The burden of HMPV and influenza associated hospitalizations in adults in New Zealand, 2012-2015.

BACKGROUND: Unlike influenza, information on the burden of human metapneumovirus (HMPV) as a cause of hospitalizations in adults with acute respiratory illness (ARI) is limited. METHODS: We compared the population-based incidence, seasonality, and clinical characteristics of these two viral infections among adults aged 20 years and over with ARI hospitalisations in Auckland, New Zealand, during 2012-2015 through the Southern Hemisphere Influenza Vaccine Effectiveness Research and Surveillance (SHIVERS) project. RESULTS: Of the 14,139 ARI hospitalisations, 276 (4.3%) of 6484 tested positive for HMPV and 1342 (19.1%) of 7027 tested positive for influenza. Crude rates of 9.8 (95% CI: 8.7-11.0) HMPV and 47.6 (95% CI: 45.1-50.1) influenza-associated ARI hospitalisations were estimated for every 100,000 adult residents annually. The highest rates for both viruses were in those aged 80 years or older, of Maori or Pacific ethnicity, or living in low socioeconomic status (SES) areas. HMPV infections were more common than influenza in those with chronic medical conditions. CONCLUSIONS: Although HMPV infections accounted for fewer hospitalisations than influenza in adults aged 20 years and over, HMPV-associated ARI hospitalisation rates were higher than influenza in older adults, Maori and Pacific people and those of low SES. This highlighted a need for vaccine/antiviral development.

Effectiveness of Immunization Products Against Medically Attended Respiratory Syncytial Virus Infection: Generic Protocol for a Test-Negative Case-Control Study.

Monitoring the real-life effectiveness of respiratory syncytial virus (RSV) products is of major public health importance. This generic protocol for a test-negative design study aims to address currently envisioned approaches for RSV prevention (monoclonal antibodies and vaccines) to study effectiveness of these products among target groups: children, older adults, and pregnant women. The generic protocol approach was chosen to allow for flexibility in adapting the protocol to a specific setting. This protocol includes severe acute respiratory infection (SARI) and acute respiratory infection (ARI), both due to RSV, as end points. These end points can be applied to studies in hospitals, primarily targeting patients with more severe disease, but also to studies in general practitioner clinics targeting ARI.

Prevalence and genetic diversity of human rhinovirus among patients with acute respiratory infections in China, 2012-2021.

To understand the prevalence of rhinovirus (RV) among acute respiratory infection (ARI) patients, 10-year ARI surveillance in multiple provinces of China were conducted during 2012-2021. Of 15 645 ARI patients, 1180 (7.54%) were confirmed to have RV infection and 820 (69.49%) were children under 5 years of age. RV typing was performed on the 527 VP1 gene sequences, and species A, B, and C accounted for 73.24%, 4.93%, and 21.82%, respectively. Although no significant difference in the proportions of age groups or disease severity was found between RV species, RV-C was more frequently detected in children under 5 years of age, RV-A was more frequently detected in elderly individuals (≥60), and the proportions of pneumonia in RV-A and RV-C patients were higher than those in RV-B patients. The epidemic peak of RV-A was earlier than that of RV-C. A total of 57 types of RV-A, 13 types of RV-B, and 35 types of RV-C were identified in RV-infected patients, and two uncertain RV types were also detected. The findings showed a few differences in epidemiological and clinical features between RV species in ARI patients, and RV-A and RV-C were more prevalent than RV-B.

Genetic characterization of pediatric SARI-associated human adenoviruses in eight Chinese provinces during 2017-2021.

