Performance Characteristics of Xpert Flu/RSV XC Assay

Expert consensus on the diagnosis, treatment, and prevention of respiratory syncytial virus infections in children

BACKGROUND

Respiratory syncytial virus (RSV) is the leading global cause of respiratory infections and is responsible for about 3 million hospitalizations and more than 100,000 deaths annually in children younger than 5 years, representing a major global healthcare burden. There is a great unmet need for new agents and universal strategies to prevent RSV infections in early life. A multidisciplinary consensus development group comprising experts in epidemiology, infectious diseases, respiratory medicine, and methodology aims to develop the current consensus to address clinical issues of RSV infections in children.

DATA SOURCES

The evidence searches and reviews were conducted using electronic databases, including PubMed, Embase, Web of Science, and the Cochrane Library, using variations in terms for "respiratory syncytial virus", "RSV", "lower respiratory tract infection", "bronchiolitis", "acute", "viral pneumonia", "neonatal", "infant" "children", and "pediatric".

RESULTS

Evidence-based recommendations regarding diagnosis, treatment, and prevention were proposed with a high degree of consensus. Although supportive care remains the cornerstone for the management of RSV infections, new monoclonal antibodies, vaccines, drug therapies, and viral surveillance techniques are being rolled out.

CONCLUSIONS

This consensus, based on international and national scientific evidence, reinforces the current recommendations and integrates the recent advances for optimal care and prevention of RSV infections. Further improvements in the management of RSV infections will require generating the highest quality of evidence through rigorously designed studies that possess little bias and sufficient capacity to identify clinically meaningful end points.

The impact of rapid diagnostic testing on hospital administrative coding accuracy for influenza

BACKGROUND

Hospital administrative coding may underestimate the true incidence of influenza-associated hospitalisation. Earlier availability of test results could lead to improved accuracy of administrative coding.

METHODS

In this study we evaluated International Classification of Diseases 10 (ICD-10) coding for influenza (with [J09-J10] or without [J11] virus identified) in adult inpatients who underwent testing in the year prior, compared to those in the 2.5 years after, the introduction of rapid PCR testing in 2017. Other factors associated with influenza coding were evaluated using logistic regression. Discharge summaries were audited to assess the impact of documentation and result availability on coding accuracy.

RESULTS

Influenza was confirmed by laboratory testing in 862 of 5755 (15%) patients tested after rapid PCR introduction compared with 170 of 926 (18%) prior. Following the introduction of rapid testing there was a significant increase in patients allocated J09 or J10 ICD-10 codes (768 of 860 [89%] vs 107 of 140 [79%], P = 0.001). On multivariable analysis, factors independently associated with correct coding were rapid PCR testing (aOR 4.36 95% CI [2.75-6.90]) and increasing length of stay (aOR 1.01, 95% CI [1.00-1.01]). Correctly coded patients were more likely to have documentation of influenza in their discharge summaries (95 of 101 [89%] vs 11 of 101 [10%], P < 0.001) and less likely to have pending results at discharge (8 of 101 [8%] vs 65 of 101 [61%], P < 0.001).

CONCLUSION

The introduction of rapid PCR testing for influenza was associated with more accurate hospital coding. One possible explanation is faster test turnaround leading to improvement in clinical documentation.

Respiratory Syncytial Virus

Human respiratory syncytial virus (RSV) is a negative sense single-stranded RNA virus that can result in epidemics of seasonal respiratory infections. Generally, one of the two genotypes (A and B) predominates in a single season and alternate annually with regional variation. RSV is a known cause of disease and death at both extremes of ages in the pediatric and elderly, as well as immunocompromised populations. The clinical impact of RSV on the hospitalized adults has been recently clarified with the expanded use of multiplex molecular assays. Among adults, RSV can produce a wide range of clinical symptoms due to upper respiratory tract infections potentially leading to severe lower respiratory tract infections, as well as exacerbations of underlying cardiac and lung diseases. While supportive care is the mainstay of therapy, there are currently multiple therapeutic and preventative options under development.

Current Status of Clinical Application of Point-of-Care Testing

CONTEXT.—

The clinical applications of point-of-care testing (POCT) are gradually increasing in many health care systems. Recently, POCT devices using molecular genetic method techniques have been developed. We need to examine clinical pathways to see where POCT can be applied to improve them.

OBJECTIVE.—

To introduce up-to-date POCT items and equipment and to provide the content that should be prepared for clinical application of POCT.

