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1.
Int J Biol Sci ; 16(10): 1698-1707, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32226287

RESUMO

As a city famous for tourism, the public healthcare system of Macau SAR has been under great pressure during the outbreak of the Coronavirus Disease 2019 (COVID-19). In this study, we report clinical and microbiological features of ten COVID-19 patients enrolled in the Centro Hospitalar Conde de São Januário (CHCSJ) between January 21 to February 16, 2020. Clinical samples from all patients including nasopharyngeal swab (NPS)/sputum, urine, and feces were collected for serial virus RNA testing by standard qRT-PCR assay. In total, seven were imported cases and three were local cases. The median duration from Macau arrival to admission in imported cases was 3 days. Four patients required oxygen therapy but none of them needed machinal ventilation. No fatal cases were noted. The most common symptoms were fever (80%) and diarrhea (80%). In the "Severe" group, there was significantly more elderly patients (p=0.045), higher lactate dehydrogenase levels (p=0.002), and elevated C-Reactive protein levels compared to the "Mild to Moderate" group (p<0.001). There were positive SARS-CoV-2 RNA signals in all patients' NPS and stool specimens but negative in all urine specimens. Based on our data on SARS-CoV-2 RNA shedding in stool and the possibility of a lag in viral detection in NPS specimens, the assessment of both fecal and respiratory specimen is recommended to enhance diagnostic sensitivity, and also to aid discharge decision before the role of viral RNA shedding in stool is clarified.


Assuntos
Betacoronavirus , Infecções por Coronavirus/diagnóstico , Fezes/virologia , Pneumonia Viral/diagnóstico , RNA Viral/isolamento & purificação , Eliminação de Partículas Virais , Adulto , Técnicas de Laboratório Clínico , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/terapia , Infecções por Coronavirus/virologia , Diarreia/virologia , Feminino , Febre/virologia , Humanos , Pulmão/diagnóstico por imagem , Macau , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Pandemias , Pneumonia Viral/terapia , Pneumonia Viral/virologia , Radiografia Torácica , Reação em Cadeia da Polimerase em Tempo Real , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Escarro/virologia , Tomografia Computadorizada por Raios X , Urina/virologia
2.
Euro Surveill ; 25(11)2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32209164

RESUMO

Data concerning the transmission of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) in paucisymptomatic patients are lacking. We report an Italian paucisymptomatic case of coronavirus disease 2019 with multiple biological samples positive for SARS-CoV-2. This case was detected using the World Health Organization protocol on cases and contact investigation. Current discharge criteria and the impact of extra-pulmonary SARS-CoV-2 samples are discussed.


Assuntos
Infecções Assintomáticas , Infecções por Coronavirus/diagnóstico , Coronavirus/isolamento & purificação , Fezes/virologia , Pulmão/diagnóstico por imagem , Nasofaringe/virologia , Pneumonia Viral/diagnóstico , Viagem , Eliminação de Partículas Virais , Anticorpos Antivirais/imunologia , Betacoronavirus , China , Busca de Comunicante , Coronavirus/genética , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Humanos , Itália , Pulmão/patologia , Masculino , Pandemias , Pneumonia Viral/terapia , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Quarentena , Radiografia Torácica , Reação em Cadeia da Polimerase em Tempo Real , Tomografia Computadorizada por Raios X , Organização Mundial da Saúde , Adulto Jovem
3.
R I Med J (2013) ; 103(2): 75-76, 2020 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-32192233

RESUMO

The novel coronavirus (now called SARS-CoV-2) initially discovered in Wuhan, China, has now become a global pandemic. We describe a patient presenting to an Emergency Department in Rhode Island on March 12, 2020 with cough and shortness of breath after a trip to Jamaica. The patient underwent nasopharyngeal swab for a respiratory pathogen panel as well as SARS-CoV-2 RT-PCR. When the respiratory pathogen panel was positive for human metapneumovirus, the patient was treated and discharged. SARS-CoV-2 RT-PCR came back positive 24 hours later. Although respiratory viral co-infection is thought to be relatively uncommon in adults, this case reflects that SARS-CoV-2 testing algorithms that exclude patients who test positive for routine viral pathogens may miss SARS-CoV-2 co-infected patients.


