• antibody phage display technology
• biosensors
• detection methods
• viruses

• 22-24-00417 Russian Science Foundation

Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.

• Cure research
• DNA
• Digital PCR
• HIV
• Infectious diseases
• PCR sensitivity
• RNA
• Virus

• COVID-19/diagnosis
• HIV Infections/diagnosis
• Humans
• RNA, Viral/analysis
• RNA, Viral/genetics
• Real-Time Polymerase Chain Reaction
• SARS-CoV-2/genetics
• Sensitivity and Specificity

• 75N91019D00024 NCI NIH HHS
• HHSN261200800001C NCI NIH HHS
• HHSN261200800001E NCI NIH HHS
• Z99 CA999999 Intramural NIH HHS

• Antibodies
• Electrical impedance
• Piezoelectric resonator
• Virus detection
• Viruses

• Animals
• Antibodies
• Biosensing Techniques/methods
• Electric Impedance
• Swine
• Viruses

• ARMS
• COVID-19
• SARS-CoV-2
• clade
• multiplex PCR
• mutations

• COVID-19/diagnosis
• COVID-19/virology
• COVID-19 Nucleic Acid Testing/economics
• COVID-19 Nucleic Acid Testing/methods
• Cost-Benefit Analysis
• Genotype
• Humans
• Multiplex Polymerase Chain Reaction
• Mutation
• Phylogeny
• Reproducibility of Results
• SARS-CoV-2/classification
• SARS-CoV-2/genetics
• SARS-CoV-2/isolation & purification

• HIV cure research
• RNA
• RT-ddPCR
• Raindance
• SIV
• Viral reservoir

Tracing the globally circulating severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) phylogenetic clades by high‐throughput sequencing is costly, time‐consuming, and labor‐intensive. We here propose a rapid, simple, and cost‐effective amplification refractory mutation system (ARMS)‐based multiplex reverse‐transcription polymerase chain reaction (PCR) assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. Our multiplex PCR is designed in a mutually exclusive way to identify V–S and G–GH–GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized with 0.2–0.6 µM primer concentration, 56–60°C annealing temperature, and 3–5 ng/µl complementary DNA to validate on 24 COVID‐19‐positive samples. Targeted Sanger sequencing further confirmed the presence of the clade‐featured mutations with another set of primers. This multiplex ARMS‐PCR assay is a fast, low‐cost alternative and convenient to discriminate the circulating phylogenetic clades of SARS‐CoV‐2.

Multiplex ARMS‐PCR (amplification refractory mutation system‐polymerase chain reaction) method for genotyping major severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2 clades).

• ARMS
• COVID-19
• SARS-CoV-2
• clade
• multiplex PCR
• mutations

• Asymptomatic
• COVID-19
• Immune responses
• Seroconversion
• Symptomatic

• ARDS
• COVID-19
• Cell therapy
• Coronavirus
• Mesenchymal stem cells
• Pneumonia
• Regenerative medicine

• COVID-19
• Coronavirus Infections/complications
• Coronavirus Infections/therapy
• Humans
• Inflammation/etiology
• Inflammation/therapy
• Mesenchymal Stem Cells
• Pandemics
• Pneumonia, Viral/complications
• Pneumonia, Viral/therapy
• Regeneration
• Regenerative Medicine/methods

Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections.

A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing.

RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution.

Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.

• RV
• Rhinovirus
• diagnostics
• epidemiology
• prevalence
• virus interactions

Organ and stem cell transplantation has been one of the greatest advances in modern medicine, and is the primary treatment modality for many end-stage diseases. As our population ages, so do the transplant recipients, and with that comes many new challenges. Respiratory viruses have been a large contributor to the mortality and morbidity of solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients. Respiratory viruses are generally a long-term complication of transplantation and primarily acquired in the community. With the emergence of molecular methods, newer respiratory viruses are being detected. Respiratory viruses appear to cause severe disease in the older transplant population. Influenza vaccine remains the mainstay of prevention in transplant recipients, although immunogenicity of current vaccines is suboptimal. Limited therapies are available for other respiratory viruses. The next decade will likely bring newer antivirals and vaccines to the forefront. Our goal is to provide the most up to date knowledge of respiratory viral infections in our aging transplant population.

