Viral etiologies of hospitalized acute lower respiratory infection patients in China, 2009-2013

Epidemiological characteristics of five non-COVID respiratory viruses among 37,139 all-age patients during 2018 - 2023 in Weifang, China: a cross-sectional study

BACKGROUND

Common non-COVID respiratory viruses, such as influenza virus (IFVA/IFVB), parainfluenza virus (PIV), respiratory syncytial virus (RSV), and adenovirus (ADV), often cause acute respiratory infections (ARIs). This study aimed to explore the epidemiological characteristics of these five viruses in patients with ARIs before, during, and after the COVID-19 pandemic from 2018 to 2023.

METHODS

A total of 37,139 serum specimens and epidemiological data from all-aged patients who presented with ARIs were collected from January 2018 to December 2023. The IgM antibodies of five non-COVID respiratory viruses were tested by an IgM kit with indirect immunofluorescent assay (lFA).

RESULTS

12,806 specimens were screened as positive for any one of the targeted viruses, with an overall positivity rate of 34.48%. Among all age groups, the most prevalent respiratory viruses were PIV (21.30%) and influenza virus (17.30% of IFVB and 9.91% of IFVA). Children aged 1-14 years were most vulnerable to lower respiratory viruses, and children aged 4-6 years have the highest prevalence no matter the positivity rate for overall viruses (53.06%) or for each virus. From 2018 to 2023, the annual percentage change (APC) revealed that the prevalence of total viruses have a 13.53% rise (p < 0.05), which increased with statistically significant for all age groups. In addition, both the infection rate and the number of samples detected have decreased significantly in the "first-level response" stage of the COVID-19 pandemic and in the "first three months" after fully lifted. Compared to those in the previous five years, the total infection rate (44.64%) and infection rate (26.93%) of the older adults (> 60 years) were all the highest in 2023, and the number of samples collected in 2023 sharply increased, increasing by 77.10% compared to the average of the number of detected in 2018-2022.

CONCLUSIONS

The data from this study indicate that the epidemiological characteristics of five non-COVID respiratory viruses are vulnerability to the environment, age, sex, and epidemics status among AIR patients, and that the detected number and positivity rate of these viruses have increased in the "post-pandemic era", which is critical for the late or retrospective diagnosis and can serve as a useful surveillance tool to inform local public policy in Weifang, China.

An Overview on Disease Burden and Management of Respiratory Syncytial Virus Infections in Older Adults in the Asia-Pacific Region

Respiratory syncytial virus (RSV) represents a significant burden on older adults (aged ≥ 50 years) globally and can lead to acute respiratory tract infections with substantial morbidity and mortality. However, there is a significant gap in knowledge regarding RSV infection in older adults, particularly in the Asia-Pacific region. This knowledge gap underscores the need for targeted and comprehensive studies to fully understand the nuanced epidemiology of RSV in ageing populations. This review synthesises data from various countries, emphasising the impact of RSV on older populations in the Asia-Pacific region. The overall proportions of RSV-related ARIs among older patients ranged from 0.2% to 5.6%. Among older adult patients with CAP, RSV accounted for 1.1%-10.3% of cases. However, it is crucial to note that the diversity in reported percentages highlights the influence of factors such as geographic location, health care settings and diagnostic practices. The most common symptoms observed in older adults with RSV infection were cough, sputum production and fever, followed by dyspnoea, sore throat and rhinorrhoea. Most of the old adults with RSV infection had underlying diseases, and RSV can cause significant morbidity and mortality in old adults. Treatment of RSV infections predominantly involve supportive care, with aerosolised ribavirin reserved for severe cases, especially immunocompromised patients. Emerging antiviral agents, including fusion and nucleoprotein inhibitors, offer promising avenues for future therapeutics. The recent approval of the bivalent RSV prefusion F protein-based vaccine for individuals aged 60 and older represents a milestone in preventive strategies. In conclusion, RSV infection remains a significant threat to older adults in the Asia-Pacific region, necessitating ongoing research and surveillance efforts. The recent vaccine approval marks a positive milestone, but further studies are crucial for refining prevention and treatment approaches.

Genomic characteristics of human respiratory syncytial virus from children in China during 2017-2020

Acute lower respiratory tract infections (ALRTIs) are a leading cause of mortality in young children worldwide due to human respiratory syncytial virus (RSV). The aim of this study was to monitor genetic variations in RSV and provide genomic data support for RSV prevention and control. A total of 105 complete RSV genome sequences were determined during 2017-2020. Phylogenetic analysis showed that all of the RSVA sequences were of genotype ON1, and all of the RSVB sequences were of genotype BA9. Notably, a phylogenetic tree based on the whole genome had more branches than a tree based on the G gene. In comparison to the RSV prototype sequences, 71.43% (50/70) of the ON1 sequences had five amino acid substitutions (T113I, V131N, N178G, H258Q, and H266L) that occurred simultaneously, and 68.57% (24/35) of the BA9 genotype sequences had 12 amino acid substitutions, four of which (A131T, T137I, T288I, and T310I) occurred simultaneously. In the F gene, there were 19 amino acid substitutions, which were mainly located in the antigenic sites Ø, II, V, and VII. Other amino acid substitutions were found in the NS1, NS2, P, SH, and L proteins. No significant evidence of recombination was found in any of the sequences. These findings provide important data that will be useful for prevention, control, and vaccine development against RSV.

Risk factor analysis and prediction model construction for severe adenovirus pneumonia in children

BACKGROUND

Severe adenovirus pneumonia in children has a high mortality rate, but research on risk prediction models is lacking. Such models are essential as they allow individualized predictions and assess whether children will likely progress to severe disease.

METHODS

A retrospective analysis was performed on children with adenovirus pneumonia who were hospitalized at the Children's Hospital of Nanjing Medical University from January 2017 to March 2024. The patients were grouped according to clinical factors, and the groups were compared using Ridge regression and multiple logistic regression to identify risk factors associated with severe adenovirus pneumonia. A prediction model was constructed, and its value in clinical application was evaluated.

RESULTS

699 patients were included in the study, with 284 in the severe group and 415 in the general group. Through the screening of 44 variables, the final risk factors for severe adenovirus pneumonia in children as the levels of neutrophils (OR = 1.086, 95% CI: 1.054‒1.119, P < 0.001), D-dimer (OR = 1.005, 95% CI: 1.003‒1.007, P < 0.001), fibrinogen degradation products (OR = 1.341, 95% CI: 1.034‒1.738, P = 0.027), B cells (OR = 1.076, 95%CI: 1.046‒1.107, P < 0.001), and lactate dehydrogenase (OR = 1.008, 95% CI: 1.005‒1.011, P < 0.001). The value of the area under the receiver operating characteristic curve was 0.974, the 95% CI was 0.963-0.985, and the P-value of the Hosmer-Lemeshow test was 0.547 (P > 0.05), indicating that the model had strong predictive power.

CONCLUSION

In this study, the clinical variables of children with adenovirus pneumonia were retrospectively analyzed to identify risk factors for severe disease. A prediction model for severe disease was constructed and evaluated, showing good application value.

Application of peripheral blood routine parameters in the diagnosis of influenza and Mycoplasma pneumoniae

OBJECTIVES

Influenza and Mycoplasma pneumoniae infections often present concurrent and overlapping symptoms in clinical manifestations, making it crucial to accurately differentiate between the two in clinical practice. Therefore, this study aims to explore the potential of using peripheral blood routine parameters to effectively distinguish between influenza and Mycoplasma pneumoniae infections.

METHODS

This study selected 209 influenza patients (IV group) and 214 Mycoplasma pneumoniae patients (MP group) from September 2023 to January 2024 at Nansha Division, the First Affiliated Hospital of Sun Yat-sen University. We conducted a routine blood-related index test on all research subjects to develop a diagnostic model. For normally distributed parameters, we used the T-test, and for non-normally distributed parameters, we used the Wilcoxon test.

RESULTS

Based on an area under the curve (AUC) threshold of ≥ 0.7, we selected indices such as Lym# (lymphocyte count), Eos# (eosinophil percentage), Mon% (monocyte percentage), PLT (platelet count), HFC# (high fluorescent cell count), and PLR (platelet to lymphocyte ratio) to construct the model. Based on these indicators, we constructed a diagnostic algorithm named IV@MP using the random forest method.