Assuntos
Betacoronavirus/isolamento & purificação , Tosse/etiologia , Dispneia/etiologia , Metapneumovirus/isolamento & purificação , Nasofaringe/virologia , Infecções por Paramyxoviridae/diagnóstico , Coinfecção , Humanos , Pessoa de Meia-Idade , Infecções por Paramyxoviridae/tratamento farmacológico , Isolamento de Pacientes , Viagem , Resultado do Tratamento
4.
Mem Inst Oswaldo Cruz ; 114: e190198, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31596309

RESUMO

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.


Assuntos
Coronaviridae/isolamento & purificação , Herpesviridae/isolamento & purificação , Nasofaringe/virologia , Parvoviridae/isolamento & purificação , Picornaviridae/isolamento & purificação , Traqueia/virologia , Coronaviridae/classificação , Coronaviridae/genética , DNA Viral/genética , Herpesviridae/classificação , Herpesviridae/genética , Humanos , Parvoviridae/classificação , Parvoviridae/genética , Picornaviridae/classificação , Picornaviridae/genética , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real , Reação em Cadeia da Polimerase Via Transcriptase Reversa
5.
BMC Res Notes ; 12(1): 628, 2019 Sep 24.
Artigo em Inglês | MEDLINE | ID: mdl-31551085

RESUMO

OBJECTIVE: We conducted four cross-sectional studies over 1 year among humans and pigs in three slaughterhouses in Central and Western Kenya (> 350 km apart) to determine infection and exposure to influenza A viruses. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from participants who reported acute respiratory illness (ARI) defined as fever, cough or running nose. Nasal swabs and blood samples were collected from pigs. Human NP/OP and pig nasal swabs were tested for influenza A virus by real-time reverse transcriptase polymerase chain reaction (PCR) and pig serum was tested for anti-influenza A antibodies by ELISA. RESULTS: A total of 288 participants were sampled, 91.3% of them being male. Fifteen (5.2%) participants had ARI but the nine swabs collected from them were negative for influenza A virus by PCR. Of the 1128 pigs sampled, five (0.4%) nasal swabs tested positive for influenza A/H1N1/pdm09 by PCR whereas 214 of 1082 (19.8%) serum samples tested for Influenza A virus antibodies. There was higher seroprevalence in colder months and among pigs reared as free-range. These findings indicate circulation of influenza A/H1N1/pdm09 among pigs perhaps associated with good adaptation of the virus to the pig population after initial transmission from humans to pigs.


Assuntos
Matadouros , Vírus da Influenza A Subtipo H1N1/genética , Influenza Humana/diagnóstico , Infecções por Orthomyxoviridae/diagnóstico , Doenças dos Suínos/diagnóstico , Adulto , Animais , Anticorpos Antivirais/sangue , Estudos Transversais , Feminino , Geografia , Humanos , Vírus da Influenza A Subtipo H1N1/fisiologia , Influenza Humana/transmissão , Influenza Humana/virologia , Quênia/epidemiologia , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Orofaringe/virologia , Infecções por Orthomyxoviridae/epidemiologia , Infecções por Orthomyxoviridae/virologia , Pandemias , Suínos , Doenças dos Suínos/epidemiologia , Doenças dos Suínos/virologia , Adulto Jovem
6.
Arch Virol ; 164(12): 2919-2930, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31520220

RESUMO

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).


