Prevalence and Seasonal Distribution of Respiratory Viruses During the 2014 - 2015 Season in Istanbul

The impact of the COVID-19 pandemic on the circulation, seasonal distribution, and research of other respiratory pathogens in Turkey

INTRODUCTION

Respiratory infections are one of the world's most common infectious diseases. Following the species, numbers, and seasonal distribution of acute respiratory agents is important for the protection of public health. Our study aimed to determine the effect of the COVID-19 pandemic on the circulation and seasonal distribution of non-SARS-CoV-2 respiratory tract agents and research on non-SARS-CoV-2 agents.

METHODS

The results of the Multiplex PCR respiratory panel of 3702 nasopharyngeal swab samples sent between January 2018 and December 2021 were evaluated retrospectively. Scientific articles on acute respiratory infections between 2010 and 2021 from Turkey were analyzed in Scopus for bibliometric analysis.

RESULTS

1.382 pathogens were detected. During the pandemic, the number of non-SARS-CoV-2 pathogens was found to be statistically significantly lower than before the pandemic. It was determined that while the most frequent agent before the pandemic was the Adenovirus, the most frequent agent was the RSV-A during the pandemic. Our network analysis of keywords indicated that academic interest in 2020-21 was directed toward COVID-19, which coincides with the pandemic period.

CONCLUSIONS

Our study determined the fact that the incidence, species, and seasonal distribution of non-SARS-COV-2 respiratory agents changed after the onset of the pandemic. Increasing the identification and following-up of these pathogens in health organizations and also presenting these data to literature and sharing with academics is important. We are of the opinion that the results of our study shall shed light on the epidemiology of changing respiratory infections and the prevention and following-up of future health problems.

Prevalence of Influenza Viruses A and B, Adenovirus, Respiratory Syncytial Virus, and Human Metapneumonia Viruses among Children with Acute Respiratory Tract Infection

Background

Acute respiratory tract infection (ARTI) is a significant cause of morbidity and mortality among children worldwide. The majority of acute respiratory infections in children are caused by viruses, with respiratory syncytial virus (RSV) being the most frequently encountered. Other important viral pathogens include human metapneumovirus, human coronaviruses, adenovirus, and influenza. These infections can lead to complications such as bronchitis and pneumonia. So, this study aimed to evaluate the prevalence of influenza viruses A and B, adenovirus, respiratory syncytial virus (RSV), and human metapneumovirus (HMPV) in children with ARTI.

Methods

The molecular diagnostic of polymerase chain reaction approach was used to detect influenza (A and B), metapneumovirus, respiratory syncytial virus (RSV), and adenovirus in respiratory samples of children with acute respiratory infection hospitalization in a teaching hospital of the Shiraz University of Medical Sciences in January 2016-March 2017.

Results

Of the 340 patients examined, 208 (61.20%) were male and the median age was 3.13 ± 2.38 years. Respiratory viruses were found in 179 (52.64%) patients. The male-to-female ratio was 1.63 : 1 in patients who were viral positive. Detection rates for influenza A, adenovirus, influenza B, RSV, and HMPV were 28.23%, 24.70%, 8.52%, 3.23%, and 2.64%, respectively, and coinfections were detected in 24.02%. The most common combination of two-virus coinfections was IFVA/AdV, followed by IFVB/AdV, AdV, IFVB/IFVA, RSV/IFVA, HMPV/AdV, RSV/AdV, and HMPV/IFVA.

Conclusion

The high prevalence of respiratory viruses in children hospitalized with ARTI suggests that viral infection may play a role in disease pathogenesis. This should be confirmed through the conduct of case-control studies and may inform the role of vaccination to prevent respiratory viral infections.

Prevalence of Common Human Coronaviruses (NL63, 229E, and OC43) in Adults before the COVID-19 Pandemic: a Single-Center Study from Turkey, 2015-2020

Common Human Coronaviruses (HCoVs), such as NL63, HKU1, 229E, and OC43, induce respiratory tract infections worldwide. Epidemiological studies of HCoVs are of paramount importance because the disease burden and trajectory (in years) have not been well addressed in adults. Here, we aimed to describe the burden of HCoVs in a hospital setting over five years before the coronavirus disease 2019 pandemic. This was a retrospective study of patients (>18 years) between January 1, 2015, and January 1, 2020, whose respiratory specimens were tested by multiplex real-time polymerase chain reaction. In total, 7,861 respiratory samples (4,540 patients) were included, 38% of which tested positive for any respiratory virus. Of these, 212 (12.2%) samples were positive for HCoVs, and their co-infection with other respiratory viruses was 30.6%. Rhinovirus (27.6%) was the most common co-infection among all three HCoVs. The overall prevalence of HCoVs tended to be the highest in the winter (40.9%). Patients aged ≥60 years had the highest prevalence of overall HCoVs (39.7%). Given the duration and large sample size, this study from Turkey is one of the largest to date among adults in the literature. These epidemiological data and molecular surveillance of HCoVs have important implications for the control and prevention of respiratory infections.

