Respiratory Tract Infections In Beijing Research Articles

Genome sequencing reveals molecular epidemiological characteristics and new recombinations of adenovirus in Beijing, China, 2014-2019.

To investigate the molecular epidemiological characteristics and genetic variations of human adenovirus (HAdV) in acute respiratory tract infections in Beijing. Whole-genome sequencing and phylogenetic analyses were performed for 83 strains of HAdV with different types in Beijing from 2014 to 2019. The clinical characteristics of HAdV infection were analyzed statistically. HAdV-B was divided into four genotypes, including B3 (n = 11), B7 (n = 13), B14 (n = 4), and B55 (n = 2). HAdV-C was divided into three genotypes, including C1 (n = 14), C2 (n = 13), and C5 (n = 10). In HAdV-C, nine recombinant adenovirus strains were identified in type 1, and seven recombinant strains were found in type 2. In type 1, we found three newly emerged intraspecific recombinant strains (A47, A48, and A52) collected in 2017, 2018, and 2019, respectively. In addition, the previously reported recombinant strains of HAdV-C1 showed more severe disease than other strains of HAdV-C, causing severe community-acquired pneumonia in both the elderly and children. Continuous population-wide molecular epidemiological surveillance of HAdV is essential for the prevention and control of respiratory infectious diseases.

Effectiveness of Oral Fluid in Pathogenic Surveillance of Acute Respiratory Infection

Objective: Oral fluid (OF) is a new safe, non-invasive, convenient, and efficient biological sample that can be used for virus nucleic acid and antibody detection. Because few studies have performed surveillance of multiple respiratory pathogens, this study sought to explore the application value of OF in this field. Methods: OF and throat swabs were collected from December 2020 to December 2021 in patients with acute respiratory tract infections in Beijing. Multiplex real-time PCR was performed, and the detection performance of two samples was compared. Results: A total of 769 OF and throat swab samples were collected. The detection rates of respiratory pathogens in throat swabs and OF were 29.26% (225/769) and 20.81% (160/769), respectively. The sensitivity and specificity of the OF assay, compared with the throat swab assay, were 71.11% (160/225) and 100% (544/544), respectively. The two assays had excellent agreement (kappa = 0.78). The detection consistency varied among pathogens. For OF samples, the most common pathogen was the influenza B virus, and the highest detection rate was in the ≤5-year-old group. The highest positivity rate was observed in December 2021. Conclusion: OF samples have excellent potential for the epidemiological surveillance of respiratory pathogens, and may have application prospects in preventing and controlling infectious diseases.

Human metapneumovirus in hospitalized children with acute respiratory tract infections in Beijing, China.

This study aims to described the epidemiology and genotypic diversity of Human metapneumovirus (HMPV) and the impact of SARS-CoV-2 on the prevalence of HMPV in hospitalized children with Acute respiratory tract infections (ARTIs) in Beijing, China. From April 2018 to March 2019 and from September 2020 to August 2021, nasopharyngeal aspirates (NPAs) from hospitalized children with ARTIs in Beijing were collected and subjected to real-time polymerase chain reaction tests for HMPV. Then genotyping, detection of 15 common respiratory viruses and clinical characteristics were analyzed on HMPV positive samples. 7.9% (124/1572) enrolled pediatric patients were identified as having HMPV infection, and the majority of children under the age of 5 (78.2%, 92/124), From April 2018 to March 2019. The detection rate of HMPV in spring and winter is significantly higher than that in summer and autumn. The co-infection rate were 37.1% (46/124), the most common co-infected virus were parainfluenza virus type 3 (HPIV-3). The main diagnosis of HMPV infection was pneumonia (92.7%,115/124), most patient have cough and fever. Of 78 HMPV-positive specimens, A2b (82.1%,64/78) were the main epidemic subtypes. Hospitalized children with HMPV genotype A infection had a higher viral load compared to genotype B. During the COVID-19 outbreak, Among 232 samples, only 4 cases were HMPV-positive. After statistical test, the detection rate of HMPV during the COVID-19 pandemic has decreased significantly compared with that before the epidemic (p=0.001). HMPV is an important cause of ARTIs in children under 5years old. The epidemic peak is generally in winter and spring, and the A2b subtype is the most common. However, under the prevention and control of the COVID-19 pandemic, the HMPV infection of hospitalized children with ARTIs has decreased significantly.

Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia

BackgroundAmong hospitalized children suffering from community-acquired pneumonia, Mycoplasma pneumoniae (MP) is one of the most common pathogens. MP often exists as a co-infection with bacteria or viruses, which can exacerbate the clinical symptoms. We investigated the pathogen spectrum in MP-positive and MP-negative samples from hospitalized children with respiratory tract infections in Beijing, China.MethodThis study included 1038 samples of nasopharyngeal aspirates obtained between April, 2017 and March, 2018 from hospitalized children under 6 years of age with respiratory tract infections. To explore the impact of MP infection on the composition of the pathogen spectrum, 185 nasopharyngeal aspirates (83 MP-positive/102 MP-negative) were randomly selected for next-generation sequencing and comprehensive metagenomics analysis. Real-time PCR was used to detect and verify common respiratory viruses.ResultsOf the 1038 samples, 454 (43.7%) were infected with MP. In children < 6 years of age, the MP infection rate gradually increased with age, with the highest rate of 74.2% in 5–6-year-olds. The results of metagenomics analysis revealed 11 human, animal and plant virus families, and bacteriophages, including common respiratory viruses, enteroviruses and anelloviruses. The virus family with the highest number of reads in both MP-positive and MP-negative samples was the Pneumoviridae, and the number of reads for human respiratory syncytial virus (HRSV) in MP-positive samples was higher than that in MP-negative samples. Among the 83 MP-positive samples, 47 (56.63%) were co-infected with viruses, the most common of which was influenza virus (IFV). The durations of hospitalization and fever were higher in patients with MP co-infection than MP single infection, but the difference was not statistically significant.ConclusionThe viral family with the highest number of reads in both groups was Pneumoviridae, and the number of reads matched to HRSV in MP-positive samples was much higher than MP-negative samples. Co-infection of MP and IFV infection were the most cases.

Epidemiology of human parainfluenza virus infection in patients with acute respiratory tract infection in Beijing, 2015–2020

Objective To understand the epidemiological characteristics of human parainfluenza virus (HPIV) infection in patients with acute respiratory tract infections (ARIs) in Beijing, and provide support for the development of prevention and control strategies for respiratory infectious diseases. Methods The throat swabs, sputum, bronchoalveolar lavage fluid, tracheal aspirates and other pathogenic samples were collected from the patients with ARIs in 35 sentinel hospitals in Beijing from 2015 to 2020. Multiple real-time PCR was used to detect HPIV-1, HPIV-2, HPIV-3, HPIV-4 and other common respiratory tract viruses. The results were analyzed with SPSS 20.0 and χ2 test was used to compare the rates between groups. Results During 2015–2020, the positive rate of HPIV was 3.90% (1622/41557). HPIV-3 was the mostly detected pathogen, accounting for 58.45%, followed by HPIV-1 (19.17%), HPIV-2 (12.70%) and HPIV-4 (10.79%). The positive rate of HPIV in 2020 (1.65%, 70/4 234) was significantly lower than that during 2015–2019 (4.52%, 1569/37 323). The HPIV infection arte showed a peak every other year. The infection peak of HPIV was from May to July. The incidence trend of HPIV-3 infection was the similar to other HPIVs. The positive rate of HPIV-1 during summer-autumn was higher than that in other seasons. There was no obvious seasonality of HPIV-2 infection. The positive rate of HPIV-4 in autumn was higher than that in other seasons. The positive rate of HPIV in men was lower than that in women. The positive rate in 0–5 years old group was highest (8.81%, 685/7 776), followed by 6–15 years old group (4.07%, 173/4 247), and ≥ 60 years old group (3.25%, 442/13 582). There was significant differences in the positive rate of HPIV-1 and HPIV-3 between upper and lower respiratory tract infection cases ( χ2=4.449, P=0.039; χ2=17.513, P Conclusion HPIV is a common respiratory pathogens in Beijing. The main affecting population of HPIV infection is children under 15 years old. In 2020, the prevention and control of COVID-19 significantly reduced the incidence of HPIV infection.

