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Mohanty M, Mishra B, Dwibedi B, Das RR, Panda S, Santra D, Mandal MC, Mamidi P, Gulla KM. Pathogenic Role of Human Rhinovirus Mono-Infection in Pediatric Lower Respiratory Tract Infection. Cureus 2024; 16:e60032. [PMID: 38854190 PMCID: PMC11162601 DOI: 10.7759/cureus.60032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Background and objective Human rhinovirus (HRV) is one of the leading causes of pediatric respiratory tract infection with a prevalence rate of 30-50%, mostly affecting children below five years of age and causing a substantial amount of economic loss. In children, it can alone or as a co-infection, cause a wide range of symptoms from mild to life-threatening ones. With the above background, the current study was carried out to emphasize the role of HRV mono-infection in pediatric acute respiratory tract infections by correlating clinical and molecular laboratory findings. Methods This study was carried out in a tertiary care teaching hospital over a duration of four years (March 2019-October 2023). Children up to 14 years of age visiting the outpatient department or admitted to the ward with diagnoses of acute respiratory tract infections (ARTIs) were included. The clinical and laboratory data were retrieved and analyzed. A nasopharyngeal swab (NPS) or throat swab (TS) was collected and sent to the Microbiology laboratory maintaining the cold chain. Nucleic acid was extracted and subjected to multiplex real-time polymerase chain reaction (RT-PCR). Result Of the 245 samples tested for the respiratory viral pathogen, 52 samples tested positive for HRV, of which 27 had HRV mono-infection. The clinico-demographic details of these 27 patients were studied in detail. The majority of the cases (24/27; 88.8%) were less than five years of age. Fever and shortness of breath were the most consistent symptoms in all. Nineteen (19/27; 62.9%) HRV mono-infection cases had underlying co-morbidities, all requiring respiratory support. The HRV mono-infection cases either developed bronchiolitis, lower respiratory tract infection, or pneumonia. All mono-infection cases had cycle threshold value (Ct) < 25, while the Ct value of HRV was > 30 in co-infection with other viruses. Conclusion Mono-infection of HRV in under-five children with underlying comorbidities and a lesser Ct value indicates severe disease manifestation and should be dealt with more cautiously.
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Affiliation(s)
- Monalisa Mohanty
- Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Baijayantimala Mishra
- Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Bhagirathi Dwibedi
- Pediatric Medicine, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Rashmi R Das
- Pediatrics, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Sailendra Panda
- Virology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Debashis Santra
- Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Madhab Charan Mandal
- Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Prabhudutta Mamidi
- Microbiology, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
| | - Krishna M Gulla
- Pediatric Medicine, All India Institute of Medical Sciences, Bhubaneswar, Bhubaneswar, IND
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Berginc N, Sočan M, Prosenc Trilar K, Petrovec M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 2024; 12:341. [PMID: 38399745 PMCID: PMC10893136 DOI: 10.3390/microorganisms12020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Maja Sočan
- Centre for Infectious Diseases, National Institute of Public Health, 1000 Ljubljana, Slovenia
| | - Katarina Prosenc Trilar
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Bastos JCS, Simas PVM, Caserta LC, Bragunde AEA, Marson FADL, Martini MC, Padilla MA, Ribeiro JD, Santos MMABD, Arns CW. Rhinoviruses as critical agents in severe bronchiolitis in infants. J Pediatr (Rio J) 2022; 98:362-368. [PMID: 34942156 PMCID: PMC9432127 DOI: 10.1016/j.jped.2021.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To detect RSV or other thirteen respiratory viruses as possible causer agent of bronchiolitis in infants. METHOD This is an epidemiological analytical study, conducted using a nasopharyngeal aspirate of 173 hospitalized children younger than two years old with severe bronchiolitis in three hospitals in the Campinas Metropolitan Region (CMR) during 2013-14. The data was statically evaluated by Pearson's chi-squared test with statistical significance of 0.05 and 95% confidence level. RESULTS As expected, the most prevalent viruses detected were RSV A and B in 47% and 16% of the samples, respectively. However, almost a third of severe bronchiolitis cases there were no detection of RSV, and the viruses more commonly detected were rhinoviruses, which were identified in almost a quarter of all positive samples for at least a viral agent. CONCLUSIONS Although nothing could be concluded from the disease severity and clinical-epidemiological data, the present study's results indicate that severe bronchiolitis is not always related to RSV infections in children younger than two years old, and the rhinoviruses were more prevalent in these cases. These findings reinforce the need to carry out a viral diagnosis in the hospital emergency would be very appropriate for all cases of respiratory infections in children, even for diseases in which the primary etiological agent seems to be well known.
