Viral etiology of common cold in children, Finland

Early-life respiratory syncytial virus disease and long-term respiratory health

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infection (LRTI), hospital admission, and mortality in children worldwide. Early-life RSV LRTI has also been associated with subsequent long-term respiratory sequelae, including recurrent LRTI, recurrent wheezing, asthma, and lung function impairment, and these effects can persist into adulthood as chronic respiratory disease. New preventive measures (maternal vaccine or long-acting monoclonal antibodies) have been licensed to reduce the burden of acute RSV LRTI in infants and children at high risk through passive immunisation. Studies of these RSV prevention products show high efficacy and effectiveness, particularly for preventing severe RSV LRTI, with implementation in many high-income countries, but limited access in low-income and middle-income countries (LMICs). These interventions might also reduce the risk of additional health outcomes and long-term morbidity. This Series paper provides the evidence for the long-term effects of early-life RSV disease, discusses mechanisms of disease development, and addresses the potential full public health value of prevention of RSV illness. Further research is needed to determine whether prevention of RSV LRTI or delay of RSV illness in early life might prevent or ameliorate the development of associated long-term respiratory disease. This potential further underscores the urgency for access and availability of new interventions to prevent early-life RSV LRTI in LMICs.

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. We designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2, providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S conformational masking and glycan shielding to balance immune evasion and receptor engagement.

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.

Increasing rhinovirus prevalence in paediatric intensive care patients since the SARS-CoV2 pandemic

BACKGROUND

Rhinovirus (HRV) is a significant seasonal pathogen in children. The emergence of SARS-CoV2, and the social restrictions introduced in, disrupted viral epidemiology. Here we describe the experience of Great Ormond Street Hospital (GOSH), where HRV almost entirely disappeared from the paediatric intensive care units (PICU) during the first national lockdown and then rapidly re-emerged with a fast-increasing incidence, leading to concerns about possible nosocomial transmission in a vulnerable population.

OBJECTIVES

To describe alterations in HRV infection amongst PICU patients at GOSH since the emergence of SARS-COV2 STUDY DESIGN: 10,950 nasopharyngeal aspirate viral PCR samples from GOSH PICU patients from 2019 to 2023 were included. 3083 returned a positive result for a respiratory virus, with 1530 samples positive for HRV. 66 HRV isolates from August 2020 - Jan 2021, the period of rapidly increasing HRV incidence, were sequenced. Electronic health record data was retrospectively collected for the same period.

RESULTS

Following a reduction in the incidence of HRV infection during the first national lockdown, multiple genotypes of HRV emerged amongst GOSH PICU patients, with the incidence of HRV infection rapidly surging to levels higher than that seen prior to the emergence of SARS-CoV2 and continuing to circulate at increased incidence year-round.

CONCLUSIONS

The incidence of HRV infection amongst GOSH PICU patients is markedly higher than prior to the emergence of SARS-CoV2, a pattern not seen in other respiratory viruses. The increased burden of HRV-infection in vulnerable PICU patients has both clinical and infection prevention and control Implications.

Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan

Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.

Rapid syndromic testing for respiratory viral infections in children attending the emergency department during COVID-19 pandemic in Lille, France, 2021-2022

OBJECTIVES

Viral respiratory infections are common in children, and usually associated with non-specific symptoms. Respiratory panel-based testing was implemented during the COVID-19 pandemic, for the rapid differentiation between SARS-CoV-2 and other viral infections, in children attending the emergency department (ED) of the teaching hospital of Lille, northern France, between February 2021 and January 2022.

METHODS

Samples were collected using nasopharyngeal swabs. Syndromic respiratory testing was performed with two rapid multiplex molecular assays: the BioFire® Respiratory Panel 2.1 - plus (RP2.1 plus) or the QIAstat-Dx Respiratory SARS-CoV-2 Panel. SARS-CoV-2 variant was screened using mutation-specific PCR-based assays and genome sequencing.

RESULTS

A total of 3517 children were included in the study. SARS-CoV-2 was detected in samples from 265 children (7.5%). SARS-CoV-2 infected patients were younger than those without SARS-CoV-2 infection (median age: 6 versus 12 months, p < 0.0001). The majority of infections (61.5%) were associated with the Omicron variant. The median weekly SARS-CoV-2 positivity rate ranged from 1.76% during the Alpha variant wave to 24.5% with the emergence of the Omicron variant. Most children (70.2%) were treated as outpatients, and seventeen patients were admitted to the intensive care unit. Other respiratory viruses were more frequently detected in SARS-CoV-2 negative children than in positive ones (82.1% versus 37.4%, p < 0.0001). Human rhinovirus/enterovirus and respiratory syncytial virus were the most prevalent in both groups.

CONCLUSIONS

We observed a low prevalence of SARS-CoV-2 infection in children attending pediatric ED, despite the significant increase due to Delta and Omicron variants, and an important circulation of other respiratory viruses. Severe disease was overall rare in children.

Characteristics and etiology of infection in febrile infants aged ≤90 days

BACKGROUND

Infants ≤90 days old can exhibit non-specific signs of infection, even in cases of serious bacterial infection (SBI).

METHODS

This prospective study included infants aged ≤90 days hospitalized for fever from June 2017 to August 2019. Nasopharyngeal swabs were tested using multiplex real-time polymerase chain reaction (PCR) tests and 16S ribosomal RNA analysis of whole blood to determine causative microorganisms. Data pertaining to inflammatory markers, maximum body temperature (BT), and respiratory symptoms of infants and their cohabiting families were collected at admission.

RESULTS

A total of 110 infants were enrolled (age range, 9-90 days), 17 (15.5%) of whom presented with SBIs. White blood cell (WBC) count and absolute neutrophil count (ANC) were significantly higher in patients with SBIs than in those without, although maximum BT did not significantly differ between the SBI and non-SBI groups (n = 93). One or more viruses were detected in 82 infants (74.5%). Viruses were detected more frequently in infants with respiratory symptoms than in those without respiratory symptoms (P = 0.038), and patients with SBIs experienced significantly less respiratory symptoms than those without SBIs (P = 0.049). Moreover, viruses were more often detected in infants from cohabiting families with respiratory symptoms than in those whose family members did not exhibit respiratory symptoms (P = 0.0018).