Clinical outcomes and economic burden of seasonal influenza and other respiratory virus infections in hospitalized adults

The cost of influenza and other respiratory virus infections should be determined to analyze the real burden of these diseases. We aimed to investigate the clinical outcomes and cost of illness due to respiratory virus infections in hospitalized adult patients. Hospitalized patients who had nasal swab sampling for a suspected viral infection between August 1, 2018 to March 31, 2019 were included. Outcome variables were oxygen requirement, mechanical ventilation need, intensive care unit admission, and cost. At least one viral pathogen was detected in 125 (47.7%) of 262 patients who were included in the study. Fifty-five (20.9%) of the patients were infected with influenza. Influenza-positive patients had higher rates for respiratory support, intensive care unit admission, and mortality compared to all other patients. The average cost of hospitalization per person was 2879.76 USD in the influenza-negative group, while the same cost was 3274.03 USD in the influenza-positive group. Although all of the vaccinated influenza-positive patients needed oxygen support, neither of them required invasive mechanical ventilation or intensive care unit admission. The average hospitalization cost per person was 779.70 USD in the vaccinated group compared to 3762.01 USD in the unvaccinated group. Disease-related direct cost of influenza in the community was estimated as 22 776 075.61 USD in the 18-65 years of age group and 15 756 120.02 USD in the 65 years of age and over group per year. Influenza, compared to other respiratory virus infections, can lead to untoward clinical outcomes and mortality as well as higher direct medical costs in adults.

Virus-virus interactions of febrile respiratory syndrome among patients in China based on surveillance data from February 2011 to December 2020

BACKGROUND

The burden of acute respiratory infections is still considerable, and virus-virus interactions may affect their epidemics, but previous evidence is inconclusive.

OBJECTIVE

To quantitatively investigate the interactions among respiratory viruses at both the population and individual levels.

METHODS

Cases tested for influenza virus (IV), respiratory syncytial virus (RSV), human parainfluenza virus (PIV), human Adenovirus (AdV), human coronavirus (CoV), human bocavirus (BoV) and rhinoviruses (RV) were collected from the pathogen surveillance for febrile respiratory syndrome (FRS) in China from February 2011 to December 2020. We used spearman's rank correlation coefficients and binary logistic regression models to analyze the interactions between any two of the viruses at the population and individual levels, respectively.

RESULTS

Among 120,237 cases, 4.5% were co-infected with two or more viruses. Correlation coefficients showed 7 virus pairs were positively correlated, namely: IV and RSV, PIV and AdV, PIV and CoV, PIV and BoV, PIV and RV, AdV and BoV, CoV and RV. Regression models showed except for the negative interaction between IV and RV (OR=0.70, 95%CI: 0.61-0.81), all other virus pairs had positive interactions.

CONCLUSION

Most of the respiratory viruses interact positively, while IV and RV interact negatively. This article is protected by copyright. All rights reserved.

Adenovirus 36 infection and obesity risk: current understanding and future therapeutic strategies

INTRODUCTION

Obesity, a multifactorial disease caused by the interaction between genetic characteristics, metabolism, lifestyle, and environmental factors, is a major global health problem and is currently defined as a pandemic phenomenon. This disease is determined by an interaction of several factors, but the imbalance between energy consumption and expenditure seems to be the crucial point. In some cases, there is no linearity between exposure to those factors that cause the onset of obesity. A striking example of the occurrence of obesity despite no obvious risk factors is that of obesity induced by viral infections. The most important of such viruses appears to be human adenovirus 36 (Adv36).

AREAS COVERED

This review covers the relation between obesity and infection by Adv36 in humans. Also, discussed are the opportunities of prevention or treatment for the effects of Adv36 in human body.

EXPERT OPINION

The role of Ad36 in the development of obesity has already been established. Future research should focus on the development of vaccines against this agent, drug discovery for infected individuals, and effective therapeutic uses of E4orf1 gene protein for diabetes and other diseases in clinical practice.