Human adenovirus (HAdV) is a significant viral pathogen causing severe acute respiratory infections (SARIs) in children. To improve the understanding of type distribution and viral genetic characterization of HAdV in severe cases, this study enrolled 3404 pediatric SARI cases from eight provinces of China spanning 2017-2021, resulting in the acquisition of 112 HAdV strains. HAdV-type identification, based on three target genes (penton base, hexon, and fiber), confirmed the diversity of HAdV types in SARI cases. Twelve types were identified, including species B (HAdV-3, 7, 55), species C (HAdV-1, 2, 6, 89, 108, P89H5F5, Px1/Ps3H1F1, Px1/Ps3H5F5), and E (HAdV-4). Among these, HAdV-3 exhibited the highest detection rate (44.6%), followed by HAdV-7 (19.6%), HAdV-1 (12.5%), and HAdV-108 (9.8%). All HAdV-3, 7, 55, 4 in this study belonged to dominant lineages circulating worldwide, and the sequences of the three genes demonstrated significant conservation and stability. Concerning HAdV-C, excluding the novel type Px1/Ps3H1F1 found in this study, the other seven types were detected both in China and abroad, with HAdV-1 and HAdV-108 considered the two main types of HAdV-C prevalent in China. Two recombinant strains, including P89H5F5 and Px1/Ps3H1F1, could cause SARI as a single pathogen, warranting close monitoring and investigation for potential public health implications. In conclusion, 5 years of SARI surveillance in China provided crucial insights into HAdV-associated respiratory infections among hospitalized pediatric patients.

High burden of acute respiratory tract infections leading to hospitalization at German pediatric hospitals: fall/winter 2022-2023.

PURPOSE: Given reduced immunity levels for seasonally occurring respiratory infections and the experience of an unusually early, severe wave of RSV infections during 2021, a preexisting clinician-led reporting system (CLRS) was updated to prospectively monitor the anticipated high burden of respiratory infections (ARI) in German pediatric hospitals during fall/winter 2022-2023. METHODS: From September 13, 2022 through March 31, 2023, children hospitalized with ARI as a primary diagnosis were monitored via a national CLRS established by the German Society for Pediatric Infectious Diseases (DGPI). Once a week, the CLRS collected overall number of new hospital admissions, ARI-related admissions according to pathogen (SARS-CoV-2, RSV, influenza, and other), plus number of patients admitted to ICU with ARI as a primary diagnosis. RESULTS: With a high participation among children's hospitals across Germany (22.8%), 76 centers submitted 1,053 survey reports. ARI-related hospital admissions showed a steep rise starting in late September 2022 and reached their highpoint in early December 2022 (50.1% of all admissions). In parallel, the average number of newly admitted patients (aNA) with RSV (3.6) peaked, as did those with influenza (2.1) one week later. The average highpoint of ARI patients on ICU (aICU) (2.9) was reached shortly thereafter. Again, RSV (1.6) und influenza (1.2) were predominant pathogens. CONCLUSION: In fall/winter 2022-2023, German hospitals reported a sharp increase in patients with ARIs. While RSV and influenza represented the greatest proportion of ARI, SARS-CoV-2 played a less significant role. Systematic, dynamic collection of ARI data is critical for assessing real burdens on the health care system.

Empowering child health: Harnessing machine learning to predict acute respiratory infections in Ethiopian under-fives using demographic and health survey insights.

BACKGROUND: A dearth of studies showed that infectious diseases cause the majority of deaths among under-five children. Worldwide, Acute Respiratory Infection (ARI) continues to be the second most frequent cause of illness and mortality among children under the age of five. The paramount disease burden in developing nations, including Ethiopia, is still ARI. OBJECTIVE: This study aims to determine the magnitude and predictors of ARI among under-five children in Ethiopia using used state of the art machine learning algorithms. METHODS: Data for this study were derived from the 2016 Ethiopian Demographic and Health Survey. To predict the determinants of acute respiratory infections, we performed several experiments on ten machine learning algorithms (random forests, decision trees, support vector machines, Naïve Bayes, and K-nearest neighbors, Lasso regression, GBoost, XGboost), including one classic logistic regression model and an ensemble of the best performing models. The prediction ability of each machine-learning model was assessed using receiver operating characteristic curves, precision-recall curves, and classification metrics. RESULTS: The total ARI prevalence rate among 9501 under-five children in Ethiopia was 7.2%, according to the findings of the study. The overall performance of the ensemble model of SVM, GBoost, and XGBoost showed an improved performance in classifying ARI cases with an accuracy of 86%, a sensitivity of 84.6%, and an AUC-ROC of 0.87. The highest performing predictive model (the ensemble model) showed that the child's age, history of diarrhea, wealth index, type of toilet, mother's educational level, number of living children, mother's occupation, and type of fuel they used were an important predicting factor for acute respiratory infection among under-five children. CONCLUSION: The intricate web of factors contributing to ARI among under-five children was identified using an advanced machine learning algorithm. The child's age, history of diarrhea, wealth index, and type of toilet were among the top factors identified using the ensemble model that registered a performance of 86% accuracy. This study stands as a testament to the potential of advanced data-driven methodologies in unraveling the complexities of ARI in low-income settings.

