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1.
Mem Inst Oswaldo Cruz ; 114: e190198, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31596309

RESUMEN

BACKGROUND: In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES: This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS: Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS: The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS: Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.


Asunto(s)
Coronaviridae/aislamiento & purificación , Herpesviridae/aislamiento & purificación , Nasofaringe/virología , Parvoviridae/aislamiento & purificación , Picornaviridae/aislamiento & purificación , Tráquea/virología , Coronaviridae/clasificación , Coronaviridae/genética , ADN Viral/genética , Herpesviridae/clasificación , Herpesviridae/genética , Humanos , Parvoviridae/clasificación , Parvoviridae/genética , Picornaviridae/clasificación , Picornaviridae/genética , ARN Viral/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa
2.
Arch Virol ; 164(12): 2919-2930, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31520220

RESUMEN

Human bocavirus (HBoV) has been detected primarily in children with acute lower respiratory tract disease (LRTD), but its occurrence, clinical profile, and role as a causative agent of RTD are not clear. The aim of this study was to investigate the prevalence and the potential clinical relevance of HBoV. Using molecular tests, we tested 1352 nasopharyngeal samples obtained between October 1, 2017 and April 30, 2018 from children up to the age of 16 with RTD for the presence of HBoV DNA and 20 other respiratory pathogens at three different hospitals in Belgium. HBoV was detected in 77 children with a median age of 10.6 months. Consecutive samples were available for 15 HBoV-positive children and showed persistent HBoV positivity in four of them. Monoinfection was observed in six infants. Four of them were born prematurely and were infected during hospitalization at the neonatal intensive care unit (NICU). Only one of these six monoinfected children was diagnosed with recurrent wheezing due to HBoV. This child was carried to term and had a high viral load. Coinfections, most frequently with rhinovirus (52.1%) and adenovirus (49.3%), were observed in 72 patients. In seventeen of them in which HBoV was present at high viral load or higher viral load than its copathogens, bronchi(oli)tis (n = 8), recurrent wheezing (n = 8) or episodic wheezing (n = 1) were diagnosed. Our results suggest that HBoV infection at high viral load in infants is associated with wheezing (P = 0.013, Cramer's V = 0.613).


Asunto(s)
Bocavirus Humano/aislamiento & purificación , Infecciones por Parvoviridae/diagnóstico , Infecciones del Sistema Respiratorio/virología , Adolescente , Bélgica/epidemiología , Niño , Preescolar , Infección Hospitalaria/epidemiología , Infección Hospitalaria/virología , ADN Viral/genética , Femenino , Bocavirus Humano/genética , Humanos , Lactante , Recién Nacido , Unidades de Cuidado Intensivo Neonatal , Masculino , Nasofaringe/virología , Infecciones por Parvoviridae/epidemiología , Nacimiento Prematuro/epidemiología , Nacimiento Prematuro/virología , Prevalencia , Estudios Retrospectivos , Carga Viral
3.
Intervirology ; 62(3-4): 112-115, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31542785

RESUMEN

OBJECTIVE: Respiratory syncytial virus (RSV) infection causes lower respiratory tract infection primarily in infants and toddlers. RSV reinfection also occurs throughout life and can be a significant cause of pneumonia and mortality in the elderly. Surges in physician offices, emergency department visits, and hospitalization often result from RSV illness. Point-of-care (POC) testing reduces healthcare costs and permits informed decisions on treatment, further testing, or hospitalization to occur during the physician-patient encounter. Optimal POC assays must be sensitive, easy to perform, and provide rapid results. METHODS: In this study, 2 POC assays (Alere i; Abbot Rapid Diagnostics and cobas Liat, Roche Molecular, Inc.) and a laboratory-based assay (Solana; Quidel, Inc.) were evaluated using 133 patient nasopharyngeal specimens. RESULTS: Sensitivity/specificity values (%) of 94.7/96.1, 98.2/96.1, and 96.5/94.7 were obtained for the Alere i, Liat, and Solana assays, respectfully. These values approximated those stated in each assay's package insert. CONCLUSION: Rapid molecular assays for RSV are sensitive and accurate. The choice of assay should reflect each healthcare institution's specific testing needs with respect to the benefits and drawbacks of each product.


Asunto(s)
Técnicas de Diagnóstico Molecular/métodos , Infecciones por Virus Sincitial Respiratorio/diagnóstico , Virus Sincitial Respiratorio Humano/aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Humanos , Lactante , Recién Nacido , Persona de Mediana Edad , Nasofaringe/virología , Pruebas en el Punto de Atención , Virus Sincitial Respiratorio Humano/genética , Sensibilidad y Especificidad , Adulto Joven
4.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(8): 904-910, 2019 Aug 10.
Artículo en Chino | MEDLINE | ID: mdl-31484252

