Epidemic 2014 enterovirus D68 cross-reacts with human rhinovirus on a respiratory molecular diagnostic platform

Coinfections and iterative detection of respiratory viruses among 17,689 patients between March 2021 and December 2022 in Southern France

OBJECTIVES

We aimed to describe coinfections and iterative infections with respiratory viruses diagnosed over a 22-month period in 2021-2022 in public university hospitals of the second largest French city.

MATERIAL AND METHODS

Respiratory virus infections were diagnosed by qPCR with the Fast Track Diagnostics Respiratory Pathogens 21 on nasopharyngeal swabs collected between 01/03/2021-31/10/2022 and sent for routine diagnosis purpose to our clinical microbiology-virology laboratory at public university hospitals of Marseille, Southern France.

RESULTS

Nasopharyngeal swabs from 17,689 patients were tested, of which 8,133 (46 %) were positive for ≥1 respiratory virus and 1,255 (15%) were co-infected with ≥2 viruses including 213 (2.6 %) with 3-7 viruses. Among them, 1,005 (80 %) were younger than 5 years, and mean age was significantly lower for coinfected than monoinfected patients (6.6 versus 23.8 years; p < 0.0001). Viruses with the highest confection rates were HBoV (97 %), HPeV (97 %), EV (92 %), ADV (68 %), and HCoV-HKU1 (63 %). Iterative infections were observed in 96 patients and they involved 10 different viruses.

CONCLUSIONS

Our study points out that coinfections with respiratory viruses vary over time in prevalence, involve majoritarily young children, and may involve concurrent acute infections or acute-on-chronic infections, which deserves further specific studies.

Enterovirus A71 and coxsackievirus A6 circulation in England, UK, 2006-2017: A mathematical modelling study using cross-sectional seroprevalence data

Enterovirus A71 (EV-A71) and coxsackievirus A6 (CVA6) primarily cause hand, foot and mouth disease and have emerged to cause potential fatal neurological and systemic manifestations. However, limited surveillance data collected through passive surveillance systems hampers characterization of their epidemiological dynamics. We fit a series of catalytic models to age-stratified seroprevalence data for EV-A71 and CVA6 collected in England at three time points (2006, 2011 and 2017) to estimate the force of infection (FOI) over time and assess possible changes in transmission. For both serotypes, model comparison does not support the occurrence of important changes in transmission over the study period, and we find that a declining risk of infection with age and / or seroreversion are needed to explain the seroprevalence data. Furthermore, we provide evidence that the increased number of reports of CVA6 during 2006-2017 is unlikely to be explained by changes in surveillance. Therefore, we hypothesize that the increased number of CVA6 cases observed since 2011 must be explained by increased virus pathogenicity. Further studies of seroprevalence data from other countries would allow to confirm this. Our results underscore the value of seroprevalence data to unravel changes in the circulation dynamics of pathogens with weak surveillance systems and large number of asymptomatic infections.

First Detection of Enterovirus D68 in Korean Children, September 2022

BACKGROUND

Enterovirus D68 (EV-D68) is a re-emerging pathogen that is particularly common in children and may cause asthma-like respiratory infection and acute flaccid myelitis. However, in Korea, EV-D68 has never been reported thus far. This study aimed to identify EV-D68 from nasopharyngeal aspirates (NPAs) in Korean children with a respiratory tract infection.

MATERIALS AND METHODS

The EV-D68 reference strain was purchased and blindly used to assess the detection ability of three commercial and one in-house mRT-PCR kit in 2018. Then, we selected children whose specimens were positive for human rhinovirus (HRV) and/or enterovirus (EV) by Allplex mRT-PCR (Seegene, Inc., Seoul, Korea) from April to December 2022. Total RNA was extracted from NPAs, and a partial 5'-UTR gene was amplified and sequenced for the identification of HRV/EV species. Additionally, PCR targeting the VP1 gene was performed to assess EV-D68-positive NPAs, followed by sequencing. Phylogenetic analysis and comparison of amino acid sequence alignments were performed using a partial VP1 gene of our and recent international EV-D68 strains.

RESULTS

Among the mRT-PCR kits tested, only the in-house kit was able to detect EV-D68 in 2018. However, we detected three EV-D68 strains among children hospitalized with fever and/or respiratory symptoms in September - December 2022 who tested positive for EV by the Allplex kit. Two of them were healthy toddlers with lower respiratory infections accompanied by new-onset wheezing but no neurologic complications. Among 34 children with lower respiratory infection who tested positive for HRV during the same period, EV-D68 was not detected. Phylogenetic analysis revealed that the first Korean EV-D68 belonged to subclade B3. Amino acid sequence alignment of international subclade B3 EV-D68 strains also showed that our strain is genetically more related to those from Europe than those from Japan.

CONCLUSION

We first detected EV-D68 in three Korean children who had EV detected by the Allplex mRT-PCR kit in 2022. EV-D68 also circulated in Korea in fall 2022, but the prevalence and severity seemed to be lower than those in previous reports from other countries.