DATA SOURCES.—

Literature review based on PubMed searches containing the terms point-of-care testing, clinical chemistry, diagnostic hematology, and clinical microbiology.

CONCLUSIONS.—

If medical resources are limited, POCT can help clinicians make quick medical decisions. As POCT technology improves and menus expand, areas where POCT can be applied will also increase. We need to understand the limitations of POCT so that it can be optimally used to improve patient management.

Cepheid Xpert® Flu/RSV and Seegene Allplex™ RP1 show high diagnostic agreement for the detection of influenza A/B and respiratory syncytial viruses in clinical practice

Background

Molecular assays based on reverse transcription‐polymerase chain reaction (RT‐PCR) provide reliable results for the detection of respiratory pathogens, although diagnostic agreement varies. This study determined the agreement between the RT‐PCR assays (Xpert^® Flu/RSV vs Allplex^™ RP1) in detecting influenza A, influenza B, and respiratory syncytial viruses (RSVs) in clinical practice.

Methods

We retrospectively identified 914 patient encounters where testing with both Xpert^® Flu/RSV and Allplex^™ RP1 was undertaken between October 2015 and September 2019 in seven hospitals across New South Wales, Australia. The diagnostic agreement of the two assays was evaluated using positive percent agreement, negative percent agreement, and prevalence and bias‐adjusted kappa.

Results

The positive percent agreement was 95.1% for influenza A, 87.5% for influenza B, and 77.8% for RSV. The negative percent agreement was 99.4% for influenza A, 99.9% for influenza B, and 100% for RSV. The prevalence and bias‐adjusted kappa was 0.98 for influenza A, 0.99 for influenza B, and 0.97 for RSV. In a sensitivity analysis, the positive percent agreement values were significantly higher during the non‐influenza season than the influenza season for influenza B and RSV.

Conclusions

The Xpert^® Flu/RSV and Allplex^™ RP1 demonstrated a high diagnostic agreement for all three viruses assessed. The seasonal variation in the positive percent agreement of the two assays for influenza B and RSV may have been due to lower numbers assessed, variability in the virology of infections outside the peak season, or changes in the physiology of the infected host in different seasons.

Rapid diagnostic tests for infectious diseases in the emergency department

Background

Rapid diagnostic tests (RDTs) for infectious diseases, with a turnaround time of less than 2 hours, are promising tools that could improve patient care, antimicrobial stewardship and infection prevention in the emergency department (ED) setting. Numerous RDTs have been developed, although not necessarily for the ED environment. Their successful implementation in the ED relies on their performance and impact on patient management.

Objectives

The aim of this narrative review was to provide an overview of currently available RDTs for infectious diseases in the ED.

Sources

PubMed was searched through August 2019 for available studies on RDTs for infectious diseases. Inclusion criteria included: commercial tests approved by the US Food and Drug Administration (FDA) or Conformité Européenne (CE) in vitro diagnostic devices with data on clinical samples, ability to run on fully automated systems and result delivery within 2 hours.

Content

A nonexhaustive list of representative commercially available FDA- or CE-approved assays was categorized by clinical syndrome: pharyngitis and upper respiratory tract infection, lower respiratory tract infection, gastrointestinal infection, meningitis and encephalitis, fever in returning travellers and sexually transmitted infection, including HIV. The performance of tests was described on the basis of clinical validation studies. Further, their impact on clinical outcomes and anti-infective use was discussed with a focus on ED-based studies.

Implications

Clinicians should be familiar with the distinctive features of each RDT and individual performance characteristics for each target. Their integration into ED work flow should be preplanned considering local constraints of given settings. Additional clinical studies are needed to further evaluate their clinical effectiveness and cost-effectiveness.

Respiratory syncytial virus infection in adults

Human respiratory syncytial virus (RSV) belongs to the recently defined Pneumoviridae family, Orthopneumovirus genus. It is a negative sense, single stranded RNA virus that results in epidemics of respiratory infections that typically peak in the winter in temperate climates and during the rainy season in tropical climates. Generally, one of the two genotypes (A and B) predominates in a single season, alternating annually, although regional variation occurs. RSV is a cause of disease and death in children, older people, and immunocompromised patients, and its clinical effect on adults admitted to hospital is clarified with expanded use of multiplex molecular assays. Among adults, RSV produces a wide range of clinical symptoms including upper respiratory tract infections, severe lower respiratory tract infections, and exacerbations of underlying disease. Here we discuss the latest evidence on the burden of RSV related disease in adults, especially in those with immunocompromise or other comorbidities. We review current therapeutic and prevention options, as well as those in development.