• Asthma
• Exacerbation
• Macrophage
• Mathematical immunology
• Respiratory tract virus

• Adolescent
• Child
• Child, Preschool
• Data Mining
• Decision Trees
• Electronic Health Records
• Female
• Hospitalization
• Humans
• Infant
• Machine Learning
• Male
• Models, Theoretical
• ROC Curve
• Respiratory Tract Infections/diagnosis
• Retrospective Studies
• Sensitivity and Specificity
• Virus Diseases/diagnosis
• Viruses/isolation & purification

• Adolescent
• Adult
• Aged
• Aged, 80 and over
• Biomarkers
• Blood Proteins
• Community-Acquired Infections/blood
• Community-Acquired Infections/diagnosis
• Community-Acquired Infections/etiology
• Comorbidity
• Diagnosis, Differential
• Electrophoresis/methods
• Female
• Humans
• Male
• Middle Aged
• Pneumonia, Bacterial/blood
• Pneumonia, Bacterial/diagnosis
• Pneumonia, Bacterial/etiology
• Pneumonia, Viral/blood
• Pneumonia, Viral/diagnosis
• Pneumonia, Viral/etiology
• ROC Curve
• Retrospective Studies
• Young Adult

Infectious processes of the trachea represent a distinct clinical entity with an evolving landscape owing to advances in airway management and vaccination practices. Untreated inflammatory processes of the trachea may present in the form of acute airway obstruction, potentially resulting in significant morbidity and even mortality. Therefore it is important to recognize the cardinal features of some of the common tracheal infectious processes to differentiate them from non-infectious pathology, as the latter is associated with a more indolent course.

As with most other infectious processes of the airway, pathogens causing tracheal infection can be bacterial, viral or fungal in nature. Viral etiology represents the most common cause of laryngotracheal infection in a child. Bacterial infections of the trachea are responsible for more significant morbidity, including prolonged hospitalization, need for endotracheal intubation and even an occasional tracheostomy. The current chapter describes the clinical features and microbiology of tracheal infections at large, explores the utility of diagnostic tests, and provides an algorithm for management.

Human parainfluenza viruses account for a significant proportion of lower respiratory tract infections in children.

To assess the prevalence of Human parainfluenza viruses as a cause of acute respiratory infection and to compare clinical data for this infection against those of the human respiratory syncytial virus.

A prospective study in children younger than five years with acute respiratory infection was conducted. Detection of respiratory viruses in nasopharyngeal aspirate samples was performed using the indirect immunofluorescence reaction. Length of hospital stay, age, clinical history and physical exam, clinical diagnoses, and evolution (admission to Intensive Care Unit or general ward, discharge or death) were assessed. Past personal (premature birth and cardiopathy) as well as family (smoking and atopy) medical factors were also assessed.

A total of 585 patients were included with a median age of 7.9 months and median hospital stay of six days. No difference between the HRSV+ and HPIV+ groups was found in terms of age, gender or length of hospital stay. The HRSV+ group had more fever and cough. Need for admission to the Intensive Care Unit was similar for both groups but more deaths were recorded in the HPIV+ group. The occurrence of parainfluenza peaked during the autumn in the first two years of the study.

Parainfluenza was responsible for significant morbidity, proving to be the second-most prevalent viral agent in this population after respiratory syncytial virus. No difference in clinical presentation was found between the two groups, but mortality was higher in the HPIV+ group.

• Acute Disease
• Brazil/epidemiology
• Child, Preschool
• Female
• Hospitalization
• Humans
• Infant
• Male
• Nasopharynx/virology
• Parainfluenza Virus 1, Human/isolation & purification
• Prospective Studies
• Respiratory Syncytial Virus Infections/virology
• Respiratory Tract Infections/epidemiology
• Respiratory Tract Infections/virology
• Respirovirus Infections/epidemiology
• Seasons

• Virus
• asthma
• asthma control
• children
• mixed-model analysis
• respiratory
• rhinovirus

