Current Best Practices for Respiratory Virus Testing

Viral co-detection of influenza virus and other respiratory viruses in hospitalized Brazilian patients during the first three years of the coronavirus disease (COVID)-19 pandemic: an epidemiological profile

Introduction

In Brazil, few studies were performed regarding the co-detection of respiratory viruses in hospitalized patients. In this way, the study aimed to describe the epidemiological profile of hospitalized patients due to influenza virus infection that presented co-detection with another respiratory virus.

Methods

The epidemiological analysis was made by collecting data from Open-Data-SUS. The study comprised patients infected by the influenza A or B virus with positive co-detection of another respiratory virus, such as adenovirus, bocavirus, metapneumovirus, parainfluenza virus (types 1, 2, 3, and 4), rhinovirus, and respiratory syncytial virus (RSV). The markers [gender, age, clinical signs and symptoms, comorbidities, need for intensive care unit (ICU) treatment, and need for ventilatory support] were associated with the chance of death. The data was collected during the first three years of the coronavirus disease (COVID)-19 pandemic-from December 19, 2019, to April 06, 2023.

Results

A total of 477 patients were included, among them, the influenza A virus was detected in 400 (83.9%) cases. The co-detection occurred, respectively, for RSV (53.0%), rhinovirus (14.0%), adenovirus (13.4%), parainfluenza virus type 1 (10.7%), parainfluenza virus type 3 (5.2%), metapneumovirus (3.8%), parainfluenza virus type 2 (3.6%), bocavirus (3.4%), and parainfluenza virus type 4 (1.5%). The co-detection rate was higher in the male sex (50.7%), age between 0-12 years of age (65.8%), and white individuals (61.8%). The most common clinical symptoms were cough (90.6%), dyspnea (78.8%), and fever (78.6%). A total of 167 (35.0%) people had at least one comorbidity, mainly cardiopathy (14.3%), asthma (8.4%), and diabetes mellitus (7.3%). The need for ICU treatment occurred in 147 (30.8%) cases, with most of them needing ventilatory support (66.8%), mainly non-invasive ones (57.2%). A total of 33 (6.9%) patients died and the main predictors of death were bocavirus infection (OR = 14.78 [95%CI = 2.84-76.98]), metapneumovirus infection (OR = 8.50 [95%CI = 1.86-38.78]), race (other races vs. white people) (OR = 3.67 [95%CI = 1.39-9.74]), cardiopathy (OR = 3.48 [95%CI = 1.13-10.71]), and need for ICU treatment (OR = 7.64 [95%CI = 2.44-23.92]).

Conclusion

Co-detection between the influenza virus and other respiratory viruses occurred, mainly with RSV, rhinovirus, and adenovirus being more common in men, white people, and in the juvenile phase. Co-detection of influenza virus with bocavirus and metapneumovirus was associated with an increased chance of death. Other factors such as race, cardiopathy, and the need for an ICU were also associated with a higher chance of death.

Modeling Respiratory Syncytial Virus Adult Vaccination in the United States With a Dynamic Transmission Model

BACKGROUND

Respiratory syncytial virus (RSV) is shown to cause substantial morbidity, hospitalization, and mortality in infants and older adults. Population-level modeling of RSV allows to estimate the full burden of disease and the potential epidemiological impact of novel prophylactics.

METHODS

We modeled the RSV epidemiology in the United States across all ages using a deterministic compartmental transmission model. Population-level symptomatic RSV acute respiratory tract infection (ARI) cases were projected across different natural history scenarios with and without vaccination of adults aged ≥60 years. The impact of vaccine efficacy against ARIs, infectiousness and vaccine coverage on ARI incidence were assessed. The impact on medical attendance, hospitalization, complications, death, and other outcomes was also derived.

RESULTS

Without a vaccine, we project 17.5-22.6 million symptomatic RSV ARI cases annually in adults aged ≥18 years in the US, with 3.6-4.8 million/year occurring in adults aged ≥60 years. Modeling indicates that up to 2.0 million symptomatic RSV-ARI cases could be prevented annually in ≥60-year-olds with a hypothetical vaccine (70% vaccine efficacy against symptomatic ARI and 60% vaccine coverage) and that up to 0.69 million/year could be prevented in the nonvaccinated population, assuming 50% vaccine impact on infectiousness.

CONCLUSIONS

The model provides estimated burden of RSV in the US across all age groups, with substantial burden projected specifically in older adults. Vaccination of adults aged ≥60 years could significantly reduce the burden of disease in this population, with additional indirect effect in adults aged <60 years due to reduced transmissibility.

Respiratory Syncytial Virus Infections in Neonates: A Persisting Problem

Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infections in young infants. It is an enveloped, single-stranded, nonsegmented, negative-strand RNA virus, a member of the family Pneumoviridae. Globally, RSV is responsible for 2.3% of deaths among neonates 0-27 days of age. Respiratory syncytial virus infection is most common in children aged below 24 months. Neonates present with cough and fever. Respiratory syncytial virus-associated wheezing is seen in 20% infants during the first year of life of which 2-3% require hospitalization. Reverse transcriptase polymerase chain reaction (RT-PCR) gives fast results and has higher sensitivity compared with culture and rapid antigen tests and are not affected by passively administered antibody to RSV. Therapy for RSV infection of the LRT is mainly supportive, and preventive measures like good hygiene and isolation are the mainstay of management. Standard precautions, hand hygiene, breastfeeding and contact isolation should be followed for RSV-infected newborns. Recent AAP guidelines do not recommend pavilizumab prophylaxis for preterm infants born at 29-35 weeks without chronic lung disease, hemodynamically significant congenital heart disease and coexisting conditions. RSV can lead to long-term sequelae such as wheezing and asthma, associated with increased healthcare costs and reduced quality of life.

Optical reflectometric measurement of SARS-CoV-2 (COVID-19) RNA based on cationic cysteamine-capped gold nanoparticles

The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a major public health outbreak in late 2019 and was proclaimed a global pandemic in March 2020. A reflectometric-based RNA biosensor was developed by using cysteamine-stabilized gold nanoparticles (cysAuNPs) as the colorimetric probe for bioassay of COVID-19 RNA (SARS-CoV-2 RNA) sequence. The cysAuNPs aggregated in the presence of DNA probes via cationic and anionic electrostatic attraction between the positively charged cysteamine ligands and the negatively charged sugar-phosphate backbone of DNA, whilst in the presence of target RNAs, the specific recognition between DNA probes and targets depleted the electrostatic interaction between the DNA probes and cysAuNPs signal probe, leading to dispersed particles. This has rendered a remarkable shifting in the surface plasmon resonance (SPR) on the basis of visual color change of the RNA biosensor from red to purplish hue at the wavelength of 765 nm. Optical evaluation of SARS-CoV-2 RNA by means on reflectance transduction of the RNA biosensor based on cysAuNPs optical sensing probes demonstrated rapid response time of 30 min with high sensitivity, good linearity and high reproducibility across a COVID-19 RNA concentration range of 25 nM to 200 nM, and limit of detection (LOD) at 0.12 nM. qPCR amplification of SARS-CoV-2 viral RNA showed good agreement with the proposed RNA biosensor by using spiked RNA samples of the oropharyngeal swab from COVID-19 patients. Therefore, this assay is useful for rapid and early diagnosis of COVID-19 disease including asymptomatic carriers with low viral load even in the presence of co-infection with other viruses that manifest similar respiratory symptoms.