RESUMEN

Objective: To analyze the etiologic and epidemiological characteristics of adult acute respiratory infections in Shanghai during 2015-2017. Methods: Data was collected from outpatients with acute respiratory infections who visited the Fever Clinics in three hospitals of different levels in three administrative regions of Shanghai, from 2015 to 2017. Basic information and nasopharyngeal swabs were collected from cases in line with the inclusion criteria. Multiplex RT-PCR and bacterial cultures were performed to detect the respiratory pathogens. Results: A total of 806 individuals were enrolled from 2015 to 2017. Respiratory pathogens were identified in 73.45% (592/806) of the cases, with the virus detection rate as 66.75% (538/806). It was found that the major respiratory pathogens for virus detection were influenza A in 326 (40.45%), influenza B in 116 (14.39%), rhinovirus/enterovirus in 39 (4.84%) of the cases. The overall detection rate of bacteria was 16.13% (130/806), including Klebsiella pneumoniae in 90 (11.17%) cases, Staphylococcus Aureus in 46 (5.71%) cases. Other kind of bacteria were not detected in our study. The detection rates on Mycoplasma pneumoniae was 5.33% (43/806) and on Chlamydia pneumonia was 0.37% (3/806). Co-infection with multiple pathogens was detected in 18.61% (150/806) of the cases, including 135 with double infection (accounting for 90.00%), 14 with triple infection and 1 with quadruple infection (accounted for 9.33% and 0.67%, respectively). Among the 150 cases with co-infections, the main identified pathogens were influenza A, Klebsiella pneumoniae, Staphylococcus aureus, and Mycoplasma pneumoniae. Pathogens of acute respiratory infections that identified among the outpatients from the Fever Clinics at different time, region or population, the characteristics were different (P<0.001). Conclusions: In 2015-2017, outpatients with acute respiratory infections in Shanghai were mainly caused by influenza virus or other viruses, however dynamically with its composition, time, region and characteristics of the population. It is necessary to strengthen and combine related medical and preventive services and to develop the appropriate strategies regarding clinical diagnosis and treatment.


Asunto(s)
Bacterias/aislamiento & purificación , Infecciones Bacterianas/diagnóstico , Gripe Humana/diagnóstico , Reacción en Cadena de la Polimerasa Multiplex/métodos , Nasofaringe , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/etiología , Virosis/diagnóstico , Virus/aislamiento & purificación , Enfermedad Aguda , Adulto , Bacterias/genética , Infecciones Bacterianas/epidemiología , Infecciones Bacterianas/microbiología , China/epidemiología , Coinfección/diagnóstico , Enterovirus/genética , Enterovirus/aislamiento & purificación , Monitoreo Epidemiológico , Humanos , Incidencia , Virus de la Influenza A/genética , Virus de la Influenza A/aislamiento & purificación , Virus de la Influenza B/genética , Virus de la Influenza B/aislamiento & purificación , Gripe Humana/epidemiología , Gripe Humana/virología , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Mycoplasma pneumoniae , Nasofaringe/microbiología , Nasofaringe/virología , Vigilancia de la Población , Infecciones del Sistema Respiratorio/diagnóstico , Rhinovirus/genética , Rhinovirus/aislamiento & purificación , Staphylococcus aureus/genética , Staphylococcus aureus/aislamiento & purificación , Virosis/epidemiología , Virosis/virología , Virus/genética
5.
Tuberk Toraks ; 67(2): 124-130, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-31414643

RESUMEN

Introduction: Exacerbations of chronic obstructive pulmonary disease (COPD) are often caused by respiratory tract infections. The aim of this study was to investigate the clinical, laboratory and computed tomography features of patients with hospitalized COPD exacerbations in which respiratory viruses were detected using a real-time polymerase chain reaction (PCR) technique. Materials and Methods: This retrospectively planned study included patients hospitalized in the chest diseases clinic due to exacerbation of COPD between November 2018-February 2019. The study included patients who had virus-specific real-time PCR, and computed tomography scans of the chest. Result: A total of 110 patients were included in the study. Respiratory viruses were identified in the nasopharyngeal swabs of 50 patients (45.5%) using the real-time PCR method, with rhinovirus (25%), influenza A (13.1%) and coronavirus (11.8%) being the most commonly isolated agents. The mean age of the patients was 68.28 ± 9.59 years in the virus-positive group and 68.20 ± 8.27 years in the virus-negative group (p= 0.963). Gender distribution, rate of smokers, exposure to biofuels, blood leukocyte count, neutrophil percentage, C-reactive protein (CRP) level, FEV1/FVC ratio did not significantly differ between the two groups (p> 0.05). Procalcitonin (PCT) and FEV1 values were significantly lower (p= 0.001 and p= 0.028, respectively) and the number of exacerbations was significantly higher in the virus-positive group (p= 0.001). The length of hospital stay was longer in the virus-positive group than in the virus-negative group (p= 0.012). Among the findings of computed tomography (CT) of the chest, bronchial wall thickening, cystic bronchiectasis, and emphysema did not differ significantly (p> 0.05). The rate of infiltrative lesions (tree-in-bud opacity, ground-glass opacity, atypical pneumonia) was significantly higher in the virus-positive group (p= 0.020). Conclusions: Viral respiratory tract infections should be considered in hospitalized patients with an exacerbation of COPD who have a history of frequent exacerbations, normal PCT value, and the absence of consolidation in CT scan of the chest. The use of broadspectrum antibiotic therapy should be avoided in patients with these features.


