Agents Of Acute Respiratory Infections Research Articles

Pathogenic agents causing acute respiratory tract infections in pediatric patients in Spring, 2023, in Beijing

Objective: To explore the pathogenic agents of acute respiratory infection (ARI) in children in Beijing. Methods: In the cross-sectional study, 3 groups of children from different departments were enrolled from Feb 6th, 2023 (6th week) to May 28th (21th week), 2023, including influenza-like case group from emergency department for nucleic acid testing of influenza virus (Flu) and human metapneumovirus (HMPV), the outpatient ARI group under nucleic acid testing for Flu, respiratory syncytial virus (RSV), adenovirus (ADV), and parainfluenza virus (PIV), and the inpatient ARI group under nucleic acid testing for Flu, RSV, HMPV, ADV, human bocavirus (HBoV), Rhinovirus (Rh), PIV, coronavirus (HCoV), Mycoplasma pneumoniae (Mp) and Chlamydia pneumonia (Cp). Results: There were 320 influenza-like cases enrolled, including 192 males and 128 females, aged 4.7 (3.6, 6.9) years, and 117 cases (36.6%) positive for Flu A, which contained similar proportion of pandemic H1N1 (H1N1) 47.0% (55/117) and H3N2 53.0% (62/117), and 13 cases for HMPV 4.1% (13/320). The rate of Flu reached its peak at the 10th week, with H1N1 as the predominant one from the 6th to 9th week (10.0%-50.0%) and then H3N2 from the 10th to 16th week (15.0%-90.0%). HMPV was detected from the 15th week 5.0% (1/20), and then reached to 30.0% (6/20) at the 20th week. In the outpatient ARI group, 7 573 were enrolled, including 4 131 males and 3 442 females, aged 4.0 (2.1, 5.3) years, and the highest positive rate for RSV 32.9% (2 491/7 573), followed by Flu A 12.1% (915/7 573). The dominant one was Flu A in weeks 6-14 (23.2%-74.7%), then RSV in the 15th week 24.8% (36/145). In the inpatient ARI group, 1 391 patients were enrolled, including 804 males and 587 females, aged 3.3 (0.4, 5.8) years, and the highest positive rate for Rh 18.7% (260/1 391), followed by RSV 12.4% (173/1 391), Flu A 10.2% (142/1 391, of which 116 cases (81.7%) were H1N1, and 26 cases (18.3%) were H3N2) and HMPV 3.1% (43/1 391). H1N1 was detected from the 7th week 10% (6/60), to peak in the 11th week 31.8% (21/66). H3N2 was detected from the 8th week 1.5% (1/68), and then kept in low level. The proportion of H1N1 among Flu was 81.7% (116/142) in the inpatient ARI group. RSV was detected from 12th week 1.3% (1/80), reaching 30.4% (35/115) at 19th week. The positive rate of HMPV reached 12.1% (14/116) at 21th week. Conclusions: In the spring of 2023, the first one in Beijing is the Flu epidemic, with H1N1 being the predominant one in the early stage and H3N2 in the later stage. Then, there is a postponed RSV epidemic and an increased HMPV detection. In addition, nucleic acid testing for outpatient children should be strengthened to provide early warning of epidemics.

Change of epidemiological characteristics of four respiratory viral infections in children before and during COVID-19 pandemic

ObjectivesViruses are the main infectious agents of acute respiratory infections (ARIs) in children. We aim to describe the changes in epidemic characteristics of viral ARIs in outpatient children before and during the COVID-19 pandemic. Patients and methodsFrom 2017 to 2022, the results of viral detection in oral pharyngeal swabs in 479,236 children with ARIs in the outpatient department of Children’s Hospital, Zhejiang University School of Medicine, were retrospectively analyzed. Viral antigens, including adenovirus (ADV), influenza A (FLUA), influenza B (FLUB) and respiratory syncytial virus (RSV) were detected by the colloidal gold method. ResultsThe median age was 3.4 (1.6–5.6) years. Among all the children, 159,895 cases (33.4 %) were positive for at least one virus. The total positive rate for ADV, FLUA and FLUB during the pandemic period was lower than during the pre-pandemic period in every season (pre-pandemic period vs. pandemic period11.7 % vs. 4.7 %, 13.9 % vs. 9.2 %, 7.0 % vs. 5.2 %, respectively, with overall p value < 0.001). However, the positive rate fir RSV was not significantly different between the pre-pandemic period and the pandemic period (5.6 % vs. 5.8 %, p = 0.117). Atypical timing of RSV (summer-autumn 2021) and FLUA (summer 2022) was noted. ConclusionsPublic health interventions for different pathogens are maximally effective. While positive rates for ADV, FLUA and FLUB decreased during the COVID-19 pandemic period, positive rates for RSV remained similar. In RSV and FLUA, off-season outbreaks were observed. Measures need to be taken to protect children from possible infection surges due to immunity debt having accrued over the last three years.