• Adrenal Cortex Hormones/therapeutic use
• Anti-Asthmatic Agents/therapeutic use
• Antigens, Dermatophagoides/blood
• Antigens, Dermatophagoides/immunology
• Asthma/complications
• Asthma/drug therapy
• Asthma/immunology
• Asthma/physiopathology
• Child
• Child, Preschool
• Cough/physiopathology
• Female
• Genotype
• Humans
• Male
• Picornaviridae Infections/complications
• Picornaviridae Infections/drug therapy
• Picornaviridae Infections/immunology
• Picornaviridae Infections/physiopathology
• Regression Analysis
• Respiratory Function Tests
• Respiratory Sounds/physiopathology
• Rhinovirus/genetics
• Rhinovirus/immunology
• Vitamin D/blood
• Vitamin D/immunology

• community-acquired pneumonia
• aetiology
• m. pneumoniae
• pneumoslide igm

• Adolescent
• Age Factors
• Child
• Child, Preschool
• China/epidemiology
• Community-Acquired Infections
• Female
• Humans
• Infant
• Infant, Newborn
• Influenza B virus
• Male
• Paramyxoviridae
• Pneumonia/epidemiology
• Pneumonia/microbiology
• Pneumonia/virology
• Pneumonia, Mycoplasma/epidemiology
• Respiratory Syncytial Viruses
• Seasons

Several studies examining the incidence of viral infection in childhood community‐acquired pneumonia (CAP) utilizing polymerase chain reaction (PCR) or real‐time PCR methods have been reported. We systematically searched Pubmed and Embase for studies reporting the incidence of respiratory viral infection in childhood CAP. The pooled incidences of viral infection were calculated with a random‐effects model. Sources of heterogeneity were explored by subgroup analysis and a univariant metaregression analysis. We included 21 eligible reports in our study. We found significant heterogeneity on the incidence of viral infection in childhood CAP. The random effects pooled incidence was 57.4% (95% confidence interval (CI): 50.8–64.1). The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6) with considerable heterogeneity. The pooled incidence of mixed infection was 29.3% (95%CI: 23.0–35.6). Rhinovirus, respiratory syncytial virus (RSV) and bocavirus were found to be the three most common viruses in childhood CAP. We also demonstrated that respiratory viruses were detected in 76.1% of patients aged ≤1 year, 63.1% of patients aged 2–5 years and 27.9% of patients aged ≥ 6 years. We conclude that respiratory viruses are widely detected in paediatric patients with CAP by PCR or real‐time PCR methods. More than half of viral infections are probably concurrent with bacterial infections. Rhinovirus, RSV and bocavirus are the three most frequent viruses identified in childhood CAP; the incidence of viral infection decreased with age.

• child
• community-acquired pneumonia
• incidence
• meta-analysis
• respiratory virus

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.

• Child
• Child, Hospitalized
• Child, Preschool
• Coronavirus/genetics
• Coronavirus/physiology
• DNA Viruses/classification
• DNA Viruses/genetics
• DNA Viruses/physiology
• DNA, Viral/analysis
• Female
• Humans
• Infant
• Male
• Nasopharynx/virology
• Phylogeny
• Pneumonia/diagnosis
• Pneumonia/virology
• RNA Viruses/classification
• RNA Viruses/genetics
• RNA Viruses/physiology
• RNA, Viral/analysis
• Respiratory Syncytial Viruses/genetics
• Respiratory Syncytial Viruses/physiology
• Respiratory Tract Infections/pathology
• Respiratory Tract Infections/virology
• Rhinovirus/genetics
• Rhinovirus/physiology
• Sequence Analysis, DNA
• Sequence Analysis, RNA

• ADAM28
• ADAM33
• IL-13
• IL-4
• Pneumonia
• Virus

• Influenza
• Medellin
• respiratory viruses
• surveillance

•

Respiratory infections represent a globally cause of mortality in childhood.

Acute viral respiratory infections represent a globally important cause of morbidity and mortality in childhood. An individual's cellular response appears to play a critical role in recovery from infections, given that individuals with impaired cellular immunity, congenital or acquired, have more severe diseases and secrete the virus for longer periods.