CONCLUSION

White blood cell count, and ANC were significantly higher, and respiratory symptoms were less in infants ≤90 days old with SBIs than in those without SBIs. Microorganisms from nasopharyngeal by multiplex real-time PCR swabs could not be judged as SBI or non-SBI.

Pharmacist's recommendations of over-the-counter treatments for the common cold - analysis of prospective cases in Poland

BACKGROUND

Common cold is a frequent illness in northern hemisphere between late autumn and early spring. Patients suffering from it frequently turn to pharmacists instead of physicians in order to receive medical advice and treatment. We studied its treatment advised by pharmacists in Poland, as well as evidence for the efficacy of their recommendations by utilizing a self-developed questionnaire and a study of existing literature.

METHODS

The data were collected by 27 pharmacists who worked in four large network community pharmacies in Lodz, Poland. The study took place from December 2019 to February 2020. Data were recorded only if the patient asked for pharmacy counselling for over-the counter (OTC) products due to common cold self-diagnosis and a product was sold. Pharmacists' recommendations were compared with the results of a literature review of best evidence to determine appropriateness of the pharmacists' decisions.

RESULTS

In four out of five cases the pharmacists recommended products contained paracetamol. In addition, in one out of three patient encounters they advised nasal decongestant, inosines and/or OTC mucolytics. There was a significant relationship between fever and recommendation frequency of some analgesics, inosines, mucolytics and sore throat products (OR > 1, p < 0.05); rhinorrhea and recommendation frequency of paracetamol, inosines, anti-histamines and alpha-mimetics (OR > 1, p < 0.05); cough and recommendation frequency of paracetamol, inosines, mucolytics and sore throat products (OR > 1, p < 0.05); and fatigue and recommendation frequency of paracetamol, acetylsalicylic acid, inosines and sore throat products (OR > 1, p < 0.05). The pharmacist recommendations were based on patients' symptoms, product price, pharmaceutical company promotion and the financial incentive. In many cases their recommendations were not in line with current best practice recommendations.

CONCLUSIONS

Our study suggests that the most common rationale for pharmacist recommendation on anti-common cold treatment was to take a "shotgun" approach. Pharmacists commonly made recommendations for products that lack strong evidence for efficacy (i.e. anti-viral agents) and are potentially unnecessary, based on presentation of the symptom. Reasons for this situation include lack of training, lack of time to evaluate the patient, lack of awareness of evidence as well as drug company marketing and financial incentives (i.e. fulfilling sale plans and target sale bonuses).

TRIAL REGISTRATION

The study was a non-interventional, observational research trial. The study registration was not required.

Changes in Seasonal Respiratory Illnesses in the United States During the Coronavirus Disease 2019 (COVID-19) Pandemic

Background

Respiratory tract infections are common, often seasonal, and caused by multiple pathogens. We assessed whether seasonal respiratory illness patterns changed during the COVID-19 pandemic.

Methods

We categorized emergency department (ED) visits reported to the National Syndromic Surveillance Program according to chief complaints and diagnosis codes, excluding visits with diagnosed SARS-CoV-2 infections. For each week during March 1, 2020 through December 26, 2020 (“pandemic period”), we compared the proportion of ED visits in each respiratory category with the proportion of visits in that category during the corresponding weeks of 2017–2019 (“pre-pandemic period”). We analyzed positivity of respiratory viral tests from two independent clinical laboratories.

Results

During March 2020, cough, shortness of breath, and influenza-like illness accounted for twice as many ED visits compared with the pre-pandemic period. During the last four months of 2020, all respiratory conditions, except shortness of breath, accounted for a smaller proportion of ED visits than during the pre-pandemic period. Percent positivity for influenza virus, respiratory syncytial virus, human parainfluenza virus, adenoviruses, and human metapneumovirus were lower in 2020 than 2019. Although test volume decreased, percent positivity was higher for rhinovirus/enterovirus during the final weeks of 2020 compared with 2019; with ED visits similar to the pre-pandemic period.

Discussion

Broad reductions in respiratory test positivity and respiratory emergency department visits (excluding COVID-19) occurred during 2020. Interventions for mitigating spread of SARS-CoV-2 likely also reduced transmission of other pathogens. Timely surveillance is needed to understand community health threats, particularly when current trends deviate from seasonal norms.

Rhinovirus spread in children during the COVID-19 pandemic despite social restrictions-A nationwide register study in Finland

Social restrictions during the coronavirus disease 2019 pandemic strongly affected the epidemiology of influenza and respiratory syncytial virus (RSV). As rhinovirus seemed to spread despite the restrictions, we aimed to analyze rhinovirus epidemiology in children during the pandemic. This register‐based study used data from the Finnish Infectious Disease Register. Nationwide rhinovirus findings from July 2015 to March 2021 were included and stratified by age (0–4, 5–9, and 10–14). Cumulative 14‐day incidence per 100000 children was calculated. Four thousand five hundred and seventy six positive rhinovirus findings were included, of which 3788 (82.8%) were among children aged 0–4. The highest recorded incidence was 36.2 among children aged 0–4 in October 2017. The highest recorded incidence during the pandemic period was 13.6 in November 2020. The impact of the restrictions was mostly seen among children aged 0–4 years of age in weeks 14–22 in 2020. The incidence has since remained near reference levels in all age groups. Strict restrictions temporarily interrupted the circulation of rhinovirus in spring 2020. Rhinovirus incidence returned to normal levels soon after the harsh restrictions were lifted. These looser social restrictions prevented RSV and influenza seasons but failed to prevent the spread of rhinovirus.

Etiology of Infectious Diseases in Acutely Ill Children at a Pediatric Hospital in Finland

This is a brief report of the etiology of infectious diseases in a pediatric emergency department. Our cohort study of 4647 children demonstrated rhinovirus as the most common etiology in a pediatric emergency department (23%) and intensive care (48%). The population-based incidence of rhinovirus-related visits was 1796/100,000/yr in children <5 years. The most common bacterial pathogen was Escherichia coli (5%).

