Etiologies of severe acute respiratory infection (SARI) and misdiagnosis of influenza in Indonesia, 2013-2016

Molecular detection and genotyping of HMPV in patients with severe acute respiratory infection in India

BACKGROUND

Human metapneumovirus (HMPV) is a common respiratory pathogen that causes respiratory tract infections. In India, HMPV has been identified as one of the leading causes of morbidity and mortality in infants and young children with respiratory tract infections. The most reported sublineages of HMPV in India are B1, B2, A2b and A2c.

OBJECTIVE

A retrospective study was conducted to determine the circulating genotypes of HMPV among SARI cases from January 2016 to December 2018.

MATERIALS AND METHODS

Positive throat swab samples were confirmed with real-time RT-PCR. Subsequently, these samples were analysed using semi-nested conventional RT-PCR targeting the G gene, followed by sequencing and phylogenetic analysis. Clinical data analysis was also performed using SPSS 15.0 software.

RESULTS

All 20 samples from the SARI cases were classified under the A2c sublineage of HMPV. Phylogenetic analysis indicated that these strains were genetically related to those circulating in Japan, China, and Croatia. Among the samples, ten showed 111-nucleotide duplications, while the other ten had 180-nucleotide duplications.

CONCLUSION

Clinical analysis showed that four cases had coinfections with other pathogens. Our extensive analysis of patient samples determined that HMPV, especially the A2c genotype, significantly contributed to SARI cases within our study population, which signifies the importance of considering HMPV as a probable aetiological agent when investigating SARI outbreaks.

Demystifying roles of exercise in immune response regulation against acute respiratory infections: A narrative review

The benefits of physical activity and exercise, especially those classified as moderate-to-vigorous activity (MVPA), have been well-established in preventing non-communicable diseases and mental health problems in healthy adults. However, the relationship between physical activity and exercise and the prevention and management of acute respiratory infection (ARI), a global high-burden disease, has been inconclusive. There have been debates and disagreements among scientific publications regarding the relationship between exercise and immune response against the causative agents of ARI. This narrative review aims to explore the theory that sufficiently explains the correlation between exercise, immune response, and ARI. The potential root causes of discrepancies come from research associated with the "open window" hypothesis. The studies have several limitations, and future improvements to address them are urgently needed in the study design, data collection, exercise intervention, subject recruitment, biomarkers for infection and inflammation, nutritional and metabolism status, and in addressing confounding variables. In conclusion, data support the clinical advantages of exercise have a regulatory contribution toward improving the immune response, which in turn potentially protects humans fromARI. However, the hypothesis related to its negative effect must be adopted cautiously.

Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses

IMPORTANCE

Since the pandemic of coronavirus diseases 2019, the use of real-time PCR assay has become widespread among people who were not familiar with it in virus detection. As a result, whether a high real-time PCR value in one time test indicates virus transmissibly became a complicated social problem, regardless of the difference in assays and/or amplification conditions, the time and number of diagnostic test during the time course of infection. In addition, the multiple positives in the test of respiratory viruses further add to the confusion in the interpretation of the infection. To address this issue, we performed virus isolation using pediatric SARI (severe acute respiratory infections) specimens on air-liquid interface culture of human bronchial/tracheal epithelial cell culture. The result of this study can be a strong evidence that the specimens showing positivity for multiple agents in real-time PCR tests possibly contain infectious viruses.

Assessment of post-COVID-19 fatigue among female survivors 2 years after hospital discharge: a nested case-control study

BACKGROUND

Fatigue is a common symptom of long COVID syndrome. Compared to male survivors, females have a higher incidence of post-COVID fatigue. Therefore, long-term follow-up is necessary to understand which groups of females are more vulnerable to post-COVID fatigue.

METHODS

This is a nested case-control study of female COVID-19 survivors who were discharged from two designated hospitals in Wuhan, China in 2020, and received 2-year follow-up from March 1 to April 6, 2022. All patients completed the Checklist Individual Strength-subscale subjective fatigue (CIS-fatigue), a chronic obstructive pulmonary disease (COPD) assessment test (CAT), and the Hospital Anxiety and Depression Scale (HADS; including the HADS-Anxiety [HADS-A] and the HADS-Depression [HADS-D]). Individuals with CIS-fatigue scores of 27 or higher were classified as cases. The risk factors for fatigue was analysed with multivariable logistic regression analysis.