A Systematic Review of Influenza Epidemiology and Surveillance in the Eastern Mediterranean and North African Region

Seasonal influenza represents a huge health burden, resulting in significant mortality and morbidity. Following the 2009 H1N1 pandemic, focus has been directed on the burden of influenza globally. Country and regional disease burden estimates play important roles in helping inform decisions on national influenza intervention programmes. Despite improvements in influenza surveillance following the 2009 pandemic, many opportunities remain unexplored in the Eastern Mediterranean and North African (EMNA) region, which has a high prevalence of patients with chronic disease and thus a population at high risk of influenza complications. We conducted a systematic literature review of Embase, Medline, Scopus and the Cochrane Database of Systematic Reviews from 1 January 1998 to 31 January 2020 covering the EMNA region with the aim to describe the epidemiology of influenza in the region and assess the influenza epidemiological surveillance research landscape. Relevant data on study characteristics, population, clinical/virology characteristics and epidemiology were extracted and summarised descriptively. Of the 112 studies identified for inclusion, 90 were conducted in the Eastern Mediterranean region, 19 in North Africa and three across the EMNA region. Data were reported on 314,058 laboratory-confirmed influenza cases, 96 of which were derived from surveillance systems. Amongst the surveillance studies, the percentage of positive cases reported ranged from 1% to 100%. The predominantly identified influenza strain was strain A; H1N1 was the most prominent circulating subtype. Typing was performed in approximately 75% and subtyping in 50% of studies, respectively. Data on those considered most at risk for influenza complications were collected in 21% of studies, highlighting a regional gap for these data. Our review reveals existing gaps in regional estimates of influenza health and economic burden, hospitalisation rates and duration, and highlights the need for robust and high-quality epidemiology data to help inform public health interventions.

Epidemiology of Human Bocavirus in the Middle East and North Africa: Systematic Review

The emergence of the COVID-19 pandemic highlighted the importance of studying newly emerging viruses that cause respiratory illnesses. Human bocavirus (HBoV) is one of the relatively newly discovered viruses that has been detected worldwide and causes respiratory and gastrointestinal infections, mainly in pediatric patients. However, little is known about the pathogenicity and evolution of HBoV. This systematic review was initiated to clarify the prevalence and circulating genotypes of HBoV in both respiratory and stool samples from patients of all age groups in the Middle East and North Africa (MENA) from 2005 to February 2021. We performed an electronic search through Science Direct, Scopus, PubMed, Mendeley and Cochrane Library databases. We included all studies reporting the detection rate of HBoV in the MENA region. Data were extracted, and the quality of the included articles was assessed. We included articles containing data on HBoV only or with other respiratory or gastrointestinal viral infections. Review articles, case studies, and animal and environmental studies were excluded. The final number of articles included in this study was 65 articles. The results showed that the HBoV prevalence in children was the lowest in Iran (0%) and the highest in Egypt (56.8%). In adults, the lowest and the highest prevalence were reported in Iran, with values of 0% and 6.6%, respectively. Regarding the respiratory cases, our findings revealed no significant difference between HBoV prevalence among the tested categories (p-value = 0.998). The present study has shown that HBoV is common in children and adults in the MENA region. This systematic review highlights the need for more data on the role of coinfection of HBoV and other viruses, for instance, SARS-CoV-2 in children with acute bronchiolitis.

Etiological and epidemiological characteristics of severe acute respiratory infection caused by multiple viruses and Mycoplasma pneumoniae in adult patients in Jinshan, Shanghai: A pilot hospital-based surveillance study

Background

Severe acute respiratory infection (SARI) results in a tremendous disease burden worldwide. Available research on active surveillance among hospitalized adult patients suffering from SARI in China is limited. This pilot study aimed to identify associated etiologies and describe the demographic, epidemiological and clinical profiles of hospitalized SARI patients aged over 16 years in Jinshan, Shanghai.

Methods

Active surveillance was conducted at 1 sentinel hospital in Jinshan district, Shanghai, from April 2017 to March 2018. Hospitalized SARI patients aged over 16 years old were enrolled, and nasopharyngeal swabs were collected within 24 hours of admission and tested for multiple respiratory viruses (including 18 common viruses) and Mycoplasma pneumoniae with real-time polymerase chain reaction. Demographic, epidemiological and clinical information was obtained from case report forms.