Human Bocavirus 1 Infection of Well-Differentiated Human Airway Epithelium

Human bocavirus 1 (HBoV1) is a small DNA virus that belongs to the Bocaparvovirus genus of the Parvoviridae family. HBoV1 is a common respiratory pathogen that causes mild to life-threatening acute respiratory tract infections in children and immunocompromised individuals, infecting both the upper and lower respiratory tracts. HBoV1 infection causes death of airway epithelial cells, resulting in airway injury and inflammation. In vitro, HBoV1 only infects well-differentiated (polarized) human airway epithelium cultured at an air-liquid interface (HAE-ALI), but not any dividing human cells. A full-length HBoV1 genome of 5543 nucleotides has been cloned from DNA extracted from a human nasopharyngeal swab into a plasmid called HBoV1 infectious clone pIHBoV1. Transfection of pIHBoV1 replicates efficiently in human embryonic kidney 293 (HEK293) cells and produces virions that are highly infectious. This article describes protocols for production of HBoV1 in HEK293 cells, generation of HAE-ALI cultures, and infection with HBoV1 in HAE-ALI. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Human bocavirus 1 production in HEK293 cells Support Protocol 1: HEK293 cell culture and transfection Support Protocol 2: Quantification of human bocavirus 1 using real-time quantitative PCR Basic Protocol 2: Differentiation of human airway cells at an air-liquid interface Support Protocol 3: Expansion of human airway epithelial cell line CuFi-8 Support Protocol 4: Expansion of human airway basal cells Support Protocol 5: Coating of plastic dishes and permeable membranes of inserts Support Protocol 6: Transepithelial electrical resistance measurement Basic Protocol 3: Human bocavirus 1 infection in human airway epithelium cultured at an air-liquid interface Support Protocol 7: Isolation of infected human airway epithelium cells from inserts Basic Protocol 4: Transduction of airway basal cells with lentiviral vector.

Incidence and clinical features of viral sore throat among children in rural Haryana, India

Background

Sore throat is one of the commonest symptoms that patients present to a primary care physician. We describe the epidemiology of sore throat and performance of an algorithm to predict viral sore throat in a part of India.

Methods

Children below 10 years of age were followed in 4 villages of Haryana, India from Aug 2012 to Aug 2014 through weekly domiciliary visits by trained field workers who screened for symptoms of acute respiratory infection (ARI) including sore throat. Nasal and throat swabs were obtained from a random sample of sore throat cases by nurses and sent in appropriate transport media for real-time polymerase chain reaction for detection of viral nucleic acid. Incidence of sore throat and viral sore throat are reported as number of sore throat episodes per 1000 child-years (EPTCY) with 95% confidence-interval (CI). Symptoms, associated with viral sore throat were identified by logistic regression, combined into a clinical score and Receiver Operating Characteristic curve was plotted.

Results

Over a two-year period, 3765 children were followed up for 5578 child years. 1069 episodes of sore throat were reported, and swabs were collected from 8% of the cases randomly. The incidence of sore throat and viral sore throat was 191.7 (95%CI: 180.5-203.6) and 60.1 (95%CI: 55.1-68.2) EPTCY, respectively. Fever (aOR 5.40,95%CI: 1.16-25.18) and running nose (aOR 10.16,95%CI: 1.01-102.42) was significantly associated with viral sore throat. The clinical score (fever, running nose, and headache) had an overall sensitivity of 86.2% (68.3-96.1%), specificity of 62% (47.2-75.3%) and AUC of 0.78 (0.67-0.87) in predicting viral sore throat.

Conclusion

Viruses contributed to one-third of burden of sore throat and clinical score can be used in primary care settings to aid antibiotic prescription by physicians.

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.

Inactivated influenza vaccine does not reduce all cause respiratory illness in children with pre-existing medical conditions

BACKGROUND

The effectiveness of inactivated influenza vaccine (IIV) immunization in preventing all cause respiratory illness (RI) in children with pre-existing medical conditions has not been fully established and varies from season to season. This study aims to quantify the overall impact of IIV immunization on primary care attended RI episodes in children with pre-existing medical conditions, using robust observational data spanning twelve influenza seasons.

METHODS

Electronic records of IIV eligible children aged 6 months to 18 years were extracted from primary care databases over the years 2004-2015. IIV eligibility criteria according to Dutch guidelines included (chronic) respiratory and cardiovascular disease and diabetes mellitus. For each year, information on IIV immunization status, primary care attended RI episodes (including influenza, acute respiratory tract infections and asthma exacerbations) and potential confounders were collected. Generalized estimating equations were used to model the association between IIV status and occurrence of at least one RI episode during the influenza epidemic period with "current year immunized" as reference group. Robustness of findings were assessed by performing various sensitivity analyzes in which (i) seasons with a mismatch between the dominant circulating influenza virus and vaccine strain were excluded, (ii) influenza periods were further restricted to weeks with at least 30% influenza virus positive specimens in sentinel surveillance (instead of 5%), (iii) propensity scores were used to adjust for confounding.

RESULTS

In total, 11,797 children (follow-up duration: 38,701 child-years) were eligible for IIV for ≥ one season with 29% immunized at least once. The adjusted odds for primary care attended RI episodes during the influenza epidemic period did not differ between current season immunized versus not immunized children (adjusted OR:1.01; 95%CI:0.90-1.13). The various sensitivity analysis showed comparable results.

CONCLUSIONS

IIV immunization in children with pre-existing medical conditions does not reduce all cause RI episodes encountered in primary care during the influenza season.

Evidence for respiratory viruses interactions in asymptomatic preschool-aged children

Aim

To prospectively evaluate interferences between viruses of the upper respiratory tract in asymptomatic preschool children.

Methods

Nasal-pharyngeal swabs from 233 preschool aged children were prospectively collected over four consecutive time periods, during one school year. The samples were tested using a RT-PCR DNA/RNA microarray system for nine respiratory viruses.

Results

Respiratory syncytial virus (RSV) was a predictor of the presence of influenza virus (INFL) (OR: 9.12, CI: 1.52–54.75, p = 0.016), and similarly, INFL predicted the presence of RSV (OR: 4.01, CI: 1.14–14.16, p = 0.030). Also, rhinovirus (RV) was a predictor of adenovirus (ADV) presence (OR: 3.66, CI: 1.10–12.14, p = 0.034), and similarly, ADV predicted the presence of RV (OR: 4.05, CI: 1.02–16.05, p = 0.046). No other significant associations between viruses were observed.