Assuntos
Bocavirus Humano/isolamento & purificação , Infecções por Parvoviridae/diagnóstico , Infecções Respiratórias/virologia , Adolescente , Bélgica/epidemiologia , Criança , Pré-Escolar , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/virologia , DNA Viral/genética , Feminino , Bocavirus Humano/genética , Humanos , Lactente , Recém-Nascido , Unidades de Terapia Intensiva Neonatal , Masculino , Nasofaringe/virologia , Infecções por Parvoviridae/epidemiologia , Nascimento Prematuro/epidemiologia , Nascimento Prematuro/virologia , Prevalência , Estudos Retrospectivos , Carga Viral
7.
Intervirology ; 62(3-4): 112-115, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31542785

RESUMO

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.


Assuntos
Técnicas de Diagnóstico Molecular/métodos , Infecções por Vírus Respiratório Sincicial/diagnóstico , Vírus Sincicial Respiratório Humano/isolamento & purificação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Humanos , Lactente , Recém-Nascido , Pessoa de Meia-Idade , Nasofaringe/virologia , Testes Imediatos , Vírus Sincicial Respiratório Humano/genética , Sensibilidade e Especificidade , Adulto Jovem
8.
Zhonghua Liu Xing Bing Xue Za Zhi ; 40(8): 904-910, 2019 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-31484252

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/diagnóstico , Influenza Humana/diagnóstico , Reação em Cadeia da Polimerase Multiplex/métodos , Nasofaringe , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/etiologia , Viroses/diagnóstico , Vírus/isolamento & purificação , Doença Aguda , Adulto , Bactérias/genética , Infecções Bacterianas/epidemiologia , Infecções Bacterianas/microbiologia , China/epidemiologia , Coinfecção/diagnóstico , Enterovirus/genética , Enterovirus/isolamento & purificação , Monitoramento Epidemiológico , Humanos , Incidência , Vírus da Influenza A/genética , Vírus da Influenza A/isolamento & purificação , Vírus da Influenza B/genética , Vírus da Influenza B/isolamento & purificação , Influenza Humana/epidemiologia , Influenza Humana/virologia , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Mycoplasma pneumoniae , Nasofaringe/microbiologia , Nasofaringe/virologia , Vigilância da População , Infecções Respiratórias/diagnóstico , Rhinovirus/genética , Rhinovirus/isolamento & purificação , Staphylococcus aureus/genética , Staphylococcus aureus/isolamento & purificação , Viroses/epidemiologia , Viroses/virologia , Vírus/genética
9.
Tuberk Toraks ; 67(2): 124-130, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31414643

RESUMO

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.


Assuntos
Doença Pulmonar Obstrutiva Crônica/complicações , Infecções Respiratórias/complicações , Viroses/complicações , Idoso , Bronquiectasia , Coronavirus/isolamento & purificação , Feminino , Humanos , Vírus da Influenza A/isolamento & purificação , Influenza Humana/complicações , Tempo de Internação , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Doença Pulmonar Obstrutiva Crônica/fisiopatologia , Doença Pulmonar Obstrutiva Crônica/virologia , Reação em Cadeia da Polimerase em Tempo Real , Testes de Função Respiratória , Infecções Respiratórias/virologia , Estudos Retrospectivos , Rhinovirus/isolamento & purificação , Tomografia Computadorizada por Raios X , Viroses/virologia
10.
Rev Soc Bras Med Trop ; 52: e20180249, 2019 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-31365620

RESUMO

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.


Assuntos
Influenza Humana/epidemiologia , Infecções por Paramyxoviridae/epidemiologia , Infecções por Vírus Respiratório Sincicial/epidemiologia , Infecções Respiratórias/virologia , Adolescente , Criança , Pré-Escolar , Estudos Transversais , Feminino , Humanos , Vírus da Influenza A/genética , Irã (Geográfico)/epidemiologia , Masculino , Metapneumovirus/genética , Nasofaringe/virologia , Reação em Cadeia da Polimerase em Tempo Real , Vírus Sincicial Respiratório Humano/genética , Infecções Respiratórias/epidemiologia
11.
Jpn J Infect Dis ; 72(5): 318-322, 2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31257239