RESULTS

A total of 899 female COVID-19 survivors were enrolled for analysis, including 47 cases and 852 controls. Compared with controls, cases had higher CAT, HADS-A and HADS-D scores, and showed a higher prevalence of symptoms, including anxiety (cases vs. controls, 44.7% vs. 4.0%, p < 0.001), chest tightness (21.2% vs. 2.3%, p < 0.001), dyspnoea (19.1% vs. 0.8%, p < 0.001) and so on. In multivariable logistic regression analysis, age (OR, 1.03; 95% CI, 1.01-1.06; p = 0.02) and cerebrovascular disease (OR, 11.32; 95% CI, 2.87-43.00; p < 0.001) were risk factors for fatigue. Fatigue had a statistically significant moderate correlation with depression (r = 0.44, p < 0.001), but not with CAT ≥ 10.

CONCLUSION

Female COVID-19 patients who had cerebrovascular disease and older age have higher risk of fatigue. Patients with fatigue have higher CAT scores, and are more likely to have concurrent depression.

Impact of PM2.5 and ozone on incidence of influenza in Shijiazhuang, China: a time-series study

Most of the studies are focused on influenza and meteorological factors for influenza. There are still few studies focused on the relationship between pollution factors and influenza, and the results are not consistent. This study conducted distributed lag nonlinear model and attributable risk on the relationship between influenza and pollution factors, aiming to quantify the association and provide a basis for the prevention of influenza and the formulation of relevant policies. Environmental data in Shijiazhuang from 2014 to 2019, as well as the data on hospital-confirmed influenza, were collected. When the concentration of PM_2.5 was the highest (621 μg/m³), the relative risk was the highest (RR: 2.39, 95% CI: 1.10-5.17). For extremely high concentration PM_2.5 (348 μg/m³), analysis of cumulative lag effect showed statistical significance from cumulative lag0-1 to lag0-6 day, and the minimum cumulative lag effect appeared in lag0-2 (RR: 0.760, 95% CI: 0.655-0.882). In terms of ozone, the RR value was 2.28(1.19,4.38), when O₃ concentration was 310 μg/m³, and the RR was 1.65(1.26,2.15), when O₃ concentration was 0 μg/m³. The RR of this lag effect increased with the increase of lag days, and reached the maximum at lag0-7 days, RR and 95% CI of slightly low concentration and extremely high concentration were 1.217(1.108,1.337) and 1.440(1.012,2.047), respectively. Stratified analysis showed that there was little difference in gender, but in different age groups, the cumulative lag effect of these two pollutants on influenza was significantly different. Our study found a non-linear relationship between two pollutants and influenza; slightly low concentrations were more associated with contaminant-related influenza. Health workers should encourage patients to get the influenza vaccine and wear masks when going out during flu seasons.

Influenza incidence and air pollution: Findings from a four-year surveillance study of prefecture-level cities in China

Background

Influenza is a serious public health problem, and its prevalence and spread show significant spatiotemporal characteristics. Previous studies have found that air pollutants are linked to an increased risk of influenza. However, the mechanism of influence and the degree of their association have not been determined. This study aimed to determine the influence of the air environment on the spatiotemporal distribution of influenza.

Methods

The kernel density estimation and Getis-Ord Gi * statistic were used to analyze the spatial distribution of the influenza incidence and air pollutants in China. A simple analysis of the correlation between influenza and air pollutants was performed using Spearman's correlation coefficients. A linear regression analysis was performed to examine changes in the influenza incidence in response to air pollutants. The sensitivity of the influenza incidence to changes in air pollutants was evaluated by performing a gray correlation analysis. Lastly, the entropy weight method was used to calculate the weight coefficient of each method and thus the comprehensive sensitivity of influenza incidence to six pollution elements.

Results

The results of the sensitivity analysis using Spearman's correlation coefficients showed the following ranking of the contributions of the air pollutants to the influenza incidence in descending order: SO2 >NO2 >CO> PM2.5 >O3 >PM10. The sensitivity results obtained from the linear regression analysis revealed the following ranking: CO>NO2 >SO2 >O3 >PM2.5 >PM10. Lastly, the sensitivity results obtained from the gray correlation analysis showed the following ranking: NO2 >CO>PM10 >PM2.5 >SO2 >O3. According to the sensitivity score, the study area can be divided into hypersensitive, medium-sensitive, and low-sensitive areas.