Conclusion

Our results indicate that respiratory viruses found in carrier stage in asymptomatic children may interact with other viruses and even facilitate their settling in the upper respiratory tract. The pathophysiological role of these interactions is not yet clear.

Viruses associated with acute respiratory infection in a community-based cohort of healthy New Zealand children

Acute respiratory infections (ARIs) are a major cause of morbidity among children. Respiratory viruses are commonly detected in both symptomatic and asymptomatic periods. The rates of infection and community epidemiology of respiratory viruses in healthy children needs further definition to assist interpretation of molecular diagnostic assays in this population. Children otherwise healthy aged 1 to 8 years were prospectively enrolled in the study during two consecutive winters, when ARIs peak in New Zealand. Parents completed a daily symptom diary for 8 weeks, during which time they collected a nasal swab from the child for each clinical ARI episode. A further nasal swab was collected by research staff during a clinic visit at the conclusion of the study. All samples were tested for 15 respiratory viruses commonly causing ARI using molecular multiplex polymerase chain reaction assays. There were 575 ARIs identified from 301 children completing the study, at a rate of 1.04 per child‐month. Swabs collected during an ARI were positive for a respiratory virus in 76.8% (307 of 400), compared with 37.3% (79 of 212) of swabs collected during asymptomatic periods. The most common viruses detected were human rhinovirus, coronavirus, parainfluenza viruses, influenzavirus, respiratory syncytial virus, and human metapneumovirus. All of these were significantly more likely to be detected during ARIs than asymptomatic periods. Parent‐administered surveillance is a useful mechanism for understanding infectious disease in healthy children in the community. Interpretation of molecular diagnostic assays for viruses must be informed by understanding of local rates of asymptomatic infection by such viruses.

During winter, children experienced acute respiratory infections at a rate of 1.04/month.

A virus was detected in 76.8% of acute respiratory infections.

Specific viruses are more likely to be associated with respiratory symptoms.

Association between viral seasonality and meteorological factors

Numerous viruses can cause upper respiratory tract infections. They often precede serious lower respiratory tract infections. Each virus has a seasonal pattern, with peaks in activity in different seasons. We examined the effects of daily local meteorological data (temperature, relative humidity, “humidity-range” and dew point) from Edinburgh, Scotland on the seasonal variations in viral transmission. We identified the seasonality of rhinovirus, adenovirus, influenza A and B viruses, human parainfluenza viruses 1–3 (HPIV), respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) from the 52060 respiratory samples tested between 2009 and 2015 and then confirmed the same by a generalised linear model. We also investigated the relationship between meteorological factors and viral seasonality. Non-enveloped viruses were present throughout the year. Following logistic regression adenovirus, influenza viruses A, B, RSV and HMPV preferred low temperatures; RSV and influenza A virus preferred a narrow “humidity-range” and HPIV type 3 preferred the season with lower humidity. A change (i.e. increase or decrease) in specific meteorological factors is associated with an increase in activity of specific viruses at certain times of the year.

Phylogenetic analysis of protein sequences based on a novel k-mer natural vector method

Based on the k-mer model for protein sequence, a novel k-mer natural vector method is proposed to characterize the features of k-mers in a protein sequence, in which the numbers and distributions of k-mers are considered. It is proved that the relationship between a protein sequence and its k-mer natural vector is one-to-one. Phylogenetic analysis of protein sequences therefore can be easily performed without requiring evolutionary models or human intervention. In addition, there exists no a criterion to choose a suitable k, and k has a great influence on obtaining results as well as computational complexity. In this paper, a compound k-mer natural vector is utilized to quantify each protein sequence. The results gotten from phylogenetic analysis on three protein datasets demonstrate that our new method can precisely describe the evolutionary relationships of proteins, and greatly heighten the computing efficiency.

Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico

Background

Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections.

Methods

This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR.

Results

The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age.

Conclusion

In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.

Human Parvoviruses

Parvovirus B19 (B19V) and human bocavirus 1 (HBoV1), members of the large Parvoviridae family, are human pathogens responsible for a variety of diseases. For B19V in particular, host features determine disease manifestations. These viruses are prevalent worldwide and are culturable in vitro, and serological and molecular assays are available but require careful interpretation of results. Additional human parvoviruses, including HBoV2 to -4, human parvovirus 4 (PARV4), and human bufavirus (BuV) are also reviewed. The full spectrum of parvovirus disease in humans has yet to be established. Candidate recombinant B19V vaccines have been developed but may not be commercially feasible. We review relevant features of the molecular and cellular biology of these viruses, and the human immune response that they elicit, which have allowed a deep understanding of pathophysiology.

Infectious Diseases of Children

Infections are the most common cause of acute illness in children. Most commonly these are respiratory infections which peak when the child starts to go to school or out-of-home day care. Although the majority of these diseases have benign course, they cause significant discomfort, anxiety, missed work, and stress to many families caring for children. Frequent office visits, and unnecessarily prescribed medications, and sometimes dubious home remedies can be reduced by following best evidence-based practice and having a good doctor-patient (and parent) relationship.

Rhinovirus Detection in Symptomatic and Asymptomatic Children: Value of Host Transcriptome Analysis

RATIONALE

Rhinoviruses (RVs) are a major cause of symptomatic respiratory tract infection in all age groups. However, RVs can frequently be detected in asymptomatic individuals.

OBJECTIVES

To evaluate the ability of host transcriptional profiling to differentiate between symptomatic RV infection and incidental detection in children.

METHODS

Previously healthy children younger than 2 years old (n = 151) were enrolled at four study sites and classified into four clinical groups: RV- healthy control subjects (n = 37), RV+ asymptomatic subjects (n = 14), RV+ outpatients (n = 30), and RV+ inpatients (n = 70). Host responses were analyzed using whole-blood RNA transcriptional profiles.