Smart Nanostructured Materials for SARS-CoV-2 and Variants Prevention, Biosensing and Vaccination

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised great concerns about human health globally. At the current stage, prevention and vaccination are still the most efficient ways to slow down the pandemic and to treat SARS-CoV-2 in various aspects. In this review, we summarize current progress and research activities in developing smart nanostructured materials for COVID-19 prevention, sensing, and vaccination. A few established concepts to prevent the spreading of SARS-CoV-2 and the variants of concerns (VOCs) are firstly reviewed, which emphasizes the importance of smart nanostructures in cutting the virus spreading chains. In the second part, we focus our discussion on the development of stimuli-responsive nanostructures for high-performance biosensing and detection of SARS-CoV-2 and VOCs. The use of nanostructures in developing effective and reliable vaccines for SARS-CoV-2 and VOCs will be introduced in the following section. In the conclusion, we summarize the current research focus on smart nanostructured materials for SARS-CoV-2 treatment. Some existing challenges are also provided, which need continuous efforts in creating smart nanostructured materials for coronavirus biosensing, treatment, and vaccination.

Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use

Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.

Viral Etiological Agent(s) of Respiratory Tract Infections in Symptomatic Individuals during the Second Wave of COVID-19 Pandemic: A Single Drive-Thru Mobile Collection Site Study

One of the tools to contain the SARS-CoV-2 pandemic was to increase the number of performed tests and to improve the access to diagnostics. To this effect, mobile collection sites (MCSs) were established. This study was performed on samples collected at the MCS between November 2020 and March 2021. We aimed to confirm/exclude SARS-CoV-2, differentiate SARS-CoV-2 variants, and detect other respiratory pathogens. SARS-CoV-2 and other respiratory viruses were identified by RT-qPCRs. A total of 876 (46.35%) SARS-CoV-2 positive specimens in the diagnostic tests were identified. The wild-type variant was determined in 667 (76.14%) samples; the remaining 209 (23.86%) samples specimens were identified as Alpha variant. A total of 51 (5.6%) non-SARS-CoV-2 cases were detected in retrospective studies. These accounted for 33 cases of mono-infection including rhinovirus (RV), human adenovirus (HAdV), human metapneumovirus (HMPV), enterovirus (EV), and influenza virus, and 18 cases of co-infection (SARS-CoV-2 with RV or HAdV or HMPV, and RV with EV). Our research shows that the results obtained from the MCS have value in epidemiological studies, reflecting national trends on a micro scale. Although the spread of COVID-19 is a major public health concern, SARS-CoV-2 is not the only pathogen responsible for respiratory infections.

Unexpected associations between respiratory viruses and bacteria with Pulmonary Function Testing in children suffering from Cystic Fibrosis (MUCOVIB study)

BACKGROUND

Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term lung function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF.

METHODS

As part of the 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria and fastidious organisms'' project, children with CF were longitudinally followed in a Swiss multicentric study. Respiratory samples included mainly throat swabs and sputa samples for bacterial culture and 16S rRNA metagenomics and nasopharyngeal swabs for respiratory virus detection by molecular assays. Percentage of predicted Forced Expiratory Volume in one second (FEV1%) and Lung Clearance Index (LCI) were recorded.

RESULTS

Sixty-one children, of whom 20 (32.8%) presented with at least one pulmonary exacerbation, were included. Almost half of the 363 nasopharyngeal swabs tested by RT-PCR were positive for a respiratory virus, mainly rhinovirus (26.5%). From linear mixed-effects regression models, P. aeruginosa (-11.35, 95%CI [-17.90; -4.80], p = 0.001) was significantly associated with a decreased FEV1%, whereas rhinovirus was associated with a significantly higher FEV1% (+4.24 95%CI [1.67; 6.81], p = 0.001). Compared to conventional culture, 16S rRNA metagenomics showed a sensitivity and specificity of 80.0% and 85.4%, respectively for detection of typical CF pathogens. However, metagenomics detected a bacteria almost twice more often than culture.

CONCLUSIONS

As expected, P. aeruginosa impacted negatively on FEV1% while rhinovirus was surprisingly associated with better FEV1%. Culture-free assays identifies significantly more pathogens than standard culture, with disputable clinical correlation.

A novel RNA detection technique for point-of-care identification of pathogens

Despite significant progress in recent years to improve capabilities to diagnose infections at point-of-care (POC), there are still technical hurdles that need to be overcome to ensure proper medical interventions. Current microbial POC tests involve polymerase chain reaction (PCR) or sandwich immunoassay (IA) based detection formats. PCR is highly sensitive but requires complex instrumentation, whereas lateral flow (LF) based IA tests are handheld but lack sensitivity. We present here a portable and sensitive technique by integrating an isothermal RNA amplification approach with IA detection format. The technique comprises i) Nucleic Acid Sequence Based isothermal Amplification (NASBA), ii) amplicon tagging with hapten labeled probes, iii) capturing the amplicon and iv) formation of a sandwich complex with an antibody (Ab) that selectively recognizes the DNA-RNA duplex. The results can be extended to develop an automated, portable and highly sensitive diagnostic platform suitable for POC applications.

Clinical and laboratory characteristics of symptomatic healthcare workers with suspected COVID-19: a prospective cohort study

A comprehensive clinical and microbiological assessments of COVID-19 in front-line healthcare workers (HCWs) is needed. Between April 10th and May 28th, 2020, 319 HCWs with acute illness were reviewed. In addition to SARS-CoV-2 RT-PCR screening, a multiplex molecular panel was used for testing other respiratory pathogens. For SARS-CoV-2 positive HCWs, the normalized viral load, viral culture, and virus neutralization assays were performed weekly. For SARS-CoV-2 negative HCWs, SARS-CoV-2 serological testing was performed one month after inclusion. Among the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; 65/67 (97.0%) developed mild form of COVID-19. Other respiratory pathogens were found in 6/66 (9.1%) SARS-CoV-2 positive and 47/241 (19.5%) SARS-Cov-2 negative HCWs (p = 0.07). The proportion of HCWs with a viral load > 5.0 log10 cp/mL (Ct value < 25) was less than 15% at 8 days after symptom onset; 12% of HCWs were positive after 40 days (Ct > 37). More than 90% of cultivable virus had a viral load > 4.5 log10 cp/mL (Ct < 26) and were collected within 10 days after symptom onset. Among negative HCWs, 6/190 (3.2%) seroconverted. Our data suggest that the determination of viral load can be used for appreciating the infectiousness of infected HCWs. These data could be helpful for facilitating their return to work.

Adhesive rolling of nanoparticles in a lateral flow inspired from diagnostics of COVID-19

Due to the lack of therapeutics and vaccines, diagnostics of COVID-19 emerges as one of the primary tools for controlling the spread of SARS-COV-2. Here we aim to develop a theoretical model to study the detection process of SARS-COV-2 in lateral flow device (LFD), which can achieve rapid antigen diagnostic tests. The LFD is modeled as the adhesion of a spherical nanoparticle (NP) coated with ligands on the surface, mimicking the SARS-COV-2, on an infinite substrate distributed with receptors under a simple shear flow. The adhesive behaviors of NPs in the LFD are governed by the ligand-receptor binding (LRB) and local hydrodynamics. Through energy balance analysis, three types of motion are predicted: (i) firm-adhesion (FA); (ii) adhesive-rolling (AR); and (iii) free-rolling (FR), which correspond to LRB-dominated, LRB-hydrodynamics-competed, and hydrodynamics-dominated regimes, respectively. The transitions of FA-to-AR and AR-to-FR are found to be triggered by overcoming LRB barrier and saturation of LRB torque, respectively. Most importantly, in the AR regime, the smaller NPs can move faster than their larger counterparts, induced by the LRB effect that depends on the radius R of NPs. In addition, a scaling law is found in the AR regime that v ∝ γ ˙ R α (rolling velocity v and shear rate γ ˙ ), with an approximate scaling factor α ∼ - 0 . 2 ± 0 . 05 identified through fitting both theoretical and numerical results. The scaling factor emerges from the energy-based stochastic LRB model, and is confirmed to be universal by examining selections of different LRB model parameters. This size-dependent rolling behavior under the control of flow strength may provide the theoretical guidance for designing efficient LFD in detecting infectious disease.