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Affiliation(s)
- Juliana Cristina Santiago Bastos
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil
| | - Paulo Vitor Marques Simas
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil; The National University of San Marcos, Veterinary School, Laboratory of Avian Pathology, Lima, Peru
| | - Leonardo Cardia Caserta
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil; Cornell University, College of Veterinary Medicine, Department of Population Medicine and Diagnostic Sciences, Ithaca, United States
| | | | | | - Matheus Cavalheiro Martini
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil
| | - Marina Aiello Padilla
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil
| | - José Dirceu Ribeiro
- Universidade Estadual de Campinas (UNICAMP), Faculdade de Ciências Médicas, Departamento de Pediatria, Campinas, SP, Brazil
| | - Márcia Mercês Aparecida Bianchi Dos Santos
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil
| | - Clarice Weis Arns
- Universidade Estadual de Campinas (UNICAMP), Instituto de Biologia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Laboratório de Virologia Animal, Campinas, SP, Brazil.
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Understanding Rhinovirus Circulation and Impact on Illness. Viruses 2022; 14:v14010141. [PMID: 35062345 PMCID: PMC8778310 DOI: 10.3390/v14010141] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 01/27/2023] Open
Abstract
Rhinoviruses (RVs) have been reported as one of the main viral causes for severe respiratory illnesses that may require hospitalization, competing with the burden of other respiratory viruses such as influenza and RSV in terms of severity, economic cost, and resource utilization. With three species and 169 subtypes, RV presents the greatest diversity within the Enterovirus genus, and despite the efforts of the research community to identify clinically relevant subtypes to target therapeutic strategies, the role of species and subtype in the clinical outcomes of RV infection remains unclear. This review aims to collect and organize data relevant to RV illness in order to find patterns and links with species and/or subtype, with a specific focus on species and subtype diversity in clinical studies typing of respiratory samples.
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Genetic diversity and epidemiology of human rhinovirus among children with severe acute respiratory tract infection in Guangzhou, China. Virol J 2021; 18:174. [PMID: 34425845 PMCID: PMC8382100 DOI: 10.1186/s12985-021-01645-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/18/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Human rhinovirus (HRV) is one of the major viruses of acute respiratory tract disease among infants and young children. This work aimed to understand the epidemiological and phylogenetic features of HRV in Guangzhou, China. In addition, the clinical characteristics of hospitalized children infected with different subtype of HRV was investigated. METHODS Hospitalized children aged < 14 years old with acute respiratory tract infections were enrolled from August 2018 to December 2019. HRV was screened for by a real-time reverse-transcription PCR targeting the viral 5'UTR. RESULTS HRV was detected in 6.41% of the 655 specimens. HRV infection was frequently observed in children under 2 years old (57.13%). HRV-A and HRV-C were detected in 18 (45%) and 22 (55%) specimens. All 40 HRV strains detected were classified into 29 genotypes. The molecular evolutionary rate of HRV-C was estimated to be 3.34 × 10-3 substitutions/site/year and was faster than HRV-A (7.79 × 10-4 substitutions/site/year). Children who experienced rhinorrhoea were more common in the HRV-C infection patients than HRV-A. The viral load was higher in HRV-C detection group than HRV-A detection group (p = 0.0148). The median peak symptom score was higher in patients with HRV-C infection as compared to HRV-A (p = 0.0543), even though the difference did not significance. CONCLUSION This study revealed the molecular epidemiological characteristics of HRV in patients with respiratory infections in southern China. Children infected with HRV-C caused more severe disease characteristics than HRV-A, which might be connected with higher viral load in patients infected with HRV-C. These findings will provide valuable information for the pathogenic mechanism and treatment of HRV infection.
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Kuypers J, Perchetti GA, Chu HY, Newman KL, Katz J, Khatry SK, LeClerq SC, Jerome KR, Tielsch JM, Englund JA. Phylogenetic characterization of rhinoviruses from infants in Sarlahi, Nepal. J Med Virol 2019; 91:2108-2116. [PMID: 31389049 PMCID: PMC6800797 DOI: 10.1002/jmv.25563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/01/2019] [Indexed: 12/29/2022]
Abstract
Problem Rhinoviruses (RVs), the most common causes of acute respiratory infections in young children and infants, are highly diverse genetically. Objective To characterize the RV types detected with respiratory illness episodes in infants in Nepal. Study methods Infants born to women enrolled in a randomized trial of maternal influenza immunization in rural, southern Nepal were followed with household‐based weekly surveillance until 180 days of age. Infants with respiratory symptoms had nasal swabs tested for twelve respiratory viruses. A subset with RV alone was selected for sequencing of the VP4/2 gene to identify RV types. Results Among 547 RV‐only positive illnesses detected from December 2012 to April 2014, 285 samples (52%) were sequenced. RV‐A, B, and C species were detected in 193 (68%), 18 (6%), and 74 (26%) specimens, respectively. A total of 94 unique types were identified from the sequenced samples, including 52 RV‐A, 11 RV‐B, and 31 RV‐C. Multiple species and types circulated simultaneously throughout the study period. No seasonality was observed. The median ages at illness onset were 88, 104, and 88 days for RV‐A, B, and C, respectively. The median polymerase chain reaction cycle threshold values did not differ between RV species. No differences between RV species were observed for reported respiratory symptoms, including pneumonia, or for medical care‐seeking. Conclusions Among very young, symptomatic infants in rural Nepal, all three species and many types of RV were identified; RV‐A was detected most frequently. There was no association between RV species and disease severity. RV infections were common among infants less than six months old in southern Nepal. All three species and 94 types of RV were identified by sequencing the VP4/2 gene. Multiple species and types circulated simultaneously throughout the study period. No symptomatic differences between RV species or types were observed.