Comparison of the Idylla™ Respiratory (IFV-RSV) panel with the GeneXpert Xpert® Flu/RSV assay: a retrospective study with nasopharyngeal and midturbinate samples

The objective of this study was to compare the performance of the Idylla™ Respiratory (IFV-RSV) panel to the GeneXpert Xpert® Flu/RSV assay and establish the performance of a midturbinate swab compared to nasopharyngeal sampling. Considering GeneXpert® assay as imperfect reference standard, a positive percentage agreement between both assays of 98-100% for influenza A and 96-99% for influenza B could be calculated when 354 nasopharyngeal and 325 midturbinate swabs were retrospectively analyzed. Comparing midturbinate samples to nasopharyngeal specimens of 321 subjects, positive percentage agreement varied from 42% to 94% depending on both target virus and assay used. Negative percentage agreements ranged from 98% to 100% for both methods and sample type comparison. The Idylla™ assay showed excellent performance compared to the GeneXpert® assay for the detection of influenza virus. The study also showed a slightly better performance for nasopharyngeal sampling compared to the use of a midturbinate swab.

Laboratory Diagnosis of Respiratory Tract Infections in Children - the State of the Art

In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach.

Systematic review of the impact of point-of-care testing for influenza on the outcomes of patients with acute respiratory tract infection

Acute respiratory tract infections are a major cause of morbidity and mortality and represent a significant burden on the health care system. Laboratory testing is required to definitively distinguish infecting influenza virus from other pathogens, resulting in prolonged emergency department (ED) visits and unnecessary antibiotic use. Recently available rapid point-of-care tests (POCT) may allow for appropriate use of antiviral and antibiotic treatments and decrease patient lengths of stay. We undertook a systematic review to assess the effect of POCT for influenza on three outcomes: (1) antiviral prescription, (2) antibiotic prescription, and (3) patient length of stay in the ED. The databases Medline and Embase were searched using MeSH terms and keywords for influenza, POCT, antivirals, antibiotics, and length of stay. Amongst 245 studies screened, 30 were included. The majority of papers reporting on antiviral prescription found that a positive POCT result significantly increased use of antivirals for influenza compared with negative POCT results and standard supportive care. A positive POCT result also led to decreased antibiotic use. The results of studies assessing the effect of POCT on ED length of stay were not definitive. The studies assessed in this systematic review support the use of POCT for diagnosis of influenza in patients suffering an acute respiratory infection. Diagnosis using POCT may lead to more appropriate prescription of treatments for infectious agents. Further studies are needed to assess the effect of POCT on the length of stay in ED.

Comparison of the Xpert Flu/RSV XC and Xpress Flu/RSV Assays

Molecular diagnostics for influenza and respiratory syncytial virus (RSV) have become commonplace, and various tests and systems have been cleared by the FDA for use in the United States. We performed a retrospective study to compare the Cepheid Xpress Flu/RSV assay with the Xpert Flu/RSV XC assay, using laboratory-developed tests (LDTs) as the reference method. The Xpress assay was 100% accurate compared to LDTs, whereas the Xpert Flu/RSV XC assay was 96.0% accurate. The Xpress test was determined to be faster and more sensitive than the XC assay.

Rapid and simple molecular tests for the detection of respiratory syncytial virus: a review

INTRODUCTION

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections. The clinical manifestations of RSV are indistinguishable from other etiologies of acute respiratory infection. Therefore, accurate and timely laboratory testing is needed to impact clinical management. There are now multiple rapid, low-complexity, commercially available assays for RSV. These tests present significant performance advantages compared to older antigen detection tests. Accurate and rapid diagnosis of RSV has the potential for enabling timely cessation of unnecessary antibiotics and implementation of good infection control practices. Furthermore, a recently approved RSV diagnostic assay can reduce the test turnaround time to 13 min or less. Areas covered: The authors aim to review the importance of rapid and accurate testing for RSV and will describe the available molecular RSV diagnostic assays approved for use at the point-of-care. Expert commentary: Further independent evaluations are needed to confirm that the accuracy of the low-complexity assays is indeed similar to reverse transcriptase polymerase chain reaction across the age spectrum, and in immunosuppressed hosts. In the future, the challenge will be to achieve a balance between increasingly sophisticated multiplex diagnostic platforms and tests that are sufficiently simple to be used at the point-of-care.