Human adenoviruses in paediatric patients with respiratory tract infections in Beijing, China

BackgroundHuman adenoviruse (HAdV) is a major pathogen of paediatric respiratory tract infections (RTIs). Mutation or recombination of HAdV genes may cause changes in its pathogenicity and transmission. We described the epidemiology and genotypic diversity of HAdV in hospitalized children with RTIs in Beijing, China.MethodsNasopharyngeal aspirates were collected from hospitalized children with RTIs from April 2018 to March 2019. HAdVs were detected by a quantitative real-time PCR, and the hexon gene was used for phylogenetic analysis.ResultsAmong 1572 samples, 90 (5.72%) were HAdV-positive. The HAdV detection rate was highest in November and July. Among HAdV-positive children, 61.11% (55/90) were co-infected with other respiratory viruses, the most common of which were human respiratory syncytial virus and human rhinovirus. The main diagnosis was bronchopneumonia, most patient have cough and fever. Children with a high viral load were more likely to have a high fever (P = 0.041) and elevated WBC count (P = 0.000). Of 55 HAdV-positive specimens, HAdV-B (63.64%), HAdV-C (27.27%), and HAdV-E (9.09%) were main epidemic species. Phylogenetic analysis indicated that hexon sequences of three samples were on the same branch with the recombinant HAdV strain (CBJ113), which was circulating in Beijing since 2016.ConclusionThe HAdV-B3 and HAdV-B7 are the main epidemic strains in Beijing, and the recombinant HAdV-C strain CBJ113 has formed an epidemic trend.

Human adenovirus among hospitalized children with respiratory tract infections in Beijing, China, 2017\u20132018

BackgroundHuman 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.MethodsNasopharyngeal 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.ResultsHAdV 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.ConclusionsHAdV 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.

Fine Particulate Air Pollution and Hospital Utilization for Upper Respiratory Tract Infections in Beijing, China.

Few studies have examined the association between fine particulate matter (PM2.5) and upper respiratory tract infections (URTI) in urban cities. The principal aim of the present study was to evaluate the short-term impact of PM2.5 on the incidence of URTI in Beijing, China. Data on hospital visits due to URTI from 1 October 2010 to 30 September 2012 were obtained from the Beijing Medical Claim Data for Employees, a health insurance database. Daily PM2.5 concentration was acquired from the embassy of the United States of America (US) located in Beijing. A generalized additive Poisson model was used to analyze the effect of PM2.5 on hospital visits for URTI. We found that a 10 μg/m3 increase in PM2.5 concentration was associated with 0.84% (95% CI, 0.05–1.64%) increase in hospital admissions for URTI at lag 0–3 days, but there were no significant associations with emergency room or outpatient visits. Compared to females, males were more likely to be hospitalized for URTI when the PM2.5 level increased, but other findings did not differ by age group or gender. The study suggests that short-term variations in PM2.5 concentrations have small but detectable impacts on hospital utilization due to URTI in adults.

Case-control study of the epidemiological and clinical features of human adenovirus 55 and human adenovirus 7 infection in children with acute lower respiratory tract infections in Beijing, China, 2008\u20132013