НОВЫЕ ВОЗМОЖНОСТИ ЛЕЧЕНИЯ И ПРОФИЛАКТИКИ ИНФЕКЦИОННО-ВОСПАЛИТЕЛЬНЫХ ЗАБОЛЕВАНИЙ РЕСПИРАТОРНОГО ТРАКТА

Management of patients with infectious and inflammatory diseases of the upper respiratory tract is one of the most pressing problems of modern medicine, which is associated with the widespread prevalence of this pathology. The main causative agents of acute respiratory infections (ARI) are viruses, but the frequency of unjustified prescription of antibiotic therapy remains high. Despite significant advances in healthcare, questions of the effectiveness and safety of treatment of patients with ARI and the prevention of complications remain largely open to the present day. In this aspect, the possibility of using the original domestic antiviral drug of plant origin Panavir® in respiratory medicine is of particular interest to doctors and patients. The action of Panavir® is aimed at increasing the body’s resistance to the effects of pathogens and the production of interferons - protective proteins produced by the body in response to pathogen invasion. Panavir® is a biologically active polysaccharide obtained from the plant Solanum tuberosum (tuberous nightshade). This substance has a long-term protective effect, prevents the development of inflammation, and accelerates the restoration of the mucous membrane.

Incidence of Acute Respiratory Infections in Dental Care Professionals

Introduction: A wide spread of causative agents of acute respiratory infections and an intensive use of aerosol-generating procedures in dentistry affect the disease incidence in dental care professionals. This issue, however, remains poorly studied. Objective: To study the incidence of acute respiratory infections in dental health personnel in order to optimize appropriate preventive measures. Materials and methods: In 2021, we conducted a descriptive retrospective epidemiological study of the workplace absence due to acute respiratory diseases among 352 dental care professionals (case study group) and 782 people unrelated to the medical field (control group). To assess the statistical significance of differences in the incidence rates, the Pearson criterion (χ2) was applied. The data were analyzed in Microsoft Office Excel 2013 and Epi Info v. 1.4.3. Results: We established that the incidence rates of viral respiratory diseases in the dental health personnel were 2.2 times higher than in the control group (301.14 and 136.83 ‰, respectively; p = 0.00001). During the respiratory illness season, the cases were 3.3 times more likely to get sick (p = 0.000001). At the same time, the incidence in the cases working in therapeutic and orthopedic departments and applying aerosol-generating procedures was 2.7 times higher compared to those working in other departments (p = 0.00153). Females generally prevailed among therapists and orthopedists (83.81 %) and the rates of viral respiratory infections in them were found to be 2.73 times higher than in male surgeons (p = 0.00134). Conclusions: The high incidence of acute respiratory infections observed in the dental care professionals, especially in those using aerosol-generating procedures in their everyday practice, shows the necessity of improving measures for prevention of respiratory tract infections in dentistry.

Clinical characteristics and outcomes of children with single or co-detected rhinovirus-associated acute respiratory infection in Middle Tennessee