Hunting for mpox (monkeypox) mimickers: Use of the Biofire meningitis/encephalitis panel on lesion swabs to support alternative viral diagnoses

BACKGROUND

Mpox (formerly monkeypox) is an emerging zoonotic disease of public health concern that presents as a rash mimicking other common viral exanthems. Unlike traditional testing algorithms relying on several assays, the BioFire FilmArray meningitis/encephalitis (ME) panel simultaneously detects common viruses causing rashes; however, Biofire ME is only licensed for testing on cerebral spinal fluid.

OBJECTIVES

This study evaluated use of the Biofire ME panel for detection and discrimination of herpes simplex virus types 1 and 2 (HSV-1 and HSV-2), varicella zoster virus (VZV), human herpesviruses type 6 (HHV-6), enteroviruses (EVs), and human paraechoviruses (HPeVs) from a dermal or mucocutaneous swabs collected in universal transport media (UTM).

STUDY DESIGN

Results of the BioFire ME panel were compared against methods used during clinical testing. Ten-fold serial dilutions in UTM of cultured viruses were used to compare analytical sensitivity, and analytical specificity was assessed using panels of microorganisms in UTM. Clinical sensitivity and specificity were assessed using 20 positive specimens each for HHV-1, HHV-2, HHV-6, VZV, EVs, and HPeV, as well as 35 known negative specimens that included 15 mpox-positive specimens.

RESULTS

Biofire ME was as sensitive as comparator methods, and correctly discriminated all HSV-1, HSV-2, VZV, HHV-6, EVs, and HPeVs from mpox and mpox-mimickers. Cross-reaction between EV and rhinoviruses A, B, and C were noted in the specificity panel.

CONCLUSIONS

Swabs in UTM collected for mpox testing are suitable for use on the Biofire ME panel, allowing more streamlined diagnostic testing for viral exanthems in patients under investigation for mpox infection.

Global prevalence and case fatality rate of Enterovirus D68 infections, a systematic review and meta-analysis

A substantial amount of epidemiological data has been reported on Enterovirus D68 (EV-D68) infections after the 2014 outbreak. Our goal was to map the case fatality rate (CFR) and prevalence of current and past EV-D68 infections. We conducted a systematic review (PROSPERO, CRD42021229255) with published articles on EV-68 infections in PubMed, Embase, Web of Science and Global Index Medicus up to January 2021. We determined prevalences using a model random effect. Of the 4,329 articles retrieved from the databases, 89 studies that met the inclusion criteria were from 39 different countries with apparently healthy individuals and patients with acute respiratory infections, acute flaccid myelitis and asthma-related diseases. The CFR estimate revealed occasional deaths (7/1353) related to EV-D68 infections in patients with severe acute respiratory infections. Analyses showed that the combined prevalence of current and past EV-D68 infections was 4% (95% CI = 3.1-5.0) and 66.3% (95% CI = 40.0-88.2), respectively. The highest prevalences were in hospital outbreaks, developed countries, children under 5, after 2014, and in patients with acute flaccid myelitis and asthma-related diseases. The present study shows sporadic deaths linked to severe respiratory EV-D68 infections. The study also highlights a low prevalence of current EV-D68 infections as opposed to the existence of EV-D68 antibodies in almost all participants of the included studies. These findings therefore highlight the need to implement and/or strengthen continuous surveillance of EV-D68 infections in hospitals and in the community for the anticipation of the response to future epidemics.

Comparative Evaluation of Allplex Respiratory Panels 1, 2, 3, and BioFire FilmArray Respiratory Panel for the Detection of Respiratory Infections

Multiplex nucleic acid amplification assays that simultaneously detect multiple respiratory pathogens in a single nasopharyngeal swab (NPS) specimen are widely used for rapid clinical diagnostics. We evaluated Allplex Respiratory Panel (RP) 1, 2, 3, and the BioFire FilmArray RP assay for detecting respiratory pathogens from NPS specimens. In all, 181 NPS specimens obtained from patients suspected of having respiratory infections during the non-influenza season (August–December 2019) were included. The Allplex RP 1, 2, and 3 detected 154 samples positive for respiratory viruses, whereas the BioFire FilmArray detected viruses in 98 samples. Co-infection with two or more viruses was detected in 41 and 17 NPS specimens by Allplex RP and the BioFire FilmArray RP, respectively. For adenoviruses, Allplex RP 1 detected 31 specimens, compared to 34 by the BioFire FilmArray. In all, 64 NPS specimens were positive for human enterovirus (HEV) and human rhinovirus (HRV) on the Allplex RP, in contrast to 39 HEV/HRV on the BioFire FilmArray. The parainfluenza virus (PIV-1–4) detection rate differed between the two systems. Most discrepant results were observed for NPS specimens with high cycle threshold values obtained by Allplex RP. This study showed concordant performance of the Allplex RP 1, 2, 3, and the BioFire FilmArray RP for the simultaneous detection of multiple respiratory viruses.

Comparison of children with acute flaccid myeltis before and after 2014

Objective

To observe whether cases of acute flaccid myelitis (AFM) before and since August 1, 2014, had important differences and to further characterize patients with AFM regarding clinical, laboratory, imaging, and treatment findings.

Methods

All pediatric patients with AFM at our institution were reviewed. Demographic, clinical, and diagnostic data were collected through medical record review. Patients with onset before August 1, 2014, and after that date were compared and when applicable compared with Centers for Disease Control and Prevention data.