Asunto(s)
Enfermedad Pulmonar Obstructiva Crónica/complicaciones , Infecciones del Sistema Respiratorio/complicaciones , Virosis/complicaciones , Anciano , Bronquiectasia , Coronavirus/aislamiento & purificación , Femenino , Humanos , Virus de la Influenza A/aislamiento & purificación , Gripe Humana/complicaciones , Tiempo de Internación , Masculino , Persona de Mediana Edad , Nasofaringe/virología , Enfermedad Pulmonar Obstructiva Crónica/fisiopatología , Enfermedad Pulmonar Obstructiva Crónica/virología , Reacción en Cadena en Tiempo Real de la Polimerasa , Pruebas de Función Respiratoria , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Rhinovirus/aislamiento & purificación , Tomografía Computarizada por Rayos X , Virosis/virología
6.
Rev Soc Bras Med Trop ; 52: e20180249, 2019 Jul 29.
Artículo en Inglés | MEDLINE | ID: mdl-31365620

RESUMEN

INTRODUCTION: Prevalence of influenza A virus (Flu-A), respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) was assessed in children with acute respiratory infections (ARIs). METHODS: Nasopharyngeal aspirates and throat swabs were subjected to real-time polymerase chain reaction (PCR) to detect RSV and Flu-A and to conventional PCR to detect hMPV. RESULTS: Of the 156 children assessed, 93 (59.6%) carried at least one virus, with 35.9% positive for RSV, 14.1% for hMPV, and 9.6% for Flu-A. The prevalence of co-infections was 2.6%. CONCLUSIONS: The high detection rate may reflect increased sensitivity of real-time PCR compared to traditional PCR and viral culture.


Asunto(s)
Gripe Humana/epidemiología , Infecciones por Paramyxoviridae/epidemiología , Infecciones por Virus Sincitial Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Adolescente , Niño , Preescolar , Estudios Transversales , Femenino , Humanos , Virus de la Influenza A/genética , Irán/epidemiología , Masculino , Metapneumovirus/genética , Nasofaringe/virología , Reacción en Cadena en Tiempo Real de la Polimerasa , Virus Sincitial Respiratorio Humano/genética , Infecciones del Sistema Respiratorio/epidemiología
7.
Jpn J Infect Dis ; 72(5): 318-322, 2019 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-31257239

RESUMEN

Respiratory viral and atypical bacterial agents lead to infections in a large spectrum, from mild symptoms to respiratory failure. In the present study, we aimed to detect multiple viral and bacterial agents in the respiratory samples of inpatients by real-time polymerase chain reaction (RT-PCR). Nasopharyngeal swabs and broncho-alveolar lavage samples from inpatients with respiratory infection symptoms at the Uludag University Hospital between December 1, 2015 and March 31,2018 were investigated. DNA/RNA was extracted using the EZ1 Virus Mini Kit v2.0 (Qiagen, Belgium) with the EZ1 extraction device (Qiagen, Belgium). The R-GENE® RT-PCR (Biomerioux, France) kit was used to detect influenza A, influenza B, respiratory syncytial virus (RSV), human metapneumovirus, rhinovirus/enterovirus (RV/EV), adenovirus, human bocavirus (hBoV), corona virus, parainfluenza virus, Chlamydia pneumoniae/Mycoplasma pneumoniae, and Legionella pneumophila in Rotor-Gene Q (Qiagen, Belgium). Patients were aged between 0 and 90 years. Overall, 177 (56.9%) patients were men and 134 (43.1%) were women. A total of 311 samples were analyzed, of which 214 (68.8%) were positive. In total, 360 agents, including 338 viruses and 22 bacteria, were detected. The commonest agents were influenza A+B (n = 65, 18,1%), hBoV (n = 64, 17.8%), RV/EV (n = 56, 15.6%), and RSV (n = 47, 13.1%). Rapid diagnosis of viral infections by RT-PCR is important for the specific treatment of patients.