CONCLUSIONS

The diagnostic algorithm demonstrated excellent diagnostic performance and was validated in a new population, with an AUC of 0.845. In addition, we developed a web tool to facilitate the diagnosis of influenza and Mycoplasma pneumoniae infections. The results of this study provide an effective tool for clinical practice, enabling physicians to accurately diagnose and differentiate between influenza and Mycoplasma pneumoniae infection, thereby offering patients more precise treatment plans.

Prevalence and predictors of antibiotic prescription among patients hospitalized with viral lower respiratory tract infections in Southern Province, Sri Lanka

BACKGROUND

Antimicrobial overprescription is common for lower respiratory tract infections (LRTI), as viral and bacterial infections generally present with similar clinical features. Overprescription is associated with downstream antimicrobial resistance. This study aims to identify the prevalence and predictors of antibiotic prescription among patients hospitalized with viral LRTI.

METHODS

A prospective cohort study was conducted among patients aged ≥1 year hospitalized with viral LRTI in a tertiary care hospital in Southern Province, Sri Lanka from 2018-2021. Demographic, clinical, and laboratory data were recorded. Nasopharyngeal and blood samples were collected for multiplex polymerase chain reaction testing for 21 respiratory pathogens and procalcitonin (PCT) detection, respectively. Demographic and clinical features associated with antibiotic prescription were identified using Chi Square and t-tests; significant variables (p<0.05) were further included in multivariable logistic regression models. The potential impact of biomarker testing on antibiotic prescription was simulated using standard c-reactive protein (CRP) and PCT cut-offs.

RESULTS

Of 1217 patients enrolled, 438 (36.0%) had ≥1 respiratory virus detected, with 48.4% of these patients being male and 30.8% children. Influenza A (39.3%) and human rhinovirus/ enterovirus (28.3%) were most commonly detected. A total of 114 (84.4%) children and 266 (87.8%) adults with respiratory viruses were treated with antibiotics. Among children, neutrophil percentage (median 63.6% vs 47.6%, p = 0.04) was positively associated with antibiotic prescription. Among adults, headache (60.6% vs 35.1%, p = 0.003), crepitations/crackles (55.3% vs 21.6%, p<0.001), rhonchi/wheezing (42.9% vs 18.9%, p = 0.005), and chest x-ray opacities (27.4% vs 8.1%, p = 0.01) were associated with antibiotic prescription. Access to CRP and procalcitonin test results could have potentially decreased inappropriate antibiotic prescription in this study by 89.5% and 83.3%, respectively.

CONCLUSIONS

High proportions of viral detection and antibiotic prescription were observed among a large inpatient cohort with LRTI. Increased access to point-of-care biomarker testing may improve antimicrobial prescription.

Molecular characterization of influenza virus circulating in Nepal in the year 2019

Influenza (sometimes referred to as "flu") is a contagious viral infection of the airways in the lungs that affects a significant portion of the world's population. Clinical symptoms of influenza virus infections can range widely, from severe pneumonia to moderate or even asymptomatic sickness. If left untreated, influenza can have more severe effects on the heart, brain, and lungs than on the respiratory tract and can necessitate hospitalization. This study was aimed to investigate and characterize all types of influenza cases prevailing in Nepal and to analyze seasonal occurrence of Influenza in Nepal in the year 2019. A cross sectional, retrospective and descriptive study was carried out at National Influenza Center (NIC), National Public Health Laboratory Kathmandu Nepal for the period of one year (Jan-Dec 2019). A total of 3606 throat swab samples from various age groups and sexes were processed at the NIC. The specimens were primarily stored at 4 °C and processed using ABI 7500 RT PCR system for the identification of Influenza virus types and subtypes. Data accessed for research purpose were retrieved from National Influenza Centre (NIC) on 1st Jan 2020. Of the total 3606 patients suspected of having influenza infection, influenza viruses were isolated from 1213 (33.6%) patients with male predominance. The highest number of infection was caused by Influenza A/Pdm09 strain 739 (60.9%) followed by Influenza B 304 (25.1%) and Influenza A/H3 169 (13.9%) and most remarkable finding of this study was the detection of H5N1 in human which is the first ever case of such infection in human from Nepal. Similar to other tropical nations, influenza viruses were detected year-round in various geographical locations of Nepal. The influenza virus type and subtypes that were in circulation in Nepal were comparable to vaccine candidate viruses, which the currently available influenza vaccine may prevent.

Epidemiology and diagnosis technologies of human metapneumovirus in China: a mini review

Human metapneumovirus (HMPV) is a newly identified pathogen causing acute respiratory tract infections in young infants worldwide. Since the initial document of HMPV infection in China in 2003, Chinese scientists have made lots of efforts to prevent and control this disease, including developing diagnosis methods, vaccines and antiviral agents against HMPV, as well as conducting epidemiological investigations. However, effective vaccines or special antiviral agents against HMPV are currently not approved, thus developing early diagnosis methods and knowing its epidemiological characteristics will be beneficial for HMPV control. Here, we summarized current research focused on the epidemiological characteristics of HMPV in China and its available detection methods, which will be beneficial to increase the public awareness and disease control in the future.

Multicenter evaluation of the Acaruiter Respiratory Panel for diagnosis of respiratory tract infections in Chinese children

IMPORTANCE

Compared to multiplex PCR assays that are available in the Chinese market, the Acaruiter Respiratory Panel (fluorescent PCR) covers a wider range of pathogens including eight viruses, five bacteria, Mycoplasma pneumoniae and Chlamydia pneumoniae, and has high accuracy and effectiveness in the detection of pathogens. This is the first study to evaluate the performance of the Acaruiter Respiratory Panel. This regent may be a promising assay for comprehensive testing for respiratory pathogens from nasopharyngeal swab specimens in Chinese children.

Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China

BACKGROUND

Human respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection and hospitalization, especially in children. Highly mutagenic nature and antigenic diversity enable the RSV to successfully survive in human population. We conducted a molecular epidemiological study during 2017-2021 to investigate the prevalence and genetic characteristics of RSV.

METHODS

A total of 6499 nasopharyngeal (NP) swabs were collected from hospitalized children at Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, China. All NP swab specimens were preliminary screened for common respiratory viruses and then tested for RSV using specific PCR assays. Partial G genes of RSV were amplified for phylogenetic analysis and genetic characterization.

RESULTS

The overall detection rate for common respiratory viruses was 16.12% (1048/6499). Among those, 405 specimens (6.20%, 405/6499) were found positive for RSV. The monthly distribution of RSV and other respiratory viruses was variable, and the highest incidence was recorded in Autumn and Winter. Based on the sequencing of hypervariable region of G gene, 93 RSV sequences were sub-grouped into RSV-A (56, 60.2%) and RSV-B (37, 39.8%). There was no coinfection of RSV-A and RSV-B in the tested samples. Phylogenetic analysis revealed that RSV-A and RSV-B strains belonged to ON1 and BA9 genotypes respectively, indicating predominance of these genotypes in Guangzhou. Several substitutions were observed which may likely change the antigenicity and pathogenicity of RSV. Multiple glycosylation sites were noticed, demonstrating high selection pressure on these genotypes.

CONCLUSION

This study illustrated useful information about epidemiology, genetic characteristics, and circulating genotypes of RSV in Guangzhou China. Regular monitoring of the circulating strains of RSV in different parts of China could assist in the development of more effective vaccines and preventive measures.

Detection of human adenoviruses in influenza-negative patients with respiratory tract infections in Nanning, China

BACKGROUND

Human adenoviruses (HAdV) have been known to cause a range of diseases, including respiratory tract infections (RTIs). However, there is limited information available regarding the genotype diversity and epidemiology of HAdV associated with RTIs in Nanning.

METHODS

Between June 2019 and December 2021, throat swab, nasal swab, or nasopharyngeal swab samples were obtained from individuals hospitalized with respiratory tract infections (RTIs). Statistical software was used to analyze the epidemiological data. The highly conserved 132-bp gene region of the HAdV hexon was targeted for the detection of HAdV using a qPCR assay. An 875-bp hexon gene fragment was subjected to phylogenetic analysis.

RESULTS

Significant variations were observed in the age and gender distribution of HAdV-positive patients (P = 0.004 and P = 0.025, respectively). The age distribution of HAdV-positive patients showed that 67.89% of those who tested positive were the age group of 0-6 years. Furthermore, the prevalence of HAdV detection was highest during spring and autumn, with a peak in February. Additionally, genotyping of the 36 HAdV-positive samples with 875-bp fragments identified the presence of circulating HAdV species B, C, and E in Nanning between 2019 and 2021.

