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Article in Chinese | WPRIM | ID: wpr-956437


Objective:To analyze common respiratory pathogens epidemiology in hospitalized children with lower respiratory tract infection (LRTI) in a single center in Shanghai, and to provide the basic data support for clinical diagnosis and treatment of children with LRTI in Shanghai.Methods:Children with LRTI in Children′s Hospital of Fudan University were enrolled from January 1, 2015 to December 31, 2019, and respiratory samples were collected and tested by direct immunofluorescence assay and real time polymerase chain reaction. The epidemiological characteristics of different respiratory pathogens were analyzed. Chi-square test was used for statistical analysis.Results:A total of 18 716 children were included, the total detection rate of respiratory pathogens was 36.96% (6 918/18 716), and the most frequent detected pathogen was Mycoplasma pneumoniae (MP) (15.31%(2 866/18 716)), followed by respiratory syncytial virus (RSV) (10.40%(1 946/18 716)) and parainfluenza virus Ⅲ (PIV-Ⅲ) (4.65%(871/18 716)). The detection rate of pathogens in female was significantly higher than that in male (38.48%(2 936/7 630) vs 35.92%(3 982/11 086), χ2=12.72, P<0.001). RSV and influenza virus A (Flu-A) infections peaked in winter. The detection rates of influenza virus B (Flu-B) and human metapneumovirus (MPV) were higher in winter and spring. PIV-Ⅲ infection peaked in spring and summer. The peak of PIV-Ⅱ infection occurred in summer and autumn. The infections of adenovirus (ADV), MP, Chlamydia trachomatis (CT) and PIV-Ⅰ were prevalent throughout the year without significant seasonality. The detection rate of RSV declined with age, while the detection rate of MP increased with age. The co-infection rate was 1.65%(309/18 716), and the predominant co-infection type was MP and RSV (0.37%(70/18 716)). Conclusions:A variety of pathogens lead to children′s LRTI in Shanghai from 2015 to 2019, with the common infection of MP, RSV and PIV-Ⅲ. Different pathogens showed different epidemiological characteristics in age and season distributions.

Article in Chinese | WPRIM | ID: wpr-909816


Objective:To investigate the epidemiological characteristics of classic human astrovirus (HAstV) among children under five years old with acute diarrhea, and to understand the role of HAstV in children acute diarrhea.Methods:A total of 1 010 fecal specimens were collected in 1 010 outpatients under five years old with acute diarrhea admitted to Children′s Hospital of Fudan University, Shanghai from January 2012 to December 2016. Reverse transcription polymerase chain reaction (PCR) or PCR was used for screening classic HAstV, group A rotavirus, norovirus and adenovirus. Genotypes of classic HAstV were determined by nucleotide sequencing and phylogenetic tree analysis.Results:The overall positive rate of classic HAstV was 2.7%(27/1 010). The detection rates of classic HAstV from 2012 to 2016 were 6.9%(10/144), 3.5%(5/144), 2.1%(3/144), 1.5%(4/265) and 1.6%(5/313), respectively. Almost 96.3%(26/27) of children infected with HAstV were 0 to 36 months of age. The prevalence of classic HAstV infections displayed a typical autumn/winter seasonality except in 2016. All the positive classic HAstV strains were genotyped as HAstV-1 with two lineages of HAstV-1a and HAstV-1b. Among them, the lineage of HAstV-1a was the predominant subtype (63.0%, 17/27). There were 77.8%(21/27) of the children with acute diarrhea only infected with classic HAstV, whereas for the remaining cases a variety of other enteric viruses were detected (three cases co-infected with HAstV and group A rotavirus, two cases co-infected with HAstV and adenovirus, and one case co-infected with HAstV, group A rotavirus and adenovirus).Conclusions:Children infected with HAstV are mainly less than 36 months of age. Although the genotype of classic HAstV detected in this study is single, but the lineages are in a state of dynamic change. Long-time and continuous monitor for the epidemiology of classic HAstV is needed to avoid outbreak of diarrhea in children.

Article in Chinese | WPRIM | ID: wpr-608453


Next generation sequencing technologies,providing high speed and throughput that contribute greatly to DNA sequencing,have many applications in clinical virology,including identification of novel or unsuspected viruses,evaluation of human viromes,investigation of viral genetic diversity and evolution,monitoring of antiviral drug resistance,and analysis of virus-host interaction.Meanwhile,due to the complexity in bioinformatics data processing and lack of quality management standards,further efforts and explorations need to be put in the application and quality management of NGS in clinical laboratory.