Profile of the Alere i Influenza A & B assay: a pioneering molecular point-of-care test

INTRODUCTION

The Alere i Influenza A & B assay incorporates the Nicking Enzyme Amplification Reaction technique on the Alere i instrument to detect and differentiate influenza virus (Flu) A and B nucleic acids in specific specimens. Areas covered: The Alere i Influenza A & B assay was cleared by the US Food and Drug Administration for use with nasal swabs (NS) and nasopharyngeal swabs, either directly or in viral transport medium. Notably, direct use on NS was the first ever CLIA-waived nucleic acid-based test. Previously published evaluations have reported sensitivities and specificities of 55.2-100% and 62.5-100% for Flu A and 45.2-100% and 53.6-100% for Flu B, respectively. Expert commentary: The Alere i Influenza A & B assay provides a rapid and simple platform for detection and differentiation of Flu A and B. Efforts are expected to further improve sensitivity and user-friendliness for effective and widespread use in the true point-of-care setting.

Respiratory syncytial virus burden among adults during flu season: an underestimated pathology

BACKGROUND

Information on the role of respiratory syncytial virus (RSV) in adult patients with influenza-like syndrome is scarce.

AIM

To assess the clinical characteristics of RSV in adult patients with respiratory manifestations during a regular influenza season.

METHODS

Prospective study in a tertiary Spanish hospital from December 2015 to February 2016. The study population included only adult patients with either community-acquired or hospital/healthcare-associated influenza-like illness, according to the European Centre for Disease Prevention and Control criteria. Samples were analysed using a rapid molecular assay (Xpert^® Flu/RSV). RSV-positive patients were compared with a randomly negative control group and with an influenza-positive control group.

FINDINGS

Twelve hundred patients with influenza-like respiratory infection were included. Overall, 114 of the samples (9%) were positive for influenza and 95 (8%) were positive for RSV. When RSV-positive and influenza-positive patients were compared, RSV-positive patients were older (57.7 vs 48.9 years; P = 0.03), and their disease was more frequently healthcare-related (26/95, 27.3% vs 5/114, 1.7%; P < 0.001). They also had significantly more antibiotics prescribed (77/95, 81.0% vs 70/114, 61.4%; P < 0.001) and more frequently needed hospital admission (93/95, 97.8% vs 69/114, 60.5%; P < 0.001). Mortality was also significantly higher in RSV-positive patients (14/95, 14.7% vs 7/114, 6.1%; P = 0.04).

CONCLUSION

RSV is a major cause of moderate-to-severe respiratory infection during the influenza season; acquisition is frequently nosocomial or healthcare-related; and mortality is significantly higher than with influenza virus infection. The use of a rapid molecular test as a first-step diagnostic technique is necessary to ensure that isolation measures are implemented and that spread is prevented.

The Drift in Molecular Testing for Influenza: Mutations Affecting Assay Performance

Influenza is associated with rapid evolution due to lack of RNA polymerase proofreading, immunogenic selection, and frequent rearrangement of gene segments. Evolutionary changes affecting the performance of diagnostic testing have long been recognized. Hence, it is not surprising that such challenges apply to nucleic acid amplification tests, even though they are designed to target highly conserved regions. Initially, case reports involved single isolates of A(H1N1)pdm09. Over the past 4 years, subtype H3N2 viruses evolved to viral clades with mutations in the WHO-recommended target region, such that almost all isolates worldwide have significantly reduced sensitivities with many commercial reverse transcription-PCR tests.

Point-of-care diagnostics for respiratory viral infections

Introduction: Successful treatment outcomes for viral respiratory tract infections presenting from primary health care to quaternary hospitals will only be achieved with rapid, sensitive and specific identification of pathogens to allow effective pathogen-specific antiviral therapy and infection control measures.

Areas covered: This review aims to explore the different point-of-care tests currently available to diagnose viral respiratory tract infections, discuss the advantages and limitations of point-of-care testing, and provide insights into the future of point-of-care tests. The following databases were searched: Medline (January 1996 to 30 September 2017) and Embase (1988 to 30 September 2017), using the following keywords: ‘point of care’, ‘respiratory virus’, ‘influenza’, ‘RSV’, ‘diagnostics’, ‘nucleic acid test’ and ‘PCR’.

Expert commentary: Viral respiratory tract infections cause significant morbidity and mortality worldwide, and point-of-care tests are facilitating the rapid identification of the pathogen responsible given the similarities in clinical presentation.