CONCLUSIONS

This study identified an association between HAdV prevalence and age as well as season. Among hospitalized patients with RTIs in Nanning, HAdV-B, HAdV-C, and HAdV-E were found to be co-circulating. The most commonly detected genotypes were HAdV-C1, HAdV-C6, and HAdV-E4.

Demographic and clinical characteristics of human bocavirus-1 infection in patients with acute respiratory tract infections during the COVID-19 pandemic in the Central Province of Sri Lanka

BACKGROUND

Human bocavirus-1 (hBoV-1) was first detected in respiratory specimens in 2005. Due to high co-infection rates and prolonged shedding of the virus, the pathogenic role of hBoV-1 as a primary causative agent of respiratory infections is still under discussion. This study aimed to determine the prevalence of hBoV-1 infection in patients with acute respiratory tract infections (ARTIs) during the COVID-19 pandemic in the Central Province of Sri Lanka.

METHODS

A total of 1021 patients (Age 12 days to ≤ 85 years) with ARTI symptoms including fever, cough, cold, sore throat and shortness of breath within first 7 days of the illness were included. The study was carried out at the National Hospital, Kandy, Sri Lanka from January 2021 to October 2022. Respiratory specimens were tested to detect 23 pathogens including hBoV-1 using a real time PCR. Prevalence of hBoV-1 co-infections with other respiratory pathogens and distribution of hBoV-1 infection among different age groups were determined. Moreover, clinical and demographic characteristics of hBoV-1 mono-infection associated ARTI were compared with that of the hBoV-1 co-infections.

RESULTS

Respiratory infections were detected in 51.5% (526/1021) of the patients and of these 82.5% were mono- and 17.1% were co-infections. hBoV-1 was detected in 66 patients and this was the most prevalent respiratory virus associated with 40% co-infections. Of the 66 hBoV-1 positive patients, 36 had co-infections and of these 33 had dual and 3 had triple infections. Most of the hBoV-1 co-infections were identified in children aged 2-<5 years. hBoV-1 co-infections were most frequently detected with respiratory syncytial virus (RSV) and Rhino/ Entero viruses (Rh/EnV). No differences were observed in age, gender and clinical presentations in those with hBoV-1 mono- compared to co-infections. Intensive care admissions were less among hBoV-1 mono-infected than hBoV-1 co-infected patients.

CONCLUSION

This study shows a prevalence of 12.5% for hBoV-1 infections in patients with ARTI. RSV and Rh/EnV were the most common co-infecting pathogens with hBoV-1. Clinical features of hBoV-1 mono-infections were not different to that of the hBoV-1 co-infections. Interactions between hBoV-1 and other respiratory pathogens need investigation to identify the role of hBoV-1 in clinical severity of co-infections.

Serum 25-Hydroxy Vitamin D Levels in Children with Acute Respiratory Infections Caused by Respiratory Virus or Atypical Pathogen Infection

We aimed to clarify the involvement of vitamin D status in virus or atypical pathogens infection in children with acute respiratory infections (ARIs). In this retrospective study, 295 patients with ARIs were attacked by a respiratory virus or a single atypical pathogen; 17 patients with ARIs induced by two pathogens, and 636 healthy children were included. Serum 25(OH)D levels of all children were measured. Oropharyngeal samples of the patients for viruses or atypical pathogens were studied by polymerase chain reaction (PCR) or reverse transcription-polymerase chain reaction (RT-PCR). In our studies, 58.98% of the 295 single-infected subjects and 76.47% of the 17 co-infected subjects had 25(OH)D levels below the recommended 50.0 nmol/L; the mean 25(OH)D levels were 48.48 ± 19.91 nmol/L and 44.12 ± 12.78 nmol/L. Low serum 25(OH)D levels were remarkable in patients with one of seven viruses or atypical pathogens infected. These results were significantly different from those in the healthy group. There were no significant differences in 25(OH)D levels between single infection and co-infection groups. There were no differences in severity among means of 25(OH)D levels. Female or >6-year-old children patients with low serum 25(OH)D levels were more vulnerable to pathogenic respiratory pathogens. However, serum 25(OH)D levels may be related to the recovery of ARIs. These findings provide additional evidence for the development of strategies to prevent ARIs in children.

Targeted Literature Review of the Burden of Respiratory Syncytial Infection among High-Risk and Elderly Patients in Asia Pacific Region

INTRODUCTION

The burden of respiratory syncytial virus (RSV), which causes acute respiratory illness, is well recognized among the pediatric population but also imposes a significant risk to the elderly (age ≥ 60) and those with underlying comorbidities. The study aimed to review the most recent data on epidemiology and burden (clinical and economic) of RSV in the elderly/high-risk populations in China, Japan, South Korea, Taiwan, and Australia.

METHODS

A targeted review was conducted of English, Japanese, Korean, and Chinese language articles published from 1 January 2010 to 7 October 2020 relevant for the purpose.

RESULTS

A total of 881 studies were identified, and 41 were included. The median proportion of elderly patients with RSV in all adult patients with acute respiratory infection (ARI) or community acquired pneumonia was 79.78% (71.43-88.12%) in Japan, 48.00% (3.64-80.00%) in China, 41.67% (33.33-50.00%) in Taiwan, 38.61% in Australia, and 28.57% (22.76-33.33%) in South Korea. RSV was associated with a high clinical burden on those patients with comorbidities such as asthma and chronic obstructive pulmonary disease. In China, inpatients with ARI showed a significantly higher rate of RSV-related hospitalization than outpatients (13.22% versus 4.08%, p < 0.01). The median length of hospital stay among elderly patients with RSV was longest in Japan (30 days) and shortest in China (7 days). Mortality data varied by region with some studies reporting rates as high as 12.00% (9/75) in hospitalized elderly patients. Finally, data on the economic burden was only available for South Korea, with the median cost of a medical admission for an elderly patient with RSV being US dollar (USD) 2933.

CONCLUSION

RSV infection is a major source of disease burden among elderly patients, especially in regions with aging populations. It also complicates the management of those with underlying diseases. Appropriate prevention strategies are required to reduce the burden among the adult, especially the elderly, population. Data gaps regarding economic burden of RSV infection in the Asia Pacific region indicates the need for further research to increase our understanding on the burden of this disease in this region.

Outbreak of acute respiratory disease caused by human adenovirus type 7 and human coronavirus-229E in Zhejiang Province, China

In 2019, an outbreak of pharyngoconjunctival fever (PCF) occurred at a swimming center in Zhejiang Province, China. A total of 97 (13.55%) of the 716 amateur swimmers had illnesses, with 24 patients (24.74%) hospitalized in the pediatric ward. Human adenovirus serotype 7 (HAdV-7) was isolated from one concentrated water from the swimming pool, and 20 of 97 positive cases without liver damage. This outbreak led to a nosocomial outbreak in the pediatric ward, in which 1 nurse had a fever and was confirmed to be adenovirus positive. The hexon, fiber, and penton genes from 20 outbreak cases, 1 water sample, and 1 nurse had 100% homology. Furthermore, 2 cases admitted to the pediatric ward, 2 parents, and 1 doctor were confirmed to be human coronaviruses (HCoV-229E) positive. Finally, all outbreak cases had fully recovered, regardless of a single infection (adenovirus or HCoV-229E) or coinfection of these two viruses simultaneously. Thus, PCF and acute respiratory disease outbreaks in Zhejiang were caused by the completely homologous type 7 adenovirus and HCoV-229E, respectively. The swimming pool water contaminated with HAdV-7 was most likely the source of the PCF outbreak, whereas nosocomial transmission might be the source of HCoV-229E outbreak.

Comparative analysis of the clinical and epidemiological characteristics of human influenza virus versus human respiratory syncytial virus versus human metapneumovirus infection in nine provinces of China during 2009-2021

A comparative analysis of confirmed cases of human influenza virus (HIFV), human respiratory syncytial virus (HRSV), and human metapneumovirus (HMPV) was conducted to describe their clinical and epidemiological characteristics. During 2009-2021, active surveillance of acute respiratory infections (ARIs) was performed in nine provinces of China. Clinical and epidemiological information and laboratory testing results of HIFV, HRSV, and HMPV were analyzed. Among 11591 ARI patients, the single-infection rates of HIFV, HRSV, and HMPV were 15.00%, 9.59%, and 2.24%, respectively; the coinfection rate of these three viruses was 0.64%. HIFV infection was mainly in adults aged 15-59 years, accounting for 39.10%. HRSV and HMPV infections were mainly in children under 5 years old, accounting for 87.13% and 83.46%, respectively. Patients with HRSV infection were younger than HMPV. HRSV and HMPV had high similarities in clinical manifestations, presenting with lower respiratory symptoms. HIFV mainly presented with an upper respiratory infection. The epidemic peak of HRSV was earlier than that of HIFV, and that of HMPV was later than those of HRSV and HFIV. A total of 85.14% of coinfection cases were children under 5 years old. Coinfection might increase the risk of pneumonia in HIFV cases. During 2020-2021, the positive rates and seasonal patterns of these three viruses changed due to the impact of the COVID-19 pandemic. Certain clinical and epidemiological features were observed in HIFV, HRSV, and HMPV infections, which could be beneficial for guiding clinical diagnosis, treatment, and prevention of these three viruses in China.