Asunto(s)
Bacterias/aislamiento & purificación , Infecciones Bacterianas/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Virosis/epidemiología , Virus/aislamiento & purificación , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Bacterias/clasificación , Infecciones Bacterianas/microbiología , Líquido del Lavado Bronquioalveolar/microbiología , Líquido del Lavado Bronquioalveolar/virología , Niño , Preescolar , Femenino , Hospitales de Enseñanza , Hospitales Universitarios , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Nasofaringe/microbiología , Nasofaringe/virología , Reacción en Cadena de la Polimerasa , Prevalencia , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Turquia/epidemiología , Virosis/virología , Virus/clasificación , Adulto Joven
8.
Biomed Environ Sci ; 32(6): 438-445, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-31262389

RESUMEN

OBJECTIVE: This study was conducted to investigate the viral and bacterial etiology and epidemiology of patients with acute febrile respiratory syndrome (AFRS) in Qinghai using a commercial routine multiplex-ligation-nucleic acid amplification test (NAT)-based assay. METHODS: A total of 445 nasopharyngeal swabs specimens from patients with AFRS were analyzed using the RespiFinderSmart22kit (PathoFinder BV, Netherlands) and the LightCycler 480 real-time PCR system. RESULTS: Among the 225 (225/445, 51%) positive specimens, 329 positive pathogens were detected, including 298 (90.58%) viruses and 31 (9%) bacteria. The most commonly detected pathogens were influenza virus (IFV; 37.39%; 123/329), adenovirus (AdV; 17.02%; 56/329), human coronaviruses (HCoVs; 10.94%; 36/329), rhinovirus/enterovirus (RV/EV; 10.03%; 33/329), parainfluenza viruses (PIVs; 8.51%; 28/329), and Mycoplasma pneumoniae (M. pneu; 8.51%; 28/329), respectively. Among the co-infected cases (17.53%; 78/445), IFV/AdV and IFV/M. pneu were the most common co-infections. Most of the respiratory viruses were detected in summer and fall. CONCLUSION: In our study, IFV-A was the most common respiratory pathogen among 22 detected pathogens, followed by AdV, HCoV, RV/EV, PIV, and M. pneu. Bacteria appeared less frequently than viruses, and co-infection was the most common phenomenon among viral pathogens. Pathogens were distributed among different age groups and respiratory viruses were generally active in July, September, and November. Enhanced surveillance and early detection can be useful in the diagnosis, treatment, and prevention of AFRS, as well as for guiding the development of appropriate public health strategies.


Asunto(s)
Síndrome Respiratorio Agudo Grave/virología , Adolescente , Adulto , Factores de Edad , Anciano , Niño , Preescolar , China/epidemiología , Femenino , Humanos , Lactante , Masculino , Persona de Mediana Edad , Nasofaringe/virología , Estaciones del Año , Vigilancia de Guardia , Síndrome Respiratorio Agudo Grave/epidemiología , Adulto Joven
9.
Diagn Microbiol Infect Dis ; 95(1): 55-58, 2019 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-31160164

RESUMEN

Respiratory syncytial virus (RSV) causes acute respiratory infections. Rapid RSV diagnosis has an impact on patient management. In a newly developed molecular assay, named reverse transcription strand invasion based amplification (RT-SIBA) RSV assay, RSV RNA is reverse transcribed to cDNA and amplified and detected under isothermal reaction conditions. The performance of this assay was evaluated. Respiratory samples that tested positive (n = 81) or negative (n = 61) for RSV with the multiplex RT-PCR Anyplex II RV16 Detection Kit (Anyplex) were analyzed with the RT-SIBA assay. Discordant samples were tested with the GeneXpert Flu/RSV XC assay. Consistent results in at least 2 of the 3 methods were defined as reference standard. The RT-SIBA assay yielded a negative result for the 61 negative samples and a positive result in 71/81 (85.5%) of the Anyplex positive samples. After a resolution of discordant samples, the positive and negative percent agreement of the RT-SIBA assay were 92% and 100%, respectively. The RT-SIBA assay is a rapid molecular assay for the detection of RSV with good performance in clinical specimens.


Asunto(s)
Infecciones por Virus Sincitial Respiratorio/diagnóstico , Virus Sincitial Respiratorio Humano/genética , Infecciones del Sistema Respiratorio/diagnóstico , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/normas , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Técnicas de Diagnóstico Molecular/normas , Nasofaringe/virología , ARN Viral/genética , Infecciones por Virus Sincitial Respiratorio/virología , Infecciones del Sistema Respiratorio/virología , Sensibilidad y Especificidad , Factores de Tiempo , Adulto Joven
10.
Virol J ; 16(1): 78, 2019 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-31196108

RESUMEN

BACKGROUND: Human adenoviruses (HAdVs) cause a wide range of diseases. However, the genotype diversity and epidemiological information relating to HAdVs among hospitalized children with respiratory tract infections (RTIs) is limited. Here, we describe the epidemiology and genotype distribution of HAdVs associated with RTIs in Beijing, China. METHODS: Nasopharyngeal aspirates (NPA) were collected from hospitalized children with RTIs from April 2017 to March 2018. HAdVs were detected by a TaqMan-based quantitative real-time polymerase chain reaction (qPCR) assay, and the hexon gene was used for phylogenetic analysis. Epidemiological data were analyzed using statistical product and service solutions (SPSS) 21.0 software. RESULTS: HAdV was detected in 72 (5.64%) of the 1276 NPA specimens, with most (86.11%, 62/72) HAdV-positives cases detected among children < 6 years of age. HAdV-B3 (56.06%, 37/66) and HAdV-C2 (19.70%, 13/66) were the most frequent. Of the 72 HAdV-infected cases, 27 (37.50%) were co-infected with other respiratory viruses, most commonly parainfluenza virus (12.50%, 9/72) and rhinovirus (9.72%, 7/72). The log number of viral load ranged from 3.30 to 9.14 copies per mL of NPA, with no significant difference between the HAdV mono- and co-infection groups. The main clinical symptoms in the HAdV-infected patients were fever and cough, and 62 (86.11%, 62/72) were diagnosed with pneumonia. Additionally, HAdVs were detected throughout the year with a higher prevalence in summer. CONCLUSIONS: HAdV prevalence is related to age and season. HAdV-B and HAdV-C circulated simultaneously among the hospitalized children with RTIs in Beijing, and HAdV-B type 3 and HAdV-C type 2 were the most frequent.