BackgroundIn adults, the emerging human adenovirus (HAdV) type 55 (HAdV-55) has been reported to cause more severe cases of adenovirus induced acute lower respiratory tract infections (ALRTIs) compared to other HAdV serotypes (HAdV-3, HAdV-7, HAdV-14). However, there is a dearth of comparative studies in children that address differences in the clinical epidemiological features between HAdV-55 and other HAdV serotypes that can also induce severe infection (such as HAdV-7).MethodsWe conducted a retrospective review of pediatric patients hospitalized at Beijing Children’s Hospital with ALRTI from April 2008 to December 2013 who had adenovirus detected from nasopharyngeal or throat samples by PCR. We further compared pediatric patients infected with HAdV-55 to those infected with HAdV-7 using a case-control methodology by matching each subject with HAdV-55 infection to 4 patients with HAdV-7 infection within 2 months of each HAdV-55 infection. Demographic, clinical, and etiological data were collected and analyzed.ResultsOver the five-year period, HAdV was detected in 194 children. Of these, 8 were HAdV-55 positive. Epidemiological results showed that HAdV-55 infection was observed only in 4% of adenovirus infected children whereas HAdV-7 infection proportioned 53%. Most cases of HAdV-55 infection were identified during March and April, whereas HAdV-7 infection occurred throughout the year. Wheezing was significantly less frequent in the HAdV-55 group. No patients infected with HAdV-55 presented with vomiting or had any underlying disease. Coinfections with other respiratory tract pathogens were frequent among children infected with either HAdV-55 or HAdV-7.ConclusionsHAdV-55 circulated in Beijing during spring and appeared to cause pediatric respiratory infections that were as severe as HAdV-7 infections. Broader surveillance studies are needed.

Prescription of antibacterial agents for acute upper respiratory tract infections in Beijing, 2010-2012.

PurposeThe purpose of this study was to describe the prescription of antibacterial agents for acute upper respiratory tract infections (URIs) in Beijing.MethodsA total of 8,588,699 outpatient cases in tertiary hospitals with acute upper respiratory tract infections (URIs) were selected from the Beijing Medical Claim Data for Employees (BMCDE) from Oct 2010 to Sep 2012. Second-generation cephalosporins, third-generation cephalosporins, fourth-generation cephalosporins, fluoroquinolones, macrolides (except for erythromycin), combinations of penicillins (including β-lactamase inhibitors), and streptomycins were classified as broad-spectrum antibacterial agents. The rates for antibiotic prescriptions and broad-spectrum antibiotic use were calculated in all cases as well as in various URI diagnosis subgroups and age (18–44, 45–64, and ≥65 years) subgroups. The most frequently prescribed antibiotic classes were identified by calculating the proportions of the different agents in all prescribed antibiotic agents.ResultsOverall, the rate of antibiotic prescription is 39.0 %, and cases diagnosed with acute tonsillitis, sinusitis, and epiglottitis have the highest prescription rate (73.6 %), followed by acute laryngitis and bronchitis (52.3 %), acute pharyngitis (40.1 %), and acute nasopharyngitis (37.2 %). Broad-spectrum agents were chosen in 82.4 % of the cases that were prescribed antibiotics, ranging from 81.9 % of cases with naspharyngitis to 87.1 % of the cases with tonsillitis, sinusitis, and epiglottitis. Second-generation cephalosporins, macrolides, fluoroquinolones, third-generation cephalosporins, and combinations of penicillins were most frequently prescribed, accounting for more than 80 % of all prescribed antibacterials.ConclusionsAntibacterial drug prescription for outpatients with acute URIs is common in tertiary hospitals in Beijing, and the prescribed antibacterials are usually broad-spectrum agents.Electronic supplementary materialThe online version of this article (doi:10.1007/s00228-015-1997-6) contains supplementary material, which is available to authorized users.

Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China.

BackgroundHPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized.MethodsThe VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays.ResultsThe prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a.ConclusionsThe prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-015-0390-5) contains supplementary material, which is available to authorized users.

Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012.