Epidemiological and etiological characteristics of 1266 patients with severe acute respiratory infection in central China, 2018-2020: a retrospective survey.

BACKGROUND: Severe acute respiratory infection (SARI), a significant global health concern, imposes a substantial disease burden. In China, there is inadequate data concerning the monitoring of respiratory pathogens, particularly bacteria, among patients with SARI. Therefore, this study aims to delineate the demographic, epidemiological, and aetiological characteristics of hospitalised SARI patients in Central China between 2018 and 2020. METHODS: Eligible patients with SARI admitted to the First Affiliated Hospital of Zhengzhou University between 1 January 2018 and 31 December 2020 were included in this retrospective study. Within the first 24 h of admission, respiratory (including sputum, nasal/throat swabs, bronchoalveolar lavage fluid, thoracocentesis fluid, etc.), urine, and peripheral blood specimens were collected for viral and bacterial testing. A multiplex real-time polymerase chain reaction (PCR) diagnostic approach was used to identify human influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human bocavirus, human coronavirus, human metapneumovirus, and rhinovirus. Bacterial cultures of respiratory specimens were performed with a particular focus on pathogenic microorganisms, including S. pneumoniae, S. aureus, K. pneumoniae, P. aeruginosa, Strep A, H. influenzae, A. baumannii, and E. coli. In cases where bacterial culture results were negative, nucleic acid extraction was performed for PCR to assay for the above-mentioned eight bacteria, as well as L. pneumophila and M. pneumoniae. Additionally, urine specimens were exclusively used to detect Legionella antigens. Furthermore, epidemiological, demographic, and clinical data were obtained from electronic medical records. RESULTS: The study encompassed 1266 patients, with a mean age of 54 years, among whom 61.6% (780/1266) were males, 61.4% (778/1266) were farmers, and 88.8% (1124/1266) sought medical treatment in 2020. Moreover, 80.3% (1017/1266) were housed in general wards. The most common respiratory symptoms included fever (86.8%, 1122/1266) and cough (77.8%, 986/1266). Chest imaging anomalies were detected in 62.6% (792/1266) of cases, and 58.1% (736/1266) exhibited at least one respiratory pathogen, with 28.5% (361/1266) having multiple infections. Additionally, 95.7% (1212/1266) of the patients were from Henan Province, with the highest proportion (38.3%, 486/1266) falling in the 61-80 years age bracket, predominantly (79.8%, 1010/1266) seeking medical aid in summer and autumn. Bacterial detection rate (39.0%, 495/1266) was higher than viral detection rate (36.9%, 468/1266), with the primary pathogens being influenza virus (13.8%, 175/1266), K. pneumoniae (10.0%, 127/1266), S. pneumoniae (10.0%, 127/1266), adenovirus (8.2%, 105/1266), P. aeruginosa (8.2%, 105/1266), M. pneumoniae (7.8%, 100/1266), and respiratory syncytial virus (7.7%, 98/1266). During spring and winter, there was a significant prevalence of influenza virus and human coronavirus, contrasting with the dominance of parainfluenza viruses in summer and autumn. Respiratory syncytial virus and rhinovirus exhibited higher prevalence across spring, summer, and winter. P. aeruginosa, K. pneumoniae, and M. pneumoniae were identified at similar rates throughout all seasons without distinct spikes in prevalence. However, S. pneumoniae showed a distinctive pattern with a prevalence that doubled during summer and winter. Moreover, the positive detection rates of various other viruses and bacteria were lower, displaying a comparatively erratic prevalence trend. Among patients admitted to the intensive care unit, the predominant nosocomial bacteria were K. pneumoniae (17.2%, 43/249), A. baumannii (13.6%, 34/249), and P. aeruginosa (12.4%, 31/249). Conversely, in patients from general wards, predominant pathogens included influenza virus (14.8%, 151/1017), S. pneumoniae (10.4%, 106/1017), and adenovirus (9.3%, 95/1017). Additionally, paediatric patients exhibited significantly higher positive detection rates for influenza virus (23.9%, 11/46) and M. pneumoniae (32.6%, 15/46) compared to adults and the elderly. Furthermore, adenovirus (10.0%, 67/669) and rhinovirus (6.4%, 43/669) were the primary pathogens in adults, while K. pneumoniae (11.8%, 65/551) and A. baumannii (7.1%, 39/551) prevailed among the elderly, indicating significant differences among the three age groups. DISCUSSION: In Central China, among patients with SARI, the prevailing viruses included influenza virus, adenovirus, and respiratory syncytial virus. Among bacteria, K. pneumoniae, S. pneumoniae, P. aeruginosa, and M. pneumoniae were frequently identified, with multiple infections being very common. Additionally, there were substantial variations in the pathogen spectrum compositions concerning wards and age groups among patients. Consequently, this study holds promise in offering insights to the government for developing strategies aimed at preventing and managing respiratory infectious diseases effectively.