Asunto(s)
Infecciones por Adenovirus Humanos/epidemiología , Hospitalización/estadística & datos numéricos , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/virología , Infecciones por Adenovirus Humanos/virología , Adenovirus Humanos/genética , Adenovirus Humanos/aislamiento & purificación , Adolescente , Beijing/epidemiología , Niño , Preescolar , Femenino , Variación Genética , Genotipo , Humanos , Lactante , Recién Nacido , Masculino , Nasofaringe/virología , Filogenia , Prevalencia , Radiografía , Reacción en Cadena en Tiempo Real de la Polimerasa , Análisis de Secuencia de ADN , Carga Viral
11.
J Med Microbiol ; 68(8): 1211-1218, 2019 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-31225788

RESUMEN

INTRODUCTION: Lower respiratory tract infections (LRTIs), particularly those acquired in hospitals, are an important cause of childhood morbidity and mortality. Understanding the aetiology and epidemiology of LRTIs is necessary for clinical management, reduction of antibiotic usage, vaccine development and prevention of nosocomial infection. AIM: In this study, we aimed to detect 13 viruses and atypical bacteria in nasopharyngeal secretion specimens from hospitalized children with LRTIs. METHODOLOGY: From January 2014 to December 2016, nasopharyngeal secretion specimens were prospectively collected from 3232 children aged between 1 and 72 months. Nucleic acid was extracted and analysed using the SureX13 respiratory pathogen multiplex kit as per the manufacturer's instructions. RESULTS: A total of 2874 (88.9 %) children tested positive for viral and/or atypical bacterial infections, and 965 (29.9 %) were co-infected with multiple pathogens. The most frequently detected respiratory tract pathogens (RTPs) were rhinovirus, respiratory syncytial virus, parainfluenza virus and adenoviruses. The rates of RTP and co-infection positivity in the toddler group were significantly higher than those in the infant and preschool groups. CONCLUSION: The SureX13 respiratory pathogen multiplex kit has the ability to effectively detect a range of RTPs in hospitalized paediatric patients with LRTIs.


Asunto(s)
Bacterias/aislamiento & purificación , Reacción en Cadena de la Polimerasa Multiplex/normas , Juego de Reactivos para Diagnóstico/normas , Infecciones del Sistema Respiratorio/diagnóstico , Virus/aislamiento & purificación , Factores de Edad , Bacterias/clasificación , Bacterias/genética , Niño Hospitalizado/estadística & datos numéricos , Preescolar , China/epidemiología , Coinfección/diagnóstico , Coinfección/epidemiología , Coinfección/microbiología , Coinfección/virología , Femenino , Humanos , Lactante , Masculino , Nasofaringe/microbiología , Nasofaringe/virología , Prevalencia , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Análisis de Secuencia de ADN , Virus/clasificación , Virus/genética
12.
Transbound Emerg Dis ; 66(5): 1884-1893, 2019 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-31059176

RESUMEN

Equine influenza is a major cause of respiratory infections in horses and can spread rapidly despite the availability of commercial vaccines. In this study, we carried out molecular characterization of Equine Influenza Virus (EIV) isolated from the Malaysian outbreak in 2015 by sequencing of the HA and NA gene segments using Sanger sequencing. The nucleotide and amino acid sequences of HA and NA were compared with representative Florida clade 1 and clade 2 strains using phylogenetic analysis. The Florida clade 1 viruses identified in this outbreak revealed numerous amino acid substitutions in the HA protein as compared to the current OIE vaccine strain recommendations and representative strains of circulating Florida sub-lineage clade 1 and clade 2. Differences in HA included amino acids located within antigenic sites which could lead to reduced immune recognition of the outbreak strain and alter the effectiveness of vaccination against the outbreak strain. Detailed surveillance and genetic information sharing could allow genetic drift of equine influenza viruses to be monitored more effectively on a global basis and aid in refinement of vaccine strain selection for EIV.