Characteristics of respiratory virus infections in autologous hematopoietic stem cell transplantation patients, a prospective study, Bern, Switzerland, 2015-2017

BACKGROUND

The epidemiology of respiratory virus infections (RVI) in patients undergoing autologous haematopoietic stem cell transplantation (auto-SCT) is not well described.

METHODS

Our goal was to describe the epidemiology of respiratory virus infections (RVI) in patients undergoing autologous haematopoietic stem cell transplantation (auto-SCT) in a single tertiary centre observation study during two respiratory virus seasons (2015-2017). All symptomatic auto-SCT patients were tested for RVI by nasopharyngeal swab.

RESULTS

156 transplantation episodes were included, 69% were male and, the median age was 57 years. We detected 19 RVIs in 156 transplantation episodes (12%). The median time to RVI after hospitalization was 13 days [IQR 7-13] and 15/19 (79%) had a possible nosocomial origin (occurrence ≥ 5 days after admission). The nosocomial infections included 5/15 (33%) 'severe' RVIs (3 influenza viruses, 1 parainfluenza virus, and 1 adenovirus) as well as 10/15 (66%) non-severe virus infections (including human rhinovirus and human coronavirus).

CONCLUSION

In approximately 10% of auto-SCT transplantation episodes, an RVI with likely nosocomial origin was detected and included 'severe viruses' such as influenza. Our study suggests that infection prevention measures in auto-SCT patients can be improved.

ABBREVIATIONS

AdV: adenovirus; ALL: acute lymphatic leukaemia; AML: acute myeloid leukaemia; auto-SCT: autologous haematopoietic stem cell transplantation; hCoV: human coronavirus; HD: Hodgkin's disease; hMPV: human metapneumovirus; HRV: human rhinovirus; HSCT: allogeneic haematopoietic stem cell transplantation; IQR: interquartile range; GCT: germ cell tumour; MM: multiple myeloma; NHL: non-Hodgkin lymphoma; PIV: parainfluenza virus; RSV: respiratory syncytial virus.

Randomly primed, strand-switching, MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses.

Epidemiology of human adenovirus associated with respiratory infection in southern Brazil

Human adenoviruses (HAdVs) are associated with respiratory infection in the human population worldwide, but HAdV is underreported and less studied than other respiratory viruses. We investigated HAdV in patients with respiratory infection in Rio Grande do Sul (RS), Brazil, between 2004 and 2018. The frequency and seasonality of HAdV, clinical symptoms and underlying diseases were analysed. Respiratory samples from outpatients with acute respiratory illness (ARI) who attended sentinel units and from inpatients with severe acute respiratory infection (SARI) were collected for HAdV detection by immunofluorescence assay; demographic and clinical data were analysed. In total, 43,514 cases of respiratory infection were analysed, of which 8,901 were ARI (20.5%), and 34,613 (79.5%) were SARI. Respiratory viruses were detected in 35.8% of the cases. The frequency of HAdV in relation to respiratory viruses was 2.8%. HAdV circulated year-round, with higher frequency during winter and early spring; increases in the average monthly temperature were associated with decreases in HAdV infections (p = 0.013). Most hospitalized patients with HAdV were male (p = 0.003). HAdV infection showed association with age (p < 0.001), and children between 1 and 5 years old accounted for 30.8% of the outpatients, whereas among cases of SARI, 88.2% were paediatric patients. Among inpatients with HAdV, 3% died, and of these, the majority had at least one underlying condition, such as cardiopathy and immunosuppression. HAdV infection of the respiratory tract causes morbidity and mortality, and individuals with heart diseases and the immunocompromised are at higher risk of fatality.

Personalizing vulvar cancer workflow in COVID-19 era: a proposal from Vul.Can MDT

INTRODUCTION

Since the community spread of Coronavirus disease 2019 (COVID-19), the practice of oncologic care at our comprehensive cancer center has changed. Postponing cancer treatment without consideration of its implications could cost more lives than can be saved. In this special situation, we must continue to provide our cancer patients with the highest quality of medical services assuring the safety. This article provides general guidance on supporting curative treatment strategies in vulvar cancer patients.

METHODS

At our institution, a vulvar cancer multidisciplinary team (Vul.Can MDT) of specialists is responsible for personalized treatment of this disease. The phase 2 period necessarily requires specific procedures for both outpatient and inpatient pathways and to provide strategies concerning the management of vulvar cancer patients even in case of an eventually concomitant SARS-CoV-2 infection. In brief, an accurate remote and in person triage must be provided routinely and patients submitted to specific diagnostic tests prior to every major treatment or procedure (surgery, RT, and CT) or in case of suspicion for COVID-19 syndrome. The decisional workflow for these women often old and frail, have been rapidly adjusted by our Vul.Can MDT to mitigate the potential risks of COVID-19.

RESULTS

The team produced two types of recommendations concerning: (1) safety regulations of care pathways, patients and health care providers, (2) personalized treatment strategies. We present a protocol that can be applied in clinical practice: the flowcharts provided, include the modulation of treatment intensity designed for surgical procedures and radiation, stratified for FIGO stage of disease and intention.

CONCLUSION

We suggest that our proposals are applicable in this setting of patients, considering anyway current international recommendations and guidelines.

How Nanophotonic Label-Free Biosensors Can Contribute to Rapid and Massive Diagnostics of Respiratory Virus Infections: COVID-19 Case

The global sanitary crisis caused by the emergence of the respiratory virus SARS-CoV-2 and the COVID-19 outbreak has revealed the urgent need for rapid, accurate, and affordable diagnostic tests to broadly and massively monitor the population in order to properly manage and control the spread of the pandemic. Current diagnostic techniques essentially rely on polymerase chain reaction (PCR) tests, which provide the required sensitivity and specificity. However, its relatively long time-to-result, including sample transport to a specialized laboratory, delays massive detection. Rapid lateral flow tests (both antigen and serological tests) are a remarkable alternative for rapid point-of-care diagnostics, but they exhibit critical limitations as they do not always achieve the required sensitivity for reliable diagnostics and surveillance. Next-generation diagnostic tools capable of overcoming all the above limitations are in demand, and optical biosensors are an excellent option to surpass such critical issues. Label-free nanophotonic biosensors offer high sensitivity and operational robustness with an enormous potential for integration in compact autonomous devices to be delivered out-of-the-lab at the point-of-care (POC). Taking the current COVID-19 pandemic as a critical case scenario, we provide an overview of the diagnostic techniques for respiratory viruses and analyze how nanophotonic biosensors can contribute to improving such diagnostics. We review the ongoing published work using this biosensor technology for intact virus detection, nucleic acid detection or serological tests, and the key factors for bringing nanophotonic POC biosensors to accurate and effective COVID-19 diagnosis on the short term.

Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

The COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study, we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription-mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther system to directly amplify and detect two separate target sequences in the open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID50)/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (n = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.

The Effect of Sample Site, Illness Duration, and the Presence of Pneumonia on the Detection of SARS-CoV-2 by Real-time Reverse Transcription PCR

Background

The performance of real-time reverse transcription polymerase chain reaction (rRT-PCR) for SARS-CoV-2 varies with sampling site(s), illness stage, and infection site.

Methods

Unilateral nasopharyngeal, nasal midturbinate, throat swabs, and saliva were simultaneously sampled for SARS-CoV-2 rRT-PCR from suspected or confirmed cases of COVID-19. True positives were defined as patients with at least 1 SARS-CoV-2 detected by rRT-PCR from any site on the evaluation day or at any time point thereafter, until discharge. Diagnostic performance was assessed and extrapolated for site combinations.