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Affiliation(s)
- Jane Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Garrett A Perchetti
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington
| | - Kira L Newman
- Department of Medicine, University of Washington, Seattle, Washington
| | - Joanne Katz
- Department of International Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Steven C LeClerq
- Department of International Health, Johns Hopkins University, Baltimore, Maryland.,Nepal Nutrition Intervention Project, Kathmandu, Nepal
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - James M Tielsch
- Department of Global Health, George Washington University, Washington, District of Colombia
| | - Janet A Englund
- Seattle Children's Hospital and Research Foundation, Seattle, Washington
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7
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Lebatteux D, Remita AM, Diallo AB. Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences. J Comput Biol 2019; 26:519-535. [PMID: 31050550 DOI: 10.1089/cmb.2018.0239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The classification of pathogens in emerging and re-emerging viruses represents major interests in taxonomic studies, functional genomics, host-pathogen interplay, prevention, and disease treatments. It consists of assigning a given sequence to its related group of known sequences sharing similar characteristics and traits. The challenges to such classification could be associated with several virus properties including recombination, mutation rate, multiplicity of motifs, and diversity. In domains such as pathogen monitoring and surveillance, it is important to detect and quantify known and novel taxa without exploiting the full and accurate alignments or virus family profiles. In this study, we propose an alignment-free method, CASTOR-KRFE, to detect discriminating subsequences within known pathogen sequences to classify accurately unknown pathogen sequences. This method includes three major steps: (1) vectorization of known viral genomic sequences based on k-mers to constitute the potential features, (2) efficient way of pattern extraction and evaluation maximizing classification performance, and (3) prediction of the minimal set of features fitting a given criterion (threshold of performance metric and maximum number of features). We assessed this method through a jackknife data partitioning on a dozen of various virus data sets, covering the seven major virus groups and including influenza virus, Ebola virus, human immunodeficiency virus 1, hepatitis C virus, hepatitis B virus, and human papillomavirus. CASTOR-KRFE provides a weighted average F-measure >0.96 over a wide range of viruses. Our method also shows better performance on complex virus data sets than multiple subsequences extractor for classification (MISSEL), a subsequence extraction method, and the Discriminative mode of MEME patterns extraction tool.
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Affiliation(s)
- Dylan Lebatteux
- Department of Computer Science, Université du Québec à Montréal, Montreal, Canada
| | - Amine M Remita
- Department of Computer Science, Université du Québec à Montréal, Montreal, Canada
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Andrés C, Peremiquel-Trillas P, Gimferrer L, Isern A, Piñana M, Rodrigo-Pendás JÁ, Codina MG, Martín MDC, Fuentes F, Rubio S, Campins-Martí M, Pumarola T, Antón A. Genetic diversity of rhinoviruses detected at a tertiary hospital in Catalonia (Spain) during the 2014-2017 seasons. Future Microbiol 2018; 13:1565-1573. [PMID: 30417657 DOI: 10.2217/fmb-2018-0151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM To describe the genetic diversity of rhinovirus (RV) from patients attended at a tertiary hospital in Barcelona (Spain) from October 2014 to May 2017. METHODS RV detection was performed by real-time multiplex RT-PCR. A specific real-time quantitive retrotranscription PCR (qRT-PCR) was carried out to select those samples (Ct < 35) for molecular characterization based on partial VP4/2 protein. RESULTS Phylogenetic characterization revealed proportions of 63% RV-A, 6% RV-B and 31% RV-C (119 different types). RV-A circulated throughout all the study period, with a minor circulation during winter, just when RV-C prevailed. Differences between age medians by RV-specie were reported. CONCLUSION The large genetic diversity of RV detected in our area is described here. The variable cocirculation of multiple RV types is also reported, showing differences by age.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - Laura Gimferrer
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Isern