Asunto(s)
Brotes de Enfermedades/veterinaria , Enfermedades de los Caballos/epidemiología , Subtipo H3N8 del Virus de la Influenza A/genética , Infecciones por Orthomyxoviridae/veterinaria , Vacunación/veterinaria , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Animales , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética , Enfermedades de los Caballos/virología , Caballos , Subtipo H3N8 del Virus de la Influenza A/aislamiento & purificación , Malasia/epidemiología , Nasofaringe/virología , Neuraminidasa/genética , Infecciones por Orthomyxoviridae/epidemiología , Infecciones por Orthomyxoviridae/virología , Filogenia , Alineación de Secuencia/veterinaria , Proteínas Virales/genética
13.
Emerg Microbes Infect ; 8(1): 662-674, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31084471

RESUMEN

Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a variety of H7N9 DI-RNA species were present in the patient samples and human bronchial epithelial cells. In several abundantly expressed DI-RNA species, long overlapping sequences have been identified around at the breakpoint region and the other side of deleted region. Influenza DI-RNA is known as a defective viral RNA with single large internal deletion. Beneficial to the long-read property of SMRT sequencing, double and triple internal deletions were identified in half of the DI-RNA species. In addition, we examined the expression of DI-RNAs in mice infected with sublethal dose of H7N9 virus at different time points. Interestingly, DI-RNAs were abundantly expressed as early as day 2 post-infection. Taken together, we reveal the diversity and characteristics of DI-RNAs found in H7N9-infected patients, cells and animals. Further investigations on this overwhelming generation of DI-RNA may provide important insights into the understanding of H7N9 viral replication and pathogenesis.


Asunto(s)
Virus Defectuosos/genética , Subtipo H7N9 del Virus de la Influenza A/crecimiento & desarrollo , Gripe Humana/patología , Gripe Humana/virología , ARN Viral/genética , Análisis de Secuencia de ADN , Animales , Bronquios/virología , Virus Defectuosos/aislamiento & purificación , Modelos Animales de Enfermedad , Células Epiteliales/virología , Genoma Viral , Humanos , Ratones , Nasofaringe/patología , Nasofaringe/virología , Infecciones por Orthomyxoviridae/patología , Infecciones por Orthomyxoviridae/virología , ARN Viral/aislamiento & purificación , Eliminación de Secuencia
14.
Rev Chilena Infectol ; 36(1): 26-31, 2019 Feb.
Artículo en Español | MEDLINE | ID: mdl-31095201

RESUMEN

BACKGROUND: Early viral detection in acute respiratory infections (ARI) is essential to establish appropriate therapy and prevent nosocomial transmission. OBJECTIVE: To compare the efficacy of indirect immunofluorescence technique (IIF) with the polymerase chain reaction (PCR) to identify respiratory viruses in children hospitalized for ARI. METHODS: 47 nasopharyngeal aspirates of children ≤ 2 years with ARI were included. IFI included respiratory syncytial virus (RSV), adenovirus, influenza A and B and parainfluenza. PCR also included the detection of metapneumovirus, enterovirus/rhinovirus, bocavirus and coronavirus. Sensitivity, specificity, positive and negative predictive value (VPP/NPV) and kappa correlation for RSV were estimated by IIF compared to PCR. RESULTS: The IIF detected only RSV (29; 61.7%). PCR detected several viruses, including RSV in 26 cases (55.3%), followed by bocavirus (29.8%), rhinovirus/enterovirus (21.3%), adenovirus (14.9%) and parainfluenza (4,3%) among others, with 35.5% of coinfection. The IIF presented sensitivity: 85.7%, specificity: 73.6%, PPV: 82.7%, NPV: 77.7% and kappa: 0.5990 (95% CI, 0.3636-0.8346) for RSV. CONCLUSION: The IIF presents good sensitivity, but moderate specificity for RSV. However, IIF fails to detect other respiratory viruses. The introduction of PCR would improve the etiological diagnosis of ARI of viral origin.


Asunto(s)
Técnica del Anticuerpo Fluorescente Indirecta/métodos , Nasofaringe/virología , Reacción en Cadena de la Polimerasa/métodos , Virus/aislamiento & purificación , Adolescente , Niño , Preescolar , Chile , Estudios Transversales , Virus ADN/aislamiento & purificación , Femenino , Humanos , Lactante , Masculino , Estudios Prospectivos , Virus ARN/aislamiento & purificación , Reproducibilidad de los Resultados , Infecciones del Sistema Respiratorio/virología , Sensibilidad y Especificidad
15.
BMC Geriatr ; 19(1): 111, 2019 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-30991957