Results

Sixteen patients were included, 6 in the pre-2014 and 10 in the post-2014 group. The mean age in the pre-2014 group was 7.4 years and in the post-2014 group was 6.4 years. Initial symptoms were similar in both groups, as were functional and motor abilities at disease nadir and the most recent follow-up. Post-2014 patients had a higher mean CSF white blood cell count (57) and neutrophil count (30%) compared with pre-2014 patients (3.2 and 0.5%, respectively). Eighty percent of post-2014 patients had positive enterovirus/rhinovirus testing, with 57% of specimens positive for enterovirus D68 (EV-D68). On acute imaging, a triad of brainstem, cervical cord gray matter involvement, and ventral nerve root/cauda equina (CE) thickening/enhancement was found in 5 patients.

Conclusion

The groups had more similarities than differences but with a more inflammatory picture in the post-2014 patients. The constellation of cervical cord gray matter, brainstem, and nerve root/CE thickening should raise suspicion for AFM in the appropriate clinical setting. Most post-2014 patients had associated enterovirus infections, and over half tested for EV-D68 were positive. There was minimal clinical improvement in both groups despite various immunotherapies.

Enterovirus D68 serosurvey: evidence for endemic circulation in the Netherlands, 2006 to 2016

BackgroundEnterovirus D68 (EV-D68) has caused major outbreaks of severe respiratory illness worldwide since 2010.AimOur aim was to evaluate EV-D68 circulation in the Netherlands by conducting a serosurvey of EV-D68 neutralising antibodies (nAb) among the Dutch general population.MethodsWe screened 280 sera from children and adults in the Netherlands and used two independent sets of samples collected in the years 2006 and 2007 and in the years 2015 and 2016, time points before and after the first EV-D68 upsurge in 2010. Neutralisation capacity of the sera was tested against the prototype Fermon EV-D68 strain isolated in 1962 and against a recent EV-D68 strain (genotype B3) isolated in France in 2016.ResultsRegardless of the time of serum collection, we found remarkably high overall seropositivity (94.3-98.3%) for nAb against both EV-D68 strains. Geometric mean titres increased in an age-dependent manner.ConclusionsOur data suggest that EV-D68 has been circulating in the Netherlands for decades and that the enterovirus surveillance does not accurately capture the prevalence of this clinically relevant pathogen.

Enterovirus D68-associated respiratory infection in southern Brazil, 2018 - A population-based laboratory surveillance

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Patients with SARI or ILI notified during epidemiological surveillance are investigated to detect respiratory virus.

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Enteroviruses were detected in 69/6535 (1%), being 39/69 (56.5 %) of SARI, and 30/69 (43.5 %) of ILI cases.

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EV-D68 was detected in the 36 samples previously identified as EV/RV co-detection.

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This finding settles the sustained circulation of EV-D68 in southern Brazil.

Enterovirus D68 (EV-D68) strain was confirmed in 36/69−52.2% of enterovirus-positive samples collected through surveillance networks for severe acute respiratory infections (SARI) and influenza-like illness (ILI) in southern Brazil in 2018. This finding settles the sustained circulation of EV-D68 in southern Brazil.

Improved diagnostic policy for respiratory tract infections essential for patient management in the emergency department

Aim:

Establishing an optimal diagnostic policy for patients with respiratory tract infections, at the emergency department (ED) of a university hospital in The Netherlands.

Methods:

Adult patients were sampled at admission, during the respiratory season (2014–2015). The FilmArray-RP was implemented at the clinical virology laboratory. Diagnostics were provided from 8 am to 10 pm, weekends included.

Results:

436/492 (89%) results were available while patients were still at the ED. Median TAT from admission to test result was 165 min (IQR: 138–214). No antibiotics were prescribed in 94/207 (45%) patients who tested positive for a virus. 185/330 (56%) hospitalized patients did not need admission with isolation measures. The value-based measure, expressed in euro–hour (€h), increased to tenfold compared with previous policy.

Conclusion:

An optimal policy is essential for patient management, by providing timely, reliable diagnostics.

Virus detections among patients with severe acute respiratory illness, Northern Vietnam

Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2–3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7–22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.

Respiratory Viruses Cause Late Morbidity in Recipients of Hematopoietic Stem Cell Transplantation

Common respiratory viral infections (CRVIs) frequently complicate hematopoietic stem cell transplantation (HSCT). We conducted a retrospective, single-center, observational cohort study to determine the incidence of CRVI in patients who received an allogeneic (allo) or autologous (auto) HSCT at the Royal Adelaide Hospital between 2009 and 2017. The median follow-up was 8.9 and 4.5 years for auto- and allo-HSCT recipients, respectively. There were 149 CRVI episodes in 74 patients, with rhinovirus being the most commonly isolated virus (n = 81, 47%). The majority of CRVIs (113/149, 75.8%) occurred more than 100 days post-HSCT and 67% were diagnosed in the outpatient setting. There was evidence of lower respiratory tract infection (LRTI) in 45.6% (68/149) of CRVIs. On multivariate logistic regression analysis, coviral infections and cytomegalovirus viremia were independent risk factors for progression of CRVI to LRTI. Ten (6.7%) CRVI episodes resulted in admission to intensive care for ventilatory support and 8 (5.4%) patients died within 30 days of CRVI diagnosis. In our study, 10.4% of HSCT recipients experienced a CRVI post-transplant, primarily causing late morbidity and potentially mortality. Prevention with strict infection control practices, vaccination, and patient education is essential.