Results

We evaluated 105 patients; 73 had active SARS-CoV-2 infection. Overall, nasopharyngeal specimens had the highest clinical sensitivity at 85%, followed by throat, 80%, midturbinate, 62%, and saliva, 38%–52%. Clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 95%, 88%, 72%, and 44%–56%, respectively, if taken ≤7 days from onset of illness, and 70%, 67%, 47%, 28%–44% if >7 days of illness. Comparing patients with upper respiratory tract infection (URTI) vs pneumonia, clinical sensitivity for nasopharyngeal, throat, midturbinate, and saliva was 92% vs 70%, 88% vs 61%, 70% vs 44%, 43%–54% vs 26%–45%, respectively. A combination of nasopharyngeal plus throat or midturbinate plus throat specimen afforded overall clinical sensitivities of 89%–92%; this rose to 96% for persons with URTI and 98% for persons ≤7 days from illness onset.

Conclusions

Nasopharyngeal specimens, followed by throat specimens, offer the highest clinical sensitivity for COVID-19 diagnosis in early illness. Clinical sensitivity improves and is similar when either midturbinate or nasopharyngeal specimens are combined with throat specimens. Upper respiratory specimens perform poorly if taken after the first week of illness or if there is pneumonia.

Comparison of a direct immunofluorescence assay (Oxoid IMAGEN®) and a multiplex RT-PCR DNA microarray assay (CLART® PneumoVir) for the detection of respiratory viruses in hospitalized children

The objective of this study was to compare the positive detection rates obtained using the Oxoid IMAGEN® direct immunofluorescence assay (designated as IF) with those obtained using the CLART® PneumoVir multiplex RT-PCR DNA microarray assay (designated as RT-PCR) in the diagnosis of respiratory viruses in hospitalized children. This was a retrospective study of 62 individuals < 18 years old who had nasopharyngeal aspirates collected for virus identification in a tertiary university hospital in south Brazil between January 1st, 2014 and December 31st, 2014. All 62 nasopharingeal aspirates were analyzed using both assay methods. The main outcome to be measured was the difference in the proportion of test samples returning a positive virus detection result between the IF and the RT-PCR. The McNemar test was used for data analysis and the results showed that the RT-PCR and the IF methods produced 55 (88.7 %) and 17 (27.4 %) virus-positive samples, respectively (p < 0.001). The most prevalent virus was rhinovirus (45.5 % of the RT-PCR positive samples). The RT-PCR method increased the detection rates of human respiratory syncytial virus, influenza A virus and parainfluenza 3 virus. The RT-PCR and IF had concordant results in 19 samples (30.6 %) and discordant results in 43 samples (69.4 %). It is concluded that in comparison to the Oxoid IMAGEN® IF method, the CLART® PneumoVir multiplex RT-PCR method had a greater potential to contribute to the clinical management of hospitalized children due its greater ability in detecting respiratory viruses than the IF method.

Determining a sampling regime for PCR detection of respiratory tract viral infection at coronial post-mortem examinations

Death due to respiratory infection is commonly encountered at autopsy. With only one opportunity to obtain samples for identification of a causative agent, it is important to ensure that sampling regimes are optimized to provide the greatest detection, without the expense and redundancy that can arise from over-sampling. This study was performed retrospectively using data from Coronial autopsies over the period 2012–2019 from which swabs from the nasopharyngeal region, trachea and lung parenchyma, in addition to samples of lung tissue, had been submitted for multiplex PCR detection of respiratory pathogens. From 97 cases with all four samples, there were 24 with at least one positive result for viral infection. Some cases had multiple positive results and a total of 27 respiratory tract viruses were identified, of which rhinovirus, influenza A virus and respiratory syncytial virus were the most common. Seventeen of the 27 viral infections (63%) were identified in all four samples. However, in nearly all cases (96%) the nasopharyngeal swab detected the infective agent when the multiplex PCR panel had detected infection in any of the four sample types. A nasopharyngeal swab is considered to be an optimal sample for detection of respiratory tract viral infection. As the samples analyzed were acquired before the appearance of the COVID-19 virus, the applicability of this finding for COVID-19 screening is not established.

Room Sharing in Hospitalized Children With Bronchiolitis and the Occurrence of Hospital-Acquired Infections: A Prospective Cohort Study

OBJECTIVES

To determine the prevalence and severity of hospital-acquired infections (HAIs) in children hospitalized for bronchiolitis when patients share a room, irrespective of the causative virus.

METHODS

A prospective cohort study during 4 winter seasons (2012-2016) was conducted in a Dutch general pediatric ward including otherwise healthy children <2 years of age hospitalized for bronchiolitis. Patients shared a 1-to-4-bed hospital room irrespective of virological diagnosis. The main outcome measures were HAIs assessed through multiplex polymerase chain reaction and disease severity.

RESULTS

HAIs occurred in 28 of 218 included patients (12.8%), most frequently with rhinovirus (17 of 28; 60.7%). In 3 (10.7%) of 28 HAIs, the same virus was identified in roommates. Only 1 patient became cross-infected with respiratory syncytial virus, although this patient never shared a room with a patient infected with respiratory syncytial virus. HAI was not associated with more severe disease. The median length of hospitalization was 3.5 days (interquartile range [IQR] 1-6) compared with 3 days (IQR 2-6; P = .86); the number of PICU admissions was 0% versus 5.3% (P = .21); the median days of oxygen supplementation was 2.5 (IQR 1-4) versus 2 (IQR 1-4; P = .58); the median days of tube feeding was 2 (IQR 0-5) versus 2 (interquartile range: 0-5; P = .77); and the readmission rate was 0% versus 5.8% (P = .19) in patients with and without HAI, respectively.

CONCLUSIONS

HAIs among patients with bronchiolitis are common but not associated with more severe disease. Room sharing with appropriate hygiene does not play a relevant role in the transmission of viruses between patients with bronchiolitis, regardless of the viruses involved. On the basis of these findings, we suggest that room sharing of patients with bronchiolitis is safe.

Comparison of the Panther Fusion and Allplex assays for the detection of respiratory viruses in clinical samples

Respiratory viral infections are the most frequent clinical syndrome affecting both children and adults, and early detection is fundamental to avoid infection-related risks and reduce the healthcare costs incurred by unnecessary antibiotic treatments. In this study, performance characteristics of two commercial methods, the Panther Fusion® assay (Hologic Inc., San Diego, CA, USA) were compared to Allplex™ respiratory panels (Seegene, Seoul, South Korea) for the detection of influenza A (Flu A), influenza B (Flu B), respiratory syncytial virus (RSV), parainfluenza virus (PIV), human metapneumovirus (hMPV), rhinovirus (RV) and adenovirus (AdV) targets. A total of 865 specimens collected prospectively and retrospectively were included, and discordant results were further examined using another commercial product, R-GENE™ respiratory kits (bioMérieux, Marcy l'Etoile, France). There was high agreement between both methods, with 98.6% concordance and a kappa (k) value of 0.9 (95% CI: 0.89-0.92). A specific analysis of both methods for each viral agent demonstrated comparable sensitivity and specificity, both ranging from 0.83 to 1 with good predictive values for the prospective part of the study. Good agreement between both methods was also found for the κ values obtained (ranging from 97.55% to 98.9%), with the lowest for hMPV (k = 0.83, 95% CI: 0.75-0.91) and RV (k = 0.73, 95% CI: 0.65-0.81). Amplification efficiency, measured according to the value of the cycle threshold (Ct) obtained in each of the amplifications in both tests, was significantly better with Panther Fusion for Flu A, Flu B, hMPV and RV. Regarding discordant results, R-GENE showed higher agreement with Panther Fusion-positive specimens (negative for Allplex; n = 28/71, 34.9%) than with Allplex-positive samples (negative for Panther Fusion; n = 7/49, 14.3%). In summary, Panther Fusion proved to be a more efficient fully-automated methodology, requiring shorter hands-on and turnaround times than Allplex.