BackgroundRhinovirus (RV) is one of the most common etiologic agents of acute respiratory infection (ARI), which is a leading cause of morbidity and mortality in young children. The clinical significance of RV co-detection with other respiratory viruses, including respiratory syncytial virus (RSV), remains unclear. We aimed to compare the clinical characteristics and outcomes of children with ARI-associated RV-only detection and those with RV co-detection—with an emphasis on RV/RSV co-detection.MethodsWe conducted a prospective viral surveillance study (11/2015–7/2016) in Nashville, Tennessee. Children < 18 years old who presented to the emergency department (ED) or were hospitalized with fever and/or respiratory symptoms of < 14 days duration were eligible if they resided in one of nine counties in Middle Tennessee. Demographics and clinical characteristics were collected by parental interviews and medical chart abstractions. Nasal and/or throat specimens were collected and tested for RV, RSV, metapneumovirus, adenovirus, parainfluenza 1–4, and influenza A–C using reverse transcription quantitative polymerase chain reaction assays. We compared the clinical characteristics and outcomes of children with RV-only detection and those with RV co-detection using Pearson’s χ2 test for categorical variables and the two-sample t-test with unequal variances for continuous variables.ResultsOf 1250 children, 904 (72.3%) were virus-positive. RV was the most common virus (n = 406; 44.9%), followed by RSV (n = 207; 19.3%). Of 406 children with RV, 289 (71.2%) had RV-only detection, and 117 (28.8%) had RV co-detection. The most common virus co-detected with RV was RSV (n = 43; 36.8%). Children with RV co-detection were less likely than those with RV-only detection to be diagnosed with asthma or reactive airway disease both in the ED and in-hospital. We did not identify differences in hospitalization, intensive care unit admission, supplemental oxygen use, or length of stay between children with RV-only detection and those with RV co-detection.ConclusionWe found no evidence that RV co-detection was associated with poorer outcomes. However, the clinical significance of RV co-detection is heterogeneous and varies by virus pair and age group. Future studies of RV co-detection should incorporate analyses of RV/non-RV pairs and include age as a key covariate of RV contribution to clinical manifestations and infection outcomes.

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.

M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV

The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is responsible for the phase change of viral activity, acting as an inhibitor or inducer of viral replication, according to the concentration of mRNA. Based on the importance of M2-2 gene and protein have to viral physiology, we performed here evaluations of genetic diversity, phylogenetic reconstructions, phylodynamics, and selection test. Our results suggested an alternative way of classifying this virus in clades A and B, based on a new phylogenetic marker, the M2-2 gene. Therefore, our study is the first one to investigate the dynamics of the evolutionary diversification process of hRSV from the perspective of the M2-2 viral gene. In our study was also identified that the M2-2 gene is under the effect of purifying selection originated by population genetic bottlenecks. Therefore, the M2-2 gene demonstrated an interesting potential to be applied in evolutionary studies involving hRSV, recovering phylogenetic signals and traits of natural selection under the evolution of this virus.

Live Influenza Vaccine Provides Early Protection against Homologous and Heterologous Influenza and May Prevent Post-Influenza Pneumococcal Infections in Mice.

Influenza and S. pneumoniae infections are a significant cause of morbidity and mortality worldwide. Intranasal live influenza vaccine (LAIV) may prevent influenza-related bacterial complications. The objectives of the study are to estimate resistance against early influenza infection and post-influenza pneumococcal pneumonia after LAIV in mice. Mice were administered intranasally the monovalent LAIV A/17/Mallard Netherlands/00/95(H7N3), A/17/South Africa/2013/01(H1N1)pdm09 or trivalent LAIV 2017–2018 years of formulation containing A/17/New York/15/5364(H1N1)pdm09 vaccine strain. LAIV demonstrated early protection against homologous and heterologous infections with A/South Africa/3626/2013 (H1N1) pdm09 influenza virus on day six, following immunization. Following boost immunization, trivalent LAIV demonstrated a pronounced protective effect both in terms of lethality and pneumococcal lung infection when S. pneumoniae infection was performed three days after the onset of influenza infection. Conclusion: LAIV provides early protection against homologous and heterologous viral infections and has a protective effect against post-influenza pneumococcal infection. These data suggest that the intranasal administration of LAIV may be useful during the cycle of circulation not only of influenza viruses, but also of other causative agents of acute respiratory infections.

ОСТРЫЕ ВИРУСНЫЕ ИНФЕКЦИИ С СОЧЕТАННЫМ ПОРАЖЕНИЕМ РЕСПИРАТОРНОГО И ЖЕЛУДОЧНО-КИШЕЧНОГО ТРАКТА - БИЧ СОВРЕМЕННОСТИ?

Viral infections continue to cause significant morbidity and mortality worldwide. The association of pathogens often changes not only the typical clinical picture of the infection, but also its course, which often becomes the reason for the delayed diagnosis and lack of adequate treatment. The variety and discovery of new respiratory viruses, their variability, the rapid formation of strains resistant to antiviral agents and modifying adaptive immune responses in humans, lead to an increase in the frequency of mixed viral infections, which dictates the need to develop and implement new diagnostic and treatment algorithms. This review is devoted to the problem of acute viral infections with combined lesions of the respiratory tract and gastrointestinal tract (GIT) among the population of children. The etiological structure of causative agents of acute respiratory infections (ARI), acute intestinal infections (AII) and infections with combined lesions of the respiratory tract and GIT in children is presented. The features of the pathogenesis and clinical features of rotavirus, coronavirus infections are considered. An algorithm for making a decision on the appointment of a treatment-and-prophylactic complex for children with AII and ARI is proposed.