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , Infecções Bacterianas/epidemiologia , Infecções Respiratórias/epidemiologia , Viroses/epidemiologia , Vírus/isolamento & purificação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/classificação , Infecções Bacterianas/microbiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , Criança , Pré-Escolar , Feminino , Hospitais de Ensino , Hospitais Universitários , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Nasofaringe/microbiologia , Nasofaringe/virologia , Reação em Cadeia da Polimerase , Prevalência , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Estudos Retrospectivos , Turquia/epidemiologia , Viroses/virologia , Vírus/classificação , Adulto Jovem
12.
PLoS One ; 14(7): e0218873, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31269055

RESUMO

Saffold virus (SAFV) is classified into the Cardiovirus genus of the Picornaviridae family. Up to now, eleven genotypes have been identified however, their clinical significance remains unclear. Here, we investigated the presence of SAFV in asymptomatic patients admitted for adenoidectomy. A total of 70 adenoid tissue samples were collected from children with clinical symptoms caused by hypertrophy of adenoids but without symptoms of airway infection. Samples were investigated for SAFV by RT-nested PCR and sequence analysis. Eleven of 70 (15.7%) samples were positive for SAFV. Nasopharyngeal swabs were available from 45 children just before surgery. SAFV was rarely found and only in children with SAFV-positive adenoids 2/8. Our findings indicate that the presence of SAFV seems to be more frequent in adenoid tissue than expected. This could support the notion of a longer than previously anticipated persistence of SAFV nucleic acids in the respiratory tract and possibly a chronic infection. Further investigations are necessary to establish the role of SAFV infection in humans.


Assuntos
Tonsila Faríngea/virologia , Cardiovirus/isolamento & purificação , Hipertrofia/virologia , Picornaviridae/isolamento & purificação , Adenoidectomia , Tonsila Faríngea/patologia , Cardiovirus/patogenicidade , Criança , Pré-Escolar , Feminino , Genótipo , Humanos , Hipertrofia/patologia , Masculino , Nasofaringe/virologia , Picornaviridae/patogenicidade
13.
Biomed Environ Sci ; 32(6): 438-445, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31262389

RESUMO

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.


Assuntos
Síndrome Respiratória Aguda Grave/virologia , Adolescente , Adulto , Fatores Etários , Idoso , Criança , Pré-Escolar , China/epidemiologia , Feminino , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Nasofaringe/virologia , Estações do Ano , Vigilância de Evento Sentinela , Síndrome Respiratória Aguda Grave/epidemiologia , Adulto Jovem
14.
PLoS One ; 14(6): e0218318, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31220115

RESUMO

Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.


Assuntos
Febre/epidemiologia , Malária/epidemiologia , Metagenoma/genética , Nasofaringe/virologia , Pré-Escolar , Citomegalovirus/genética , Citomegalovirus/isolamento & purificação , Citomegalovirus/patogenicidade , Fezes/parasitologia , Fezes/virologia , Feminino , Febre/sangue , Febre/parasitologia , Febre/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Lactente , Malária/sangue , Malária/parasitologia , Malária/virologia , Masculino , Plasmodium falciparum/genética , Plasmodium falciparum/isolamento & purificação , Plasmodium falciparum/patogenicidade , Vírus Sinciciais Respiratórios/genética , Vírus Sinciciais Respiratórios/isolamento & purificação , Vírus Sinciciais Respiratórios/patogenicidade , Estudos Retrospectivos , Rhinovirus/genética , Rhinovirus/isolamento & purificação , Rhinovirus/patogenicidade , Uganda/epidemiologia
15.
J Med Microbiol ; 68(8): 1211-1218, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31225788

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , Reação em Cadeia da Polimerase Multiplex/normas , Kit de Reagentes para Diagnóstico/normas , Infecções Respiratórias/diagnóstico , Vírus/isolamento & purificação , Fatores Etários , Bactérias/classificação , Bactérias/genética , Criança Hospitalizada/estatística & dados numéricos , Pré-Escolar , China/epidemiologia , Coinfecção/diagnóstico , Coinfecção/epidemiologia , Coinfecção/microbiologia , Coinfecção/virologia , Feminino , Humanos , Lactente , Masculino , Nasofaringe/microbiologia , Nasofaringe/virologia , Prevalência , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/microbiologia , Infecções Respiratórias/virologia , Análise de Sequência de DNA , Vírus/classificação , Vírus/genética
16.
Virol J ; 16(1): 78, 2019 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-31196108

RESUMO

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.