BackgroundHuman adenoviruses (HAdV) play a significant role in pediatric respiratory tract infections. To date, over 60 types of HAdV have been identified. Here, HAdV types are characterized in children in the Beijing area with acute lower respiratory tract infections (ALRTIs) and the clinical features and laboratory findings of hospitalized HAdV-infected cases are described.MethodsRespiratory specimens were collected from pediatric patients with ALRTIs in the emergency department or from those admitted to Beijing Children’s Hospital between March 2007 and December 2012. Infections with common respiratory viruses were determined by PCR or RT-PCR. HAdV positive samples were further typed by PCR and sequencing.ResultsAmong 3356 patients with ALRTIs, 194 (5.8 %) were found to have HAdV infection. HAdV infection was primarily confined to children (88.35 %) less than 5 years of age. A total of 11 different types of HAdV were detected throughout the study period, with HAdV-B7 (49.0 %) and HAdV-B3 (26.3 %) as the most prevalent types, followed by HAdV-C2 (7.7 %) and HAdVC1 (4.6 %). Newly emerging and re-emergent types or variants, HAdV-B55 (n = 5), HAdV-C57 (n = 3), and HAdV-B14p1 (n = 1), were identified. Results also included the reported first case of co-infection with HAdV-C2 and HAdV-C57. Clinical entities of patients with single HAdV infection (n = 49) were similar to those with mixed HAdV/respiratory syncytial virus (RSV) infections (n = 41). Patients with HAdV-B7 infection had longer duration of fever and higher serum levels of muscle enzymes than HAdV-B3-infected patients.ConclusionsDuring the study period, HAdV-B7 and HAdV-B3 were the predominant types identified in pediatric ALRTIs. HAdV-B7 infection tends to have more severe clinical consequences. The presence of newly emerging types or variants and co-infection with different types of HAdV highlights the need for constant and close surveillance of HAdV infection.

Prevalence of human coronaviruses in adults with acute respiratory tract infections in Beijing, China

Human coronaviruses (HCoVs) are a common etiological agent of acute respiratory tract infections. HCoV infections, especially those caused by the two HCoVs identified most recently, NL63 and HKU‐1, have not been characterized fully. To evaluate the prevalence and clinical presentations of HKU1 and NL63 in adults with acute respiratory tract infections, an investigation of HCoV infections in Beijing, China from 2005 to 2009 was performed by using reverse transcriptase PCR assays and sequencing analysis. Among 8,396 respiratory specimens studied, 87 (1%) clinical samples were positive for HCoVs, of which 50 samples (0.6% of the total) were positive for HCoV‐OC43, 15 (0.2%) for HCoV‐229E, 14 (0.2%) for HCoV‐HKU1, and 8 (0.1%) for HCoV‐NL63. The prevalence of HCoV infection in adults exhibited distinct seasonal fluctuations during the study period. In addition, patients positive for HCoV‐229E infections were more likely to be co‐infected with other respiratory viruses. Enterovirus, rhinovirus, and parainfluenza virus type 3 were the most common viruses found in patients with HCoV infections. The demographic and clinical data present in this study of HCoV infections in adults with acute respiratory tract infections should improve our understanding of the pathogenesis of HCoVs. J. Med. Virol. 83:291–297, 2011. © 2010 Wiley‐Liss, Inc.

Prevalence of human respiratory viruses in adults with acute respiratory tract infections in Beijing, 2005–2007

To determine the aetiological role and epidemiological profile of common respiratory viruses in adults with acute respiratory tract infections (ARTIs), a 2-year study was conducted in Beijing, China, from May 2005 to July 2007. Nose and throat swab samples from 5808 ARTI patients were analysed by PCR methods for common respiratory viruses, including influenza viruses (IFVs) A, B, and C, parainfluenza viruses (PIVs) 1–4, enteroviruses (EVs), human rhinoviruses (HRVs), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), human coronaviruses (HCoVs) OC43, 229E, NL63, and HKU1, and adenoviruses (ADVs). Viral pathogens were detected in 34.6% of patient samples, and 1.6% of the patients tested positive for more than one virus. IFVs (19.3%) were the dominant agents detected, followed by HRVs (6.5%), PIVs (4.3%), EVs (3.2%), and HCoVs (1.1%). ADVs, RSV and HMPV were also detected (<1%). The viral detection rates differed significantly between infections of the lower and upper respiratory tracts in the sample population: PIVs, the second most commonly detected viral agents in lower acute respiratory tract infections (LRTIs), were more prevalent than in upper acute respiratory tract infections, indicating that the pathogenic role of PIVs in LRTIs should be investigated. Currently, this study is the largest-scale investigation of respiratory virus infections in China with multiple agent detection, providing baseline data for further studies of respiratory virus infections in adults with ARTIs.

Human Rhinovirus Group C Infection in Children with Lower Respiratory Tract Infection

Human Rhinovirus Group C Infection in Children with Lower Respiratory Tract Infection