2% (1/47). Of 14 positive samples, 9 isolates were successfully sequenced, showing the follow group distribution: 6 group A, 1 group B and 2 group C HRVs. CONCLUSIONS The high incidence of HRV during the months of the influenza season requires further study regarding HRV infection impact on respiratory complications among this population. Infection caused by HRV is very frequent and may contribute to increasing the already high demand for healthcare during the influenza season.
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148
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Flanagan ML, Parrish CR, Cobey S, Glass GE, Bush RM, Leighton TJ. Anticipating the species jump: surveillance for emerging viral threats. Zoonoses Public Health 2011; 59:155-63. [PMID: 21914152 PMCID: PMC4948863 DOI: 10.1111/j.1863-2378.2011.01439.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zoonotic disease surveillance is typically triggered after animal pathogens have already infected humans. Are there ways to identify high‐risk viruses before they emerge in humans? If so, then how and where can identifications be made and by what methods? These were the fundamental questions driving a workshop to examine the future of predictive surveillance for viruses that might jump from animals to infect humans. Virologists, ecologists and computational biologists from academia, federal government and non‐governmental organizations discussed opportunities as well as obstacles to the prediction of species jumps using genetic and ecological data from viruses and their hosts, vectors and reservoirs. This workshop marked an important first step towards envisioning both scientific and organizational frameworks for this future capability. Canine parvoviruses as well as seasonal H3N2 and pandemic H1N1 influenza viruses are discussed as exemplars that suggest what to look for in anticipating species jumps. To answer the question of where to look, prospects for discovering emerging viruses among wildlife, bats, rodents, arthropod vectors and occupationally exposed humans are discussed. Finally, opportunities and obstacles are identified and accompanied by suggestions for how to look for species jumps. Taken together, these findings constitute the beginnings of a conceptual framework for achieving a virus surveillance capability that could predict future species jumps.
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Affiliation(s)
- M L Flanagan
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA 16802, USA.
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149
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Abstract
Viral infections affect wheezing and asthma in children and adults of all ages. In infancy, wheezing illnesses are usually viral in origin, and children with more severe wheezing episodes are more likely to develop recurrent episodes of asthma and to develop asthma later in childhood. Children who develop allergen-specific immunoglobulin E (allergic sensitization) and those who wheeze with human rhinoviruses (HRV) are at especially high risk for asthma. In older children and adults, HRV infections generally cause relatively mild respiratory illnesses and yet contribute to acute and potentially severe exacerbations in patients with asthma. These findings underline the importance of understanding the synergistic nature of allergic sensitization and infections with HRV in infants relative to the onset of asthma and in children and adults with respect to exacerbations of asthma. This review discusses clinical and experimental evidence of virus-allergen interactions and evaluates theories which relate immunologic responses to respiratory viruses and allergens to the pathogenesis and disease activity of asthma. Greater understanding of the relationship between viral respiratory infections, allergic inflammation, and asthma is likely to suggest new strategies for the prevention and treatment of asthma.
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Affiliation(s)
- Monica L. Gavala
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin‐Madison, Madison, WI, USA
| | - Paul J. Bertics
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin‐Madison, Madison, WI, USA
| | - James E. Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin‐Madison, Madison, WI, USA
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin‐Madison, Madison, WI, USA
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150
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Rhinovirus genome variation during chronic upper and lower respiratory tract infections. PLoS One 2011; 6:e21163. [PMID: 21713005 PMCID: PMC3119694 DOI: 10.1371/journal.pone.0021163] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 05/21/2011] [Indexed: 02/02/2023] Open
Abstract
Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5′UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.
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