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José Ángel Rodrigo-Pendás
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Del Carmen Martín
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco Fuentes
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susana Rubio
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Magda Campins-Martí
- Preventive Medicine & Epidemiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Vall Hebron Research Institute, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
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Interferon lambda receptor 1 (IFNL1R) transcript is highly expressed in rhinovirus bronchiolitis and correlates with disease severity. J Clin Virol 2018; 102:101-109. [PMID: 29549834 DOI: 10.1016/j.jcv.2018.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/23/2018] [Accepted: 03/09/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND As the expression of type III IFN receptor is restricted to the mucosal surfaces, its evaluation could be crucial to characterize the role of IFNλs during bronchiolitis. OBJECTIVES This study was designed to investigate airway type III IFN receptor (IFNLR1/IL10RB) expression during respiratory syncytial virus (RSV) or human rhinovirus (HRV) bronchiolitis. STUDY DESIGN Seventy-one 1-6 month old infants hospitalized with their first episode of acute RSV or HRV bronchiolitis were selected for this study. Expression of IFNLR1, IL10RB and IFN-stimulated genes (ISGs) MxA and ISG56 in cells of nasopharyngeal washings taken within the first 48 h of admission were determined by a real-time hydrolysis probe RT-PCR assay. The ability of types I and III IFNs to induce the expression of both IFNLR1 and IL10RB in vitro was also evaluated. RESULTS Airway IFNLR1 transcript levels were significantly higher in HRV bronchiolitis infants compared to those with RSV bronchiolitis. No differences were recorded for IL10RB-mRNA between RSV or HRV infection. IFNLR1 mRNA levels increased significantly in infants infected with the C species of HRV and in those with a higher clinical score index and with an eosinophil count >3%. There were no correlations in vivo between type III IFN receptors and those of ISGs and neither IFNLR1 nor IL10RB were induced in vitro by IFNs. CONCLUSIONS These results suggest that IFNLR1 are increased in HRV-infected infants with more severe bronchiolitis and blood eosinophilia and in those infected with the HRVC species.
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Droz N, Enouf V, Bidet P, Mohamed D, Behillil S, Simon AL, Bachy M, Caseris M, Bonacorsi S, Basmaci R. Temporal Association Between Rhinovirus Activity and Kingella kingae Osteoarticular Infections. J Pediatr 2018; 192:234-239.e2. [PMID: 29246347 DOI: 10.1016/j.jpeds.2017.09.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/21/2017] [Accepted: 09/21/2017] [Indexed: 01/17/2023]
Abstract
OBJECTIVE To determine whether the seasonal distribution of Kingella kingae osteoarticular infections is similar to that of common respiratory viruses. STUDY DESIGN Between October 2009 and September 2016, we extracted the results of K kingae-specific real-time polymerase chain reaction analyses performed for bone or joint specimens in patients from 2 pediatric tertiary care centers in Paris. We used data of respiratory virus detection from the Réseau National des Laboratoires network with coordination with the National Influenza Center of France. The Spearman rank correlation was used to assess a correlation between weekly distributions, with P < .05 denoting a significant correlation. RESULTS During the 7-year study period, 322 children were diagnosed with K kingae osteoarticular infection, and 317 testing episodes were K kingae-negative. We observed high activity for both K kingae osteoarticular infection and human rhinovirus (HRV) during the fall (98 [30.4%] and 2401 [39.1%] cases, respectively) and low activity during summer (59 [18.3%] and 681 [11.1%] cases, respectively). Weekly distributions of K kingae osteoarticular infection and rhinovirus activity were significantly correlated (r = 0.30; P = .03). In contrast, no significant correlation was found between the weekly distribution of K kingae osteoarticular infection and other respiratory viruses (r = -0.17, P = .34 compared with respiratory syncytial virus; r = -0.13, P = .34 compared with influenza virus; and r = -0.22, P = .11 compared with metapneumovirus). CONCLUSION A significant temporal association was observed between HRV circulation and K kingae osteoarticular infection, strengthening the hypothesis of a role of viral infections in the pathophysiology of K kingae invasive infection.