Estimated Burden of Community-Onset Respiratory Syncytial Virus-Associated Hospitalizations Among Children Aged <2 Years in the United States, 2014-15

BACKGROUND

Respiratory syncytial virus (RSV) is a major cause of hospitalizations in young children. We estimated the burden of community-onset RSV-associated hospitalizations among US children aged <2 years by extrapolating rates of RSV-confirmed hospitalizations in 4 surveillance states and using probabilistic multipliers to adjust for ascertainment biases.

METHODS

From October 2014 through April 2015, clinician-ordered RSV tests identified laboratory-confirmed RSV hospitalizations among children aged <2 years at 4 influenza hospitalization surveillance network sites. Surveillance populations were used to estimate age-specific rates of RSV-associated hospitalization, after adjusting for detection probabilities. We extrapolated these rates using US census data.

RESULTS

We identified 1554 RSV-associated hospitalizations in children aged <2 years. Of these, 27% were admitted to an intensive care unit, 6% needed mechanical ventilation, and 5 died. Most cases (1047/1554; 67%) had no underlying condition. Adjusted age-specific RSV hospitalization rates per 100 000 population were 1970 (95% confidence interval [CI],1787 to 2177), 897 (95% CI, 761 to 1073), 531 (95% CI, 459 to 624), and 358 (95% CI, 317 to 405) for ages 0-2, 3-5, 6-11, and 12-23 months, respectively. Extrapolating to the US population, an estimated 49 509-59 867 community-onset RSV-associated hospitalizations among children aged <2 years occurred during the 2014-2015 season.

CONCLUSIONS

Our findings highlight the importance of RSV as a cause of hospitalization, especially among children aged <2 months. Our approach to estimating RSV-related hospitalizations could be used to provide a US baseline for assessing the impact of future interventions.

Self-collected compared with professional-collected swabbing in the diagnosis of influenza in symptomatic individuals: A meta-analysis and assessment of validity

Self-collected nasal swabs offer a cheaper alternative to professional-collected swabs for influenza testing. However, the diagnostic accuracy of self-collection has not been quantitatively reviewed. We identified 14 studies that compared diagnostic accuracy of self-collected to professional-collected swabs in influenza symptomatic individuals. Self-collected swabs were found to be highly acceptable, simple and comfortable to use. Data from nine studies were meta-analyzed. Pooled sensitivity was 87% (95% CI: 80%, 92%) and specificity was 99% (95% CI: 98%, 100%), compared to professional-collected swabs in the diagnosis of influenza. Pooled sensitivity and specificity estimates were used to assess the potential bias that would be introduced in studies had self-collected rather than professional-collected samples been used. While self-collected swabbing should not replace the role of clinical testing, our findings support the use of self-collected swabs for influenza research and surveillance. This method will be an important tool for evaluating novel influenza vaccines and vaccination strategies.

Antiviral Response in the Nasopharynx Identifies Patients With Respiratory Virus Infection

Background

Despite the high burden of respiratory infection and the importance of early and accurate diagnosis, there is no simple diagnostic test to rule in viral infection as a cause of respiratory symptoms.

Methods

We performed RNA sequencing on human nasal epithelial cells following stimulation of the intracellular viral recognition receptor RIG-I. Next, we evaluated whether measuring identified host mRNAs and proteins from patient nasopharyngeal swabs could predict the presence of a respiratory virus in the sample.

Results

Our first study showed that a signature of 3 mRNAs, CXCL10, IFIT2, and OASL, predicted respiratory virus detection with an accuracy of 97% (95% confidence interval [CI], 0.9–1.0), and identified proteins correlating with virus detection. In a second study, elevated CXCL11 or CXCL10 protein levels identified samples containing respiratory viruses, including viruses not on the initial test panel. Overall area under the curve (AUC) values were: CXCL11 AUC = 0.901 (95% CI, 0.86–0.94); CXCL10 AUC = 0.85 (95% CI, 0.80–0.91).

Conclusions

Host antiviral mRNAs and single host proteins detectable using nasopharyngeal swabs accurately predict the presence of viral infection. This approach holds promise for developing rapid, cost-effective tests to improve management of patients with respiratory illnesses.

Multiplex Platforms for the Identification of Respiratory Pathogens: Are They Useful in Pediatric Clinical Practice?

Respiratory tract infections (RTIs) are extremely common especially in the first year of life. Knowledge of the etiology of a RTI is essential to facilitate the appropriate management and the implementation of the most effective control measures. This perspective explains why laboratory methods that can identify pathogens in respiratory secretions have been developed over the course of many years. High-complexity multiplex panel assays that can simultaneously detect up to 20 viruses and up to four bacteria within a few hours have been marketed. However, are these platforms actually useful in pediatric clinical practice? In this manuscript, we showed that these platforms appear to be particularly important for epidemiological studies and clinical research. On the contrary, their routine use in pediatric clinical practice remains debatable. They can be used only in the hospital as they require specific equipment and laboratory technicians with considerable knowledge, training, and experience. Moreover, despite more sensitive and specific than other tests routinely used for respiratory pathogen identification, they do not offer significantly advantage for detection of the true etiology of a respiratory disease. Furthermore, knowledge of which virus is the cause of a respiratory disease is not useful from a therapeutic point of view unless influenza virus or respiratory syncytial virus are the infecting agents as effective drugs are available only for these pathogens. On the other hand, multiplex platforms can be justified in the presence of severe clinical manifestations, and in immunocompromised patients for whom specific treatment option can be available, particularly when they can be used simultaneously with platforms that allow identification of antimicrobial resistance to commonly used drugs. It is highly likely that these platforms, particularly those with high sensitivity and specificity and with low turnaround time, will become essential when new drugs effective and safe against most of the respiratory viruses will be available. Further studies on how to differentiate carriers from patients with true disease, as well as studies on the implications of coinfections and identification of antimicrobial resistance, are warranted.

Economic and operational impact of an improved pathway using rapid molecular diagnostic testing for patients with influenza-like illness in a German emergency department

To evaluate the economic and operational effects of implementing a shorted diagnostic pathway during influenza epidemics. This retrospective study used emergency department (ED) data from the 2014/2015 influenza season. Alere i influenza A & B rapid molecular diagnostic test (RDT) was compared with the polymerase chain reaction (PCR) pathway. Differences in room occupancy time in the ED and inpatient ward and cost differences were calculated for the 14-week influenza season. The process flow was more streamlined with the RDT pathway, and the necessary isolation time in the ED was 9 h lower than for PCR. The difference in the ED examination room occupancy time was 2.9 h per patient on a weekday and 4 h per patient on a weekend day, and the difference in the inpatient room occupancy time was 2 h per patient on a weekday and 3 h per patient on a weekend day. Extrapolated time differences across the influenza season were projected to be 2733 h in the ED examination room occupancy and 1440 h in inpatient room occupancy. In patients with a negative diagnosis, the RDT was also estimated to reduce the total diagnostic costs by 41.52 € per patient compared with PCR. The total cost difference was projected to be 31,892 € across a 14-week influenza season. The improved process and earlier diagnosis with the RDT pathway compared with conventional PCR resulted in considerable savings in ED, inpatient room occupancy time and cost across the influenza season.

Evaluation of national guidelines for bronchiolitis: AGREEments and controversies

AIM

Bronchiolitis is a common respiratory illness and is a leading cause of hospitalisation in infancy. We aimed to appraise three recent national bronchiolitis guidelines produced by the Australasian Paediatric Research in Emergency Departments International Collaborative, the National Institute for Health and Care Excellence in the UK and the American Academy of Pediatrics.

METHODS

A group of final-year medical students and one senior clinician used the AGREE II tool to appraise each guideline in two stages. First, two students appraised each guideline independently and presented their results. Second, two self-selected students met with the senior clinicians to review all scores to ensure completeness of the appraisal and consistency of AGREE II application.