Evaluation of the molecular Xpert Xpress Flu/RSV assay vs. Alere i Influenza A & B assay for rapid detection of influenza viruses

A new FDA-approved Xpert Xpress Flu/RSV assay has been released for rapid influenza virus detection. We collected 134 nasopharyngeal specimens to compare the diagnostic performance of the Xpert assay and the Alere i Influenza A & B assay for influenza A and B virus detection. The Xpert assay demonstrated 100% and 96.3% sensitivity to influenza A and influenza B virus respectively. Its specificity was 100% for both viruses. The Alere i assay demonstrated slightly lower sensitivity but similar specificity to the Xpert Xpress assay. Although the Xpert assay (30 min) required longer processing time than the Alere assay (15 min), the handling procedure of the Alere assay was more complicated than the Xpert assay. As the GenXpert system has higher throughput than the Alere system, it is more suitable for hospital clinical laboratories. Overall, the new Xpert Xpress Flu/RSV assay is a reliable and useful tool for rapid influenza detection.

Respiratory Syncytial Virus Infection Control Challenges with a Novel Polymerase Chain Reaction Assay in a Tertiary Medical Center

OBJECTIVES To evaluate host characteristics, mode of infection acquisition, and infection control procedures in patients with a positive respiratory syncytial virus (RSV) test result after the introduction of the GenXpert Influenza/RSV polymerase chain reaction (PCR) assay. DESIGN Retrospective cohort study. PATIENTS Adults with a positive PCR test result for RSV who were hospitalized in a tertiary academic medical center between January 2015 and December 2016 were included in this study. Our infection control policy applies contact isolation precautions only for immunocompromised patients. METHODS Patients were identified through 2 databases, 1 consisting of patients isolated because of RSV infection and 1 with automatically collected laboratory results. Baseline and clinical characteristics were collected through a retrospective medical chart review. The rate of and clinical factors associated with healthcare-associated RSV infections were evaluated. RESULTS In total, 108 episodes in 106 patients hospitalized with a positive Xpert RSV test result were recorded during the study period. Among them, 11 episodes were healthcare-associated infections (HAIs) and 97 were community-acquired infections (CAIs). The mean length of hospital stay (LOS, 40.2 vs 11.2 days), the mean number of room switches (3.5 vs 1.7) and ward switches (1.5 vs 0.4), and the mean numbers of contact patients (9.9 vs 3.8) were significantly longer and higher in the HAI group than in the CAI group (P<.0001). Surveillance of microbiology records and clinical data did not reveal evidence for a cluster or an epidemic during the 2-year observation period. CONCLUSIONS The introduction of a rapid molecular diagnostic test systematically applied to patients with influenza-like illness may challenge current infection control policies. In our study, patients with HAIs had a prolonged hospital stay and a high number of contact patients, and they switched rooms and wards frequently. Infect Control Hosp Epidemiol 2017;38:1291-1297.

Respiratory Syncytial Virus: Infection, Detection, and New Options for Prevention and Treatment

Respiratory syncytial virus (RSV) infection is a significant cause of hospitalization of children in North America and one of the leading causes of death of infants less than 1 year of age worldwide, second only to malaria. Despite its global impact on human health, there are relatively few therapeutic options available to prevent or treat RSV infection. Paradoxically, there is a very large volume of information that is constantly being refined on RSV replication, the mechanisms of RSV-induced pathology, and community transmission. Compounding the burden of acute RSV infections is the exacerbation of preexisting chronic airway diseases and the chronic sequelae of RSV infection. A mechanistic link is even starting to emerge between asthma and those who suffer severe RSV infection early in childhood. In this article, we discuss developments in the understanding of RSV replication, pathogenesis, diagnostics, and therapeutics. We attempt to reconcile the large body of information on RSV and why after many clinical trials there is still no efficacious RSV vaccine and few therapeutics.

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.

Performance of the Alere™ i Influenza A&B and the Cepheid Xpert® Flu/RSV XC assays

Aim: To evaluate the Alere™ i Influenza A&B assay and the Xpert® Flu/RSV XC assay using nasopharyngeal aspirates and swabs not provided in the commercial kits. Methods: Specimens were tested with the Alere i Influenza A&B and the Xpert Flu/RSV XC assays and compared with reference methods. Results: Compared with the comparator methods and following discordant analysis, the sensitivity of the i Influenza A&B assay was 63.3% for influenza A and 83.3% for influenza B. For the Xpert Flu/RSV XC assay, sensitivity was 100% for influenza A and B and respiratory syncytial virus. The specificity for all test systems was 100%. Conclusion: The Xpert Flu/RSV XC assay out-performed the Alere i Influenza A&B assay in all diagnostic characteristics evaluated.