RESUMEN

BACKGROUND: In children suffering from severe lower airway illnesses, respiratory virus detection has given good prognostic information, but such reports in the elderly are scarce. Therefore, our aim was to study whether the detection of nasopharyngeal viral pathogens and conventional inflammatory markers in the frail elderly correlate to the presence, signs and symptoms or prognosis of radiographically-verified pneumonia. METHODS: Consecutive episodes of hospital care of patients 65 years and older with respiratory symptoms (N = 382) were prospectively studied as a cohort. Standard clinical questionnaire was filled by the study physician. Laboratory analyses included PCR diagnostics of nasopharyngeal swab samples for 14 respiratory viruses, C-reactive protein (CRP) and white blood cell count (WBC). Chest radiographs were systematically analysed by a study radiologist. The length of hospital stay, hospital revisit and death at ward were used as clinical endpoints. RESULTS: Median age of the patients was 83 years (range 76-90). Pneumonia was diagnosed in 112/382 (29%) of the studied episodes. One or more respiratory viruses were detected in 141/382 (37%) episodes and in 34/112 (30%) episodes also diagnosed with pneumonia. Pneumonia was associated with a WBC over 15 × 109/L (P = .006) and a CRP value over 80 mg/l (P < .05). A virus was detected in 30% of pneumonia episodes and in 40% of non-pneumonia episodes, but this difference was not significant (P = 0.09). The presence of a respiratory virus was associated with fewer revisits to the hospital (P < .05), whereas a CRP value over 100 mg/l was associated with death during hospital stay (P < .05). Respiratory virus detections did not correlate to WBC or CRP values, signs and symptoms or prognosis of radiographically-verified pneumonia episodes. CONCLUSION: Among the elderly with respiratory symptoms, respiratory virus detection was not associated with an increased risk of pneumonia or with a more severe clinical course of the illness. CRP and WBC remain important indicators of pneumonia, and according to our findings, pneumonia should be treated as a bacterial disease regardless of the virus findings. Our data does not support routine virus diagnostics for the elderly patients with pneumonia outside the epidemic seasons.


Asunto(s)
Nasofaringe/virología , Neumonía Viral/diagnóstico , Neumonía Viral/epidemiología , Estaciones del Año , Anciano , Anciano de 80 o más Años , Estudios de Cohortes , Femenino , Estudios de Seguimiento , Humanos , Tiempo de Internación/tendencias , Masculino , Neumonía Viral/sangre , Estudios Prospectivos , Infecciones del Sistema Respiratorio/sangre , Infecciones del Sistema Respiratorio/diagnóstico , Infecciones del Sistema Respiratorio/epidemiología
16.
Jpn J Infect Dis ; 72(4): 237-242, 2019 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-30814460

RESUMEN

Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are the leading causes of acute respiratory tract infection in children, and clinical manifestations of these virus infections are considered similar. To investigate the differences in clinical characteristics between HMPV and RSV infections in young children, we prospectively enrolled children < 3 years old who required hospitalization with acute respiratory tract infection due to HMPV or RSV at 10 hospitals in Japan. We enrolled 48 children with HMPV infection and 141 with RSV infection. Patients with HMPV infection were older than those with RSV infection. High-grade fever was more frequently observed in patients with HMPV infection, whereas no significant differences in respiratory symptoms were apparent. Abnormal serum lactate dehydrogenase values and consolidation shadows on chest X-ray were more frequently observed in patients with HMPV infection. During hospitalization, nasal mucus suction was more frequently required in patients with RSV infection. On the other hand, ß2-adrenergic agonists, corticosteroids, and leukotriene receptor antagonists were more frequently used in patients with HMPV infection. These findings suggest that HMPV and RSV infections show similar respiratory symptoms, but HMPV infection is more likely to lead to the development of pneumonia, at least among hospitalized young children.


Asunto(s)
Metapneumovirus , Infecciones por Paramyxoviridae/patología , Infecciones por Virus Sincitial Respiratorio/patología , Virus Sincitial Respiratorio Humano , Infecciones del Sistema Respiratorio/patología , Infecciones del Sistema Respiratorio/virología , Enfermedad Aguda , Preescolar , Femenino , Hospitalización , Humanos , Lactante , Japón , Masculino , Nasofaringe/virología , Infecciones por Paramyxoviridae/terapia , Neumonía Viral/patología , Neumonía Viral/terapia , Neumonía Viral/virología , Infecciones por Virus Sincitial Respiratorio/terapia , Infecciones del Sistema Respiratorio/terapia
17.
Bioengineered ; 10(1): 33-42, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-30913952

RESUMEN

The diagnosis of influenza A virus is essential since it can be confused with influenza A like illness and lead to inaccurate drug prescription. In this study, the M2e peptide, a strategic antigen that is conserved in all virus subtypes, was used as a diagnostic marker of influenza A. For the first time, M2e-specific IgY antibody was covalently conjugated to alkaline phosphatase (ALP) enzyme in the presence of glutaraldehyde. The antibody-enzyme bioconjugate was characterized by fluorescence and Fourier-transform infrared spectroscopy. Subsequently, the diagnostic value of this bioconjugate was evaluated by direct sandwich ELISA using nasopharyngeal swab samples positive/negative for H1N1 and H3N2, which were previously analyzed by rRT-PCR for influenza. In conclusion, the M2e-specific IgY-ALP bioconjugate demonstrated positive results for Influenza A in samples that were diagnosed as Influenza A via the RT-PCR method.