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Affiliation(s)
- Nina Droz
- Pediatric-Emergency Department, Louis-Mourier Hospital, AP-HP, Colombes, France
| | - Vincent Enouf
- Coordinating Center of the National Reference Center for Influenza Viruses, Institut Pasteur, UMR 3569 CNRS, Paris Diderot-Paris 7 University, Sorbonne Paris Cité
| | - Philippe Bidet
- Department of Microbiology, Robert Debré Hospital, AP-HP, Associated-National Reference Center for Escherichia Coli, Paris, France; IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité
| | - Damir Mohamed
- Unit of Clinical Epidemiology, Robert Debré Hospital, AP-HP, Paris, France; Inserm, CIC-EC 1426, Paris, France
| | - Sylvie Behillil
- Coordinating Center of the National Reference Center for Influenza Viruses, Institut Pasteur, UMR 3569 CNRS, Paris Diderot-Paris 7 University, Sorbonne Paris Cité
| | - Anne-Laure Simon
- Department of Pediatric Orthopedic Surgery, Robert Debré Hospital, AP-HP, Paris, France
| | - Manon Bachy
- Department of Pediatric Orthopedic Surgery, Armand Trousseau Hospital, APHP, Pierre et Marie Curie Paris 6 University, Paris, France
| | - Marion Caseris
- Department of Pediatric Infectious Diseases, Robert Debré Hospital, AP-HP, Paris, France
| | - Stéphane Bonacorsi
- Department of Microbiology, Robert Debré Hospital, AP-HP, Associated-National Reference Center for Escherichia Coli, Paris, France; IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité
| | - Romain Basmaci
- Pediatric-Emergency Department, Louis-Mourier Hospital, AP-HP, Colombes, France; IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité.
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Fiscon G, Weitschek E, Cella E, Lo Presti A, Giovanetti M, Babakir-Mina M, Ciotti M, Ciccozzi M, Pierangeli A, Bertolazzi P, Felici G. MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification. BioData Min 2016; 9:38. [PMID: 27980679 PMCID: PMC5139023 DOI: 10.1186/s13040-016-0116-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/20/2016] [Indexed: 12/04/2022] Open
Abstract
Background Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods. Results We propose a supervised method based on a genetic algorithm to identify small genomic subsequences that discriminate among different species. The method identifies multiple subsequences of bounded length with the same information power in a given genomic region. The algorithm has been successfully evaluated through its integration into a rule-based classification framework and applied to three different biological data sets: Influenza, Polyoma, and Rhino virus sequences. Conclusions We discover a large number of small subsequences that can be used to identify each virus type with high accuracy and low computational time, and moreover help to characterize different genomic regions. Bounding their length to 20, our method found 1164 characterizing subsequences for all the Influenza virus subtypes, 194 for all the Polyoma viruses, and 11 for Rhino viruses. The abundance of small separating subsequences extracted for each genomic region may be an important support for quick and robust virus identification. Finally, useful biological information can be derived by the relative location and abundance of such subsequences along the different regions. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0116-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giulia Fiscon
- Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy
| | - Emanuel Weitschek
- Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.,Department of Engineering, Uninettuno International University, Corso Vittorio Emanuele II 39, Rome, 00186 Italy
| | - Eleonora Cella
- Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.,Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185 Italy
| | - Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy
| | - Marta Giovanetti
- Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy.,Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, Rome, 00133 Italy
| | | | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Viale Oxford 81, Rome, 00133 Italy
| | - Massimo Ciccozzi
- Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy.,Department of Infectious Diseases, Istituto Superiore di Sanita, Viale Regina Margherita 299, Rome, 00161 Italy
| | - Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, Viale di Porta Tiburtina 2, Rome, 00185 Italy
| | - Paola Bertolazzi
- Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy
| | - Giovanni Felici
- Institute of Systems Analysis and Computer Science A. Ruberti (IASI), National Research Council (CNR), Via dei Taurini 19, Rome, 00185 Italy
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12
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Prevalence of rhinoviruses in young children of an unselected birth cohort from the Netherlands. Clin Microbiol Infect 2016; 22:736.e9-736.e15. [PMID: 27265373 PMCID: PMC7128250 DOI: 10.1016/j.cmi.2016.05.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022]
Abstract
Rhinovirus (RV) is a frequent pathogen in young children, eliciting symptoms ranging from common colds to wheezing illnesses and lower respiratory tract infections. The recently identified RV-C seems to be associated with asthma exacerbations and more severe disease, but results vary. We studied the prevalence and severity of infection with RV in an unselected birth cohort. Children with respiratory symptoms entered the symptomatic arm of the cohort and were compared with asymptomatic children. Severity of wheezing and other respiratory symptoms was registered. Respiratory viruses were evaluated using throat and nasopharyngeal swabs on first presentation and after recovery (wheezing children). RV genotyping was performed on RV-PCR positive samples. RV was the most prevalent respiratory virus and was found in 58/140 symptomatic children (41%), 24/96 (25%) control children and 19/74 (26%) wheezing symptomatic children after recovery (p <0.05) and did not differ between wheezing and non-wheezing symptomatic children—respectively, 42% (38/90) and 40% (20/50). RV-A was the most commonly detected species (40/68, 59%), followed by RV-C (22/68, 32%) and RV-B (6/68, 9%). RV-B was more frequently detected in asymptomatic children (5/6, p <0.05). There was no significant difference in the frequency of RV species between wheezing and non-wheezing symptomatic children. Children with RV mono-infection had more severe symptoms, but no association between RV species and severity of disease was seen. In an unselected birth cohort from the Netherlands with mild respiratory disease RV was the most prevalent respiratory virus. RV(-C) infection was not associated with more severe disease or wheezing.