The aim of this study was to immunohistochemically evaluate the expression of the cell surface antigens CD4, CD8, CD25, CD14 and CD74, in pneumonic infiltrates in the alveolar septa using paraffin-embedded lung samples from autopsies of immunocompetent children who died of lethal, non-pandemic, severe acute respiratory infections.

From 794 cases of pediatric autopsies of patients with severe respiratory disease (between 1960 and 2004), 193 cases were selected for this study. To identify subpopulations of inflammatory cells in the alveolar septa, cell surface antigen expression was assessed by immunohistochemistry using the following primary antibodies: anti-CD4, anti-CD8, anti-CD14, anti-CD25 and anti-CD74.

The TCD8+ lymphocyte count was higher in the virus-positive group (p = 0.04) and was also much higher among cases that were positive for more than three viral types (p = 0.016). There were fewer CD14+ cells in cases of AdV (adenovirus) infection (p = 0.002), and there was a predominance of CD74+ cells in the histopathological pattern defined as interstitial pneumonitis (p = 0.037).

The results of this study demonstrate that TCD8+ lymphocytes present in the alveolar septa participate to a greater extent in the response toward viral pneumonia, while CD14+ cell numbers are often reduced in cases of AdV.

• Autopsy
• Childhood
• Immunohistochemistry
• Pneumonia
• Virus

• airway inflammation
• bacterial infections
• bronchitis
• co-infection
• respiratory tract
• viral infections

• Bacterial Infections/diagnosis
• Bronchoalveolar Lavage
• Bronchoalveolar Lavage Fluid/microbiology
• Bronchoscopy
• Child, Preschool
• Coinfection
• Cough/etiology
• Diagnosis, Differential
• Female
• Humans
• Infant
• Male
• Neutrophils/pathology
• Prospective Studies
• Respiratory Tract Infections/diagnosis
• Virus Diseases/diagnosis

Background. The role of human adenoviruses (HAdVs) in chronic respiratory disease pathogenesis is recognized. However, no studies have performed molecular sequencing of HAdVs from the lower airways of children with chronic endobronchial suppuration. We thus examined the major HAdV genotypes/species, and relationships to bacterial coinfection, in children with protracted bacterial bronchitis (PBB) and mild bronchiectasis (BE).

Methods. Bronchoalveolar lavage (BAL) samples of 245 children with PBB or mild (cylindrical) BE were included in this prospective cohort study. HAdVs were genotyped (when possible) in those whose BAL had HAdV detected (HAdV⁺). Presence of bacterial infection (defined as ≥10⁴ colony-forming units/mL) was compared between BAL HAdV⁺ and HAdV negative (HAdV⁻) groups. Immune function tests were performed including blood lymphocyte subsets in a random subgroup.

Results. Species C HAdVs were identified in 23 of 24 (96%) HAdV⁺ children; 13 (57%) were HAdV-1 and 10 (43%) were HAdV-2. An HAdV⁺ BAL was significantly associated with bacterial coinfection with Haemophilus influenzae, Moraxella catarrhalis, or Streptococcus pneumoniae (odds ratio [OR], 3.27; 95% confidence interval, 1.38–7.75; P = .007) and negatively associated with Staphylococcus aureus infection (P = .03). Young age was related to increased rates of HAdV⁺. Blood CD16 and CD56 natural killer cells were significantly more likely to be elevated in those with HAdV (80%) compared with those without (56.1%) (P = .027).

Conclusions. HAdV-C is the major HAdV species detected in the lower airways of children with PBB and BE. Younger age appears to be an important risk factor for HAdV⁺ of the lower airways and influences the likelihood of bacterial coinfection.

• bronchiectasis
• children
• protracted bacterial bronchitis
• respiratory bacteria
• respiratory viruses

The comparative yield of respiratory virus detection from nasopharyngeal aspirate (NPA) versus bronchoalveolar lavage (BAL) is uncertain. Furthermore, the significance of virus detection and its relationship to lower airway neutrophilic inflammation is poorly studied.

To evaluate the sensitivity, specificity and predictive values of NPA for detecting respiratory viruses in BAL; and to determine the relationship between viruses and lower airway neutrophilia in children with non-acute respiratory illness.