The clinical and virological features of two children's coinfections with human adenovirus type 7 and human coronavirus-229E virus

Objective

Human adenovirus (HAdV) coinfection with other respiratory viruses is common, but adenovirus infection combined with human coronavirus-229E (HCoV-229E) is very rare.

Study design and setting

Clinical manifestations, laboratory examinations, and disease severity were compared between three groups: one coinfected with HAdV-Ad7 and HCoV-229E, one infected only with adenovirus (mono-adenovirus), and one infected only with HCoV-229E (mono-HCoV-229E).

Results

From July to August 2019, there were 24 hospitalized children: two were coinfected with HAdV-Ad7 and HCoV-229E, and 21 were infected with a single adenovirus infection. Finally, one 14-year-old boy presented with a high fever, but tested negative for HAdV-Ad7 and HCoV-229E. Additionally, three adult asymptotic cases with HCoV-229E were screened. No significant difference in age was found in the coinfection and mono-adenovirus groups (11 vs. 8 years, p = 0.332). Both groups had the same incubation period (2.5 vs. 3 days, p = 0.8302), fever duration (2.5 vs. 2.9 days, p = 0.5062), and length of hospital stay (7 vs. 6.76 days, p = 0.640). No obvious differences were found in viral loads between the coinfection and mono-adenovirus groups (25.4 vs. 23.7, p = 0.570), or in the coinfection and mono-HCoV-229E groups (32.9 vs. 30.06, p = 0.067). All cases recovered and were discharged from the hospital.

Conclusion

HAdV-Ad7 and HCoV-229E coinfection in healthy children may not increase the clinical severity or prolong the clinical course. The specific interaction mechanism between the viruses requires further study.

Comparison of infections with respiratory syncytial virus between children and adults: a multicenter surveillance from 2015 to 2019 in Beijing, China

The objective of this study is to investigate the epidemiological and clinical characteristics of the acute respiratory tract infections (ARTI) caused by respiratory syncytial virus (RSV) among the population of all age categories in Beijing, China. Outpatients and inpatients with ARTI were enrolled from 35 sentinel hospitals in Beijing between March 2015 and February 2019. They were interviewed and their medical records were collected using a standardized form. Their respiratory specimens were collected and tested for the nucleic acid of RSV. The RSV-positive specimens were further genotyped into RSV-A and RSV-B groups. A total of 29,923 cases were included in this study. RSV was detected in 623 (2%, 623/29923) patients, with 391 (62.8%) genotypd as RSV-A, 126 (20.2%) as RSV-B, and 106 (17.0%) untyped. The RSV epidemic season usually occurred between October and March covering approximately 90% of annual RSV infections. The RSV-infected children aged < 5 years accounted for 52.2% of the total RSV infections with cough and fever as the most common manifestations. The RSV-infected elderly adults aged ≥ 60 years have the second largest proportion (25.2%) with dyspnea and lymphocytopenia as the most common manifestations and showed an elevated rate of hospitalization, an increased rate of ICU admission, an extended length of hospital stay, and an elevated mortality compared to the RSV-infected children. The RSV infections aged ≥ 60 years old, as the second largest population of the total annual RSV infections, usually developed worse outcomes than children and should be taken seriously.

Epidemiologic and clinical characteristics of human bocavirus infection in children hospitalized for acute respiratory tract infection in Qingdao, China

Persistent infection and prolonged shedding of human bocavirus 1 (HBoV1) in children have been reported, and the role of HBoV1 as a sole causative pathogen in acute respiratory infection (ARI) is yet to be established. While the reported prevalence of HBoV infection varies due to different detection methods and sampling criteria, determining the viral and bacterial etiology of HBoV infection using multiplex real-time PCR is yet to be reported. Herein, we aimed to further explore the pathogenicity of HBoV in patients with ARI by screening the viral and bacterial infections in children with ARI in Qingdao and comparing the epidemiological, clinical characteristics, and etiological results. Human bocavirus was identified in 28.1% of the samples, and further sequencing analysis of the detected HBoV confirmed 96.4% as HBoV1. The rate of HBoV as a single viral infection was 75%, and the rate of coinfection with bacteria was 66.1%, suggesting the need for continued monitoring of HBoV in children with ARIs. Clinical characterization suggested that HBoV infection may affect the function of organs, such as the liver, kidney, and heart, and the blood acid–base balance. Additionally, it is essential to promote awareness about the importance of disinfection and sterilization of the hospital environment and standardizing operations. The interactions between HBoV and other pathogens remain to be investigated in further detail in the future.

Viral etiology among children hospitalized for acute respiratory tract infections and its association with meteorological factors and air pollutants: a time-series study (2014-2017) in Macao

Background

The associations between viral etiology of acute respiratory infections (ARI) with meteorological factors and air pollutants among children is not fully understood. This study aimed to explore the viral etiology among children hospitalized for ARI and the association of meteorological factors and air pollutants with children hospitalization due to viral ARI.

Methods

Electronic health record data about children (aged between 1 month and 14 years) admitted for ARI at Kiang Wu Hospital in Macao between 2014 and 2017 was analyzed retrospectively. xMAP multiplex assays were used to detect viruses in the nasopharyngeal swab and distributed-lag nonlinear model (DLNM) was used to evaluate associations.

Results

Among the 4880 cases of children hospitalization due to ARI, 3767 (77.2%) were tested positive for at least one virus and 676 (18%) exhibited multiple infections. Enterovirus (EV)/rhinovirus (HRV), adenovirus (ADV), respiratory syncytial virus (RSV) and influenza virus (IFV) were the most common viral pathogens associated with ARI and human bocavirus (hBOV) exhibited the highest multiple infection rates. Meteorological factors and air pollutants (PM₁₀, PM_2.5 and NO₂) were associated with the risk of viral ARI hospitalization. The relative risk of viral infection increased with daily mean temperature but plateaued when temperature exceeded 23 °C, and increased when the relative humidity was < 70% and peaked at 50%. The effect of solar radiation was insignificant. Air pollutants (including PM₁₀, PM_2.5, NO₂ and O₃) showed strong and immediate effect on the incidence of viral infection.

Conclusions

The effects of mean temperature, relative humidity and air pollutants should be taken into account when considering management of ARI among children.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07585-y.

The A2c 111nt-dup Variants of Human Metapneumovirus Predominantly Circulating in Qingdao, China, during 2018 and 2019

BACKGROUND

Human metapneumovirus (HMPV) plays an important role in acute respiratory tract infections, especially in children. We investigated the epidemiology of HMPV associated with acute respiratory tract infections (ARTIs) among pediatric inpatients and identified HMPV genetic variations in Qingdao, China, from January 2018 to June 2019.

METHODS

HMPV-positive samples were identified from throat swabs by multiplex real-time RT-PCR. The G gene sequences of HMPV were obtained, followed by phylogenetic analysis.

RESULTS

As a result, 71 out of 1051 (6.76%) patients were HMPV positive, and the HMPV-positive rate in children under 5 years of age was three times higher than that in those aged 5-17 years. The epidemic season of HMPV was in spring, with a peak mainly in March. Thirty-two nucleotide sequences of the HMPV G gene successfully obtained were clustered into 3 genotypes, A2c (25/32, 78.13%), B1 (3/32, 9.38%) and B2 (4/32, 12.50%). In addition, 76% (19/25) of A2c viruses were identified as the emerging A2c_111nt-dup variants, which were predominantly circulating among pediatric inpatients with ARTIs between January 2018 and June 2019 in Qingdao.

CONCLUSIONS

The emerging A2c_111nt-dup variants have spread between countries and cities and might spread more widely in the future. Further prevalence monitoring of this duplication variant is needed to clarify the potentially expanding transmission and to provide a scientific basis for disease control and vaccine development. This article is protected by copyright. All rights reserved.