Results

In total, 397 SARI patients were enrolled; the median age was 68 years, and 194 (48.9%) patients were male. A total of 278 (70.0%) patients had at least one underlying chronic medical condition. The most frequent symptoms were cough (99.2%) and sputum production (88.4%). The median duration of hospitalization was 10 days. A total of 250 infection patients (63.0%) were positive for at least one pathogen, of whom 198 (49.9%) were positive for a single pathogen and 52 (13.1%) were positive for multiple pathogens. The pathogens identified most frequently were M. pneumoniae (23.9%, 95/397), followed by adenovirus (AdV) (11.6%, 46/397), influenza virus A/H3N2 (Flu A/H3N2) (11.1%, 44/397), human rhinovirus (HRhV) (8.1%, 32/397), influenza virus B/Yamagata (Flu B/Yamagata) (6.3%, 25/397), pandemic influenza virus A/H1N1 (Flu A/pH1N1) (4.0%, 16/397), parainfluenza virus (PIV) type 1 (2.0%, 8/397), human coronavirus (HCoV) type NL63 (2.0%, 8/397), HCoV 229E (1.5%, 6/397), HCoV HKU1 (1.5%, 6/397), PIV 3 (1.5%, 6/397), human metapneumovirus (HMPV) (1.5%, 6/397), PIV 4 (1.3%, 5/397), HCoV OC43 (1.0%, 4/397), influenza virus B/Victoria (Flu B/Victoria) (0.5%, 2/397), respiratory syncytial virus (RSV) type B (0.5%, 2/397), and human bocavirus (HBoV) (0.3%, 1/397). The seasonality of pathogen-confirmed SARI patients had a bimodal distribution, with the first peak in the summer and the second peak in the winter. Statistically significant differences were observed with respect to the rates of dyspnea, radiographically diagnosed pneumonia and the presence of at least one comorbidity in patients who were infected with only M. pneumoniae, AdV, HRhV, Flu A/H3N2, Flu A /pH1N1 or Flu B/Yamagata. The differences in the positivity rates of the above 6 pathogens among the different age groups were nonsignificant.

Conclusions

M. pneumoniae, AdV and Flu A/H3N2 were the main pathogens detected in hospitalized SARI patients aged over 16 years old in Jinshan district, Shanghai. Our findings highlight the importance of sustained multipathogen surveillance among SARI patients in sentinel hospitals, which can provide useful information on SARI etiologies, epidemiology, and clinical characteristics.

Advanced "lab-on-a-chip" to detect viruses - Current challenges and future perspectives

Massive viral outbreaks draw attention to viruses that have not been thoroughly studied or understood. In recent decades, microfluidic chips, known as "lab-on-a-chip", appears as a promising tool for the detection of viruses. Here, we review the development of microfluidic chips that could be used in response to viral detection, specifically for viruses involved in more recent outbreaks. The advantages as well as the disadvantages of microfluidic systems are discussed and analyzed. We also propose ideas for future development of these microfluidic chips and we expect this advanced technology to be used in the future for viral outbreaks.

The burden of laboratory-confirmed pertussis in low- and middle-income countries since the inception of the Expanded Programme on Immunisation (EPI) in 1974: a systematic review and meta-analysis

BACKGROUND

An effective vaccine against Bordetella pertussis was introduced into the Expanded Programme on Immunisation (EPI) by WHO in 1974, leading to a substantial global reduction in pertussis morbidity and mortality. In low- and middle-income countries (LMICs), however, the epidemiology of pertussis remains largely unknown. This impacts negatively on pertussis control strategies in these countries. This study aimed to systematically and comprehensively review published literature on the burden of laboratory-confirmed pertussis in LMICs over the 45 years of EPI.

METHODS

Electronic databases were searched for relevant literature (1974 to December 2018) using common and MeSH terms for pertussis. Studies using PCR, culture or paired serology to confirm Bordetella pertussis and parapertussis in symptomatic individuals were included if they had clearly defined numerators and denominators to determine prevalence and mortality rates.

RESULTS

Eighty-two studies (49,167 participants) made the inclusion criteria. All six WHO regions were represented with most of the studies published after 2010 and involving mainly upper middle-income countries (n = 63; 77%). PCR was the main diagnostic test after the year 2000. The overall median point prevalence of PCR-confirmed Bordetella pertussis was 11% (interquartile range (IQR), 5-27%), while culture-confirmed was 3% (IQR 1-9%) and paired serology a median of 17% (IQR 3-23%) over the period. On average, culture underestimated prevalence by 85% (RR = 0.15, 95% CI, 0.10-0.22) compared to PCR in the same studies. Risk of pertussis increased with HIV exposure [RR, 1.4 (95% CI, 1.0-2.0)] and infection [RR, 2.4 (95% CI, 1.1-5.1)]. HIV infection and exposure were also related to higher pertussis incidences, higher rates of hospitalisation and pertussis-related deaths. Pertussis mortality and case fatality rates were 0.8% (95% CI, 0.4-1.4%) and 6.5% (95% CI, 4.0-9.5%), respectively. Most deaths occurred in infants less than 6 months of age.