MEASUREMENTS AND MAIN RESULTS

RV infection induced a robust transcriptional signature, which was validated in three independent cohorts and by quantitative real-time polymerase chain reaction with high prediction accuracy. The immune profile of symptomatic RV infection was characterized by overexpression of innate immunity and underexpression of adaptive immunity genes, whereas negligible changes were observed in asymptomatic RV+ subjects. Unsupervised hierarchical clustering identified two main clusters of subjects. The first included 93% of healthy control subjects and 100% of asymptomatic RV+ subjects, and the second comprised 98% of RV+ inpatients and 88% of RV+ outpatients. Genomic scores of healthy control subjects and asymptomatic RV+ children were similar and significantly lower than those of RV+ inpatients and outpatients (P < 0.0001).

CONCLUSIONS

Symptomatic RV infection induced a robust and reproducible transcriptional signature, whereas identification of RV in asymptomatic children was not associated with significant systemic transcriptional immune responses. Transcriptional profiling represents a useful tool to discriminate between active infection and incidental virus detection.

Respiratory Virus Detection and Clinical Diagnosis in Children Attending Day Care

BACKGROUND

Respiratory viruses often have been studied in children with respiratory tract infection (RTI), but less knowledge exists about viruses in asymptomatic children. We have studied the occurrence of a broad panel of respiratory viruses in apparently healthy children attending day care, taking into account the influence of possible confounding factors, such as age, clinical signs of respiratory tract infection (RTI), location (day-care section) and season.

METHODS

We have studied 161 children in two day-care centers, each with separate sections for younger and older children, during four autumn and winter visits over a two-year period. A total of 355 clinical examinations were performed, and 343 nasopharyngeal samples (NPS) were analyzed by semi-quantitative, real-time, polymerase chain reaction (PCR) tests for 19 respiratory pathogens.

RESULT

Forty-three percent of all NPS were PCR-positive for ≥ 1 of 13 virus species, with high species variation during visits. Rhinovirus 26% (88/343 NPS), enterovirus 12% (40/343) and parechovirus 9% (30/343) were detected in every visit, and the rates varied in relation to age, day-care section and season. Ten other viruses were detected in ≤ 3% of the NPS. Generally, viruses occurred together in the NPS. In 24% (79/331) of the clinical examinations with available NPS, the children had clear signs of RTI, while in 41% (135/331) they had mild signs, and in 35% (117/331) the children had no signs of RTI. Moreover, viruses were found in 70% (55/79) of children with clear signs of RTI, in 41% (55/135) with mild signs and in 30% (35/117) without any signs of RTI (p < 0.001).

CONCLUSIONS

Positive PCR tests for respiratory viruses, particularly picornaviruses, were frequently detected in apparently healthy children attending day care. Virus detection rates were related to age, presence of clinical signs of RTI, location in day care and season.

Respiratory viruses and children

Respiratory viruses place a great disease burden especially on the youngest children in terms of high rates of infection, bacterial complications and hospitalizations. In developing countries, some viral infections are even associated with substantial mortality in children. The interaction between viruses and bacteria is probably much more common and clinically significant than previously understood. Respiratory viruses frequently initiate the cascade of events that ultimately leads to bacterial infection. Effective antiviral agents can substantially shorten the duration of the viral illness and prevent the development of bacterial complications. Viral vaccines have the potential to not only prevent the viral infection but also decrease the incidence of bacterial complications. At present, antivirals and vaccines are only available against influenza viruses, but new vaccines and antivirals against other viruses, especially for RSV, are being developed.

Lung Infection by Human Bocavirus Induces the Release of Profibrotic Mediator Cytokines In Vivo and In Vitro

Human Bocavirus subtype 1 (HBoV1) is associated with respiratory diseases and may contribute to chronic lung diseases by persisting in the infected host. Here the question was addressed if HBoV infections could contribute to fibrogenesis processes as suggested by previously published clinical observations. Cytokine profiles induced by HBoV infection in CuFi-8 air-liquid interphase cell cultures and in bronchoalveolar lavage fluid (BALF) of 20 HBoV-positive and 12 HBoV-negative patients were analysed by semi-quantitative Western spot blot analyses. Although lots of cytokines were regulated independently of HBoV status, several cytokines associated with lung fibrosis and tumour development, e.g., EGF, VEGF, TARC (CCL17), TNF-α, TNF-β, TIMP-1, were clearly upregulated in the HBoV-positive cohort. These findings suggest that the development of lung fibrosis might be triggered by HBoV induced cytokine expression.

Comprehensive real-time epidemiological data from respiratory infections in Finland between 2010 and 2014 obtained from an automated and multianalyte mariPOC® respiratory pathogen test

Respiratory viruses cause seasonal epidemics every year. Several respiratory pathogens are circulating simultaneously and typical symptoms of different respiratory infections are alike, meaning it is challenging to identify and diagnose different respiratory pathogens based on symptoms alone. mariPOC® is an automated, multianalyte antigen test which allows the rapid detection of nine respiratory infection pathogens [influenza A and B viruses, respiratory syncytial virus (RSV), human metapneumovirus, adenovirus, parainfluenza 1–3 viruses and pneumococci] from a single nasopharyngeal swab or aspirate samples, and, in addition, can be linked to laboratory information systems. During the study period from November 2010 to June 2014, a total of 22,485 multianalyte respi tests were performed in the 14 participating laboratories in Finland and, in total, 6897 positive analyte results were recorded. Of the tested samples, 25 % were positive for one respiratory pathogen, with RSV (9.8 %) and influenza A virus (7.2 %) being the most common findings, and 0.65 % of the samples were multivirus-positive. Only small geographical variations in seasonal epidemics occurred. Our results show that the mariPOC® multianalyte respi test allows simultaneous detection of several respiratory pathogens in real time. The results are reliable and give the clinician a picture of the current epidemiological situation, thus minimising guesswork.

Viral aetiology of common colds of outpatient children at primary care level and the use of antibiotics

Although antibiotics are ineffective against viral respiratory infections, studies have shown high rates of prescriptions worldwide. We conducted a study in Brazil to determine the viral aetiologies of common colds in children and to describe the use of antibiotics for these patients. Children up to 12 years with common colds were enrolled from March 2008-February 2009 at a primary care level facility and followed by regular telephone calls and medical consultations. A nasopharyngeal wash was obtained at enrollment and studied by direct fluorescence assay and polymerase chain reaction for nine different types of virus. A sample of 134 patients was obtained, median age 2.9 years (0.1-11.2 y). Respiratory viruses were detected in 73.9% (99/134) with a coinfection rate of 30.3% (30/99). Rhinovirus was the most frequent virus (53/134; 39.6%), followed by influenza (33/134; 24.6%) and respiratory syncytial virus (8/134; 13.4%). Antibiotic prescription rate was 39.6% (53/134) and 69.8% (37/53) were considered inappropriate. Patients with influenza infection received antibiotics inappropriately in a greater proportion of cases when compared to respiratory syncytial virus and rhinovirus infections (p = 0.016). The rate of inappropriate use of antibiotics was very high and patients with influenza virus infection were prescribed antibiotics inappropriately in a greater proportion of cases.