Genomic analysis of serologically untypable human enteroviruses in Taiwan

BACKGROUND

Human enteroviruses contain over 100 serotypes. We have routinely conducted enterovirus surveillance in northern Taiwan; but about 10% of isolates could not be serotyped using traditional assays. Next-generation sequencing (NGS) is a powerful tool for genome sequencing.

METHODS

In this study, we established an NGS platform to conduct genome sequencing for the serologically untypable enterovirus isolates.

RESULTS

Among 130 serologically untypable isolates, 121 (93%) of them were classified into 29 serotypes using CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer)-based RT-PCR to amplify VP1 genes (VP1-CODEHOP). We further selected 52 samples for NGS and identified 59 genome sequences from 51 samples, including 8 samples containing two virus genomes. We also detected 23 genome variants (nucleotide identity < 90% compared with genome sequences in the public domain) which were potential genetic recombination, including 9 inter-serotype recombinants and 14 strains with unknown sources of recombination.

CONCLUSIONS

We successfully integrated VP1-CODEHOP and NGS techniques to conduct genomic analysis of serologically untypable enteroviruses.

The Resource Burden of Infections With Rhinovirus/Enterovirus, Influenza, and Respiratory Syncytial Virus in Children

We reviewed the resource utilization of patients with human rhinovirus/enterovirus (HRV/ENT), influenza A/B (FLU), or respiratory syncytial virus (RSV). A total of 2013 patients with nasopharyngeal swabs positive for HRV/ENT, RSV, or FLU were included. Records were reviewed for respiratory support, vascular access procedures, emergency department care only versus admission versus pediatric intensive care unit (PICU) care, antibiotics, length of stay, and billing data. Of the 2013 subjects, 1251 tested positive for HRV/ENT, 558 for RSV, and 204 for FLU. Fewer HRV/ENT patients were discharged from the emergency department ( P < .001); and they were more likely to be admitted to the pediatric intensive care unit ( P < .001). HRV/ENT and RSV patients were more likely to require invasive procedures ( P = .01). Median hospital costs for HRV/ENT patients were more than twice that of FLU patients ( P < .001). HRV/ENT infection in pediatric patients poses a significant resource and cost burden, even when compared with other organisms.

Genetic diversity of rhinoviruses detected at a tertiary hospital in Catalonia (Spain) during the 2014-2017 seasons

AIM

To describe the genetic diversity of rhinovirus (RV) from patients attended at a tertiary hospital in Barcelona (Spain) from October 2014 to May 2017.

METHODS

RV detection was performed by real-time multiplex RT-PCR. A specific real-time quantitive retrotranscription PCR (qRT-PCR) was carried out to select those samples (Ct < 35) for molecular characterization based on partial VP4/2 protein.

RESULTS

Phylogenetic characterization revealed proportions of 63% RV-A, 6% RV-B and 31% RV-C (119 different types). RV-A circulated throughout all the study period, with a minor circulation during winter, just when RV-C prevailed. Differences between age medians by RV-specie were reported.

CONCLUSION

The large genetic diversity of RV detected in our area is described here. The variable cocirculation of multiple RV types is also reported, showing differences by age.

Enterovirus D68 - The New Polio?

Enterovirus D68 (EV-D68) has emerged over the recent years, with large outbreaks worldwide. Increased occurrence has coincided with improved clinical awareness and surveillance of non-polio enteroviruses. Studies showing its neurotropic nature and the change in pathogenicity have established EV-D68 as a probable cause of Acute Flaccid Myelitis (AFM). The EV-D68 storyline shows many similarities with poliovirus a century ago, stimulating discussion whether EV-D68 could be ascertaining itself as the "new polio." Increasing awareness amongst clinicians, incorporating proper diagnostics and integrating EV-D68 into accessible surveillance systems in a way that promotes data sharing, will be essential to reveal the burden of disease. This will be a necessary step in preventing EV-D68 from becoming a threat to public health.

Evaluation of Performance Characteristics of Panther Fusion Assays for Detection of Respiratory Viruses from Nasopharyngeal and Lower Respiratory Tract Specimens

Accurate and rapid diagnosis is needed for timely intervention and clinical management of acute respiratory infections. This study evaluated performance characteristics of the Panther Fusion assay for the detection of influenza A virus (Flu A), influenza B virus (Flu B), respiratory syncytial virus (RSV), parainfluenza viruses 1 to 3 (Para 1 to 3), human metapneumovirus (hMPV), rhinovirus (RV), and adenovirus (Adeno) targets in comparison to those of the eSensor and Lyra assays using 395 nasopharyngeal (NP) and 104 lower respiratory tract (LRT) specimens. Based on the consensus positive result established (positive result in 2 of the 3 assays), the NP specimens for the Fusion and eSensor assays had 100% positive percent agreement (PPA) for all the analytes and the Lyra assays had 100% PPA for Flu A and Adeno analytes. A 100% negative percent agreement (NPA) was observed for all the Lyra analytes, whereas those for the Fusion targets ranged from 98.4 to 100% and those for the eSensor ranged from 99.4 to 100% for all the analytes except RV. For the LRT specimens, Fusion had 100% PPA and 100% NPA for all the targets except hMPV. There was a 100% PPA for eSensor analytes; the NPA ranged from 98 to 100%, except for RV. For the Lyra assays, the PPA ranged between 50 and 100%, while the NPA was 100% for all the targets except Adeno. The Fusion assay performed similarly to the eSensor assay for majority of the targets tested and provides laboratories with a fully automated random-access system to test for a broad array of viral respiratory pathogens.