Human Adenovirus Serotype 3 Infection Modulates the Biogenesis and Composition of Lung Cell-Derived Extracellular Vesicles.

Adenovirus (Ad) is a major causal agent of acute respiratory infections. However, they are a powerful delivery system for gene therapy and vaccines. Some Ad serotypes antagonize the immune system leading to meningitis, conjunctivitis, gastroenteritis, and/or acute hemorrhagic cystitis. Studies have shown that the release of small, membrane-derived extracellular vesicles (EVs) may offer a mechanism by which viruses can enter cells via receptor-independent entry and how they influence disease pathogenesis and/or host protection considering their existence in almost all bodily fluids. We proposed that Ad3 could alter EV biogenesis, composition, and trafficking and may stimulate various immune responses in vitro. In the present study, we evaluated the impact of in vitro infection with Ad3 vector on EV biogenesis and composition in the human adenocarcinoma lung epithelial cell line A549. Cells were infected in an exosome-free media at different multiplicity of infections (MOIs) and time points. The cell viability was determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and fluorometric calcein-AM. EVs were isolated via ultracentrifugation. Isolated EV proteins were quantified and evaluated via nanoparticle tracking, transmission electron microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunoblotting assays. The cell viability significantly decreased with an increase in MOI and incubation time. A significant increase in particle mean sizes, concentrations, and total EV protein content was detected at higher MOIs when compared to uninfected cells (control group). A549 cell-derived EVs revealed the presence of TSG101, tetraspanins CD9 and CD63, and heat shock proteins 70 and 100 with significantly elevated levels of Rab5, 7, and 35 at higher MOIs (300, 750, and 1500) when compared to the controls. Our findings suggested Ad3 could modulate EV biogenesis, composition, and trafficking which could impact infection pathogenesis and disease progression. This study might suggest EVs could be diagnostic and therapeutic advancement to Ad infections and other related viral infections. However, further investigation is warranted to explore the underlying mechanism(s).

Respiratory infections of combined etiology in the clinical practice of the pediatrician

Acute respiratory infections hold the leading position in the structure of infectious pathology in children and are one of the main reasons for visits to the doctor. Most often causative agents of acute respiratory infections are viruses. In recent years, respiratory infections of combined etiology are becoming an increasingly significant problem, the proportion of which is increasing.In co-infections, clinical diagnosis is difficult, which once again emphasizes the importance of the widespread introduction of highly sensitive etiological diagnostic methods, in particular polymerase chain reaction. Data on the tendency to a more severe course of co-infections compared to mono-infections are ambiguous, which seems to depend on the specific causative agent and the level of viral load. Another urgent problem of acute respiratory infections in children is the frequent registration of concomitant respiratory viral and herpes virus infections. The clinical picture of acute respiratory tract infections is not very diverse: fever, intoxication symptoms, cough, nasal congestion, rhinorrhea, sore throat, etc. At the same time, pathognomonic symptoms can be identified in some monoinfections, but in coinfections such clinical diagnosis is difficult, suggesting the importance of etiological diagnosis, especially polymerase chain reaction (PCR).All of the above, as well as age and clinical manifestations largely determine the rational selection of antiviral therapy simultaneously effective against both respiratory viruses and herpes viruses. One such drug is Cycloferon, which has not only a broad antiviral spectrum, but also a high level of safety.Inclusion of an interferon inducer in the treatment of acute respiratory infections will reduce the need to prescribe other drugs, including antibiotics, and reduce the medication load on the body.

Epidemiological characteristics of four common respiratory viral infections in children