150 paired NPA and BAL samples were obtained from 75 children aged <18 years undergoing flexible bronchoscopy for investigation of chronic respiratory symptoms. Viral studies were performed using polymerase chain reaction (PCR). Cellularity studies were performed on BALs. Diagnostic parameters of NPA compared to BAL and associations between viruses and lower airway %neutrophils were evaluated.

NPA had a higher yield than BAL for detection of any respiratory virus (52 versus 38, respectively). NPA had a high sensitivity (92%) and low specificity (57%) for detecting HRV in BAL with poor kappa agreement value of 0.398 (95% CI 0.218–0.578, p < 0.001). NPA had a fair sensitivity (69%) and good specificity (90.3%) for detecting HAdV on BAL, kappa agreement was 0.561 (95% CI 0.321–0.801, p < 0.001). HAdV positivity on NPA, compared to negativity, was independently associated with heightened airway neutrophilia [mean difference (95% CI): 18 (1,35); p = 0.042].

NPA has a higher yield for respiratory virus detection than BAL, however its diagnostic accuracy is dependent on viral species. Adenovirus positivity is associated with significantly heightened lower airway neutrophilia in children with chronic respiratory symptoms.

• BAL
• Bacteria
• Co-infection
• HAdV
• HBoV
• HCoV – NL63, OC43, 229E, HKU1
• HPIV1–3
• HRV
• Human adenovirus
• Human rhinovirus
• IFAV
• IFBV
• KI polyomavirus
• KIPyV
• NPA
• Neutrophilic airway inflammation
• PCR
• Polymerase chain reaction
• RSV
• RVI
• WU polyomavirus
• WUPyV
• bronchoalveolar lavage
• hMPV
• human adenovirus
• human bocavirus
• human coronaviruses
• human influenza A virus
• human influenza B virus
• human metapneumovirus
• human para-influenza virus 1–3
• human rhinovirus
• nasopharyngeal aspirate
• polymerase chain reaction
• respiratory syncytial virus
• respiratory virus infection

• virology
• multiplex pcr
• molecular assays
• clinical impact
• cost-effectiveness
• respiratory virus
• infection control
• public health
• immunocompromised patients
• cystic fibrosis
• neonatology
• copd

• Animals
• Coinfection/diagnosis
• Coinfection/virology
• Communicable Disease Control
• Cost-Benefit Analysis
• Humans
• Influenza A virus/genetics
• Molecular Diagnostic Techniques/economics
• Multiplex Polymerase Chain Reaction/economics
• Respiratory Tract Infections/diagnosis
• Respiratory Tract Infections/virology

• Acute Disease
• Adult
• Chi-Square Distribution
• Cohort Studies
• Humans
• Nasopharynx/virology
• Oropharynx/virology
• Pharyngitis/diagnosis
• Pharyngitis/virology
• Real-Time Polymerase Chain Reaction
• Sensitivity and Specificity
• Specimen Handling/methods
• Virology/methods
• Virus Diseases/diagnosis
• Virus Diseases/virology

Eight novel human polyomaviruses have been discovered since 2007. Prevalence rates and tissue tropism for the most recent members HPyV 6, 7, 9, TSPyV and MWPyV are largely unknown. We used real-time PCR to determine the presence of HPyV 6, 7, 9, TSPyV and MWPyV in feces (n = 263), urine (n = 189), blood (n = 161), respiratory swabs (n = 1385) and cerebrospinal fluid (n = 171) from both healthy control children and children and adults undergoing diagnostic testing. Whole genome sequencing was able to be performed on 9 MWPyV positive specimens. Novel polyomaviruses were only detected in respiratory swabs and feces, with no detections of HPyV 9 in any sample type. MWPyV was found to be the most prevalent novel polyomavirus, being detected in 18 (1.5%) respiratory specimens from symptomatic patients, 16 (9.8%) respiratory sample from healthy control children, 11 (5.9%) fecal specimens from patient suffering gastrointestinal illness, and in 13 (15.3%) of feces from healthy control children. MWPyV was found only in respiratory and fecal specimens from children, the oldest being 9 years old. HPyV 6, 7, 9 and TSPyV were also detected in respiratory specimens and fecal specimens at low prevalence (<1.3%). The majority of these detections were found in immunocompromised patients. Our findings suggest that MWPyV can result in a subclinical infection, persistent or intermittent shedding, particularly in young children. The other novel polyomaviruses were also found in respiratory and fecal specimens, but at lower prevalence and most commonly in immunocompromised individuals.