Critical evaluation of FDA-approved respiratory multiplex assays for public health surveillance

Introduction: Clinical management and identification of respiratory diseases has become more rapid and increasingly specific due to widespread use of PCR(polymerase chain reaction) multiplex technologies. Although significantly improving clinical diagnosis, multiplexed PCR assays could have a greater impact on local and global disease surveillance. The authors wish to propose methods of evaluating respiratory multiplex assays to maximize diagnostic yields specifically for surveillance efforts.

Areas covered: The authors review multiplexed assays and critically assess what barriers have limited these assays for disease surveillance and how these barriers might be addressed. The manuscript focuses specifically on the case study of using multiplexed assays for surveillance of respiratory pathogens. The authors also provide a method of validation of specific surveillance measures.

Expert commentary: Current commercially available respiratory multiplex PCR assays are widely used for clinical diagnosis; however, specific barriers have limited their use for surveillance. Key barriers include differences in testing phase requirements and diagnostic performance evaluation. In this work the authors clarify phase testing requirements and introduce unique diagnostic performance measures that simplify the use of these assays on a per target basis for disease surveillance.

An array-based melt curve analysis method for the identification and classification of closely related pathogen strains

PCR-based techniques are widely used to identify disease causing bacterial and viral pathogens, especially in point-of-care or near-patient clinical settings that require rapid results and sample-to-answer workflows. However, such techniques often fail to differentiate between closely related species that have highly variable genomes. Here, a homogenous (closed-tube) pathogen identification and classification method is described that combines PCR amplification, array-based amplicon sequence verification, and real-time detection using an inverse fluorescence fluorescence-resonance energy transfer technique. The amplification is designed to satisfy the inclusivity criteria and create ssDNA amplicons, bearing a nonradiating quencher moiety at the 5'-terminus, for all the related species. The array includes fluorescent-labeled probes which preferentially capture the variants of the amplicons and classify them through solid-phase thermal denaturing (melt curve) analysis. Systematic primer and probe design algorithms and empirical validation methods are presented and successfully applied to the challenging example of identification of, and differentiation between, closely related human rhinovirus and human enterovirus strains.

Clinical characteristics and outcomes of human rhinovirus positivity in hospitalized children

BACKGROUND:

The clinical relevance of positive human rhinovirus (HRV) in hospitalized patients is unclear. Our objective was to describe the clinical characteristics and outcomes of HRV positivity in a heterogeneous population of hospitalized children, compared to those positive for another respiratory virus and those where no respiratory virus was detected.

METHODS:

A retrospective case–control study of children hospitalized between January 2014 to April 2015 who had a respiratory viral specimen collected. Clinical and laboratory data were collected, and baseline characteristics and clinical variables were compared.

RESULTS:

During the study period, there were 671 specimens obtained from 577 patients that were processed for the respiratory viral polymerase chain reaction assay, of which 198 were positive for HRV, 167 positive for another respiratory virus, and 306 where no respiratory virus was detected. A history of asthma was significantly associated with HRV-positive patients (odds ratio [OR] 3.71; P < 0.001). On multivariate analysis, HRV-positive patients had a higher requirement for mechanical ventilation (OR 1.44), lower rates of readmission (OR 0.53), and lower mortality (OR 0.35) compared to patients with no respiratory virus isolated; however, none were statistically significant. HRV-positive patients did have a significantly shorter length of stay (LOS) compared with patients with no respiratory virus isolated (difference–0.35; P = 0.001). Similar outcomes were seen in patients positive for other respiratory viruses.

CONCLUSIONS:

HRV-positive hospitalized pediatric patients with a heterogeneous set of clinical diagnoses had higher association with asthma compared to patients who had another, or no, respiratory virus isolated. HRV-positive patients had shorter LOS compared to patients who had no respiratory viruses isolated. These findings suggest that HRV positivity in hospitalized pediatric patients may not lead to adverse clinical outcomes, although asthma is a risk factor regardless of clinical comorbidities and diagnoses. Further research is warranted to understand the predisposition of asthma to HRV positivity.

Interpretation and Relevance of Advanced Technique Results

Advanced techniques in the field of diagnostic microbiology have made amazing progress over the past 25 years due largely to a technological revolution in the molecular aspects of microbiology [1, 2]. In particular, rapid molecular methods for nucleic acid amplification and characterization combined with automation in the clinical microbiology laboratory as well as user-friendly software and robust laboratory informatics systems have significantly broadened the diagnostic capabilities of modern clinical microbiology laboratories. Molecular methods such as nucleic acid amplification tests (NAATs) rapidly are being developed and introduced in the clinical laboratory setting [3, 4]. Indeed, every section of the clinical microbiology laboratory, including bacteriology, mycology, mycobacteriology, parasitology, and virology, has benefited from these advanced techniques. Because of the rapid development and adaptation of these molecular techniques, the interpretation and relevance of the results produced by such molecular methods continues to lag behind. The purpose of this chapter is to review, update, and discuss the interpretation and relevance of results produced by these advanced molecular techniques.