Review of Non-Bacterial Infections in Respiratory Medicine: Viral Pneumonia

Although bacteria are the main pathogens involved in community-acquired pneumonia, a significant number of community-acquired pneumonia are caused by viruses, either directly or as part of a co-infection. The clinical picture of these different pneumonias can be very similar, but viral infection is more common in the pediatric and geriatric populations, leukocytes are not generally elevated, fever is variable, and upper respiratory tract symptoms often occur; procalcitonin levels are not generally affected. For years, the diagnosis of viral pneumonia was based on cell culture and antigen detection, but since the introduction of polymerase chain reaction techniques in the clinical setting, identification of these pathogens has increased and new microorganisms such as human bocavirus have been discovered. In general, influenza virus type A and syncytial respiratory virus are still the main pathogens involved in this entity. However, in recent years, outbreaks of deadly coronavirus and zoonotic influenza virus have demonstrated the need for constant alert in the face of new emerging pathogens. Neuraminidase inhibitors for viral pneumonia have been shown to reduce transmission in cases of exposure and to improve the clinical progress of patients in intensive care; their use in common infections is not recommended. Ribavirin has been used in children with syncytial respiratory virus, and in immunosuppressed subjects. Apart from these drugs, no antiviral has been shown to be effective. Prevention with anti-influenza virus vaccination and with monoclonal antibodies, in the case of syncytial respiratory virus, may reduce the incidence of pneumonia.

Seasonal variations of respiratory viruses and etiology of human rhinovirus infection in children

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Nasal aspirates were subjected to real-time PCR to detect 16 respiratory viruses.

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One or more viruses were detected in 83% of specimens.

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Rhinoviruses were the most frequently detected viruses.

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Seasonal distribution was seen for each virus.

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The clinical severity did not differ among main respiratory viral infections.

Background

Using the polymerase chain reaction (PCR) method it is possible to detect uncultivable viruses and discover multiple viral infections. However, the clinical importance of these findings in relation to symptoms is not known.

Objectives

The seasonal fluctuations of respiratory viruses and the clinical outcomes of single infections and dual infections were investigated.

Study design

Nasal aspirate samples were obtained from outpatients and inpatients of a children’s hospital and these samples were subjected to real-time PCR to detect 16 respiratory viruses. Seasonal variations of the 16 viruses and the clinical outcomes such as wheezing, the need for oxygenation and prolonged hospitalization of patients with single viral infections and multiple infections were determined for the 5 most often detected viruses.

Results

Among 512 specimens analyzed, one or more viruses were detected in 424 (83%) specimens. Two or more viruses were detected in 160 samples (31% of all samples). The epidemic peaks of the viruses did not coincide with each other. Rhinoviruses were the most frequently detected viruses and their coinfection rates were also higher. However, the disease severity in the lower respiratory tract did not differ in most respiratory viral infections regardless of whether there was single infection or dual infection with a rhinovirus and other respiratory virus.

Conclusions

Seasonal distribution was seen for each virus. There were no significant differences in clinical symptoms in the children studied. Because the infection of rhinoviruses is the common occurrence in children, it is hypothesized that the factors related to disease severity are mainly the underlying conditions of the children.

Molecular epidemiology of severe respiratory disease by human rhinoviruses and enteroviruses at a tertiary paediatric hospital in Barcelona, Spain

In order to describe the molecular epidemiology of human rhinovirus (HRV) and enterovirus (EV) infection in severely ill children, we studied all episodes of bronchospasm/bronchopneumonia in 6-month-old to 18-year-old patients from January 2010 to May 2012 who required mechanical ventilation. HRV/EVs were detected in 55 (57.3%) of 96 patients, of which 50 (91%) were HRV (HRV-A, 16; HRV-B, 1; HRV-C, 18) and 5 (9%) were EVs (EV-D68, 3). No significant differences in epidemiologic and clinical characteristics were found between different types. In six of the 13 patients who required invasive mechanical ventilation, HRV was the only pathogen detected.

Review of Non-Bacterial Infections in Respiratory Medicine: Viral Pneumonia

Although bacteria are the main pathogens involved in community-acquired pneumonia, a significant number of community-acquired pneumonia are caused by viruses, either directly or as part of a co-infection. The clinical picture of these different pneumonias can be very similar, but viral infection is more common in the pediatric and geriatric populations, leukocytes are not generally elevated, fever is variable, and upper respiratory tract symptoms often occur; procalcitonin levels are not generally affected. For years, the diagnosis of viral pneumonia was based on cell culture and antigen detection, but since the introduction of polymerase chain reaction techniques in the clinical setting, identification of these pathogens has increased and new microorganisms such as human bocavirus have been discovered. In general, influenza virus type A and syncytial respiratory virus are still the main pathogens involved in this entity. However, in recent years, outbreaks of deadly coronavirus and zoonotic influenza virus have demonstrated the need for constant alert in the face of new emerging pathogens. Neuraminidase inhibitors for viral pneumonia have been shown to reduce transmission in cases of exposure and to improve the clinical progress of patients in intensive care; their use in common infections is not recommended. Ribavirin has been used in children with syncytial respiratory virus, and in immunosuppressed subjects. Apart from these drugs, no antiviral has been shown to be effective. Prevention with anti-influenza virus vaccination and with monoclonal antibodies, in the case of syncytial respiratory virus, may reduce the incidence of pneumonia.

Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China

BACKGROUND

Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China.

METHODS

Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses--influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV)--by multiplex real-time PCR.

RESULTS

We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3.

CONCLUSIONS

This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies.