Exploring the link between particulate matter pollution and acute respiratory infection risk in children using generalized estimating equations analysis: a robust statistical approach.

BACKGROUND: India is facing a burdensome public health challenge due to air pollution, with a particularly high burden of acute respiratory infections (ARI) among children. To address this issue, our study aims to evaluate the association between exposure to fine particulate matter (PM2.5) and ARI incidence in young children in India. MATERIALS AND METHODS: Our study used PM2.5 data provided by the Atmospheric Composition Analysis Group at Washington University to assess the association between PM2.5 exposure and ARI incidence in 223,375 children sampled from the 2019-2021 Demographic Health Survey in India. We employed the generalized estimating equation and reported odds ratios and 95% confidence intervals for a 10 µg/m3 increase in PM2.5 and quartiles of PM2.5 exposure. RESULTS: Each 10 µg/m3 increase in PM2.5 levels was associated with an increased odds of ARI (OR: 1.23, 95% CI: 1.19-1.27). A change from the first quartile of PM2.5 (2.5-34.4 µg/m3) to the second quartile (34.5-51.5 µg/m3) of PM2.5 was associated with a two-fold change (OR: 2.06, 95% CI: 1.60-2.66) in the odds of developing ARI. Similarly, comparing the first quartile to the fourth quartile of PM2.5 exposure (78.3-128.9 µg/m3) resulted in an over four-fold increase in the odds of ARI (OR: 4.45, 95% CI: 3.37-5.87). CONCLUSION: Mitigation efforts must be continued implementing higher restrictions in India and to bring new interventions to ensure safe levels of air for reducing the burden of disease and mortality associated with air pollution in India.

Magnitude and determinant of healthcare-seeking behavior for childhood acute respiratory tract infections in Ethiopia: a cross-sectional study.

BACKGROUND: Acute respiratory infections (ARIs) remain a major public health concern which become the leading cause of mortality and morbidity in children under the age of five. A large percentage of childhood deaths and complications can be avoided by seeking proper medical care. Therefore, this study aimed to assess the magnitude, and individual and community-level determinants of mothers' healthcare-seeking behavior for their children under the age of five who had ARI symptoms in Ethiopia. METHOD: A secondary data analysis was conducted using the 2016 Ethiopian Demographic and Health Surveys(EDHS) with a total weighted sample of 643 under-five children who had ARI symptoms within two weeks of the survey. Due to the hierarchical nature of the EDHS data, a multi-level logistic regression model was used to identify the individual and community-level factors influencing mothers' health care-seeking behavior for their children with ARI symptoms. In the multivariable multilevel analysis, those variables with a p-value < 0.05 were considered to be significant predictors of the outcome variable. RESULTS: Healthcare-seeking behavior among mothers or caregivers for children with symptoms of ARIs was 32.61% (95% CI: 29.08-36.33%) in Ethiopia. The ICC in the null model indicated that about 55% of the total variability of treatment-seeking behavior was due to differences between clusters. Child aged > 24 months [AOR = 0.35; 0.19-0.63], having primary education [AOR = 3.25; 1.27-8.32], being media exposed [AOR = 2.49; 1.15, 5.38], female household head[AOR = 3.90; 1.35, 11.24], and delivery at health institution[AOR = 2.24; 1.00, 5.01] were significant predictors of health care seeking behavior of mother for their children with ARI symptoms. CONCLUSION: There is poor treatment-seeking behavior for children with symptoms of ARI in Ethiopia with significant community level variations. The multilevel logistic regression analysis showed that improving mothers' education, women's empowerment, facilitating institutional delivery and media accessibility are critical to promoting health-seeking behaviors among mothers or caregivers of under-five children with ARI symptoms. Hence, concerned bodies should design targeted interventions that increase mothers' or caregivers' treatment-seeking behavior for childhood ARI to reduce child morbidity and mortality.