A chip-based rapid genotyping assay to discriminate between rhinovirus species A, B and C

BACKGROUND

Human rhinoviruses (RVs) are increasingly associated with severe disease of the respiratory tract. Multiple studies highlighted the clinical significance of different RV species; RV-C is linked to asthma exacerbations and increased disease severity in children, whereas RV-B seems to correlate with milder disease.

OBJECTIVES

Current typing strategies for differentiation of RV species are time consuming and require extensive equipment. Here we present a novel genotyping tool to discriminate RV species A, B and C.

STUDY DESIGN

The method encompasses a VP4/VP2 polymerase chain reaction (PCR), followed by hybridization of the product on a macro array with probes covering RV-A, B, and C, produced by Chipron as custom array. Validation was performed with respiratory specimens submitted for diagnostic evaluation to the Academic Medical Center. A selection of RV PCR-positive samples genotyped based on VP4/VP2 sequencing was evaluated. Diagnostic performance was tested on respiratory samples positive for RV in an in-house multiplex respiratory PCR from January 2016 to January 2017. In-house primers and additional genotype-specific primers were used for sequencing to investigate array-negative and array-double-positive samples.

RESULTS

The majority of samples pretyped RVs (n = 135) were classified correctly, except for one that was assigned RV-C instead of RV-A, and 3 samples tested negative. The array gave four double-positive results; the presence of more than one genotype was confirmed in two samples. In 173/187 (92.5%) RV-positive tested patient samples from 2016, the test resulted in a designated species. RV species A was identified in 109 specimens (58.3%), RV-B in 26 (13.9%), and RV-C in 56 (29.9%) samples. Sequencing of the probe region of 14 (7.6%) negative samples revealed up to 3 mismatches to the probes for 12 samples; in 2 cases no PCR product was generated. Notably, in 18 samples the chip detected more than one species, of which 16 were confirmed by sequencing.

DISCUSSION

The Chipron LCD RV array provides a fast and highly sensitive method for discrimination between rhinovirus species, and has the power to detect dual infections.

A comparison of hospitalized children with enterovirus D68 to those with rhinovirus

BACKGROUND

During the Fall of 2014, numerous children were hospitalized with asthma or respiratory distress related to Enterovirus D68 (EV-D68). A large proportion initially tested positive for rhinovirus. During this period our laboratory noted a cross-reactivity between EV-D68 and the rhinovirus component of the GenMark multiplex respiratory viral panel. Many other laboratories used assays not designed to distinguish these Picornoviridae.

METHODS

To compare the presentation and outcomes of patients with rhinovirus and EV-D68, 103 GenMark rhinovirus positive nasopharyngeal swabs from hospitalized children were retested for EV-D68.

RESULTS

EV-D68 positive patients versus EV-D68 negative patients were more likely to have a history of asthma (33.3% vs. 11.0%, P = 0.02) and to present with acute respiratory illness (66.7% vs. 40.2%, P = 0.048), especially status asthmaticus (47.6% vs. 2.4%, P < 0.001). On admission they had more wheezing, respiratory distress, and lower respiratory tract involvement, and were more likely to be treated with steroids and discharged home on asthma medications. Respiratory viral coinfection was less common in EV-D68 positive vs EV-D68 negative patients. In patients without a respiratory viral coinfection the overall findings were similar.

CONCLUSION

Patients with EV-D68 versus rhinovirus were more likely to have a history of asthma, to present with status asthmaticus, to wheeze on admission, and to receive treatment with asthma medications in hospital and at discharge. The inability of common assays to distinguish EV-D68 from rhinoviruses raises the possibility that the role of EV-D68 as a viral trigger of asthma has been under appreciated. Pediatr Pulmonol. 2017;52:827-832. © 2017 Wiley Periodicals, Inc.

Rhinovirus - From bench to bedside

Rhinovirus has been neglected in the past because it was generally perceived as a respiratory virus only capable of causing mild common cold. Contemporary epidemiological studies using molecular assays have shown that rhinovirus is frequently detected in adult and pediatric patients with upper or lower respiratory tract infections. Severe pulmonary and extrapulmonary complications are increasingly recognized. Contrary to popular belief, some rhinoviruses can actually replicate well at 37 °C and infect the lower airway in humans. The increasing availability of multiplex PCR panels allows rapid detection of rhinovirus and provides the opportunity for timely treatment and early recognition of outbreaks. Recent advances in the understanding of host factors for viral attachment and replication, and the host immunological response in both asthmatic and non-asthmatic individuals, have provided important insights into rhinovirus infection which are crucial in the development of antiviral treatment. The identification of novel drugs has been accelerated by repurposing clinically-approved drugs. As humoral antibodies induced by past exposure and vaccine antigen of a particular serotype cannot provide full coverage for all rhinovirus serotypes, novel vaccination strategies are required for inducing protective response against all rhinoviruses.