Assuntos
Infecções por Adenovirus Humanos/epidemiologia , Hospitalização/estatística & dados numéricos , Infecções Respiratórias/epidemiologia , Infecções Respiratórias/virologia , Infecções por Adenovirus Humanos/virologia , Adenovírus Humanos/genética , Adenovírus Humanos/isolamento & purificação , Adolescente , Pequim/epidemiologia , Criança , Pré-Escolar , Feminino , Variação Genética , Genótipo , Humanos , Lactente , Recém-Nascido , Masculino , Nasofaringe/virologia , Filogenia , Prevalência , Radiografia , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA , Carga Viral
17.
Diagn Microbiol Infect Dis ; 95(1): 55-58, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31160164

RESUMO

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.


Assuntos
Infecções por Vírus Respiratório Sincicial/diagnóstico , Vírus Sincicial Respiratório Humano/genética , Infecções Respiratórias/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/normas , Nasofaringe/virologia , RNA Viral/genética , Infecções por Vírus Respiratório Sincicial/virologia , Infecções Respiratórias/virologia , Sensibilidade e Especificidade , Fatores de Tempo , Adulto Jovem
18.
Transbound Emerg Dis ; 66(5): 1884-1893, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31059176

RESUMO

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.


Assuntos
Surtos de Doenças/veterinária , Doenças dos Cavalos/epidemiologia , Vírus da Influenza A Subtipo H3N8/genética , Infecções por Orthomyxoviridae/veterinária , Vacinação/veterinária , Sequência de Aminoácidos , Substituição de Aminoácidos , Animais , Glicoproteínas de Hemaglutininação de Vírus da Influenza/genética , Doenças dos Cavalos/virologia , Cavalos , Vírus da Influenza A Subtipo H3N8/isolamento & purificação , Malásia/epidemiologia , Nasofaringe/virologia , Neuraminidase/genética , Infecções por Orthomyxoviridae/epidemiologia , Infecções por Orthomyxoviridae/virologia , Filogenia , Alinhamento de Sequência/veterinária , Proteínas Virais/genética
19.
Emerg Microbes Infect ; 8(1): 662-674, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31084471

RESUMO

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.


Assuntos
Vírus Defeituosos/genética , Subtipo H7N9 do Vírus da Influenza A/crescimento & desenvolvimento , Influenza Humana/patologia , Influenza Humana/virologia , RNA Viral/genética , Análise de Sequência de DNA , Animais , Brônquios/virologia , Vírus Defeituosos/isolamento & purificação , Modelos Animais de Doenças , Células Epiteliais/virologia , Genoma Viral , Humanos , Camundongos , Nasofaringe/patologia , Nasofaringe/virologia , Infecções por Orthomyxoviridae/patologia , Infecções por Orthomyxoviridae/virologia , RNA Viral/isolamento & purificação , Deleção de Sequência
20.
Rev Chilena Infectol ; 36(1): 26-31, 2019 Feb.
Artigo em Espanhol | MEDLINE | ID: mdl-31095201

RESUMO

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.


Assuntos
Técnica Indireta de Fluorescência para Anticorpo/métodos , Nasofaringe/virologia , Reação em Cadeia da Polimerase/métodos , Vírus/isolamento & purificação , Adolescente , Criança , Pré-Escolar , Chile , Estudos Transversais , Vírus de DNA/isolamento & purificação , Feminino , Humanos , Lactente , Masculino , Estudos Prospectivos , Vírus de RNA/isolamento & purificação , Reprodutibilidade dos Testes , Infecções Respiratórias/virologia , Sensibilidade e Especificidade
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