CONCLUSIONS

Despite the widespread use of pertussis vaccines, the prevalence of pertussis remains high in LMIC over the last three decades. There is a need to increase access to PCR-based diagnostic confirmation in order to improve surveillance. Disease control measures in LMICs must take into account the persistent significant infant mortality and increased disease burden associated with HIV infection and exposure.

Prevalence of prescription medication use in preschool-age children seen in pediatric otolaryngology

OBJECTIVE

To examine the prevalence of daily medication use and prescribing patterns in preschool aged children presenting to otolaryngology clinics.

STUDY DESIGN

Retrospective summary of prescription-related data from PEDSnet database of two tertiary care children's hospitals within single health system.

METHODS

All new patients between birth and 5 years of age seen in otolaryngology clinics from October 1, 2016 through September 30, 2017 were included. Existing diagnoses, active prescriptions at time of visit, prescription dates, and demographics were abstracted. Summary analysis was performed on medication prevalence, quantity and duration of use, comparing all variables between age, gender, and geographical regions.

RESULTS

Of 7532 patient encounters, 20% presented with active daily medication use. Eustachian tube dysfunction and otitis media were the most common diagnoses regardless of daily medication usage. Corticosteroids, specifically hydrocortisone (Delaware) and Flovent (Florida), were the most common medication prescribed. The number of medications strongly correlated with the number of encounter diagnoses. Overall, patients in Delaware were 4.5 times more likely to have at least one prescription prior to encounter (p < 0.05, 95% CI 3.2-4.8). This pattern was preserved across age and gender. Patients with medication in Delaware and Florida had a median of 2 (IQR 3.0-1.0) and 1 prescriptions (IQR 2.0-1.0), respectively (p < 0.001). There were no differences based on insurance type and no correlations between medication count and age or gender.

CONCLUSION

Children in Delaware presented to otolaryngology clinics with significantly more prescribed medications than in Florida. Regional differences were consistent across age and gender. Most children were on these medications for a significant duration.

Molecular Diagnosis of Pneumonia Using Multiplex Real-Time PCR Assay RespiFinder® SMART 22 FAST in a Group of Moroccan Infants

Background

In Morocco, pediatric pneumonia remains a serious public health problem, as it constitutes the first cause of mortality due to infectious diseases. The etiological diagnosis of acute respiratory tract infections is difficult. Therefore, it is necessary to use Multiplex real-time polymerase chain reaction assay tests in a routine setting for exact and fast identification.

Objectives

In this paper, we present the clinical results of pediatric pneumonia and describe their etiology by using molecular diagnosis. Study design: Tracheal secretion was collected from infants presenting respiratory distress isolated or associated with systemic signs, attending the unit of Neonatology between December 1, 2016, and Mai 31, 2018. Samples were tested with the multiplex RespiFinder® SMART 22 FAST which potentially detects 18 viruses and 4 bacteria.

Results

Of the 86 infants considered in this study (mean age 31 ± 19 days) suspected of acute respiratory tract infections, 71 (83%) were positive for one or multiple viruses or/and bacteria. The majority of acute respiratory tract infections had a viral origin (95%): respiratory syncytial viruses (A and B) (49%), rhinovirus (21%), coronaviruses 229E (11%), humain metapneumovirus (5%), influenza A (3%), influenza H1N1 (1%), adenovirus (2%), and parainfluenza virus type 4 (2%). Among our patients, 6% had Mycoplasma pneumoniae. Coinfections were not associated with severe respiratory symptoms.

Conclusion

The clinical spectrum of respiratory infections is complex and often nonspecific. Thus, the early and fast detection of related causative agents is crucial. The use of multiplex real time polymerase chain reaction may help choose an accurate treatment, reduce the overall use of unnecessary antibiotics, preserve intestinal flora, and decrease nosocomial infection by reducing the length of hospitalization.