Epidemiologic Analysis of Respiratory Viral Infections Mainly in Hospitalized Children and Adults in a Midwest University Medical Center After the Implementation of a 14-Virus Multiplex Nucleic Acid Amplification Test

OBJECTIVES

To investigate the etiology of viral respiratory tract infections mainly in hospitalized children and adults over a 12-month consecutive period after implementation of a 14-virus multiplex nucleic acid amplification test.

METHODS

From January 2014 to January 2015, a total of 2,237 respiratory samples were analyzed with the US Food and Drug Administration-cleared eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA).

RESULTS

Of the 2,237 specimens tested, 788 specimens were positive for at least one virus, giving a positivity rate of 35.2%, and because of viral codetection, a total of 862 viral targets were identified. The age groups with the highest positivity rates were the 0- to 1-year (73.5%) and 2- to 6-year (78.4%) age groups. The overall viral codetection rate was 9.1%. Human rhinovirus (HRV) was the most prevalent respiratory virus found in children and adults. The peak of HRV seen in September 2014 represented a combination of HRV and enterovirus D68, 2014 epidemic respiratory infections.

CONCLUSION

The ability to detect a wider range of respiratory viruses gave us a better understanding of the etiology of respiratory infections in our population, particularly for HRV and enhanced our ability to detect viral coinfection.

Performance Evaluation of Allplex Respiratory Panels 1, 2, and 3 for Detection of Respiratory Viruses and Influenza A Virus Subtypes

The Allplex respiratory panels 1, 2, and 3 (Allplex) comprise a one-step real-time reverse transcription-PCR assay for the detection of respiratory viruses (RVs) and influenza A subtypes based on multiple detection temperature (MuDT) technology. The performance of the Allplex assay was compared with those of the AdvanSure RV real-time PCR kit (AdvanSure) and the PowerChek pandemic H1N1/H3N2/H5N1 real-time PCR kit (PowerChek) using 417 clinical respiratory specimens. In comparison with the AdvanSure assay for RV detection by each virus, the ranges of positive percent agreement, negative percent agreement, and kappa values with the Allplex assay were 82.8 to 100%, 95.5 to 100%, and 0.85 to 1.00, respectively. For influenza A virus (INF A) subtyping, the kappa values between the Allplex and PowerChek assays were 0.67 and 1.00 for the INF A H1N1-pdm09 and H3 subtypes, respectively. Uniplex PCR and sequencing for samples with discrepant results demonstrated that the majority of results were concordant with those from the Allplex assay. When testing 24 samples, the turnaround and hands-on time required to perform the Allplex assay were 4 h 15 min and 15 min, respectively. In conclusion, the Allplex assay produced results comparable to those from the AdvanSure and PowerChek assays.

Laboratory Diagnosis of Central Nervous System Infection

Central nervous system (CNS) infections are potentially life threatening if not diagnosed and treated early. The initial clinical presentations of many CNS infections are non-specific, making a definitive etiologic diagnosis challenging. Nucleic acid in vitro amplification-based molecular methods are increasingly being applied for routine microbial detection. These methods are a vast improvement over conventional techniques with the advantage of rapid turnaround and higher sensitivity and specificity. Additionally, molecular methods performed on cerebrospinal fluid samples are considered the new gold standard for diagnosis of CNS infection caused by pathogens, which are otherwise difficult to detect. Commercial diagnostic platforms offer various monoplex and multiplex PCR assays for convenient testing of targets that cause similar clinical illness. Pan-omic molecular platforms possess potential for use in this area. Although molecular methods are predicted to be widely used in diagnosing and monitoring CNS infections, results generated by these methods need to be carefully interpreted in combination with clinical findings. This review summarizes the currently available armamentarium of molecular assays for diagnosis of central nervous system infections, their application, and future approaches.

A molecular epidemiological perspective of rhinovirus types circulating in Amsterdam from 2007 to 2012

Rhinoviruses (RVs) are frequently detected respiratory viruses that cause mild common cold symptoms, but may also lead to more severe respiratory tract infections. The large number of RV types, classified into species A, B and C, hampers clear insights into the epidemiology and clinical significance of each RV type. The aim of this study was to map the circulation of RV types in the Amsterdam area. RV-positive nasopharyngeal and oropharyngeal samples, collected from 2007 to 2012 in the Academic Medical Centre (Amsterdam, the Netherlands), were typed based on the sequence of the region coding for capsid proteins VP4 and VP2. RV-A, RV-B and RV-C were found in proportions of of 52.4% (334/637), 11.3% (72/637), and 36.2% (231/637), respectively. We detected 129 of the 167 currently classified types. RVs circulated throughout the entire year with a peak in the autumn and a decline in the summer. Some RV types were observed throughout the entire sampling period and others had a more seasonal pattern. Nine RV-A and four RV-B novel provisionally assigned types were identified. This study provides an insight into the molecular epidemiology of RVs in the Amsterdam area. The RVs circulating are diverse and include several provisionally new types.

The Emergence of Enterovirus-D68

Enterovirus-D68 (EV-D68) is a unique enterovirus, similar to human rhinoviruses, spread via the respiratory route and primarily causing respiratory disease. Increasing clusters of EV-D68 associated respiratory disease have been reported since 2008, with the largest reported outbreak occurring in North America in 2014. Epidemiologic data and biological plausibility support an association of EV-D68 with the neurologic condition, acute flaccid myelitis. Diagnosis requires EV-D68 specific PCR or viral sequencing of respiratory specimens. Treatment consists of supportive care, as there are no currently available effective vaccines or antiviral therapies. Further research is needed to prepare for future EV-D68 outbreaks of respiratory or neurologic disease.