Conclusion

The influenza incidence showed a strong spatial correlation and associated sensitivity to changes in concentrations of air pollutants. Hypersensitive areas were mainly located in the southeastern part of northeastern China, the coastal areas of the Yellow River Basin, the Beijing-Tianjin-Hebei region and surrounding areas, and the Yangtze River Delta. The influenza incidence was most sensitive to CO, NO2, and SO2, with the occurrence of influenza being most likely in areas with elevated concentrations of these three pollutants. Therefore, the formulation of targeted influenza prevention and control strategies tailored for hypersensitive, medium-sensitive, low-sensitive, and insensitive areas are urgently needed.

Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period

Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae, Paramoxyviridae, Pneumoviridae, Picobirnaviridae, Totiviridae, and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.

Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Pathogen interference is the ability of one pathogen to alter the course and clinical outcomes of infection by another. With up to 3000 species of human pathogens the potential combinations are vast. These combinations operate within further immune complexity induced by infection with multiple persistent pathogens, and by the role which the human microbiome plays in maintaining health, immune function, and resistance to infection. All the above are further complicated by malnutrition in children and the elderly. Influenza vaccination offers a measure of protection for elderly individuals subsequently infected with influenza. However, all vaccines induce both specific and non-specific effects. The specific effects involve stimulation of humoral and cellular immunity, while the nonspecific effects are far more nuanced including changes in gene expression patterns and production of small RNAs which contribute to pathogen interference. Little is known about the outcomes of vaccinated elderly not subsequently infected with influenza but infected with multiple other non-influenza winter pathogens. In this review we propose that in certain years the specific antigen mix in the seasonal influenza vaccine inadvertently increases the risk of infection from other non-influenza pathogens. The possibility that vaccination could upset the pathogen balance, and that the timing of vaccination relative to the pathogen balance was critical to success, was proposed in 2010 but was seemingly ignored. Persons vaccinated early in the winter are more likely to experience higher pathogen interference. Implications to the estimation of vaccine effectiveness and influenza deaths are discussed.

Aetiology of childhood pneumonia in low- and middle-income countries in the era of vaccination: a systematic review

Background

This systematic review aimed to describe common aetiologies of severe and non-severe community acquired pneumonia among children aged 1 month to 9 years in low- and middle-income countries.

Methods

We searched the MEDLINE, EMBASE, and PubMed online databases for studies published from January 2010 to August 30, 2020. We included studies on acute community-acquired pneumonia or acute lower respiratory tract infection with ≥1 year of continuous data collection; clear consistent case definition for pneumonia; >1 specimen type (except empyema studies where only pleural fluid was required); testing for >1 pathogen including both viruses and bacteria. Two researchers reviewed the studies independently. Results were presented as a narrative summary. Quality of evidence was assessed with the Quality Assessment Tool for Quantitative Studies. The study was registered on PROSPERO [CRD42020206830].

Results

We screened 5184 records; 1305 duplicates were removed. The remaining 3879 titles and abstracts were screened. Of these, 557 articles were identified for full-text review, and 55 met the inclusion criteria - 10 case-control studies, three post-mortem studies, 11 surveillance studies, eight cohort studies, five cross-sectional studies, 12 studies with another design and six studies that included patients with pleural effusions or empyema. Studies which described disease by severity showed higher bacterial detection (Streptococcus pneumoniae, Staphylococcus aureus) in severe vs non-severe cases. The most common virus causing severe disease was respiratory syncytial virus (RSV). Pathogens varied by age, with RSV and adenovirus more common in younger children. Influenza and atypical bacteria were more common in children 5-14 years than younger children. Malnourished and HIV-infected children had higher rates of pneumonia due to bacteria or tuberculosis.

Conclusions

Several viral and bacterial pathogens were identified as important targets for prevention and treatment. Bacterial pathogens remain an important cause of moderate to severe disease, particularly in children with comorbidities despite widespread PCV and Hib vaccination.

Epidemiology of community-acquired pneumonia among hospitalised children in Indonesia: a multicentre, prospective study

OBJECTIVE

To identify aetiologies of childhood community-acquired pneumonia (CAP) based on a comprehensive diagnostic approach.

DESIGN

'Partnerships for Enhanced Engagement in Research-Pneumonia in Paediatrics (PEER-PePPeS)' study was an observational prospective cohort study conducted from July 2017 to September 2019.

SETTING

Government referral teaching hospitals and satellite sites in three cities in Indonesia: Semarang, Yogyakarta and Tangerang.

PARTICIPANTS

Hospitalised children aged 2-59 months who met the criteria for pneumonia were eligible. Children were excluded if they had been hospitalised for >24 hours; had malignancy or history of malignancy; a history of long-term (>2 months) steroid therapy, or conditions that might interfere with compliance with study procedures.