Epidemiology of Mycoplasma pneumoniae prevalence in Iranian patients: a systematic review and meta-analysis

Introduction. Mycoplasma pneumoniae is regarded as the important infectious agent of acute respiratory infections (ARIs) in the world. However, there is little knowledge about the prevalence of M. pneumoniae in Iran. Therefore, the aim of this study was to investigate the prevalence of M. pneumoniae in Iran through a meta-analysis of included studies.Methods. A systematic search was done by using electronic databases from papers that were published by Iranian authors to the end of February 2019. Then, 12 publications, which met our inclusion criteria, were enrolled for data extraction and analysis by using the 'metaprop program' in stata version 14.0.Results. The pooled prevalence of M. pneumoniae was 9 % (95 % confidence intervals: 5-16 %) ranging from 1 to 26 %. There was a significant heterogeneity among the 12 studies (X²=128.29; P<0.001; I ²=91.43 %). The funnel plot for publication bias showed no evidence of asymmetry.Conclusions. The frequency of M. pneumoniae in Iran is comparable with other parts of the world. Although the overall prevalence of M. pneumoniae was low, awareness about the distribution of these agent is very important because of higher infection rates in susceptible groups. In addition, these results showed the rates of M. pneumoniae had variation based on location, type of infection and sample, gender and detection rate and there was evidence of publication bias.

Viral and Bacterial Etiology of Acute Febrile Respiratory Syndrome among Patients in Qinghai, China

OBJECTIVE

This study was conducted to investigate the viral and bacterial etiology and epidemiology of patients with acute febrile respiratory syndrome (AFRS) in Qinghai using a commercial routine multiplex-ligation-nucleic acid amplification test (NAT)-based assay.

METHODS

A total of 445 nasopharyngeal swabs specimens from patients with AFRS were analyzed using the RespiFinderSmart22kit (PathoFinder BV, Netherlands) and the LightCycler 480 real-time PCR system.

RESULTS

Among the 225 (225/445, 51%) positive specimens, 329 positive pathogens were detected, including 298 (90.58%) viruses and 31 (9%) bacteria. The most commonly detected pathogens were influenza virus (IFV; 37.39%; 123/329), adenovirus (AdV; 17.02%; 56/329), human coronaviruses (HCoVs; 10.94%; 36/329), rhinovirus/enterovirus (RV/EV; 10.03%; 33/329), parainfluenza viruses (PIVs; 8.51%; 28/329), and Mycoplasma pneumoniae (M. pneu; 8.51%; 28/329), respectively. Among the co-infected cases (17.53%; 78/445), IFV/AdV and IFV/M. pneu were the most common co-infections. Most of the respiratory viruses were detected in summer and fall.

CONCLUSION

In our study, IFV-A was the most common respiratory pathogen among 22 detected pathogens, followed by AdV, HCoV, RV/EV, PIV, and M. pneu. Bacteria appeared less frequently than viruses, and co-infection was the most common phenomenon among viral pathogens. Pathogens were distributed among different age groups and respiratory viruses were generally active in July, September, and November. Enhanced surveillance and early detection can be useful in the diagnosis, treatment, and prevention of AFRS, as well as for guiding the development of appropriate public health strategies.

An updated roadmap for MERS-CoV research and product development: focus on diagnostics

Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management.

Bacterial and Viral Identification Rate in Acute Exacerbation of Chronic Obstructive Pulmonary Disease in Korea

PURPOSE

The most common cause of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is respiratory infection. Most studies of bacterial or viral cause in AECOPD have been conducted in Western countries. We investigated bacterial and viral identification rates in AECOPD in Korea.

MATERIALS AND METHODS

We reviewed and analyzed medical records of 736 cases of AECOPD at the Korea University Guro Hospital. We analyzed bacterial and viral identification rates and classified infections according to epidemiological factors, such as Global Initiative for Chronic Obstructive Lung Disease stage, mortality, and seasonal variation.

RESULTS

The numbers of AECOPD events involving only bacterial identification, only viral identification, bacterial-viral co-identification, and no identification were 200 (27.2%), 159 (21.6%), 107 (14.5%), and 270 (36.7%), respectively. The most common infectious bacteria identified were Pseudomonas aeruginosa (13.0%), Streptococcus pneumoniae (11.4%), and Haemophilus influenzae (5.3%); the most common viruses identified were influenza virus (12.4%), rhinovirus (9.4%), parainfluenza virus (5.2%), and metapneumovirus (4.9%). The bacterial identification rate tended to be higher at more advanced stages of chronic obstructive pulmonary disease (p=0.020 overall, p=0.011 for P. aeruginosa, p=0.048 for S. pneumoniae). Staphylococcus aureus and Klebsiella pneumoniae were identified more in mortality group (p=0.003 for S. aureus, p=0.009 for K. pneumoniae). All viruses were seasonal (i.e., greater prevalence in a particular season; p<0.050). Influenza virus and rhinovirus were mainly identified in the winter, parainfluenza virus in the summer, and metapneumovirus in the spring.