Atypical age distribution and high disease severity in children with RSV infections during two irregular epidemic seasons throughout the COVID-19 pandemic, Germany, 2021 to 2023.

BackgroundNon-pharmaceutical interventions (NPIs) during the COVID-19 pandemic affected respiratory syncytial virus (RSV) circulation worldwide.AimTo describe, for children aged < 5 years, the 2021 and 2022/23 RSV seasons in Germany.MethodsThrough data and 16,754 specimens from outpatient sentinel surveillance, we investigated RSV seasonality, circulating lineages, and affected children's age distributions in 2021 and 2022/23. Available information about disease severity from hospital surveillance was analysed for patients with RSV-specific diagnosis codes (n = 13,104). Differences between RSV seasons were assessed by chi-squared test and age distributions trends by Mann-Kendall test.ResultsRSV seasonality was irregular in 2021 (weeks 35-50) and 2022/23 (weeks 41-3) compared to pre-COVID-19 2011/12-2019/20 seasons (median weeks 51-12). RSV positivity rates (RSV-PR) were higher in 2021 (40% (522/1,291); p < 0.001) and 2022/23 (30% (299/990); p = 0.005) than in prior seasons (26% (1,430/5,511)). Known globally circulating RSV-A (lineages GA2.3.5 and GA2.3.6b) and RSV-B (lineage GB5.0.5a) strains, respectively, dominated in 2021 and 2022/23. In 2021, RSV-PRs were similar in 1 - < 2, 2 - < 3, 3 - < 4, and 4 - < 5-year-olds. RSV hospitalisation incidence in 2021 (1,114/100,000, p < 0.001) and in 2022/23 (1,034/100,000, p < 0.001) was approximately double that of previous seasons' average (2014/15-2019/20: 584/100,000). In 2022/23, proportions of RSV patients admitted to intensive care units rose (8.5% (206/2,413)) relative to pre-COVID-19 seasons (6.8% (551/8,114); p = 0.004), as did those needing ventilator support (6.1% (146/2,413) vs 3.8% (310/8,114); p < 0.001).ConclusionsHigh RSV-infection risk in 2-4-year-olds in 2021 and increased disease severity in 2022/23 possibly result from lower baseline population immunity, after NPIs diminished exposure to RSV.

Use of proxy indicators for automated surveillance of severe acute respiratory infection, the Netherlands, 2017 to 2023: a proof-of-concept study.

BackgroundEffective pandemic preparedness requires robust severe acute respiratory infection (SARI) surveillance. However, identifying SARI patients based on symptoms is time-consuming. Using the number of reverse transcription (RT)-PCR tests or contact and droplet precaution labels as a proxy for SARI could accurately reflect the epidemiology of patients presenting with SARI.AimWe aimed to compare the number of RT-PCR tests, contact and droplet precaution labels and SARI-related International Classification of Disease (ICD)-10 codes and evaluate their use as surveillance indicators.MethodsPatients from all age groups hospitalised at Leiden University Medical Center between 1 January 2017 up to and including 30 April 2023 were eligible for inclusion. We used a clinical data collection tool to extract data from electronic medical records. For each surveillance indicator, we plotted the absolute count for each week, the incidence proportion per week and the correlation between the three surveillance indicators.ResultsWe included 117,404 hospital admissions. The three surveillance indicators generally followed a similar pattern before and during the COVID-19 pandemic. The correlation was highest between contact and droplet precaution labels and ICD-10 diagnostic codes (Pearson correlation coefficient: 0.84). There was a strong increase in the number of RT-PCR tests after the start of the COVID-19 pandemic.DiscussionAll three surveillance indicators have advantages and disadvantages. ICD-10 diagnostic codes are suitable but are subject to reporting delays. Contact and droplet precaution labels are a feasible option for automated SARI surveillance, since these reflect trends in SARI incidence and may be available real-time.