MAIN OUTCOMES MEASURES

Causative bacterial, viral or mixed pathogen(s) for pneumonia were determined using microbiological, molecular and serological tests from routinely collected specimens (blood, sputum and nasopharyngeal swabs). We applied a previously published algorithm (PEER-PePPeS rules) to determine the causative pathogen(s).

RESULTS

188 subjects were enrolled. Based on our algorithm, 48 (25.5%) had a bacterial infection, 31 (16.5%) had a viral infection, 76 (40.4%) had mixed bacterial and viral infections, and 33 (17.6%) were unable to be classified. The five most common causative pathogens identified were Haemophilus influenzae non-type B (N=73, 38.8%), respiratory syncytial virus (RSV) (N=51, 27.1%), Klebsiella pneumoniae (N=43, 22.9%), Streptococcus pneumoniae (N=29, 15.4%) and Influenza virus (N=25, 13.3%). RSV and influenza virus diagnoses were highly associated with Indonesia's rainy season (November-March). The PCR assays on induced sputum (IS) specimens captured most of the pathogens identified in this study.

CONCLUSIONS

Our study found that H. influenzae non-type B and RSV were the most frequently identified pathogens causing hospitalised CAP among Indonesian children aged 2-59 months old. Our study also highlights the importance of PCR for diagnosis and by extension, appropriate use of antimicrobials.

TRAIL REGISTRATION NUMBER

NCT03366454.

Co-infection of SARS-CoV-2 with other viral respiratory pathogens in Yogyakarta, Indonesia: A cross-sectional study

Background

Growing evidence shows that viral co-infection is found repeatedly in patients with Coronavirus Disease–2019 (COVID-19). This is the first report of SARS-CoV-2 co-infection with viral respiratory pathogens in Indonesia.

Methods

Over a one month period of April to May 2020, SARS-CoV-2 positive nasopharyngeal swabs in our COVID-19 referral laboratory in Yogyakarta, Indonesia, were tested for viral respiratory pathogens by real-time, reverse transcription polymerase chain reaction (RT-PCR). Proportion of co-infection reported in percentage.

Results

Fifty-nine samples were positive for other viral respiratory pathogens among a total of 125 samples. Influenza A virus was detected in 32 samples, Influenza B in 16 samples, Human metapneumovirus in 1 sample, and adenovirus in 10 samples. We did not detect any co-infection with respiratory syncytial virus. Nine (7.2%) patients had co-infection with more than two viruses.

Conclusion

Viral co-infection with SARS-CoV-2 is common. These results will provide a helpful reference for diagnosis and clinical treatment of patients with COVID-19.

•

Viral co-infection with SARS-CoV-2 is common.

•

Co-infection by two viral respiratory pathogens is prevalent.

•

Pandemic transmission control may also impact in other viral respiratory infections.

•

Early identification of co-infection is necessary, given differences in treatment.

•

Simple laboratory diagnosis algorithm may be applied to screen viral co-infection.

Spatio-temporal Differentiation in the Incidence of Influenza and Its Relationship with Air Pollution in China from 2004 to 2017

The Healthy China Initiative is a major health strategy being pursued by the country. To prevent and control different types of diseases as well as their complex variants, research on the spatio-temporal differentiation among and mechanisms of influence of epidemic diseases is growing worldwide. This study analyzed monthly data on the incidence of influenza by using different methods, including Moran's I, the hotspot analysis model, concentration analysis, and correlation analysis, to determine the characteristics of spatio-temporal differentiation in the incidence of influenza across prefecture-level cities in China from 2004 to 2017, and to examine its relationship with air pollution. According to the results, the overall incidence of influenza in China exhibited a trend of increase from 2004 to 2017, with small peaks in 2009 and 2014. More cases of influenza were recorded in the first and fourth quarters of each year. Regions with higher incidences of influenza were concentrated in northwestern and northern China, and in the coastal areas of southeastern China. Over time, the distribution of regions with a higher incidence of influenza has shifted from the west to the east of the country. A significant relationship was observed between the incidence of influenza and factors related to air pollution. The contents of five air pollutants (PM2.5, PM10, SO2, NO2, and CO) were significantly positively correlated with the incidence of influenza, with a decreasing order of contribution to it of SO2 > CO > NO2 > PM2.5 > PM10. The content of O3 in the air was negatively correlated with the incidence of influenza. The influence of air pollution-related factors on the incidence of influenza in different regions and seasons showed minor differences. The large-scale empirical results provided here can supply a scientific basis for governmental disease control authorities to formulate strategies for regional prevention and control.