CONCLUSION

This information on the epidemiology of respiratory infections in AECOPD will improve the management of AECOPD using antibiotics and other treatments in Korea.

Epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in Northern Italy

Acute respiratory tract infections (ARTIs) are among the leading causes of morbidity and mortality in children. The viral etiology of ARTIs was investigated over 3 years (October 2012–September 2015) in 2575 children in Parma, Italy, using indirect immunofluorescent staining of respiratory samples for viral antigens, cell culture, and molecular assays. Respiratory viruses were detected in 1299 cases (50.44%); 1037 (79.83%) were single infections and 262 (20.17%) mixed infections. The highest infection incidence was in children aged >6 months to ≤3 years (57.36%). Human respiratory syncytial virus (27.12%) and human adenovirus (23.58%) were the most common viruses identified. The virus detection rate decreased significantly between the first and third epidemic season (53.9% vs. 43.05%, P < 0.0001). The simultaneous use of different diagnostic tools allowed us to identify a putative viral etiology in half the children examined and to provide an estimate of the epidemiology and seasonality of respiratory viruses associated with ARTIs.

•

Respiratory viruses were assessed in children from October 2012 to September 2015.

•

Viruses were detected using antigen and molecular assays, and cell culture.

•

Respiratory syncytial virus and adenovirus were the most common viruses detected.

•

Influenza virus and respiratory syncytial virus detection showed seasonal variation.

•

Respiratory virus detection was highest in children aged >6 months to ≤3 years.

Respiratory viral infections in infants with possible sepsis

Background

Knowledge of infections leading to sepsis is needed to develop comprehensive infection prevention and sepsis, as well as early recognition and treatment strategies.The aim of this study was to investigate the etiology of sepsis and evaluate the proportion of respiratory viral pathogens in infants under two years of age with possible sepsis.

Methods

The prospective study was performed in two years. Multiplex reverse transcriptase polymerase chain reaction (RT‐PCR) was performed to detect viral pathogens. All patients who were included in this study had sepsis symptoms as defined by the Surviving Sepsis Campaign.

Results

We compared 90 patients with sepsis into three groups as patients (n = 33) who had only viral positivity in nasopharyngeal swab, patients (17) had proven bacterial infection with or without viral infection, and patients (40) without the pathogen detection. Human rhinovirus (16.7%) and influenza (7.8%) were the most commonly seen viruses. A cough was more common in the viral infection group than other groups ( P = 0.02) and median thrombocyte count was lower in the bacterial infection group than the others ( P = 0.01). Patients having bacterial sepsis had the longest duration of hospitalization than the other groups ( P = 0.04). During winter and spring seaons, patients with sepsis had more viral infection; however, in summer and autumn period, patients were mostly in a state that we could not prove infection agents ( P = 0.02).

Conclusions

Our results suggest that respiratory tract viruses may play an important role in patients with sepsis and they should be kept in mind, especially during winter and spring seasons. In overall infection, viral respiratory viruses as a single pathogen with a detection rate of 36.6% in sepsis etiology.

Prevalence of Human Bocavirus in Africa and Other Developing Countries between 2005 and 2016: A Potential Emerging Viral Pathogen for Diarrhea

BACKGROUND

Human Bocavirus (HBoV) is an emerging virus discovered in 2005 from individuals suffering gastroenteritis and respiratory tract infections. Numerous studies related to the epidemiology and pathogenesis of HBoV have been conducted worldwide. This review reports on HBoV studies in individuals with acute gastroenteritis, with and without respiratory tract infections in Africa between 2005 and 2016.

MATERIAL AND METHOD

The search engines of PubMed, Google Scholar, and Embase database for published articles of HBoV were used to obtain data between 2005 and 2016. The search words included were as follows: studies performed in Africa or/other developing countries or/worldwide; studies for the detection of HBoV in patients with/without diarrhea and respiratory tract infection; studies using standardized laboratory techniques for detection.

RESULTS

The search yielded a total of 756 publications with 70 studies meeting the inclusion criteria. Studies included children and individuals of all age groups. HBoV prevalence in Africa was 13% in individuals suffering gastroenteritis with/without respiratory tract infection.

CONCLUSION

Reports suggest that HBoV infections are increasingly being recognized worldwide. Therefore, surveillance of individuals suffering from infections in Africa is required to monitor the prevalence of HBoV and help understand the role of HBoV in individuals suffering from gastroenteritis with/without respiratory tract infection.