Real-time investigation of an influenza A(H3N2) virus outbreak in a refugee community, November 2022.

OBJECTIVES: To report epidemiological and virological results of an outbreak investigation of influenza-like illness (ILI) among refugees in Northern Italy. STUDY DESIGN: Outbreak investigation of ILI cases observed among nearly 100 refugees in Northern Italy unvaccinated for influenza. METHODS: An epidemiological investigation matched with a differential diagnosis was carried out for each sample collected from ILI cases to identify 10 viral pathogens (SARS-CoV-2, influenza virus type A and B, respiratory syncytial virus, metapneumovirus, parainfluenza viruses, rhinovirus, enterovirus, parechovirus, and adenovirus) by using specific real-time PCR assays according to the Centers for Disease Control and Prevention (CDC) protocols. In cases where the influenza virus type was identified, complete hemagglutinin (HA) gene sequencing and the related phylogenetic analysis were conducted. RESULTS: The outbreak was caused by influenza A(H3N2): the attack rate was 83.3% in children aged 9-14 years, 84.6% in those aged 15-24 years, and 28.6% in adults ≥25 years. Phylogenetic analyses uncovered that A(H3N2) strains were closely related since they segregated in the same cluster, showing both a high mean nucleotide identity (100%), all belonging to the genetic sub-group 3C.2a1b.2a.2, as those mainly circulating into the general population in the same period. CONCLUSIONS: The fact that influenza outbreak strains as well as the community strains were genetically related to the seasonal vaccine strain suggests that if an influenza prevention by vaccination strategy had been implemented, a lower attack rate of A(H3N2) and ILI cases might have been achieved.

SARS-CoV-2 infection decreases cardiorespiratory fitness and time-trial performance even two months after returning to regular training - Insights from a longitudinal case series of well-trained kayak athletes.

Objective: The aims of this study were to examine the effect of SARS-CoV-2 infection on cardiorespiratory fitness (CRF) and time-trial performance in vaccinated well-trained young kayak athletes. Methods: This is a longitudinal observational study. Sixteen (7 male, 9 female) vaccinated kayakers underwent body composition assessment, maximal graded exercise test, and 1000-m time-trial tests 21.9 ± 1.7 days before and 66.0 ± 2.2 days after the SARS-CoV-2 infection. The perception of training load was quantified with Borg's CR-10 scale before and after the infection return to sport period. Results: There were significant decreases in peak oxygen uptake (-9.7 %; effect size [ES] = 1.38), peak oxygen pulse (-5.7 %; ES = 0.96), and peak heart rate (-1.9 %; ES = 0.61). Peak minute ventilation, and minute ventilation/carbon dioxide production slope were unchanged after infection compared to the pre-infection values. In the entire 1000-m, the impaired tendencies were found in completion time, mean power, and mean speed (-2.4 to 1.2 %; small ESs = -0.40 to 0.47) as well as significant changes in stroke rate and stroke length (-4.5 to 3.7 %; ESs = -0.60 to 0.73). Conclusion: SARS-CoV-2 infection decreased CRF and time-trial performance even two months after return to regular training in vaccinated athletes.

The Influence of Rapid Influenza Diagnostic Testing on Clinician Decision-Making for Patients With Acute Respiratory Infection in Urgent Care.