RESULTS

The guidelines scored well overall, with particular strengths in the domains of clarity of presentation, scope and purpose and rigour of development. Comparison of the recommendations across each guideline demonstrated a high degree of consistency. Notable differences included recommendations for the role of palivizumab in prevention of bronchiolitis, the use of continuous pulse oximetry monitoring in the hospitalised patient and the value of respiratory virus testing.

CONCLUSIONS

Our appraisal of bronchiolitis guidelines from three high-income countries demonstrated that they were of high quality, with substantial areas of agreement. Most aspects of clinical practice should be uniform for this common paediatric condition. Areas of guideline weakness were in the domains of applicability and editorial independence. We identified three areas of controversy where further research is needed to support stronger evidence-based recommendations.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Pulmonary Impairment after Respiratory Viral Infections Is Associated with High Mortality in Allogeneic Hematopoietic Cell Transplant Recipients

Pulmonary impairment predicts increased mortality in many settings, and respiratory viral infection (RVI) causes considerable morbidity and mortality in allogeneic hematopoietic cell transplant recipients (allo-HCT). We hypothesized that pulmonary impairment after RVI, defined as a decline of forced expiratory volume in 1 second values by ≥10%, may identify allo-HCT recipients at high risk for mortality. We studied all allo-HCT recipients at our institution who had RVI with respiratory syncytial virus, parainfluenza virus, or influenza from 2004 to 2013 and had pre-RVI and post-RVI pulmonary function tests. We used competing risk regression models to identify risk factors for 2-year nonrelapse mortality (NRM) as the primary outcome after RVI and relapse-related mortality as a competing risk. From 223 eligible patients, pulmonary impairment after RVI was associated with over a 3-fold increase in 2-year NRM (pulmonary impairment, 25.3%; no impairment, 7.4%; univariate subhazard ratio [SHR], 3.9; 95% confidence interval [CI], 1.9 to 8.1; P < .001). After adjusting for age and systemic steroid use, pulmonary impairment after RVI was still associated with increased 2-year NRM (SHR, 3.3 [95% CI, 1.6 to 6.9]; P = .002). After adjustment for race and graft-versus-host disease (GVHD) prophylaxis, chronic GVHD at the time of RVI (odds ratio [OR], 2.8 [95% CI, 1.4 to 5.4]; p = .003) and lymphopenia (OR, 2.2 [95% CI, 1.1 to 4.2]; P = .02) were associated with increased odds of pulmonary impairment, whereas use of nonmyeloablative conditioning was associated with reduced odds of pulmonary impairment (OR, .4 [95% CI, .2 to .8]; P = .006). In allo-HCT recipients with RVIs, pulmonary impairment after RVI is associated with high NRM at 2years.

Rapid Antigen Tests for Influenza: Rationale and Significance of the FDA Reclassification

Rapid antigen tests for influenza, here referred to as rapid influenza diagnostic tests (RIDTs), have been widely used for the diagnosis of influenza since their introduction in the 1990s due to their ease of use, rapid results, and suitability for point of care (POC) testing. However, issues related to the diagnostic sensitivity of these assays have been known for decades, and these issues gained greater attention following reports of their poor performance during the 2009 influenza A(H1N1) pandemic. In turn, significant concerns arose about the consequences of false-negative results, which could pose significant risks to both individual patient care and to public health efforts. In response to these concerns, the FDA convened an advisory panel in June 2013 to discuss options to improve the regulation of the performance of RIDTs. A proposed order was published on 22 May 2014, and the final order published on 12 January 2017, reclassifying RIDTs from class I to class II medical devices, with additional requirements to comply with four new special controls. This reclassification is a landmark achievement in the regulation of diagnostic devices for infectious diseases and has important consequences for the future of diagnostic influenza testing with commercial tests, warranting the prompt attention of clinical laboratories, health care systems, and health care providers.

Temporal relationship between occurrences of hand, foot and mouth disease, respiratory virus detection and febrile seizures in children in tropical Singapore: a time-series analysis

Febrile seizure (FS) in children is a common complication of infections with respiratory viruses and hand, foot and mouth disease (HFMD). We conducted a retrospective ecological time-series analysis to determine the temporal relationship between hospital attendances for FS and HFMD or respiratory virus infections. Epilepsy attendance was used as a control. Data from 2004 to 2012 FS and epilepsy hospital attendance, HFMD notifications to the Ministry of Health and from laboratory-confirmed viral respiratory infections among KK Women's and Children's Hospital inpatients were used. A multivariate linear regression analysis was conducted to evaluate the relationship between FS and the virus time series. Relative risks of FS by age were calculated using Bayesian statistical methods. Paediatric accident and emergency (A&E) attendances for FS were found to be associated with influenza A (extra 0.47 FS per influenza A case), B (extra 0.32 per influenza B case) and parainfluenza 3 (extra 0.35 per parainfluenza type 3 case). However, other viruses were not significantly associated with FS. None of the viruses were associated with epileptic seizure attendance. Influenza A, B and parainfluenza 3 viruses contributed to the burden of FS resulting in A&E attendance. Children at risk of FS should be advised to receive seasonal influenza vaccination.

Comparison of the Cepheid Xpert Xpress Flu/RSV Assay to in-house Flu/RSV triplex real-time RT-PCR for rapid molecular detection of Influenza A, Influenza B and Respiratory Syncytial Virus in respiratory specimens

This study compared the performance of the commercially available Xpert Xpress Flu/RSV assay to an in-house FluAB/RSV triplex real-time RT-PCR assay for the detection of influenza A/B viruses and respiratory syncitial virus (RSV) from both nasopharyngeal aspirate (NPA) and nasopharyngeal flocked swab (NPS). A total of 20 external quality assurance (EQA) samples and 172 clinical respiratory samples were tested prospectively using both the Xpert Xpress Flu/RSV assay and the in-house FluAB/RSV triplex assay. For the EQA samples, concordance rate was 100 % when tested with both assays. For clinical samples, there was 100 % agreement between the two assays for detection of influenza A and influenza B, 96.7 % agreement for detection of RSV and 99.7 % agreement for negative results. With a shortened turnaround time and good diagnostic performance, application of the Xpert Xpress Flu/RSV assay can facilitate patient triage for prompt implementation of infection control measures and management of high-risk patients during influenza epidemics.

Effectiveness of Live Attenuated vs Inactivated Influenza Vaccines in Children During the 2012-2013 Through 2015-2016 Influenza Seasons in Alberta, Canada: A Canadian Immunization Research Network (CIRN) Study

IMPORTANCE

Recent observational studies report conflicting results regarding the effectiveness of live attenuated influenza vaccine (LAIV), particularly against influenza A(H1N1)pdm09.

OBJECTIVE

To compare the effectiveness of LAIV and inactivated influenza vaccine (IIV) against laboratory-confirmed influenza.

DESIGN, SETTING, AND PARTICIPANTS

A test-negative study to estimate influenza vaccine effectiveness (VE) using population-based, linked, individual-level laboratory, health administrative, and immunization data. Data were obtained from 10 169 children and adolescents aged 2 to 17 years (children) who were tested for influenza in inpatient or outpatient settings during periods when influenza was circulating based on a threshold level of 5% weekly test positivity for the province during the 4 influenza seasons spanning from November 11, 2012, to April 30, 2016, in Alberta, Canada. Logistic regression was used to estimate VE by vaccine type, influenza season, and influenza type and subtype. The relative effectiveness of each vaccine type was assessed by comparing the odds of laboratory-confirmed influenza infection for LAIV recipients with that for IIV recipients.

EXPOSURES

The primary exposure was receipt of LAIV or IIV before testing for influenza.

MAIN OUTCOMES AND MEASURES

The primary outcome was influenza case status as determined by reverse-transcriptase polymerase chain reaction testing.