Detection of Viruses and Mycoplasma pneumoniae in Hospitalized Patients with Severe Acute Respiratory Infection in Northern China, 2015-2016

Severe acute respiratory infection (SARI) presents a huge disease and economic burden worldwide. The present study described the frequency and types of different infectious etiologies among hospitalized patients with SARI in Tianjin, China, during 2015 and 2016. Basic information, in addition to a throat or serum sample, was collected from SARI patients. Nine viruses were detected using reverse transcription polymerase chain reaction, and Mycoplasma pneumoniae was detected using the Serodia Myco II gelatin particle agglutination test. A total of 585 specimens from 2,290 SARI cases were collected. The most common infection (19.66%, 115/585) was M. pneumoniae, followed by influenza virus A/B (6.15%, 36/585), and respiratory syncytial virus (4.96%, 29/585). Identification of viral or M. pneumoniae infections was the highest in the pediatric medicine ward (74.84%, 119/159), followed by the intensive care unit (37.04%, 80/216) and respiratory medicine ward (34.29%, 72/210). M. pneumoniae was highest (38.71%, 24/62) in the 5-14-year age group. Influenza was the main infection in January 2015 and March 2016. The correlation coefficient for the proportion of hospitalized cases of SARI and the positive detection rate within the same week was 0.25. M. pneumoniae and influenza were the leading pathogens among hospitalized SARI patients. A continued surveillance of hospitalized cases of SARI can detect emerging diseases, such as avian influenza A (H7N9) virus and other respiratory disease outbreaks.

The rapid diagnosis of viral respiratory tract infections and its impact on antimicrobial stewardship programs

We aimed to describe the potential benefit of new rapid molecular respiratory tests (MRT) in decreasing inappropriate antibiotic use among the inpatients presenting with influenza-like illness (ILI). We included patients from inpatient and outpatient departments who had ILI and performed MRT between 1 January 2015 and 31 December 2016 in a 265-bed private hospital in Istanbul. At the end of 2015, we implemented antimicrobial stewardship including systematic use of MRT. Then, we compared our observations between the year 2015 and the year 2016. We designed the study according to the STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) tool. A U.S. Food and Drug Administration (FDA)-cleared multiplexed polymerase chain reaction (PCR) system (BioFire FilmArray, Idaho Technology, Salt Lake City, UT) which detects 17 viruses and three bacteria was used for diagnosis. In total, 1317 patients were included; 630 (48%) were inpatients and 569 (43%) were older than 16 years of age. At least one virus was detected in 747 (57%) patients. Rhinovirus/enterovirus, influenza virus, and adenovirus were the most commonly detected. Among hospitalized patients, in children, a significant decrease in antibiotic use (44.5% in 2015 and 28.8% in 2016, p = 0.009) was observed, but in adults, the decrease was not statistically significant (72% in 2015 and 63% in 2016, p = 0.36). The duration of antibiotic use after the detection of virus was significantly decreased in both children and adults (p < 0.001 and p = 0.007, respectively). By using MRT, inappropriate antibiotic use and, also, duration of inappropriate antibiotic use after the detection of virus was significantly decreased. It is time to increase the awareness about the viral etiology in respiratory tract infections (RTIs) and implement MRT in clinical practice.

Admission predictability of children with acute asthma

OBJECTIVES

We aimed to evaluate the seasonal variations of acute asthma presentation in children and the utility of the pediatric asthma score (PAS) and its components in early admission prediction.

METHODS

As part of a randomized controlled trial addressing the clinical efficacy of budesonide nebulization in the treatment of acute asthma in children, the PAS was measured at baseline, 1^st, 2^nd, 3^rd, and 4^th h from the start of medications. Decision of admission was taken at or beyond the 2^nd h.

RESULTS

Out of a total 906 emergency department (ED) visits with moderate-to-severe acute asthma, 157 children were admitted. June to September had the lowest number of visits. The admission-to-discharge ratio varied throughout the year. During the ED stay, between baseline and 3^rd h, admission predictability of the total score improved progressively with a small difference between the 2^nd and 3^rd h. The total score remained the strongest predictor of admission at every time point compared to its individual components. The drop of PAS from baseline to the 2^nd h was not a good predictor of admission. Oxygen saturation (OS) and respiratory rate (RR) had relatively higher predictability than other components.

CONCLUSIONS

Decision of admission could be made to many children with moderate-to-severe acute asthma at the 2^nd h of ED stay based on their total PAS. OS and RR should be part of any scoring system to evaluate acute asthma in children.