Epidemiological and Clinical Characteristics of Respiratory Syncytial Virus Infections in Children Aged <5 Years in China, from 2014−2018

Respiratory syncytial virus (RSV) is an important pathogen that causes acute respiratory tract infections in children. To understand the epidemiological and clinical characteristics of RSV in children, we analyzed the RSV diagnostic testing results from the 2014−2018 surveillance of acute respiratory infections in China. Among children aged <5 years, RSV incidence during 2014−2018 was 17.3% (3449/19,898), and 89.1% of RSV-positive individuals were inpatients. Children aged < 6 months had a high proportion in RSV infected individual (n = 1234; 35.8%). The highest RSV detection rate was in winter, RSV-A and RSV-B co-circulated year-round and jointly prevailed in 2015−2016. Cough was the common symptom of RSV infection 93.2% (3216/3449). Compared with older children, those aged <6 months were more likely to show breathing difficulty or lung rale that further developed into bronchopneumonia (p < 0.001). The symptoms such as cough, running nose, and diarrhea had significant differences between the RSV-A and RSV-B groups. The rate of RSV co-detection with other viruses or bacteria was 35.4%. Those coinfected with other viruses had a significantly higher incidence of fever, whereas those coinfected with bacteria had higher incidences of breathing difficulty and severe pneumonia. Our findings highlight the need for accumulating epidemiological information for the prevention and control of RSV.

The Impact and Vaccination Coverage of Seasonal Influenza among Children Aged 6-59 Months in China in 2017-2018: An Internet Panel Survey

Seasonal influenza vaccination is highly recommended for 6-59-month-old children. To determine the impact of seasonal influenza and the factors affecting influenza vaccine uptake among children, we conducted an opt-in Internet panel survey of parents from 21 March 2018 to 1 April 2018. Overall, 40.5% (1913/4719) of children experienced influenza-like illness (ILI), 92.4% of parents sought medical care for children with ILI (outpatients: 61.2%, inpatients: 12.8%), 39.6% of parents preferred to take their sick child to a tertiary hospital, and 57.3% of family members requested leave to care for children with ILI. There was a median of three days of absenteeism (2, 5) per sick child, and 39.4% of children received the influenza vaccine during the 2017-2018 influenza season. Vaccine coverage among children aged 6-11 months and 48-59 months was lower than that among 12-47-month-old children. The top three reasons for not vaccinating were: the influenza vaccine was not recommended by healthcare workers (21.1%), no knowledge about the influenza vaccine (19.2%), and lack of confidence in the vaccine's effectiveness (14.3%). Our findings highlight the need for awareness about the severity of influenza, hygiene behavior, and effectiveness of the influenza vaccine among children and their family members in China.

Hospitalization rate of respiratory syncytial virus-associated acute lower respiratory infection among young children in Suzhou, China, 2010-2014

Background

There is a limited amount of data in China on the disease burden of respiratory syncytial virus‐ (RSV) associated acute lower respiratory infection (ALRI) among young children. This study aimed to estimate the hospitalization rate of RSV‐associated ALRI (RSV‐ALRI) among children aged 0–59 months in Suzhou, China.

Methods

All cases from children hospitalized with ALRI who were aged 0–59 months in Suzhou University Affiliated Children's Hospital during January 2010 to December 2014 were retrospectively identified. Detailed diagnosis and treatment data were collected by reviewing each individual's medical chart. In accordance with the World Health Organization (WHO) influenza disease burden estimation, the hospitalization rate of RSV‐ALRI among children aged 0–59 months in Suzhou, China, was then estimated.

Results

Out of the 28,209 ALRI cases, 19,317 (68.5%) were tested for RSV, of which the RSV positive proportion was 21.3% (4107/19,317). The average hospitalization rate of RSV‐ALRI for children aged 0–59 months was 14 (95% confidence interval [CI]:14–14)/1000 children years, and that for children aged 0–5, 6–11, 12–23, and 24–59 months were 70 (95% CI: 67–73), 31 (95% CI: 29–33), 11 (95% CI: 10–12), and 3 (95% CI: 3–3)/1000 children years, respectively.

Conclusion

A considerable degree of RSV‐ALRI hospitalization exists among children aged 0–59 months, particularly in those under 1 year of age. Therefore, an effective monoclonal antibody or vaccine is urgently needed to address the substantial hospitalization burden of RSV infection.

A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019

Human respiratory syncytial virus (RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015-2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A (RSV-A) was the predominant subgroup during this research period except in 2016. Totally, 535 sequences of the second hypervariable region (HVR-2) of the G gene were obtained. Combined with 182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1 (512), NA1 (6) and GA5 (3), respectively; while 196 RSV-B sequences fell in BA9 (193) and SAB4 (3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258Q and H266L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than 10%, while the sequences with T290I and T312I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites (296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015-2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.

Etiological and epidemiological features of acute respiratory infections in China

Nationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients' demography, geographic locations and season of illness in China.

Detection and differentiation of respiratory syncytial virus subgroups A and B with colorimetric toehold switch sensors in a paper-based cell-free system

Respiratory syncytial virus (RSV) infection is the most common clinical infectious disease threatening the safety of human life. Herein, we provided a sensitive and specific method for detection and differentiation of RSV subgroups A (RSVA) and B (RSVB) with colorimetric toehold switch sensors in a paper-based cell-free system. In this method, we applied the toehold switch, an RNA-based riboswitch, to regulate the translation level of β-galactosidase (lacZ) gene. In the presence of target trigger RNA, the toehold switch sensor was activated and the expressed LacZ hydrolyzed chromogenic substrates to produce a colorimetric result that can be observed directly with the naked eye in a cell-free system. In addition, nucleic acid sequence-based amplification (NASBA) was used to improve the sensitivity by amplifying target trigger RNAs. Under optimal conditions, our method produced a visible result for the detection of RSVA and RSVB with the detection limit of 52 aM and 91 aM, respectively. The cross-reaction of this method was validated with other closely related respiratory viruses, including human coronavirus HKU1 (HCoV-HKU1), and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Furthermore, we used the paper-based carrier material that allows stable storage of our detection elements and rapid detection outside laboratory. In conclusion, this method can sensitively and specifically differentiate RSVA and RSVB and generate a visible colorimetric result without specialized operators and sophisticated equipment. Based on these advantages above, this method serves as a simple and portable detector in resource-poor areas and point-of-care testing (POCT) scenarios.

Hospital utilization rates for influenza and RSV: a novel approach and critical assessment

BACKGROUND

Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone.

METHODS

This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease.

RESULTS

For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation.

CONCLUSIONS

This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.

Prevalence of human respiratory syncytial virus, parainfluenza and adenoviruses in East Africa Community partner states of Kenya, Tanzania, and Uganda: A systematic review and meta-analysis (2007-2020)

Background

Viruses are responsible for a large proportion of acute respiratory tract infections (ARTIs). Human influenza, parainfluenza, respiratory-syncytial-virus, and adenoviruses are among the leading cause of ARTIs. Epidemiological evidence of those respiratory viruses is limited in the East Africa Community (EAC) region. This review sought to identify the prevalence of respiratory syncytial virus, parainfluenza, and adenoviruses among cases of ARTI in the EAC from 2007 to 2020.

Methods

A literature search was conducted in Medline, Global Index Medicus, and the grey literature from public health institutions and programs in the EAC. Two independent reviewers performed data extraction. We used a random effects model to pool the prevalence estimate across studies. We assessed heterogeneity with the I² statistic, and Cochran’s Q test, and further we did subgroup analysis. This review was registered with PROSPERO under registration number CRD42018110186.

Results

A total of 12 studies met the eligibility criteria for the studies documented from 2007 to 2020. The overall pooled prevalence of adenoviruses was 13% (95% confidence interval [CI]: 6–21, N = 28829), respiratory syncytial virus 11% (95% CI: 7–15, N = 22627), and parainfluenza was 9% (95% CI: 7–11, N = 28363). Pooled prevalence of reported ARTIs, all ages, and locality varied in the included studies. Studies among participants with severe acute respiratory disease had a higher pooled prevalence of all the three viruses. Considerable heterogeneity was noted overall and in subgroup analysis.

Conclusion

Our findings indicate that human adenoviruses, respiratory syncytial virus and parainfluenza virus are prevalent in Kenya, Tanzania, and Uganda. These three respiratory viruses contribute substantially to ARTIs in the EAC, particularly among those with severe disease and those aged five and above.