Pulmonary and extrapulmonary complications of human rhinovirus infection in critically ill patients

BACKGROUND

Human rhinovirus (HRV) is frequently detected in patients with respiratory tract infection. However, the full clinical spectrum of HRV infection in critically ill patients is not well characterized.

OBJECTIVE

To evaluate the clinical and virological characteristics of critically ill patients with HRV infection.

STUDY DESIGN

HRV-specific reverse transcription-polymerase chain reaction (RT-PCR) was performed on nasopharyngeal aspirate (NPA) specimens from 294 adult patients who required admission into the intensive care unit (ICU). Clinical characteristics were analyzed. HRV genotyping using the 5'UTR-VP4-VP2 region was performed.

RESULTS

HRV was detected in NPA specimens of 22 patients (7.5%) by RT-PCR. Dyspnea was the most common presenting symptom (16/22; 72.7%), but seizure also occurred in 5 (22.7%) patients. Exacerbation of underlying disease occurred in 12 (54.5%) patients. Four (18.2%) patients died, and HRV was considered to play a role as the cause of death in 3 patients. Thirteen (59.1%) patients had pneumonia, and the most common radiological finding was consolidation (6/13; 46.2%). Streptococcus pneumoniae was the most common co-pathogen among patients with pneumonia. Among the 9 patients without pneumonia, 3 patients had exacerbation of underlying lung diseases, 3 patients had acute pulmonary edema, 2 patients with diabetes mellitus had acute complications from poor glycemic control, and 1 patient had status epilepticus. HRV-A was the most common species (64.3%), but there was no clear relationship between HRV species and clinical presentation.

CONCLUSION

Both pulmonary and extrapulmonary complications of HRV were common in critically ill patients.

BioFire FilmArray Respiratory Panel for Detection of Enterovirus D68

During the enterovirus D68 (EV-D68) outbreak of 2014, the BioFire FilmArray (FA) respiratory panel was used to detect rhinovirus/enterovirus in respiratory specimens; suspected EV-D68-positive specimens were sent to CDC for confirmation. Positive rhinovirus/enterovirus FA targets revealed patterns loosely associated with EV-D68 that may be useful for confirmation triaging.

Enterovirus D68 Infection

First described in 1962 in children hospitalized for pneumonia and bronchiolitis, the Enterovirus D68 (EV-D68) is an emergent viral pathogen. Since its discovery, during the long period of surveillance up to 2005, EV-D68 was reported only as a cause of sporadic outbreaks. In recent years, many reports from different countries have described an increasing number of patients with respiratory diseases due to EV-D68 associated with relevant clinical severity. In particular, an unexpectedly high number of children have been hospitalized for severe respiratory disease due to EV-D68, requiring intensive care such as intubation and mechanical ventilation. Moreover, EV-D68 has been associated with acute flaccid paralysis and cranial nerve dysfunction in children, which has caused concerns in the community. As no specific antiviral therapy is available, treatment is mainly supportive. Moreover, because no vaccines are available, conventional infection control measures (i.e., standard, for contacts and droplets) in both community and healthcare settings are recommended. However, further studies are required to fully understand the real importance of this virus. Prompt diagnosis and continued surveillance of EV-D68 infections are essential to managing and preventing new outbreaks. Moreover, if the association between EV-D68 and severe diseases will be confirmed, the development of adequate preventive and therapeutic approaches are a priority.

2014 outbreak of enterovirus D68 in North America

Enterovirus D68 (EV-D68) is an emerging picornavirus which causes severe respiratory disease, predominantly in children. In 2014, the largest and most widespread outbreak of EV-D68 described to date was reported in North America. Hospitals throughout the United States and Canada reported surges in patient volumes and resource utilization from August to October, 2014. In the US a total of 1,153 infections were confirmed in 49 states, although this is an underestimate of the likely millions of cases that occurred but were not tested. EV-D68 was detected in 14 patients who died; the role of the virus in these deaths is unknown. A possible association between EV-D68 and cases of acute flaccid paralysis with spinal cord gray matter lesions, known as acute flaccid myelitis, was observed during the outbreak and is under investigation. The 2014 outbreak of EV-D68 in North America demonstrates the public health importance of this emerging pathogen.

Enterovirus D-68: an emerging cause of infection

The outbreak of Enterovirus D-68 (EV-D68) in the United States in 2014 raised great interest due to it affecting large numbers of people and because patients presented with severe respiratory and/or central nervous system involvement. Many studies have tried to evaluate the biologic and genetic characteristics of this virus, its association with disease development and the possibility of infection prevention and therapy. The main aim of this paper is to discuss what is presently known and what might be expected in the future regarding EV-D68. We highlight that further studies are needed to precisely define the epidemiology and total burden of EV-D68, the real age prevalence, and the factors that may lead to negative outcomes in some patients and not in others. Moreover, if recently reported clinical data are confirmed, specific efficacious prophylactic and therapeutic measures should be urgently developed.