BackgroundViruses are the main infectious agents of acute respiratory infections in children. We aim to describe the epidemiological characteristics of viral pathogens of acute respiratory tract infections in outpatient children.MethodsFrom April 2018 to March 2019, the results of viral detection using oral pharyngeal swabs from 103,210 children with acute respiratory tract infection in the outpatient department of the Children’s Hospital, Zhejiang University School of Medicine, were retrospectively analyzed. Viral antigens, including adenovirus (ADV), influenza A (FLUA), influenza B (FLUB) and respiratory syncytial virus (RSV), were detected by the colloidal gold method.ResultsAt least one virus was detected in 38,355 cases; the positivity rate was 37.2%. A total of 1910 cases of mixed infection with two or more viruses were detected, and the positivity rate of multiple infection was 1.9%. The ADV positivity rate was highest in the 3–6-year-old group (18.7%), the FLUA positivity rate was highest in the > 6-year-old group (21.6%), the FLUB positivity rate was highest in the > 6-year-old group (6.6%), and the RSV positivity rate was highest in the < 1-year-old group (10.6%). There was a significant difference in the positivity rate of viral infection among different age groups (χ2 = 1280.7, P < 0.001). The rate of positive viral infection was highest in winter (47.1%). The ADV infection rate was highest in spring (18.2%). The rates of FLUA and FLUB positivity were highest in winter (28.8% and 3.6%, respectively). The rate of RSV positivity was highest in autumn (17.4%). The rate of positive viral infection in different seasons was significantly different (χ2 = 6459.1, P < 0.001).ConclusionsViral infection rates in children differ for different ages and seasons. The positivity rate of ADV is highest in the preschool period and that of RSV is highest in infants; that of FLU increases with age. The total positive rate of viral infection in different seasons is highest in winter, as is the rate of FLU positivity.

Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains.

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

Human adenoviruses associated with respiratory illness in neonates, infants, and children in the Sousse area of Tunisia

BackgroundThe human Adenovirus (HAdV) is a common agent of acute respiratory infections (ARIs). Its clinical impact in immunocompetent children and in the context of coinfections remains unclear in Tunisia.Material and methodsHAdV‐ARIs were studied in hospitalized patients from birth to the age of 5 years from 2013 to 2014. Clinical and demographic characteristics, coinfections, and molecular characterization of HAdV were established.ResultsHAdV‐positivity was detected in 114/583 specimens (19.6%) including 6.1% single infections and 93.9% coinfections. Adenoviral coinfections mostly comprised human Rhinovirus (50.9%), Streptococcus pneumoniae (34.2%), human Respiratory Syncytial virus A/B (29.8%), and human Coronaviruses (21.9%). HAdV infection was predominant in the pediatric population (25.0% vs 10.0% in neonates, P < .001) and peaked in February 2014 (21.1%). HAdV severity of pediatric cases is characterized by low saturation of oxygen (<94%, 33.8%, P = .05) and long duration of oxygen support (≥5 days, 32.7%, P = .02). Severe HAdV infections were described with S. pneumoniae coinfection, which seemed to increase the risk of death. HAdV genotyping identified HAdV‐C as the most common species. Severe ARIs were observed in all HAdV‐identified types. Phylogenetic analysis revealed that sequences were variable suggesting the circulation of different HAdV strains sharing more similarities to strains circulating in Europe or Asia than those from Africa.ConclusionThis first molecular study of HAdV in Tunisia demonstrated that it has an important role in severe ARIs with HAdV‐C being the most common species. S. pneumoniae codetection seems to increase the severity of HAdV‐ARIs.

Molecular evolution of the hemagglutinin-neuraminidase (HN) gene in human respirovirus 3

Human respirovirus 3 (HRV3) is a major causative agent of acute respiratory infections in humans. HRV3 can manifest as a recurrent infection, although exactly how is not known. In the present study, we conducted detailed molecular evolutionary analyses of the major antigen-coding hemagglutinin-neuraminidase (HN) gene of this virus detected/isolated in various countries. We performed analyses of time-scaled evolution, similarity, selective pressure, phylodynamics, and conformational epitope prediction by mapping to HN protein models. In this way, we estimated that a common ancestor of the HN gene of HRV3 and bovine respirovirus 3 diverged around 1815 and formed many lineages in the phylogenetic tree. The evolutionary rates of the HN gene were 1.1 × 10−3 substitutions/site/year, although the majority of these substitutions were synonymous. Some positive and many negative selection sites were predicted in the HN protein. Phylodynamic fluctuations of the gene were observed, and these were different in each lineage. Furthermore, most of the predicted B cell epitopes did not correspond to the neutralization-related mouse monoclonal antibody binding sites. The lack of a link between the conformational epitopes and neutralization sites may explain the naturally occurring HRV3 reinfection.

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.

Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010–2013

BackgroundData on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years. MethodsWorld Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October–April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis. ResultsA total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype. ConclusionsThis study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.

Epidemiological, clinical and genotypic features of human Metapneumovirus in patients with influenza-like illness in Senegal, 2012 to 2016

BackgroundHuman metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal.MethodsThis retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing.ResultsIn total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July–September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014.ConclusionIn summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.