Incidence, risk factors, and viral etiology of community-acquired acute lower respiratory tract infection among older adults in rural north India

BACKGROUND

There are limited data on incidence, risk factors and etiology of acute lower respiratory tract infection (LRTI) among older adults in low- and middle-income countries.

METHODS

We established a cohort of community dwelling older adults ≥60 years and conducted weekly follow-up for acute respiratory infections (ARI) during 2015-2017. Nurses assessed ARI cases for LRTI, collecting combined nasal/throat swabs from all LRTI cases and an equal number of age- and sex-matched asymptomatic neighbourhood controls. Swabs were tested for influenza viruses, respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and parainfluenza viruses (PIV) using polymerase chain reaction. LRTI and virus-specific LRTI incidence was calculated per 1000 person-years. We estimated adjusted incidence rate ratios (IRR) for risk factors using Poisson regression and calculated etiologic fractions (EF) using adjusted odds ratios for detection of viral pathogens in LRTI cases vs controls.

RESULTS

We followed 1403 older adults for 2441 person-years. LRTI and LRTI-associated hospitalization incidences were 248.3 (95% confidence interval (CI) = 229.3-268.8) and 12.7 (95% CI = 8.9-18.1) per 1000 person-years. Persons with pre-existing chronic bronchitis as compared to those without (incidence rate ratio (IRR) = 4.7, 95% CI = 3.9-5.6); aged 65-74 years (IRR = 1.6, 95% CI = 1.3-2.0) and ≥75 years (IRR = 1.8, 95% CI = 1.4-2.4) as compared to 60-64 years; and persons in poorest wealth quintile (IRR = 1.4, 95% CI = 1.1-1.8); as compared to those in wealthiest quintile were at higher risk for LRTI. Virus was detected in 10.1% of LRTI cases, most commonly influenza (3.8%) and RSV (3.0%). EF for RSV and influenza virus was 83.9% and 83.6%, respectively.

CONCLUSION

In this rural cohort of older adults, the incidence of LRTI was substantial. Chronic bronchitis was an important risk factor; influenza virus and RSV were major viral pathogens.

Evaluation of the Xpert Xpress SARS-CoV-2/Flu/RSV Assay for Simultaneous Detection of SARS-CoV-2, Influenza A and B Viruses, and Respiratory Syncytial Virus in Nasopharyngeal Specimens

Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A (flu A), influenza B (flu B), and respiratory syncytial virus (RSV) have overlapping clinical presentations, but the approaches to treatment and management of infections caused by these viruses are different. Therefore, rapid diagnosis in conjunction with infection prevention measures is important to prevent transmission of the diseases. Recently, a new Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4-in-1) assay enables the detection and differentiation of SARS-CoV-2, flu A, flu B, and RSV in upper respiratory tract specimens. In this study, we evaluated the performance of the Xpert 4-in-1 assay by comparing it with that of the Xpert Xpress SARS-CoV-2 and Xpert Xpress Flu/RSV assays for the detection of the four viruses in nasopharyngeal (NP) specimens. A total of 279 NP specimens, including 66, 56, 64, and 53 specimens positive for SARS-CoV-2, flu A, flu B, and RSV, respectively, were included. The Xpert 4-in-1 assay demonstrated high concordance with the comparator assays, with overall agreement for SARS-CoV-2, flu A, flu B, and RSV at 99.64%, 100%, 99.64%, and 100%, respectively, and a high Cohen's kappa (κ) value ranging from 0.99 to 1.00, indicating an almost perfect correlation between assays. The cycle threshold value association between positive samples also showed a good correlation between assays. In conclusion, the overall performance of the Xpert 4-in-1 assay was highly comparable to that of the Xpert SARS-CoV-2 and Xpert Flu/RSV assays for the detection and differentiation of SARS CoV-2, flu A, flu B, and RSV in NP specimens.

The clinical application of Filmarray respiratory panel in children especially with severe respiratory tract infections

BACKGROUND

Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children.

METHODS

Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated.

RESULTS

A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0-2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3-5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6-14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05).

CONCLUSIONS

This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.

Global Seasonality of Human Coronaviruses: A Systematic Review

In the context of the coronavirus disease 2019 pandemic, we aimed to systematically address the global seasonal patterns of human coronavirus (HCoV) infections. We identified relevant articles from MEDLINE, EMBASE, and CINAHL Plus as of May 11, 2020. The main outcomes were the peak months of HCoV infections each year and the months during which more than 5% of positive respiratory specimen tests were attributable to HCoV. Of 707 articles reviewed, 22 met the inclusion criteria. The annual percentage of HCoV infections reached a peak in February globally. We found a higher HCoV positivity rate among studies that tested only children (median: 5.9%, range: 0.9%–18.4%), compared with other studies of adults alone (median: 5.2%, range: 3.3%–7.1%) or the entire population (median: 1.9%, range: 0.2%–8.1%). We found the largest global peak of HCoV during the winter season, with the highest rate of positivity among children.

Epidemiological characteristics of respiratory viruses in patients with acute respiratory infections during 2009-2018 in southern China

BACKGROUND

Acute respiratory infections (ARIs) remain a significant public threat with high morbidity and mortality worldwide; viruses are significant pathogens that cause ARIs. This study was conducted to better understand the epidemiological characteristics of respiratory viruses circulating in southern China.

METHODS

We collected 22,680 respiratory samples from ARI patients in 18 hospitals in southern China during 2009-2018; seven common respiratory viruses including Flu, RSV, PIV, hMPV, ADV, HCoV, and HBoV were screened using in-house real-time PCR.

RESULTS

Of all samples, 9760 ARI cases (9760/22680, 43.03%) tested positive for the seven common respiratory viruses. The most detected virus was Flu (14.15%), followed by RSV (10.33%) and PIV (5.43%); Flu-A, PIV3, and HCoV-OC43 were the predominant subtypes. Although most of the viruses were detected in male inpatients, Flu was more likely detected in female outpatients. Flu infection was more likely to cause URTI (upper respiratory tract infection), whereas RSV infection was more likely to cause pneumonia and bronchitis. The prevalence of Flu was particularly high in 2009. The epidemic level was found notably high in 2014-2018 for RSV, in 2016-2018 for PIV, in the summer of 2018 for ADV, in the summer of 2016 and winter of 2018 for HCoV, and in the summer of 2011 and autumn of 2018 for HBoV. The co-detection rate of the seven viruses was 4.70%; RSV, PIV, and Flu were the most commonly co-detected viruses.

CONCLUSIONS

This work demonstrates the epidemiological characteristics of seven common respiratory viruses in ARI patients in southern China.

Etiological analysis of virus, mycoplasma pneumoniae and chlamydia pneumoniae in hospitalized children with acute respiratory infections in Huzhou

BACKGROUND

Acute respiratory infections are a common disease in children with high mortality and morbidity. Multiple pathogens can cause acute respiratory infections. A 2-year survey of hospitalized children was conducted to understand the epidemic situation, seasonal spread of pathogens and the improvement of clinical diagnosis, treatment and prevention of disease in Huzhou, China.

METHODS

From September 2017 to August 2019, 3121 nasopharyngeal swabs from hospitalized children with acute respiratory infections were collected, and real-time PCR was used to detect various pathogens. Then, pathogen profiles, frequency and seasonality were analyzed.

RESULTS

Of the 3121 specimens, 14.45% (451/3121) were positive for at least one pathogen. Of the single-pathogen infections, RSV (45.61%, 182/399) was the most frequent pathogen, followed by PIVs (14.79%, 59/399), ADV (14.54%, 58/399), MP (10.78%, 43/399), and IAV (5.26%, 21/399). Of the 52 coinfections, RSV + PIVs viruses were predominantly identified and accounted for 40.38% (21/52) of cases. RSV was the most frequent pathogen in all four groups. The highest positive rate of the pathogens occurred in the winter (21.26%), followed by autumn (14.98%), the summer (14.11%) and the spring (12.25%).

CONCLUSION

Viruses are the main pathogens in hospitalized children with acute respiratory infections in Huzhou city, Zhejiang Province, China. Among the pathogens, RSV had the highest detection rate, and MP is also a common pathogen among children with acute respiratory infections. This study provided a better understanding of the distribution of pathogens in children of different ages and seasons, which is conducive to the development of more reasonable treatment strategies and prevention and control measures.

Influenza virus detection in the stool of children with acute gastroenteritis

OBJECTIVES

To determine if the clinical characteristics of children with gastroenteritis and influenza identified in their stool differ from those whose stool was influenza-negative.