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13
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Pulmonary and extrapulmonary complications of human rhinovirus infection in critically ill patients. J Clin Virol 2016; 77:85-91. [PMID: 26921740 DOI: 10.1016/j.jcv.2016.02.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/29/2016] [Accepted: 02/16/2016] [Indexed: 01/28/2023]
Abstract
BACKGROUND Human rhinovirus (HRV) is frequently detected in patients with respiratory tract infection. However, the full clinical spectrum of HRV infection in critically ill patients is not well characterized. OBJECTIVE To evaluate the clinical and virological characteristics of critically ill patients with HRV infection. STUDY DESIGN HRV-specific reverse transcription-polymerase chain reaction (RT-PCR) was performed on nasopharyngeal aspirate (NPA) specimens from 294 adult patients who required admission into the intensive care unit (ICU). Clinical characteristics were analyzed. HRV genotyping using the 5'UTR-VP4-VP2 region was performed. RESULTS HRV was detected in NPA specimens of 22 patients (7.5%) by RT-PCR. Dyspnea was the most common presenting symptom (16/22; 72.7%), but seizure also occurred in 5 (22.7%) patients. Exacerbation of underlying disease occurred in 12 (54.5%) patients. Four (18.2%) patients died, and HRV was considered to play a role as the cause of death in 3 patients. Thirteen (59.1%) patients had pneumonia, and the most common radiological finding was consolidation (6/13; 46.2%). Streptococcus pneumoniae was the most common co-pathogen among patients with pneumonia. Among the 9 patients without pneumonia, 3 patients had exacerbation of underlying lung diseases, 3 patients had acute pulmonary edema, 2 patients with diabetes mellitus had acute complications from poor glycemic control, and 1 patient had status epilepticus. HRV-A was the most common species (64.3%), but there was no clear relationship between HRV species and clinical presentation. CONCLUSION Both pulmonary and extrapulmonary complications of HRV were common in critically ill patients.
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14
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Howard LM, Johnson M, Gil AI, Griffin MR, Edwards KM, Lanata CF, Williams JV, Grijalva CG. Molecular Epidemiology of Rhinovirus Detections in Young Children. Open Forum Infect Dis 2016; 3:ofw001. [PMID: 26900577 PMCID: PMC4759584 DOI: 10.1093/ofid/ofw001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/01/2016] [Indexed: 02/06/2023] Open
Abstract
Background. Human rhinoviruses (HRVs) are frequently detected in children with acute respiratory illnesses (ARIs) but also in asymptomatic children. We compared features of ARI with HRV species (A, B, C) and determined genotypes associated with repeated HRV detections within individuals. Methods. We used clinical data and respiratory samples obtained from children <3 years old during weekly active household-based surveillance. A random subset of samples in which HRV was detected from individuals during both ARI and an asymptomatic period within 120 days of the ARI were genotyped. Features of ARI were compared among HRV species. Concordance of genotype among repeated HRV detections within individuals was assessed. Results. Among 207 ARI samples sequenced, HRV-A, HRV-B, and HRV-C were detected in 104 (50%), 20 (10%), and 83 (40%), respectively. Presence of fever, decreased appetite, and malaise were significantly higher in children with HRV-B. When codetections with other viruses were excluded (n = 155), these trends persisted, but some did not reach statistical significance. When 58 paired sequential HRV detections during asymptomatic and ARI episodes were sequenced, only 9 (16%) were identical genotypes of HRV. Conclusions. Clinical features may differ among HRV species. Repeated HRV detections in young children frequently represented acquisition of new HRV strains.