Article in Chinese | WPRIM | ID: wpr-502275


Objective To compare the molecular epidemic characteristics of human astrovirus (HAstV) between outpatient and hospitalized children with acute diarrhea,and to investigate the relationship between HAstY infection and diarrhea in children.Methods A total of 298 cases were randomly collected from hospitalized children from January 2008 to December 2010 in Children's Hospital of Fudan University,and 360 specimens were collected from outpatients with acute diarrhea from August 2010 to July 2011.Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect rotavirus (RV),human calicivirus (HuCV),HAstV and human adenovirus (HAdV).H AstV genotype was determined by gene sequencing and phylogenetic analysis.Results Epidemiology of HAstV in hospitalized children was as follows:among the included 298 samples,HAstV was detected in 27.2% (81/298) of the patients,compared with 33.9% (42/124),33.8% (25/74) and 14.0% (14/100),respectively from 2008 to 2010.HAstV diarrhea occurred throughout the year and peaked in January,March,and April.95.1% (77/81) of the infected children were 0-35 months old.All the episodes of HAstV were mixed with other diarrhea virus infection.Molecular epidemiology of HAstV in outpatient children with diarrhea was as follows:the overall incidence of HAstV was 1.9 % among the 360 cases (7/360).The seasonal distribution of HAstV's gastroenteritis showed a peak in November.All the outpatient children were 0-35 months old.Three cases were single infection with HAstV and the others were coinfection with RV (3 cases) or HAdV (1 case).All of the detected HAstV,either in inpatients or outpatients,belonged to HAstV-1.Conclusions The detection rate of HAstV in hospitalized children is significantly higher than that in outpatients.Most HAstV infections in hospitalized children are ascribed to nosocomial infections.Most episodes of HAstV infection were accompanied with other diarrhea viruses infection.HAstY single infection is seen in outpatient children while the detection rate is very low,implying that HAstV co-infection with other viruses plays a main role in diarrhea in most instances.

Article in Chinese | WPRIM | ID: wpr-424853


Objective To obtain the molecular epidemiology of human Parechovirus (HPeV)infections m children with central nervous system (CNS)-related disease and sepsis,as well as understand the pathogenic properties of HPeV infections by detecting HPeV in cerebrospinal fluid (CSF) and blood samples.Methods From January to December in the year of 2009,a total of 359enterovirus-negative specimens including 210 CSF and 149 blood samples were collected from 328children <14 years of age who were hospitalized for CNS-related disease and sepsis at Children's Hospital,Fudan University,Shanghai,China.HPeV was detected by nested reverse transcription polymerase chain reaction (RT-PCR),and then directly genotyped by sequencing nested RT-PCR product of VP3/VP1 region.Ninty-nine blood samples from healthy children were collected as controls during the same period.Results Twenty-seven children (8.2%) were HPeV positive in 328 children.HPeV infections were found in all age groups of children and the highest frequency was seen in children <3 months old (18.2%,12/66).HPeV was detected in several months,with the peak in December (18.8%,9/48).Of all the positive samples,20 were genotyped successfully and identified to be HPeV1.No HPeV infections were found in blood of healthy controls.ConclusionsHPeV is the pathogen of CNS infections and sepsis in children.HPeV screening should be enrolled in the routine virus testing in specimens obtained from children.HPeV1 is the prevalent type in children in the year of 2009 in Shanghai.

Article in Chinese | WPRIM | ID: wpr-419053


Objective To investigate the dynamic characteristic of molecular epidemiology of group A Rotavirus (RV) by analyzing viral genotypes,disease seasonality,and the patients' age distribution,so that to provide theoretical basis for preyention and control of RV diarrhea in children.MethodsA total of 380 RV antigen positive samples were selected from 5176 stool specimens collected from <5 year-old patients with acute diarrhea who were admitted to Children's Hospital of Fudan University during January 2006 to December 2008. Multiplex nested reverse transcription polymerase chain reaction (RT-PCR) was used to analyze the RV genotypes.ResultsDuring 2006-2008,the incidence of RV related diarrhea peaked from October to December and about 96.8% of all RV episodes occurred in patients younger than 3 years old,The predominant genotype was G3 which accounted for 58.4% (222/380),G9 was an emerging genotype with the prevalence rate as high as 10.8% (41/380).G1 and G2 types were rarely found during the three years.Infections with both G3 and G9 were the major mixed genotype G infection. Genotype P [8] was predominant with the prevalence rates of 64.6% (53/82) and 46.8% (58/124) in 2006 and 2008,respectively,whereasgenotype P[4] was predominant in 2007 (38,5%,67/174).P[6] and P[9] were found as minor types.The major mixed genotype P infection were genotype P[4] and P[8]. The proportion of undetermined genotype G and genotype P strains tended to increasing during 2006-2008.Genotype P [8]G3 was the major RV strain (20.5%) in Shanghai during 2006-2008 and the other prevalent genotypes included P[4]G3 and P[m]G3.Conclusion The infection of group A RV in Shanghai presents some new molecular epidemiology characteristics during 2006-2008,such as switch of predominant genotypes and diversification of prevalent genotypes.