METHODS

Children <18-years with gastroenteritis whose stool tested negative for enteropathogen were tested for influenza in stool. The clinical features between influenza-positive and influenza-negative gastroenteritis cases were compared. Stools from controls without infection were also tested for influenza.

RESULTS

Among the 440 gastroenteritis cases, those who were influenza test-positive were older [median age 4.0 (IQR: 2.3, 5.5) vs. 1.5 (IQR: 0.5, 4.0) years; P = 0.008], more likely to present in fall or winter (92.3 % vs. 48.0 %; P = 0.001), be febrile (84.6 % vs. 30.6 %; P < 0.001), have respiratory symptoms (91.7 % vs. 44.8 %; P = 0.002), have dehydration [median Clinical Dehydration Scale score: 4 (IQR: 1.5, 4.5) vs. 2 (IQR: 0, 3); P = 0.034], and have higher Modified Vesikari Scale scores [median: 13 (IQR: 10.5, 14.0) vs. 10 (IQR: 9.0, 13.0); P = 0.044], than those who tested negative. Thirteen gastroenteritis cases (13/440; 3.0 %) including one child without respiratory symptoms vs. one control (1/250; 0.4 %) were influenza stool positive.

CONCLUSIONS

Fever, respiratory symptoms, more severe illness, and older age were more common in children with gastroenteritis with influenza detected in stool, compared to those tested negative.

COVID-19: An Early Review of Its Global Impact and Considerations for Parkinson's Disease Patient Care

While many infectious disorders are unknown to most neurologists, COVID-19 is very different. It has impacted neurologists and other health care workers, not only in our professional lives but also through the fear and panic within our own families, colleagues, patients and their families, and even in the wider public. COVID-19 affects all sorts of individuals, but the elderly with underlying chronic conditions are particularly at risk of severe disease, or even death. Parkinson's disease (PD) shares a common profile as an age-dependent degenerative disorder, frequently associated with comorbidities, particularly cardiovascular diseases, so PD patients will almost certainly fall into the high-risk group. Therefore, the aim of this review is to explore the risk of COVID-19 in PD based on the susceptibility to severe disease, its impact on PD disease severity, potential long-term sequelae, and difficulties of PD management during this outbreak, where neurologists face various challenges on how we can maintain effective care for PD patients without exposing them, or ourselves, to the risk of infection. It is less than six months since the identification of the original COVID-19 case on New Year's Eve 2019, so it is still too early to fully understand the natural history of COVID-19 and the evidence on COVID-19-related PD is scant. Though the possibilities presented are speculative, they are theory-based, and supported by prior evidence from other neurotrophic viruses closely related to SARS-CoV-2. Neurologists should be on high alert and vigilant for potential acute and chronic complications when encountering PD patients who are suspected of having COVID-19.

[The Effects and Management of Viral Pneumonia on Lung Cancer Patients]

The worldwide epidemic of three coronaviruses and one influenza virus in 21st century have seriously threatened human health. Infection with these viruses can cause respiratory symptoms. The patients with lung cancer are more susceptible to viral infection and have a worse prognosis due to the advanced age and the systemic immunosuppressive state caused by malignancy itself and the anticancer treatments. In addition, without sufficient clinical awareness, a missed diagnosis of viral pneumonia may occur due to the fever and respiratory symptoms caused by lung cancer and its secondary diseases. Furthermore, control measures against viral outbreaks may interfere with routine diagnosis and treatment of lung cancer patients. Therefore, scientific protection and individualized management of lung cancer patients are particularly important during virus epidemic prevention and control. Here, we systematically reviewed the epidemiological and clinical characteristics of viral pneumonia, its impact on patients with lung cancer and the differential diagnosis of lung cancer-related respiratory manifestations, aiming to provide guidance for the individual management of lung cancer patients during the prevention and control of viral pneumonia epidemic.

Meteorological factors affecting respiratory syncytial virus infection: A time-series analysis

INTRODUCTION

Respiratory syncytial virus (RSV) infection is a major cause of hospitalization in children. Meteorological factors are known to influence seasonal RSV epidemics, but the relationship between meteorological factors and RSV infection in children is not well understood. We aimed to explore the relationship between meteorological factors and RSV infections among hospitalized children, using different statistical models.

METHODS

We conducted a retrospective review concerning children with RSV infections admitted to a tertiary pediatric hospital in Wenzhou, China, between January 2008 and December 2017. The relationship between meteorological factors (average daily temperatures, average daily relative humidity, rainfall, rainfall days, and wind speed) and the incidence of RSV in hospitalized children was analyzed using three time-series models, namely an autoregressive integrated moving average (ARIMA) model, a generalized additive model (GAM), and a least absolute shrinkage and selection operator (LASSO)-based model.

RESULTS

In total, 15 858 (17.6%) children tested positive for RSV infection. The ARIMA model revealed a marked seasonal pattern in the RSV detection rate, which peaked in winter and spring. The model was a good predictor of RSV incidence (R² : 83.5%). The GAM revealed that a lower temperature and higher wind speed preceded increases in RSV detection. The LASSO-based model revealed that temperature and relative humidity were negatively correlated with RSV detection.

CONCLUSIONS

Seasonality of RSV infection in hospitalized children correlated strongly with temperature. The LASSO-based model can be used to predict annual RSV epidemics using weather forecast data.

The burden of respiratory syncytial virus in adults: a systematic review and meta-analysis

Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/10⁵ population in Africa and Asia and from 190 to 254/10⁵ population in the USA. Higher incidence rates (195–1790/10⁵ population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.

Respiratory Syncytial Virus Seasonality, Beijing, China, 2007-2015

During July 2007-June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. We defined season as the period during which >10% of total PCRs performed each week were RSV positive. We identified 8 distinctive RSV seasons. On average, the season onset occurred at week 41 (mid-October) and lasted 33 weeks, through week 20 of the next year (mid-May); 97% of all RSV-positive cases occurred during the season. RSV seasons occurred 3-5 weeks earlier and lasted ≈6 weeks longer in RSV subgroup A-dominant years than in RSV subgroup B-dominant years. Our analysis indicates that monitoring such RSV subgroup shifts might provide better estimates for the onset of RSV transmission. PCR-based tests could be a flexible or complementary way of determining RSV seasonality in locations where RSV surveillance is less well-established, such as local hospitals throughout China.

Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China

Background

No comparison data have been reported on viral and epidemiological profiles of hospitalized children with severe acute respiratory infection (SARI) in Beijing or Shanghai, China.

Methods

We collected 700 nasopharyngeal aspirates (NPA) from hospitalized children with SARI in Beijing (northern China) and Shanghai (southern China). Multiple respiratory viruses (including 15 common viruses) were screened by validated polymerase chain reaction (PCR) or real-time reverse transcription-PCR assays and confirmed by sequencing. Demographic data and the distribution of viral infections were also examined.

Results

Of 700 samples, 547 (78.1%) tested positive for viral infections. The picornaviruses (PIC), which included rhinovirus (RV) and enterovirus (EV), were the most common (34.0%), followed by respiratory syncytial virus (RSV) (28.3%), human bocavirus (HBoV) (19.1%), adenovirus (ADV) (13.7%), human coronaviruses (HCoV) (10.7%), influenza A and B (8.9%), parainfluenza virus (PIV 1–3) (7.9%), and human metapneumovirus (HMPV) (5.0%). PIC (RV/EV) and RSV were the most prevalent etiological agents of SARI in both cities. The total and age-matched prevalence of RSV, HCoV, and hMPV among SARI children under 5 years old were significantly higher in Beijing than in Shanghai. Different age and seasonal distribution patterns of the viral infections were found between Beijing and Shanghai.

Conclusions

Viral infection was tested and shown to be the most prevalent etiological agent among children with SARI in either the Beijing or the Shanghai area, while showing different patterns of viral and epidemiological profiles. Our findings provide a better understanding of the roles of geographic location and climate in respiratory viral infections in hospitalized children with SARI.

Human adenovirus among hospitalized children with respiratory tract infections in Beijing, China, 2017-2018

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.

The spectrum of viral pathogens in children with severe acute lower respiratory tract infection: A 3-year prospective study in the pediatric intensive care unit

Background

No comprehensive analysis is available on the viral etiology and clinical characterization among children with severe acute lower respiratory tract infection (SALRTI) in Southern China.

Methods

Cohort of 659 hospitalized children (2 months to 14 years) with SALRTI admitted to the Pediatric Intensive Care Unit (PICU) in the Guangzhou from May 2015 to April 2018 was enrolled in this study. Nasopharyngeal aspirate specimens or induced sputum were tested for eight categories respiratory viral targets. The viral distribution and its clinical characters were statistically analyzed.