Chimeric rhinoviruses obtained via genetic engineering or artificially induced recombination are viable only if the polyprotein coding sequence derives from the same species

Recombination is a widespread phenomenon that ensures both the stability and variation of RNA viruses. This phenomenon occurs with different frequencies within species of the Enterovirus genus. Intraspecies recombination is described frequently among non-rhinovirus enteroviruses but appears to be sporadic in rhinoviruses. Interspecies recombination is even rarer for rhinoviruses and mostly is related to ancient events which contributed to the speciation of these viruses. We reported that artificially engineered 5' untranslated region (UTR) interspecies rhinovirus/rhinovirus or rhinovirus/non-rhinovirus enterovirus recombinants are fully viable. Using a similar approach, we demonstrated in this study that exchanges of the P1-2A polyprotein region between members of the same rhinovirus species, but not between members of different species, give rise to competent chimeras. To further assess the rhinovirus intra- and interspecies recombination potential, we used artificially induced recombination by cotransfection of 5'-end-deleted and 3'-end-deleted and replication-deficient genomes. In this system, intraspecies recombination also resulted in viable viruses with high frequency, whereas no interspecies rhinovirus recombinants could be recovered. Mapping intraspecies recombination sites within the polyprotein highlighted recombinant hotspots in nonstructural genes and at gene boundaries. Notably, all recombinants occurring at gene junctions presented in-frame sequence duplications, whereas most intragenic recombinants were homologous. Taken together, our results suggest that only intraspecies recombination gives rise to viable rhinovirus chimeras in the polyprotein coding region and that recombination hotspots map to nonstructural genes with in-frame duplications at gene boundaries. These data provide new insights regarding the mechanism and limitations of rhinovirus recombination.

IMPORTANCE

Recombination represents a means to ensure both the stability and the variation of RNA viruses. While intraspecies recombination is described frequently among non-rhinovirus enteroviruses, it seems to occur more rarely in rhinoviruses. Interspecies recombination is even rarer in this virus group and is mostly related to ancient events, which contributed to its speciation. We used engineered chimeric genomes and artificially induced RNA recombination to study experimentally the recombination potential of rhinoviruses and analyze recombination sites. Our results suggest that only intraspecies recombination gives rise to viable chimeras in the polyprotein coding region. Furthermore, characterization of intraspecies chimeras provides new insight into putative recombination hotspots within the polyprotein. In summary, we applied two powerful and complementary experimental approaches to improve current knowledge on rhinovirus recombination.

Is there still room for novel viral pathogens in pediatric respiratory tract infections?

Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.

The use of a multiplex real-time PCR assay for diagnosing acute respiratory viral infections in children attending an emergency unit

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Evaluate the use of multiplex real-time PCR for diagnosing respiratory infections.

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857/966 samples from 914 children were positive for one or multiple viruses.

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Respiratory syncytial virus and rhinovirus were the most prevalent.

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Co-infections were associated with severe respiratory symptoms.

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The spread of respiratory viruses returned to the one it was before the flu outbreak.

Background

The use of a multiplex molecular technique to identify the etiological pathogen of respiratory viral infections might be a support as clinical signs are not characteristic.

Objectives

The aim of the study was to evaluate a multiplex molecular real-time assay for the routine diagnosis of respiratory viruses, to analyze the symptoms associated with the pathogens detected and to determine the spread of virus during the period.

Study design

Respiratory samples were collected from children presenting with respiratory symptoms and attending the emergency unit during the 2010–2011 winter seasons. Samples were tested with the multiplex RespiFinder^® 15 assay (PathoFinder™) which potentially detects 15 viruses.

Results

857 (88.7%) of the 966 samples collected from 914 children were positive for one (683 samples) or multiple viruses (174 samples). The most prevalent were the respiratory syncytial virus (39.5%) and the rhinovirus (24.4%). Influenza viruses were detected in 139 (14.4%) samples. Adenovirus was detected in 93 (9.6%) samples, coronaviruses in 88 (9.1%), metapneumovirus in 51 (5.3%) and parainfluenzae in 47 (4.9%). Rhinovirus (40%) was the most prevalent pathogen in upper respiratory tract infections while respiratory syncytial virus (49.9%) was the most prevalent in lower respiratory tract infections. Co-infections were associated with severe respiratory symptoms.

Conclusion

The multiplex assay detected clinically important viruses in a single genomic test and thus will be useful for detecting several viruses causing respiratory tract disorders.

Neutralizing antibody responses to enterovirus and adenovirus in healthy adults in China

Hand, foot and mouth disease (HFMD) is an important public health problem that has emerged over the past several years. HFMD predominantly infects children under seven years old and occasionally causes severe disease in adults. Among the enteroviruses, enterovirus 71 (EV71) and coxsackievirus 16 (CA16) are the major causative agents of HFMD. In addition, adenovirus cocirculates with enterovirus and has become a possible additional pathogenic factor for HFMD in some cases. Here, we have investigated the neutralizing antibody responses to both enterovirus and adenovirus in adults, with the aim of exploring the prevalence trends of these viruses and the nature of protective immunity in humans to these viral infections. Sera from 391 healthy adults from 21 provinces and cities in China were tested for the presence of antibodies against EV71, CA16, adenovirus human serotype 5 (AdHu5) and chimpanzee adenovirus pan7 (AdC7) using neutralization tests. High seroprevalence rates of EV71, CA16 and AdHu5 were found in the population (85.7%, 58.8% and 74.2%, respectively). The coseropositivity rate of these three viruses was 39.4% (154 of 391), with median neutralizing antibody titers of 80, 40 and 640, respectively, and the neutralizing antibody titer for EV71 was found to be correlated with those of CA16 and AdHu5. AdC7 was found to be a rare adenovirus serotype in the human population, with a seropositivity rate of 11.8%, suggesting that it could be a good choice for a vaccine carrier that could be used in vaccine development.

Human rhino- and enteroviruses in children with respiratory symptoms in Luanda, Angola

OBJECTIVES

The role of human rhinoviruses (HRV) and human enteroviruses (HEV) in common colds, as well as their seasonality, remains largely unknown in tropical environments. The study aimed to define the frequency and clinical features of HRV and HEV in children with respiratory symptoms in tropical Africa during autumn and winter.