BACKGROUND: The potential benefits of using rapid influenza diagnostic tests (RIDTs) in urgent care facilities for clinical care and prescribing practices are understudied. We compared antiviral and antibiotic prescribing, imaging, and laboratory ordering in clinical encounters with and without RIDT results. METHODS: We compared patients with acute respiratory infection (ARI) symptoms who received an RIDT and patients who did not at 2 urgent care facilities. Primary analysis using 1-to-1 exact matching resulted in 1145 matched pairs to which McNemar 2 × 2 tests were used to assess the association between the likelihood of prescribing, imaging/laboratory ordering, and RIDT use. Secondary analysis compared the same outcomes using logistic regression among the RIDT-tested population between participants who tested negative (RIDT(-)) and positive (RIDT(+)). RESULTS: Primary analysis revealed that compared to the non-RIDT-tested population, RIDT(+) patients were more likely to be prescribed antivirals (OR, 10.23; 95% CI, 5.78-19.72) and less likely to be prescribed antibiotics (OR, 0.15; 95% CI, .08-.27). Comparing RIDT-tested to non-RIDT-tested participants, RIDT use increased antiviral prescribing odds (OR, 3.07; 95% CI, 2.25-4.26) and reduced antibiotic prescribing odds (OR, 0.52; 95% CI, .43-.63). Secondary analysis identified increased odds of prescribing antivirals (OR, 28.21; 95% CI, 18.15-43.86) and decreased odds of prescribing antibiotics (OR, 0.20; 95% CI, .13-.30) for RIDT(+) participants compared with RIDT(-). CONCLUSIONS: Use of RIDTs in patients presenting with ARI symptoms influences clinician diagnostic and treatment decision-making, which could lead to improved patient outcomes, population-level reductions in influenza burden, and a decreased threat of antibiotic resistance.

Viruses responsible for acute respiratory infections before (2016-2019) and during (2021) circulation of the SARS-CoV-2 virus in pediatric patients in a reference center at Barranquilla Colombia: A pattern analysis.

OBJECTIVE: To evaluate the behavior of the viruses responsible for acute respiratory infections before (2016-2019) and after (2020-2021) the start of the circulation of the SARS-CoV-2 virus in pediatric patients treated at a reference center from Barranquilla, Colombia. MATERIALS AND METHODS: A descriptive observational study was carried out, and data were obtained by reviewing the influenza-like illness and severe acute respiratory infection database in the pediatric population of the sentinel surveillance reference center in the district of Barranquilla during the years 2016-2021, applying inclusion and exclusion criteria. RESULTS: During 2016-2019, the average age of individuals was 1.3 (±1.7) years, during 2021, it was 2.3 (±3.5) years. The distribution by sex was similar, predominantly male. August and February were the months with the highest record of symptoms for 2016-2019 and 2021, respectively, the most frequent being cough, fever, shortness of breath, and diarrhea. By 2021 there was a higher use of antibiotics and antivirals reported than in 2016-2019. Most patients tested negative for viral detection. When comparing the percentage of viruses detected by age group and years of detection, positivity was lower in 2021 by every age group, and respiratory syncytial virus (RSV) was the most frequently detected. CONCLUSIONS: There was less virus positivity in viral detection tests in the pediatric population in 2021. RSV persists as the main etiology affecting this population, especially infants. The use of antibiotic therapy in viral infections continues to be a problematic practice in their management. Sentinel surveillance can be strengthened throughout the country.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Continuous evolution and emerging lineage of seasonal human coronaviruses: A multicenter surveillance study.

The seasonal human coronaviruses (HCoVs) have zoonotic origins, repeated infections, and global transmission. The objectives of this study are to elaborate the epidemiological and evolutionary characteristics of HCoVs from patients with acute respiratory illness. We conducted a multicenter surveillance at 36 sentinel hospitals of Beijing Metropolis, China, during 2016-2019. Patients with influenza-like illness (ILI) and severe acute respiratory infection (SARI) were included, and submitted respiratory samples for screening HCoVs by multiplex real-time reverse transcription-polymerase chain reaction assays. All the positive samples were used for metatranscriptomic sequencing to get whole genomes of HCoVs for genetical and evolutionary analyses. Totally, 321 of 15 677 patients with ILI or SARI were found to be positive for HCoVs, with an infection rate of 2.0% (95% confidence interval, 1.8%-2.3%). HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1 infections accounted for 18.7%, 38.3%, 40.5%, and 2.5%, respectively. In comparison to ILI cases, SARI cases were significantly older, more likely caused by HCoV-229E and HCoV-OC43, and more often co-infected with other respiratory pathogens. A total of 179 full genome sequences of HCoVs were obtained from 321 positive patients. The phylogenetical analyses revealed that HCoV-229E, HCoV-NL63 and HCoV-OC43 continuously yielded novel lineages, respectively. The nonsynonymous to synonymous ratio of all key genes in each HCoV was less than one, indicating that all four HCoVs were under negative selection pressure. Multiple substitution modes were observed in spike glycoprotein among the four HCoVs. Our findings highlight the importance of enhancing surveillance on HCoVs, and imply that more variants might occur in the future.