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Affiliation(s)
- Leigh M Howard
- Division of Infectious Diseases, Department of Pediatrics; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Monika Johnson
- Department of Pediatrics , University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center , Pennsylvania
| | - Ana I Gil
- Instituto de Investigacion Nutricional , Lima , Peru
| | - Marie R Griffin
- Department of Health Policy , Vanderbilt University, Tennessee
| | - Kathryn M Edwards
- Division of Infectious Diseases, Department of Pediatrics; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Claudio F Lanata
- Division of Infectious Diseases, Department of Pediatrics; Instituto de Investigacion Nutricional, Lima, Peru
| | - John V Williams
- Department of Pediatrics , University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center , Pennsylvania
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15
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Abstract
Human rhinoviruses (HRVs) are widespread respiratory pathogens and a major cause of acute respiratory tract infections. The aim of this study was to investigate the molecular epidemiology of rhinovirus infections in children in Cyprus over three consecutive winter seasons. From a total of 116 rhinovirus-positive samples, 68 were sequenced in the 5'-UTR and VP4/VP2 regions. Thirty-six (52.9%) samples were identified as HRV-A and 27 (39.7%) as HRV-C, with only five (7.4%) samples belonging to the HRV-B species. Of these, a total of 46 different genotypes were identified. In the VP2/VP4 phylogenetic tree all strains clustered in three different well-defined clades, whereas the 5'-UTR tree exhibited clades with a mixed clustering of HRV-A and HRV-C strains reflecting the evolutionary history of recombination between HRV-A and HRV-C that has been observed previously. In summary, a high intra- and inter-season diversity of HRV types was observed. Despite its geographical isolation the frequency of HRV species in Cyprus is comparable to that reported in other regions of the world supporting the concept of an unrestricted global circulation. This study assesses, for the first time, the epidemiology of rhinovirus infections in Cypriot children and will be helpful to clinicians and researchers interested in the treatment and control of viral respiratory tract infections.
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16
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Lu QB, Wo Y, Wang LY, Wang HY, Huang DD, Zhang XA, Liu W, Cao WC. Molecular epidemiology of human rhinovirus in children with acute respiratory diseases in Chongqing, China. Sci Rep 2014; 4:6686. [PMID: 25328042 PMCID: PMC4202208 DOI: 10.1038/srep06686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/01/2014] [Indexed: 01/10/2023] Open
Abstract
Human rhinovirus-C (HRV-C) has been increasingly detected in patients with acute respiratory diseases (ARDs). Prolonged surveillance was performed on children with ARD to investigate the molecular epidemiology and clinical characteristics of HRV in Chongqing, China. Nasopharyngeal aspirates (NPA) were collected from hospitalized children with ARD during 2009–2012. HRV-C was genotyped by sequencing the VP4/VP2 coding region. Among the 1,567 NPAs obtained, 223 (14.2%) were HRV positive, and 75.3% of these 223 NPAs were co-infected with other viruses. HRV-A (54.7%) and HRV-C (39.9%) accounted for the majority of HRV infections. Logistic regression models demonstrated significant associations between HRV-A, HRV-C, and asthma attacks, as well as between HRV-C and wheezing. A phylogenetic tree showed that HRV-C2 was the predominant type of HRV-C, followed by HRV-C43, HRV-C1, and HRV-C17. Three novel genotypes were proposed on the basis of a low identity with the known HRVs. Our results showed that HRV-A and HRV-C were the predominant types of HRV infection, and HRV-C showed a high genetic variation in Chongqing, China. HRV infection was associated with asthma attacks and wheezing; furthermore, HRV infections played a minor role in causing severe pneumonia. This knowledge provides information for the prevention and control of HRV associated with ARDs.
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Affiliation(s)
- Qing-Bin Lu
- School of Public Health, Peking University, Beijing100191, P. R. China
| | - Ying Wo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China
| | - Li-Yuan Wang
- 1] State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China [2] Graduate School of Anhui Medical University, Hefei. 230032, P. R. China
| | - Hong-Yu Wang
- 1] State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China [2] Graduate School of Anhui Medical University, Hefei. 230032, P. R. China
| | - Dou-Dou Huang
- 1] State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China [2] Graduate School of Anhui Medical University, Hefei. 230032, P. R. China
| | - Xiao-Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing. 100071, P. R. China
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17
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Linder JE, Plachco TE, Libster R, Miller EK. Sequencing human rhinoviruses: direct sequencing versus plasmid cloning. J Virol Methods 2014; 211:64-9. [PMID: 25286177 DOI: 10.1016/j.jviromet.2014.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 09/17/2014] [Accepted: 09/24/2014] [Indexed: 01/08/2023]
Abstract
Human rhinoviruses (RV) are associated with the majority of viral respiratory illnesses in infants, children and adults. Over the last several years, researchers have begun to sequence the many different species and strains of RV in order to determine if certain species were associated with increased disease severity. There are a variety of techniques employed to prepare samples for sequencing. One method utilizes plasmid-cloning, which is expensive and takes several hours to complete. Recently, some investigators have instead used direct sequencing to sequence RV strains, allowing for omission of the time- and labor-intensive cloning step. This study formally compares and contrasts the sequencing results obtained from plasmid-cloning and direct Sanger sequencing of a 500 base pair PCR product covering the VP4/VP2 region of RV. A slightly longer sequence (by 65 base pairs on average) was obtained when specimens were plasmid-cloned, and the sequences were 86% similar. After trimming the extra base pairs from the cloned sequences, the sequences were 99.7% identical. Overall success of directly sequencing samples was similar to that of cloning, 5% on average failed for each technique. Therefore, in many instances, directly sequencing samples may be considered in lieu of the more expensive and time-consuming plasmid-cloning technique.