Consensus and variations in cell line specificity among human metapneumovirus strains.

Human metapneumovirus (HMPV) has been a notable etiological agent of acute respiratory infection in humans, but it was not discovered until 2001, because HMPV replicates only in a limited number of cell lines and the cytopathic effect (CPE) is often mild. To promote the study of HMPV, several groups have generated green fluorescent protein (GFP)-expressing recombinant HMPV strains (HMPVGFP). However, the growing evidence has complicated the understanding of cell line specificity of HMPV, because it seems to vary notably among HMPV strains. In addition, unique A2b clade HMPV strains with a 180-nucleotide duplication in the G gene (HMPV A2b180nt-dup strains) have recently been detected. In this study, we re-evaluated and compared the cell line specificity of clinical isolates of HMPV strains, including the novel HMPV A2b180nt-dup strains, and six recombinant HMPVGFP strains, including the newly generated recombinant HMPV A2b180nt-dup strain, MG0256-EGFP. Our data demonstrate that VeroE6 and LLC-MK2 cells generally showed the highest infectivity with any clinical isolates and recombinant HMPVGFP strains. Other human-derived cell lines (BEAS-2B, A549, HEK293, MNT-1, and HeLa cells) showed certain levels of infectivity with HMPV, but these were significantly lower than those of VeroE6 and LLC-MK2 cells. Also, the infectivity in these suboptimal cell lines varied greatly among HMPV strains. The variations were not directly related to HMPV genotypes, cell lines used for isolation and propagation, specific genome mutations, or nucleotide duplications in the G gene. Thus, these variations in suboptimal cell lines are likely intrinsic to particular HMPV strains.

MULTIPLEX RT-PCR BASED DETECTION OF HUMAN BOCAVIRUS AND OTHER RESPIRATORY VIRUSES IN INFANTS AND YOUNG CHILDREN WITH LOWER RESPIRATORY TRACT INFECTION

Background: Human Bocavirus (hBoV) has recently been identified as a causative agent of acute respiratory infection (ARI) in infant and young children. However, there is little information about its frequency and importance as a cause of lower respiratory tract infection (LRTI) in Iraq. Objective:To assess the frequency of hBoV and co-infection rate in infants and young children with LRTI. Methods: Nasopharyngeal/throat swabs were collected during the peak winter months from 100 hospitalized infants and young children less than 5 years of age with LRTI in Baghdad, Iraq. Five viruses were investigated by Multiplex Real-Time Polymerase Chain Reaction (RT-PCR). Results: It was found that 71 (71%) had a viral infection either single or mixed. Six out of 100 samples (6%) were hBoV positive, 10 (10%) were parainfluenza virus positive, 12 (12%) tested positive for adenovirus, 58 (58%) were rhinovirus positive and none of the samples gave positive results for coronavirus. Sixteen samples showed mixed infection with rhinovirus, eight of these (8%) with parainfluenza virus, 6 (6%) with adenovirus, and 2 (2%) with hBoV. There were no significant differences between the viral infected and non-infected patients with respect to age, gender, crowding status, gestational age, diagnosis at presenting and hospital stay (the average stay of viral-infected patients in the hospital was three days). In contrast, exposure to smoking was significantly more associated with viral-infected children than virus-free children (80% vs. 44.83%, P&lt;0.001). In addition, viral-infected children showed significantly less proportion for need for intensive care unit than virus-free children (15.5% vs. 79.31%, P&lt;0.001). Breastfeeding was found to have significant adverse association with viral infection (P&lt;0.001). About one-third of viral-infected children had a medical history involving a disease other than respiratory infection (P&lt;0.001). Finally, viral-infected children were reported to have longer period of illness before hospital admission (6.32±5.49 days) than virus-free children (6.32±5.49 days vs. 3.38±2.37 days, P&lt;0.01). Conclusion: More than two third of children with respiratory tract infection have been viral infection either single or mixed. Multiplex RT-PCR has the potential for clinical use in the rapid and differential detection of viral infection. Keywords: Viral respiratory tract infection, Children, Multiplex Real Time PCR Citation: Rasheed ZS, Al-Shuwaikh AMA, Issa KR. Multiplex RT-PCR based detection of Human Bocavirus and other respiratory viruses in infants and young children with lower respiratory tract infection. Iraqi JMS. 2019; 17(1): 74-82. doi: 10.22578/IJMS.17.1.11