METHODS

Clinical data and PCR assays of nasopharyngeal swabs (NPS) were collected from 67 (66%) children with and 35 (34%) children without chronic illnesses who were attending different outpatient clinics at a paediatric tertiary-care hospital in Luanda, Angola.

RESULTS

Thirty-six (35%) children had HIV infection, and 27 (26%) were malnourished. Thirty-seven (36%) out of 102 NPS specimens were virus-positive: 34 (33%) for HRV and 10 (10%) for HEV. Seven (7%) had co-infection. The highest HRV-positivity rate (47%) occurred in July (P = 0·02), a mid-winter month with high relative humidity but no precipitation. Virus positivity was associated with younger age (median 36 vs 52 months, P = 0·02) but not with specific symptoms or findings.

CONCLUSIONS

HRVs play a major role in young children's respiratory infections in urban tropical Angola during autumn and winter. A better understanding is required of the seasonality and clinical outcomes of these viruses in children living in resource-poor tropical countries.

Human rhinovirus and disease severity in children

OBJECTIVE

To evaluate retrospectively human rhinovirus (HRV) infections in children up to 5 years old and factors involved in disease severity.

METHODS

Nasopharyngeal aspirates from 434 children presenting a broad range of respiratory infection symptoms and severity degrees were tested for presence of HRV and 8 other respiratory viruses. Presence of host risk factors was also assessed.

RESULTS

HRV was detected in 181 (41.7%) samples, in 107 of them as the only agent and in 74 as coinfections, mostly with respiratory syncytial virus (RSV; 43.2%). Moderate to severe symptoms were observed in 28.9% (31/107) single infections and in 51.3% (38/74) coinfections (P = .004). Multivariate analyses showed association of coinfections with lower respiratory tract symptoms and some parameters of disease severity, such as hospitalization. In coinfections, RSV was the most important virus associated with severe disease. Prematurity, cardiomyopathies, and noninfectious respiratory diseases were comorbidities that also were associated with disease severity (P = .007).

CONCLUSIONS

Our study showed that HRV was a common pathogen of respiratory disease in children and was also involved in severe cases, causing symptoms of the lower respiratory tract. Severe disease in HRV infections were caused mainly by presence of RSV in coinfections, prematurity, congenital heart disease, and noninfectious respiratory disease.

Genetic analysis of human parainfluenza viruses circulating in Korea, 2006

Human parainfluenza viruses (HPIV) are important causes of respiratory tract infections in young children. To characterize the molecular epidemiology of an HPIV outbreak occurring in Korea during 2006, genetic analysis of 269 cell culture isolates from HPIV-infected children, was conducted using nested reverse transcription-PCR (RT-PCR). HPIV-1 was detected in 70.3% of tested samples (189/269). The detection rate of HPIV-2 and HPIV-3 was 1.5% (4/269) and 9.3% (25/269), respectively. Mixed HPIV-1, -2 and -3 infections were detected in 19.0% (51/269): HPIV-1 and HPIV-2 in 15, HPIV-1 and HPIV-3 in 26, HPIV-2 and HPIV-3 in 6, and HPIV-1, -2 and -3 in 4. Of these positive samples for three different types HIPV-1, -2, and -3, two each representative strains were selected, the full length of hemagglutinin-neuraminidase (HN) gene for HPIV was amplified by RT-PCR, and sequenced. Multiple alignment analysis, based on reference sequence of HPIV-1, -2, and -3 strains available in GenBank, showed that the identity of nucleotide and deduced amino acid sequences was 92.4-97.6% and 92.7-97.9%, respectively, for HPIV-1, 88.5-99.8% and 88.6-100% for HPIV-2, and 96.3-99.5% and 95.0-99.3% for HPIV-3, respectively. Phylogenetic analysis showed that HPIV-1, -2, and -3 strains identified in this study were closely related among the strains in the same type with no significant genetic variability. These results show that HPIV of multiple imported sources was circulating in Korea.

[Upper airway infections]

Background

Upper airway infections contribute significantly to paediatric morbidity and hospitalization especially of young children, are often treated polypragmatically, and are one of the main reasons for antibiotic prescriptions. The severity varies between mild, self-limiting and potentially life-threatening airway obstructions.

Diagnosis

The physician involved can normally make the right diagnosis based on the patient's history and physical findings; additional diagnostic procedures (blood tests, imaging) should be restricted to unclear cases.

Therapy

Antibiotic stewardship should be applied. Imminent airway obstruction will require early and competent paediatric intensive care interventions. Since viral and bacterial upper airway infections can present with similar features, it is useful to approach them under topographical aspects.

Prevention

Following immunization recommendations can prevent an enormous amount of severe potentially life threatening airway infections.

Distribution of influenza and other acute respiratory viruses during the first year after the 2009-2010 influenza pandemic in the English- and Dutch-speaking Caribbean countries

BACKGROUND

Limited specimen collection and testing for influenza occurred in the English and Dutch-speaking Caribbean countries prior to the 2009/2010 influenza pandemic. Caribbean Epidemiology Centre (CAREC) member countries rapidly mobilized to collect specimens during the pandemic and a vast majority of confirmed cases during the pandemic period were influenza A(H1N1)pdm09.

OBJECTIVES

To describe the aetiology and distribution of acute respiratory illness (ARI) among laboratory confirmed cases during the first year after the 2009/2010 influenza pandemic in the English- and Dutch-speaking Caribbean.

RESULTS

In total, 774 specimens were tested and 394 (52.7%) cases had positive laboratory confirmation. Respiratory syncytial virus (RSV) (28.4%) and influenza A(H3N2) (23.1%) were most frequently detected. RSV activity peaked in July 2011 while influenza A(H3N2) peaked in October 2010. Influenza was responsible for illness in greater numbers in persons 15-64 years while RSV was seen in primarily in children<5 years and adults>65 years. Other agents confirmed include rhinovirus (12.9%), influenza B (10.9%) and influenza A(H1N1)pdm09 (9.4%).

CONCLUSIONS

RSV and influenza A(H3N2) were the most common viruses identified during the first year after the influenza A(H1N1)pdm09 pandemic. Influenza was detected every month with peak activity corresponding to that typically seen in North America (October to March). In order to determine the seasonality of influenza and RSV, laboratory data from subsequent years and increased specimen submission is needed.