Integrated Polymerase Chain Reaction Technologies (Sample-to-Answer Technologies)

The tools available for both infectious disease diagnostics and human identity testing have benefitted from major technological advances in the automation of nucleic acid purification, amplification, and detection methods. The seamless integration of these processes into a fully automated microscale format has led to the development of rapid, user-friendly sample-to-answer assay systems. The application of these systems for human identity testing allows for DNA profiles to be generated in a field-forward environment where they can be used to generate investigative leads in crimes or other actionable intelligence. When used for infectious disease diagnostics, the sensitivity and specificity of these assay systems meets or exceeds that of more conventional strategies for the detection of respiratory, gastrointestinal, nervous system, and sexually transmitted pathogens. The anticipated medical benefits of this technology include shorter hospital stays, the elimination of unnecessary or ineffectual treatment, improved patient outcomes, and an overall quantifiable reduction in healthcare costs.

Comparison of NxTAG Respiratory Pathogen Panel and Anyplex II RV16 Tests for Multiplex Detection of Respiratory Pathogens in Hospitalized Children

Multiplex molecular techniques can detect a diversity of respiratory viruses and bacteria that cause childhood acute respiratory infection rapidly and conveniently. However, currently available techniques show high variation in performance. We sought to compare the diagnostic accuracy of the novel multiplex NxTAG respiratory pathogen panel (RPP) RUO test versus a routine multiplex Anyplex II RV16 assay in respiratory specimens collected from children <18 years of age hospitalized with nonspecific symptoms of acute lower respiratory infection. Parallel testing was performed on nasopharyngeal aspirates prospectively collected at referral Children's Hospital Sant Joan de Déu (Barcelona, Spain) between June and November 2015. Agreement values between the two tests and kappa coefficients were assessed. Bidirectional sequencing was performed for the resolution of discordant results. A total of 319 samples were analyzed by both techniques. A total of 268 (84.0%) of them yielded concordant results. Positive percent agreement values ranged from 83.3 to 100%, while the negative percent agreement was more than 99% for all targets except for enterovirus/rhinovirus (EV/RV; 94.4%). Kappa coefficients ranged from 0.83 to 1.00. Discrepancy analysis confirmed 66.0% of NxTAG RPP RUO results. A total of 260 viruses were detected, with EV/RV (n = 105, 40.4%) being the most prevalent target. Viral coinfections were found in 44 (14.2%) samples. In addition, NxTAG RPP RUO detected single bacterial and mixed viral-bacterial infections in seven samples. NxTAG RPP RUO showed high positive and negative agreement with Anyplex II RV16 for main viruses that cause acute respiratory infections in children, coupled with an additional capability to detect some respiratory bacteria.

Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15

The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary.

Comparison of Cepheid Xpert Flu/RSV XC and BioFire FilmArray for Detection of Influenza A, Influenza B, and Respiratory Syncytial Virus

The Xpert Flu/RSV XC was compared to the FilmArray respiratory panel for detection of influenza (Flu) A, Flu B, and respiratory syncytial virus (RSV), using 128 nasopharyngeal swabs. Positive agreements were 100% for Flu A and RSV and 92.3% for Flu B. The Xpert may be useful in clinical situations when extensive testing is not required and may serve an important role in laboratories already performing broader respiratory panel testing.

Severe sensitivity loss in an influenza A molecular assay due to antigenic drift variants during the 2014/15 influenza season

The 2014-2015 influenza season in Belgium was dominated by the circulation of 2 influenza A(H3N2) subgroups: 3C.2a and 3C.3b. Analysis of 166 nasopharyngeal aspirates, collected in patients with respiratory illness at the start of the epidemic season, showed a decreased sensitivity for the detection of influenza A(H3N2)/3C.2a using a commercially available multiplex assay. Gene sequencing of the matrix protein showed a point mutation (C163T) leading to a mismatch with the assay probes.

Sample-to-result molecular infectious disease assays: clinical implications, limitations and potential

Molecular infectious disease diagnostic tests have undergone major advances in the past decade and will continue to rapidly evolve. Assays have become extraordinarily simple to perform, eliminating the need for pre-analytic sample preparation and post-amplification analysis. This allows these tests to be performed in settings without sophisticated expertise in molecular biology, including locations with limited resources. Additionally, the sensitivity and specificity of these assays is superb and many offer extremely fast turn-around times. These tests have major impacts on patient care, but also have some limitations.