RESULTS

A total of 10 779 respiratory specimens (from 10 169 children) collected and tested for influenza during the 4 influenza seasons were included, with 53.4% from males; the mean (SD) age was 7.0 (4.6) years. Across the 4 influenza seasons, 3161 children tested positive for influenza. Combining the 4 influenza seasons, the adjusted VE against influenza A(H1N1)pdm09 was 69% (95% CI, 56%-78%) for LAIV compared with 79% (95% CI, 70%-86%) for IIV. Vaccine effectiveness against influenza A(H3N2) was 36% (95% CI, 14%-53%) for LAIV and 43% (95% CI, 22%-59%) for IIV. Against influenza B, VE was 74% (95% CI, 62%-82%) for LAIV and 56% (95% CI, 41%-66%) for IIV. There were no significant differences in the odds of influenza infection for LAIV recipients compared with IIV recipients except for influenza B during the 2015-2016 season, when LAIV recipients had lower odds of infection than IIV recipients (odds ratio, 0.36; 95% CI, 0.17-0.76).

CONCLUSIONS AND RELEVANCE

There was no evidence to support the lack of effectiveness of LAIV against influenza A(H1N1)pdm09. These results support administration of either vaccine type in this age group.

Non-mumps Viral Parotitis During the 2014-2015 Influenza Season in the United States

Background

During the 2014-2015 US influenza season, 320 cases of non-mumps parotitis (NMP) among residents of 21 states were reported to the Centers for Disease Control and Prevention (CDC). We conducted an epidemiologic and laboratory investigation to determine viral etiologies and clinical features of NMP during this unusually large occurrence.

Methods

NMP was defined as acute parotitis or other salivary gland swelling of >2 days duration in a person with a mumps- negative laboratory result. Using a standardized questionnaire, we collected demographic and clinical information. Buccal samples were tested at the CDC for selected viruses, including mumps, influenza, human parainfluenza viruses (HPIVs) 1-4, adenoviruses, cytomegalovirus, Epstein-Barr virus (EBV), herpes simplex viruses (HSVs) 1 and 2, and human herpes viruses (HHVs) 6A and 6B.

Results

Among the 320 patients, 65% were male, median age was 14.5 years (range, 0-90), and 67% reported unilateral parotitis. Commonly reported symptoms included sore throat (55%) and fever (48%). Viruses were detected in 210 (71%) of 294 NMP patients with adequate samples for testing, ≥2 viruses were detected in 37 samples, and 248 total virus detections were made among all samples. These included 156 influenza A(H3N2), 42 HHV6B, 32 EBV, 8 HPIV2, 2 HPIV3, 3 adenovirus, 4 HSV-1, and 1 HSV-2. Influenza A(H3N2), HHV6B, and EBV were the most frequently codetected viruses.

Conclusions

Our findings suggest that, in addition to mumps, clinicians should consider respiratory viral (influenza) and herpes viral etiologies for parotitis, particularly among patients without epidemiologic links to mumps cases or outbreaks.

Survey of diagnostic testing for respiratory syncytial virus (RSV) in adults: Infectious disease physician practices and implications for burden estimates

Respiratory syncytial virus (RSV) often causes respiratory illness in adults. Over 40 RSV vaccine and monoclonal antibody products are currently in preclinical development or clinical trials. Because RSV diagnostic practices may impact disease burden estimates, we investigated infectious disease physicians' RSV diagnostic practices among their adult patients.

Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

OBJECTIVES

To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections.

METHODS

A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay.

RESULTS

Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA.

CONCLUSIONS

Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.

Vaccine effectiveness against laboratory-confirmed influenza hospitalizations among young children during the 2010-11 to 2013-14 influenza seasons in Ontario, Canada

Uncertainty remains regarding the magnitude of effectiveness of influenza vaccines for preventing serious outcomes, especially among young children. We estimated vaccine effectiveness (VE) against laboratory-confirmed influenza hospitalizations among children aged 6-59 months. We used the test-negative design in hospitalized children in Ontario, Canada during the 2010-11 to 2013-14 influenza seasons. We used logistic regression models adjusted for age, season, and time within season to calculate VE estimates by vaccination status (full vs. partial), age group, and influenza season. We also assessed VE incorporating prior history of influenza vaccination. We included specimens from 9,982 patient hospitalization episodes over four seasons, with 12.8% testing positive for influenza. We observed variation in VE by vaccination status, age group, and influenza season. For the four seasons combined, VE was 60% (95%CI, 44%-72%) for full vaccination and 39% (95%CI, 17%-56%) for partial vaccination. VE for full vaccination was 67% (95%CI, 48%-79%) for children aged 24-59 months, 48% (95%CI, 12%-69%) for children aged 6-23 months, 77% (95%CI, 47%-90%) for 2010-11, 59% (95%CI, 13%-81%) for 2011-12, 33% (95%CI, -18% to 62%) for 2012-13, and 72% (95%CI, 42%-86%) for 2013-14. VE in children aged 24-59 months appeared similar between those vaccinated in both the current and previous seasons and those vaccinated in the current season only, with the exception of 2012-13, when VE was lower for those vaccinated in the current season only. Influenza vaccination is effective in preventing pediatric laboratory-confirmed influenza hospitalizations during most seasons.

Multiplex Respiratory Virus Testing for Antimicrobial Stewardship: A Prospective Assessment of Antimicrobial Use and Clinical Outcomes Among Hospitalized Adults

Background

Respiratory tract infections are frequent causes of hospitalization and initiation of empirical antimicrobial therapy. Testing for a broad panel of respiratory viruses has been advocated as a useful tool for antibiotic stewardship. We conducted a prospective observational study to assess the impact of rapid viral test results on antimicrobial prescriptions and clinical outcomes among hospitalized adults.

Methods

Eight hundred patients admitted with respiratory symptoms were tested by a 12-virus respiratory panel (RVP) during 3 consecutive winters in Montreal, Canada. The primary outcome measure was change in antimicrobial prescriptions (ie, de-escalation of empirical antimicrobial therapy or commencement of new antimicrobial therapy) after RVP results were available. Clinical outcomes were also assessed.

Results

Influenza virus was identified in 53% of individuals in the study population, and other viruses were identified in 10%. Influenza virus positivity was associated with shorter duration of hospitalization and appropriate antiviral management. Antibiotic management was most significantly correlated with radiographic suspicion of pneumonia and less so with results of the RVP. Positivity for viruses other than influenza virus was not correlated with significantly different outcomes.

Conclusions

Physicians respond to results of testing for influenza virus when managing hospitalized adult patients but respond less to test results for other viruses. These data can inform the design of stewardship interventions and the selection of viral testing panels for hospitalized patients.

Determining the Seasonality of Respiratory Syncytial Virus in the United States: The Impact of Increased Molecular Testing

Background

In the United States, the seasonality of respiratory syncytial virus (RSV) has traditionally been defined on the basis of weeks during which antigen-based tests detect RSV in >10% of specimens (hereafter, the "10% threshold"). Because molecular testing has become more widely used, we explored the extent of polymerase chain reaction (PCR)-based RSV testing and its impact on determining the seasonality of RSV.

Methods

We assessed antigen- and PCR-based RSV reports submitted to the National Respiratory and Enteric Virus Surveillance System during July 2005-June 2015. To characterize RSV seasons by using PCR-based reports, we assessed the traditional 10% threshold; subsequently, we developed 3 methods based on either PCR-based detections or the percentage of positive test results.

Results

The annual number of PCR-based reports increased 200-fold during 2005-2015, while the annual number of antigen-based reports declined. The weekly percentage of specimens positive for RSV by PCR was less than that for antigen-detection tests; accordingly, the 10% threshold excluded detections by PCR and so was imprecise for characterizing RSV seasons. Among our PCR-specific approaches, the most sensitive and consistent method captured 96%-98% of annual detections within a season, compared with 82%-94% captured using the traditional method.

Conclusions

PCR-based reports are increasingly relevant for RSV surveillance and determining the seasonality of RSV. These PCR-specific methods provide a more comprehensive understanding of RSV trends, particularly in settings where testing and reporting are most active. Diagnostic practices will vary by locality and should be understood before choosing which method to apply.