• Adult
• Blood/virology
• Cerebrospinal Fluid/virology
• Child
• Feces/virology
• Genome, Viral/genetics
• Humans
• Polyomavirus/genetics
• Polyomavirus Infections/epidemiology
• Polyomavirus Infections/genetics
• Prevalence
• Queensland/epidemiology
• Real-Time Polymerase Chain Reaction
• Respiratory System/virology
• Sequence Analysis, DNA
• Species Specificity
• Urine/virology

• amoxycillin-clavulanate
• azithromycin
• bronchiectasis
• placebo
• pulmonary exacerbations
• randomized controlled trial

• Amoxicillin-Potassium Clavulanate Combination/therapeutic use
• Anti-Bacterial Agents/therapeutic use
• Azithromycin/therapeutic use
• Bronchiectasis/drug therapy
• Clinical Protocols
• Double-Blind Method
• Humans
• Outcome Assessment, Health Care
• Sample Size

• molecular diagnostic methods
• pediatric respiratory infections
• nucleic acid tests
• virus isolation

• amoxicillin-clavulanic acid
• azithromycin
• bronchiectasis
• placebo
• pulmonary exacerbations
• randomised controlled trial

• Administration, Oral
• Adolescent
• Age Factors
• Amoxicillin-Potassium Clavulanate Combination/administration & dosage
• Amoxicillin-Potassium Clavulanate Combination/therapeutic use
• Anti-Bacterial Agents/therapeutic use
• Australia
• Azithromycin/administration & dosage
• Azithromycin/therapeutic use
• Bronchiectasis/diagnosis
• Bronchiectasis/drug therapy
• Bronchiectasis/physiopathology
• Bronchiectasis/psychology
• Child
• Child, Preschool
• Disease Progression
• Double-Blind Method
• Hospitalization
• Humans
• Infant
• Infant, Newborn
• New Zealand
• Quality of Life
• Research Design
• Time Factors
• Treatment Outcome

• Adolescent
• Bacteria/isolation & purification
• Bacterial Infections/microbiology
• Child
• Child, Preschool
• Cystic Fibrosis/complications
• Female
• Humans
• Male
• Molecular Diagnostic Techniques/methods
• Multiplex Polymerase Chain Reaction/methods
• Nasal Mucosa/microbiology
• Nasal Mucosa/virology
• Respiratory Tract Infections/microbiology
• Respiratory Tract Infections/virology
• Virus Diseases/virology
• Viruses/isolation & purification
• Young Adult

Acute respiratory illnesses (ARIs) with unconfirmed infectious aetiologies peak at different times of the year. Molecular diagnostic assays reduce the number of unconfirmed ARIs compared to serology- or culture-based techniques. Screening of 888 inpatient and outpatient respiratory specimens spanning late autumn through to early spring, 2004, identified the presence of a human coronavirus (HCoV) on 74 occasions (8.3% of all specimens and 26.3% of all respiratory virus detections). Prevalence peaked in August (late winter in the southern hemisphere) when they were detected in 21.9% of specimens tested. HCoV-HKU1 and HCoV-OC43 comprised 82.4% of all HCoVs detected. Positive specimens were used to develop novel reverse transcriptase real-time PCRs (RT-rtPCRs) for HCoV detection. An objective clinical severity score was assigned to each positive HCoV patient. Severity scores were similar to those from a random selection of young children who were positive for respiratory syncytial virus at a different time but from the same specimen population. During the cooler months of 2004, sensitive and specific RT-rtPCRs identified the concurrent circulation of all four HCoVs, a quarter of which co-occurred with another virus and most of which were from children under the age of two years.

• HCoV-229E
• HCoV-HKU1
• HCoV-NL63
• HCoV-OC43
• clinical impact
• coronavirus
• real-time PCR
• respiratory virus