Asunto(s)
Fosfatasa Alcalina/química , Anticuerpos Antivirales/química , Antígenos Virales/inmunología , Inmunoglobulinas/química , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Subtipo H3N2 del Virus de la Influenza A/aislamiento & purificación , Gripe Humana/diagnóstico , Fosfatasa Alcalina/inmunología , Secuencia de Aminoácidos , Animales , Anticuerpos Antivirales/biosíntesis , Anticuerpos Antivirales/aislamiento & purificación , Antígenos Virales/administración & dosificación , Antígenos Virales/química , Pollos , Reactivos de Enlaces Cruzados/química , Ensayo de Inmunoadsorción Enzimática/métodos , Epítopos/química , Femenino , Glutaral/química , Humanos , Inmunización , Inmunoconjugados/química , Inmunoglobulinas/biosíntesis , Inmunoglobulinas/aislamiento & purificación , Subtipo H1N1 del Virus de la Influenza A/química , Subtipo H1N1 del Virus de la Influenza A/inmunología , Subtipo H3N2 del Virus de la Influenza A/química , Subtipo H3N2 del Virus de la Influenza A/inmunología , Gripe Humana/inmunología , Gripe Humana/virología , Nasofaringe/virología , Péptidos/administración & dosificación , Péptidos/química , Péptidos/inmunología , Espectroscopía Infrarroja por Transformada de Fourier
18.
Influenza Other Respir Viruses ; 13(4): 339-353, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30891896

RESUMEN

BACKGROUND: Respiratory syncytial virus (RSV) is one of the main viral causes of lower respiratory tract illness (LRTI), especially in young children. RSV vaccines, including maternal and infant vaccines, are under development; however, more epidemiological studies are needed to develop effective vaccination strategies. OBJECTIVES: To estimate detailed age-specific incidence rates and severity of RSV-associated LRTI (RSV-LRTI) using data from a community-based prospective cohort study in the Philippines. PATIENTS/METHODS: Cohort children who visited health facilities due to acute respiratory symptoms were identified, and nasopharyngeal swabs were collected to detect RSV. The severity of RSV-LRTI was assessed using the severity definition proposed by the World Health Organization. Risk factors for developing RSV-LRTI and contribution of SpO2 measurement were also evaluated. RESULTS: A total of 395 RSV episodes which occurred in children aged 2-59 months were categorised as 183 RSV-LRTI, 72 as severe RSV-LRTI and 29 as very severe RSV-LRTI. Children aged 3-5 months had the highest incidence rate of RSV-LRTI, at 207.4 per 1000 child-years (95% CI: 149.0-279.5). Younger age group, place of living and low educational level of caregivers were associated with developing RSV-LRTI. Clinical manifestations had low levels of agreement with hypoxaemia as measured by pulse oximeter. CONCLUSION: The highest burden of RSV was observed in young infants aged 3-5 months, whereas the burden was also high in those aged 12-20 months. Future vaccination strategies should consider the protection of older children, especially those aged one year, as well as young infants.


Asunto(s)
Infecciones por Virus Sincitial Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/epidemiología , Factores de Edad , Preescolar , Femenino , Hospitalización , Humanos , Incidencia , Lactante , Pulmón/virología , Masculino , Nasofaringe/virología , Filipinas/epidemiología , Estudios Prospectivos , Vacunas contra Virus Sincitial Respiratorio , Virus Sincitial Respiratorio Humano , Infecciones del Sistema Respiratorio/virología , Factores de Riesgo
19.
J Infect Chemother ; 25(8): 578-583, 2019 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-30905631

RESUMEN

Recently, rapid molecular detection systems have been used for point-of-care testing for the diagnosis of influenza worldwide. Here, we evaluated the performance of the cobas Liat system and the cobas Influenza A/B assay (Liat) using fresh nasopharyngeal samples collected from a Japanese population between December 2017 and February 2018. The performance of the examination was compared with that of antigen testing and a conventional polymerase chain reaction (nested-PCR) method. A total of 159 patients were included in this study, and 77 tested positive using Liat. The concordance rate between Liat and nested PCR was 97.5%. The median time between the ordering of testing and completion of molecular analyses using Liat was 30 min (interquartile range: 28-35 min). The overall sensitivity and specificity of antigen testing were 57.1% and 100%, respectively. The duration from symptom onset to examination did not alter antigen testing sensitivity. The current study demonstrates the high performance of Liat for the rapid molecular identification of the influenza virus.


Asunto(s)
Virus de la Influenza A/genética , Virus de la Influenza B/genética , Gripe Humana/diagnóstico , Adolescente , Adulto , Anciano , Femenino , Humanos , Gripe Humana/virología , Masculino , Persona de Mediana Edad , Técnicas de Diagnóstico Molecular/métodos , Nasofaringe/virología , Sistemas de Atención de Punto , Reacción en Cadena de la Polimerasa/métodos , Estudios Prospectivos , Sensibilidad y Especificidad , Adulto Joven
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