The epidemiology of medically attended respiratory syncytial virus in older adults in the United States: A systematic review

Objective

This review was undertaken to assess the historical evidence of the disease incidence and burden of laboratory-confirmed respiratory syncytial virus (RSV) in medically attended older adults.

Design

A qualitative systematic literature review was performed; no statistical synthesis of the data was planned, in anticipation of expected heterogeneity across studies in this population.

Methods

A literature search of PubMed, Embase, and the Cochrane Library was conducted for studies of medically attended RSV in older adults (≥ 50 years) published in the last 15 years. Two independent reviewers screened titles and abstracts based on predefined inclusion and exclusion criteria.

Results

From 10 studies reporting incidence proportions, RSV may be the causative agent in up to 12% of medically attended acute respiratory illness in older adults unselected for comorbidities, with variations in clinical setting and by year. In multiple studies, medically attended–RSV incidence among older adults not selected for having underlying health conditions increased with increasing age. Of prospectively followed lung transplant recipients, 16% tested positive for RSV. In hospitalized adults with chronic cardiopulmonary diseases, 8% to 13% were infected with RSV during winter seasons (8%-13%) or metapneumovirus season (8%). Hospitalizations for RSV in older adults typically lasted 3 to 6 days, with substantial proportions requiring intensive care unit admission and mechanical ventilation. Among older adults hospitalized with RSV, the mortality rate was 6% to 8%.

Conclusions

Protection of older adults against RSV could reduce respiratory-related burden, especially as age increases and the prevalence of comorbidities (especially cardiopulmonary comorbidities) grows.

Impact of Respiratory Virus Infections in Exacerbation of Acute and Chronic Rhinosinusitis

Rhinosinusitis (RS) is a symptomatic disease classification of many causes and is a major economic burden worldwide. It is widely accepted that RS is further classified into acute (ARS) and chronic (CRS) rhinosinusitis based on the duration of the symptoms, and that viral infection plays a large role in initiating or potentiating the disease. In this review, we examine the role of respiratory virus infection in the exacerbation of ARS and CRS. We explore the epidemiology of viral exacerbation of ARS and CRS and highlight key viruses that may cause exacerbation. We also review the current understanding of viral infections in the upper airway to further explain the putative underlying mechanisms of inflammatory events in ARS and CRS exacerbation. Advances in accurate diagnosis of the etiologic respiratory viruses of ARS and CRS symptoms which can lead to better disease management are also surveyed. In addition to the current treatments which provide symptomatic relief, we also explore the potential of harnessing existing antiviral strategies to prevent ARS and CRS exacerbation, especially with improved viral diagnostic tools to guide accurate prescription of antivirals against causative respiratory viruses.

Respiratory RNA Viruses

Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.

Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens

Respiratory illness causes significant morbidity especially in children, the elderly and the immunocompromised. The sample type taken and the quality of that sample are of great significance in providing an accurate diagnosis. Gargle samples are easy to take and sample the same area as a throat swab (THS). In this study, we assessed the utility of gargle samples for the molecular detection of common respiratory infections. Paired gargle and THS samples collected on the same day from the same patient were compared. We also included in our analysis paired THS and gargle samples that were collected within three days of each other as these samples are likely to have been taken during the same illness. Overall the data suggests that gargle samples are a more sensitive sample type than THS samples as overall the diagnostic yield was higher in the gargle samples and the Ct value of the gargle samples was stronger for the majority of samples in comparison to THS samples. Similar data was seen in the paired samples collected within one to three days of each other, as although the diagnostic yield between the sample types was similar (similar discrepant results), the majority of gargles had stronger Ct values than THS samples. This paper highlights the usefulness of gargle samples as non-invasive sensitive respiratory sample in comparison to THS samples. We recommend that other testing sites should consider using gargle samples for respiratory diagnosis as it will bring benefits in terms of sensitivity and sampling ease of use.

Frequency of respiratory virus infections and next-generation analysis of influenza A/H1N1pdm09 dynamics in the lower respiratory tract of patients admitted to the ICU

Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014–2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p<0.05). Overall, a greater number of H1N1pdm09 virus variants were observed using next generation sequencing on partial HA sequences (codons 180–286) in clinical samples from the LRT as compared to URT. In addition, 222G/N/A mutations were observed in 30% of LRT samples from ICU patients. Finally, intra-host evolution analysis showed the presence of different dynamics of viral population in LRT of patients hospitalized in ICU with a severe influenza infection.

An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections

Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases.

Nasopharyngeal viral PCR in immunosuppressed patients and its association with virus detection in bronchoalveolar lavage by PCR

Background and objective

Pulmonary infiltrates are common in immunosuppressed patients. Bronchoscopy with bronchoalveolar lavage (BAL) is often used to evaluate their aetiology. However, it may not always be easily performed. Thus, alternative diagnostic strategies may be needed. There is limited data on the correlation of nasopharyngeal (NP) respiratory viral panel (RVP)‐PCR testing compared with BAL. We aimed to identify the predictive value of NP RVP‐PCR samples compared with samples obtained from BAL in immunosuppressed patients with pulmonary infiltrates.

Methods

We conducted an observational retrospective study of immunosuppressed adults who underwent bronchoscopy in the Pulmonary Department at the University of Rochester Medical Center between January 2011 and June 2016. We compared the positive and negative predictive values, sensitivity, specificity and false negative rate of NP RVP‐PCR and BAL RVP‐PCR, as well as identified clinical predictors of positive viral BAL RVP‐PCR.

Results

Eighty‐nine immunosuppressed patients had both NP and bronchoalveolar RVP‐PCR testing. Twenty‐one patients had NP(+)BAL(+) RVP‐PCR testing. Seven patients had false negative (NP(−)BAL(+)) RVP‐PCR testing. Three patients had NP(+)BAL(−) RVP‐PCR testing. The positive and negative predictive values of NP RVP‐PCR testing were 88% and 89%, respectively. Allogeneic bone marrow transplantation and testing performed in the winter and spring months were significantly associated with positive BAL RVP‐PCR (OR = 3.3 (1.19–9.12); OR = 4.62 (1.64–12.99), respectively).

Conclusion

NP RVP‐PCR testing has high concordance with testing performed on BAL samples. Repeat testing through BAL is beneficial when there is high concern for viral infection after initial NP RVP‐PCR testing is negative.

There are limited data on nasopharyngeal (NP) testing compared with bronchoscopy in immunosuppressed patients. NP PCR testing has a false negative rate of 8%, positive predictive value of 88% and negative predictive value of 89%.

http://onlinelibrary.wiley.com/doi/10.1111/resp.13061/abstract

Aptamers for respiratory syncytial virus detection

The identification of the infectious agents is pivotal for appropriate care of patients with viral diseases. Current viral diagnostics rely on selective detection of viral nucleic acid or protein components. In general, detection of proteins rather than nucleic acids is technically more suitable for rapid tests. However, protein-based virus identification methods depend on antibodies limiting the practical applicability of these approaches. Aptamers rival antibodies in target selectivity and binding affinity, and excel in terms of robustness and cost of synthesis. Although aptamers have been generated for virus identification in laboratory settings, their introduction into routine virus diagnostics has not been realized, yet. Here, we demonstrate that the rationally designed SELEX protocol can be applied on whole virus to select aptamers, which can potentially be applied for viral diagnostics. This approach does not require purified virus protein or complicated virus purification. The presented data also illustrate that corroborating the functionality of aptamers with various approaches is essential to pinpoint the most appropriate aptamer amongst the panel of candidates obtained by the selection. Our protocol yielded aptamers capable of detecting respiratory syncytial virus (RSV), an important pathogen causing severe disease especially in young infants, at clinically relevant concentrations in complex matrices.