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Affiliation(s)
- Jodell E Linder
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
| | - Tatyana E Plachco
- Hospital de Pediatria SAMIC Prof. Dr. Juan P Garrahan, Buenos Aires, Argentina; Hospital Materno Infantil Ramon Sarda, Buenos Aires, Argentina.
| | | | - E Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Medical Center North, Nashville, TN 37232, United States.
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18
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Selvaggi C, Pierangeli A, Fabiani M, Spano L, Nicolai A, Papoff P, Moretti C, Midulla F, Antonelli G, Scagnolari C. Interferon lambda 1-3 expression in infants hospitalized for RSV or HRV associated bronchiolitis. J Infect 2014; 68:467-77. [PMID: 24389019 PMCID: PMC7172705 DOI: 10.1016/j.jinf.2013.12.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/19/2013] [Accepted: 12/24/2013] [Indexed: 12/30/2022]
Abstract
OBJECTIVES The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. As an additional objective we sought to determine whether a different expression of IFN lambda 1-3 was associated with different harboring viruses, the clinical course of bronchiolitis or with the levels of well established IFN stimulated genes (ISGs), such as mixovirus resistance A (MxA) and ISG56. METHODS The analysis was undertaken in 118 infants with RSV or HRV bronchiolitis. Nasopharyngeal washes were collected for virological studies and molecular analysis of type III IFN responses. RESULTS RSV elicited higher levels of IFN lambda subtypes when compared with HRV. A similar expression of type III IFN was found in RSVA or RSVB infected infants and in those infected with HRVA or HRVC viruses. Results also indicate that IFN lambda 1 and IFN lambda 2-3 levels were correlated with each other and with MxA and ISG56-mRNAs. In addition, a positive correlation exists between the IFN lambda1 levels and the clinical score index during RSV infection. In particular, higher IFN lambda 1 levels are associated to an increase of respiratory rate. CONCLUSIONS These findings show that differences in the IFN lambda 1-3 levels in infants with RSV or HRV infections are present and that the expression of IFN lambda 1 correlates with the severity of RSV bronchiolitis.
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Affiliation(s)
- Carla Selvaggi
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Alessandra Pierangeli
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Marco Fabiani
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Lucia Spano
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Ambra Nicolai
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Paola Papoff
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Corrado Moretti
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Fabio Midulla
- Department of Pediatrics PICU, Sapienza University of Rome, Rome, Italy
| | - Guido Antonelli
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy
| | - Carolina Scagnolari
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Molecular Medicine, Laboratory of Virology, Sapienza University of Rome, Rome, Italy.
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19
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Daleno C, Piralla A, Scala A, Senatore L, Principi N, Esposito S. Phylogenetic analysis of human rhinovirus isolates collected from otherwise healthy children with community-acquired pneumonia during five successive years. PLoS One 2013; 8:e80614. [PMID: 24260436 PMCID: PMC3833952 DOI: 10.1371/journal.pone.0080614] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022] Open
Abstract
In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify HRV, and the HRV-positive samples were used for sequencing analysis and to reconstruct the phylogenetic tree. HRV was identified in 198 samples (42.2%), and the VP4/VP2 region was successfully amplified in 151 (76.3%). HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%) and HRV-C in 59 (39.1%). Forty-seven (31.1%) of the children with HRV infection were aged <1 year, 71 (47.0%) were aged 1-3 years, and 33 (21.9%) were aged ≥4 years. Blast and phylogenetic analyses showed that the HRV strains were closely related to a total of 66 reference genotypes, corresponding to 29 HRV-A, 9 HRV-B and 28 HRV-C strains. Nucleotide variability was 37% between HRV-A and HRV-B, 37.3% between HRV-A and HRV-C, and 39.9% between HRV-B and HRV-C. A number of sequences clustered with known serotypes and, within these clusters, there were strains circulating during several seasons. The most frequently detected genotypes were HRV-A78 (n=17), HRV-A12 (n=9) and HRV-C2 (n=5). This study shows that, although it is mainly associated with HRV-A, pediatric CAP can also be diagnosed in subjects infected by HRV-C and, more rarely, by HRV-B. Moreover, a large number of genotypes may be involved in causing pediatric CAP and can be different from year to year. Although the prolonged circulation of the same genotypes can sometimes be associated with a number of CAP episodes in different years.
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Affiliation(s)
- Cristina Daleno
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Piralla
- Virolog Uni, Fondazion IRCCS Policlinic Sa Matte, Pavi, Ital
| | - Alessia Scala
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Senatore
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nicola Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Susanna Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- * E-mail:
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