Surveillance, isolation and genomic characterization of Pteropine orthoreovirus of probable bat origin among patients with acute respiratory infection in Malaysia.

Pteropine orthoreovirus (PRV), an emerging bat-borne virus, has been linked to cases of acute respiratory infections (ARI) in humans. The prevalence, epidemiology and genomic diversity of PRV among ARI of unknown origin were studied. Among 632 urban outpatients tested negative for all known respiratory viruses, 2.2% were PRV-positive. Patients mainly presented with moderate to severe forms of cough, sore throat and muscle ache, but rarely with fever. Phylogenetic analysis revealed that over 90% of patients infected with the Melaka virus (MelV)-like PRV, while one patient infected with the Pulau virus previously found only in fruit bats. Human oral keratinocytes and nasopharyngeal epithelial cells were susceptible to clinical isolates of PRV, including the newly isolated MelV-like 12MYKLU1034. Whole genome sequence of 12MYKLU1034 using Nanopore technique revealed a novel reassortant strain. Evolutionary analysis of the global PRV strains suggests the continuous evolution of PRV through genetic reassortment among PRV strains circulating in human, bats and non-human primate hosts, creating a spectrum of reassortant lineages with complex evolutionary characteristics. In summary, the role of PRV as a common etiologic agent of ARI is evident. Continuous monitoring of PRV prevalence, pathogenicity and diversity among human and animal hosts is important to trace the emergence of novel reassortants.

Used paper tissues for pathogen identification in acute respiratory infection.

During the Belgian winter and spring season 2022-2023, we investigated the potential of used paper tissue (UPT) as a noninvasive sampling method for the diagnosis of acute respiratory infections. Screening for respiratory pathogens was done using an in-house developed respiratory panel for simultaneous detection of 22 respiratory viruses and seven nonviral pathogens. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. Pathogens that were identified in nasal swabs could also be detected in concurrent UPT from the same patient. In all cases that tested positive on an antigen-detection rapid diagnostic test, the corresponding virus could be detected in UPT. The collection of UPT could be useful in epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 and other coronaviruses, as well as other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses including EV-D68, parainfluenzaviruses, and Streptococcus pneumoniae. Multiple respiratory pathogens could be detected in UPTs of collectivities, confirming its applicability for community testing. This is especially interesting for screening in nursing homes, centers for the disabled, schools or other settings were taking nasal or nasopharyngeal samples is cumbersome.

Epidemiology and clinical severity of the serotypes of human parainfluenza virus in children with acute respiratory infection.

BACKGROUND: Acute respiratory infections (ARI) are a threat to human health and survival, resulting in many paediatric hospitalisations. However, the epidemiological and clinical severity characteristics of the human parainfluenza virus (PIV), one of the most prevalent respiratory viruses, are not well understood in children. METHODS: To identify the epidemiological features of PIV infection, in 2019, hospitalised children with ARI were screened using multiplex polymerase chain reaction (PCR) for PIV and 10 other common respiratory pathogens. Subtyping of randomly selected PIV-positive samples was performed using reverse transcription-PCR. Demographics, epidemiology, clinical manifestations, diagnosis, and outcomes were compared between PIV subtypes. RESULTS: The annual detection rate for PIV was 14.9%, with a peak from April to September. Children under one year of age had the highest rate of PIV infection (45.5%) compared to other age groups. Of the 121 sequenced samples, 58.7%, 36.4% and 4.9% were positive for PIV-3, PIV-1 and PIV-2, respectively, and no PIV-4 was detected. Severe infections were associated with pre-existing underlying diseases and co-infections, but not with PIV serotype. After excluding cases of co-infection, we found that PIV-2 infection was associated with upper respiratory tract infections, whereas PIV-1 and PIV-3 mainly caused lower respiratory tract infections. Apart from the proportion of patients with fever, there were no significant differences among the three subtypes in terms of clinical symptoms, severity, and outcome. CONCLUSION: Here, PIV was the main pathogen causing ARI in hospitalised children. Appropriate attention should be paid to children with underlying diseases and co-infections to prevent the worsening of severe PIV infection.