Results

Viral pathogen was detected in 326 (49.5%) of children with SALRTI and there were 36 (5.5%) viral coinfections. Overall, the groups of viruses identified were, in descending order of prevalence: Influenza virus (IFV) (n = 94, 14.3%), respiratory syncytial virus (RSV) (n = 75, 11.4%), human rhinovirus (HRV) (n = 56, 8.5%), adenovirus (ADV) (n = 55, 8.3%), parainfluenza (PIV) (n = 47, 7.1%), human coronavirus (HCoV) (n = 15, 2.3%), human metapneumovirus (HMPV) (n = 14, 2.1%) and human bocavirus (HBoV) (n = 11, 1.7%). The positive rate in younger children (< 5 years) was significantly higher than the positive rate detected in elder children (> 5 years) (52.5% vs 35.1%, P = 0.001). There were clear seasonal peaks for IFV, RSV, HRV, ADV, PIV, and HMPV. And the individuals with different viral infection varied significantly in terms of clinical profiles.

Conclusions

Viral infections are present in a consistent proportion of patients admitted to the PICU. IFV, RSV, HRV, and ADV accounted for more than two‐thirds of all viral SALRTI. Our findings could help the prediction, prevention and potential therapeutic approaches of SALRTI in children.

Viral infections are present in a consistent proportion of patients admitted to the Pediatric Intensive Care Unit.

Influenza virus, respiratory syncytial virus, human rhinovirus and adenovirus accounted for more than two‐thirds of all viral SALRTI.

Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR

OBJECTIVE

To determine the frequency of respiratory pathogens in infants diagnosed with acute lower respiratory tract infections.

METHODS

A prospective cross-sectional observational study was conducted in infants hospitalized with a diagnosis of acute lower respiratory tract infection (ALRTI), in a tertiary care hospital in a metropolitan city of Western India. Nasopharyngeal swabs were analyzed by multiplex real time polymerase chain reaction, for 18 viruses and 3 bacteria (H. influenzae type b, C. pneumoniae and M. pneumoniae). The entire data was entered in Microsoft excel sheet and frequencies were determined.

RESULTS

One hundred eligible infants were enrolled. Pathogens were detected in 82 samples, which included Respiratory syncytial viruses (RSV) A / B (35.4%), Human rhinovirus (25.6%), Adenovirus (22%), Human Parainfluenza viruses (11%), Human bocavirus (9.8), Human metapneumovirus A / B (8.5%), Influenza A (H1N1) pdm 09 (6.1%), Parechovirus (3.7%), Human coronaviruses (3.66%), Haemophilus influenzae type b (6.1%), Chlamydia pneumoniae (2.4%) and Mycoplasma pneumoniae (2.4%). Influenza A (other than H1N1), Influenza B, Human Coronavirus 229E and Enterovirus were not detected. The rate of coinfection was 34% and rhinovirus was the most common of the multiple pathogens.

CONCLUSIONS

Spectrum of viral etiologies of ALRTI is highlighted. Etiological diagnosis of ALRTI would enable specific antiviral therapy, restrict antibiotic use and help in knowing burden of disease.

Human bocaviruses and paediatric infections

Human bocavirus 1 (HBoV1), belonging to the Parvoviridae family, was discovered in 2005, in nasopharyngeal samples from children with respiratory tract infections. Three additional bocaviruses, HBoV2-4, were discovered in 2009-10. These viruses have mainly been found in faecal samples and their role in human diseases is still uncertain. HBoV1 causes a wide spectrum of respiratory diseases in children, including common cold, acute otitis media, pneumonia, bronchiolitis, and asthma exacerbations. HBoV1 DNA can persist in airway secretions for months after an acute infection. Consequently, acute HBoV1 infection cannot be diagnosed with standard DNA PCR; quantitative PCR and serology are better diagnostic approaches. Because of their high clinical specificity, diagnostic developments such as HBoV1 mRNA and antigen detection have shown promising results. This Review summarises the knowledge on human bocaviruses, with a special focus on HBoV1.

Characteristics and Outcomes of Young Children Hospitalized With Laboratory-confirmed Influenza or Respiratory Syncytial Virus in Ontario, Canada, 2009-2014

BACKGROUND

Respiratory illnesses are a major contributor to pediatric hospitalizations, with influenza and respiratory syncytial virus (RSV) causing substantial morbidity and cost each season. We compared the characteristics and outcomes of children 0-59 months of age who were hospitalized with laboratory-confirmed influenza or RSV between 2009 and 2014 in Ontario, Canada.

METHODS

We included hospitalized children who were tested for influenza A, influenza B and RSV and were positive for a single virus. We characterized individuals by their demographics and healthcare utilization patterns and compared their hospital outcomes, in-hospital cost and postdischarge healthcare use by virus type and by presence of underlying comorbidities.

RESULTS

We identified and analyzed 7659 hospitalizations during which a specimen tested positive for influenza or RSV. Children with RSV were the youngest whereas children with influenza B were the oldest [median ages 6 months (interquartile range: 2-17 months) and 25 months (interquartile range: 10-45 months), respectively]. Complex chronic conditions were more prevalent among children with all influenza (sub)types than RSV (31%-34% versus 20%). In-hospital outcomes were similar by virus type, but in children with comorbidities, postdischarge outcomes varied. We observed no differences in in-hospital cost between viruses or by presence of comorbidities [overall median cost: $4150 Canadian dollars (interquartile range: $3710-$4948)].

CONCLUSIONS

Influenza and RSV account for large numbers of pediatric hospitalizations. RSV and influenza were similar in terms of severity and cost in hospitalized children. Influenza vaccination should be promoted in pregnant women and young children, and a vaccine against RSV would mitigate the high burden of RSV.

A combination of naso- and oropharyngeal swabs improves the diagnostic yield of respiratory viruses in adult emergency department patients

BACKGROUND

Along with the current development of molecular diagnostic methods of respiratory viruses, the bedside patient sampling techniques need to be evaluated. We here asked the question whether the addition of an oropharynx swab to the traditional nasopharynx swab might improve the diagnostic yield of multiplex PCR analysis. Ct values from the two sampling sites were compared as well as patient tolerability.

METHODS

In an emergency department in Malmö, Sweden, 98 adult patients with respiratory disease were sampled both from the nasopharynx and oropharynx for virus diagnostics by PCR.

RESULTS

Influenza (AH1, AH3, B), human metapneumovirus (hMPV) or respiratory syncytial virus (RSV) were detected by PCR in 58 subjects. The diagnostic yield was improved by combining nasopharyngeal and oropharyngeal sampling - a virus was detected in another 6 patients compared to traditional nasopharyngeal sampling (p = .031, McNemar's test). In 38/55 subjects viral load was higher in the nasopharynx than in the oropharynx. Self-reported discomfort was significantly lower from oropharyngeal sampling than from nasopharyngeal sampling.

CONCLUSIONS

Adding an oropharynx sample to a nasopharynx sample increased the diagnostic yield of respiratory viruses. Oropharyngeal sampling was well tolerated.

Comparison of the Cepheid Xpert Xpress Flu/RSV assay and commercial real-time PCR for the detection of influenza A and influenza B in a prospective cohort from China

BACKGROUND

The Xpert Xpress Flu/RSV assay is released by FDA for rapid detection of influenza A (FluA), influenza B (FluB), and respiratory syncytial virus (RSV). This study aimed to evaluate its clinical performance in comparison to that of the RT-PCR assay cleared by China FDA (CFDA-PCR).

METHODS

Nasopharyngeal specimens were collected from patients and tested by the two assays side by side. Discordant results were tested with a laboratory-developed real-time PCR for resolution. Viral load in the sample was quantified with a droplet digital PCR.

RESULTS

A total of 658 specimens were involved and gave 94.7%-99.1% agreement between the two assays. The Xpert assay showed higher sensitivity for FluA (100% vs. 89.8%) and FluB detection (100% vs. 95.3%), and also higher accuracy (98.9% vs. 95.7%) for FluA than the CDFA-PCR. The positive and negative predictive values (NPV) for the three viruses ranged from 90.5% to 100% in the two assays, with higher NPV for FluA and FluB in Xpert assay. Moreover, the Xpert Ct values showed a linear correlation with virus titer in specimens tested.

CONCLUSION

Overall, the Xpert assay is a reliable and sensitive tool for the detection of FluA, FluB and RSV in our clinical settings.