Comparison of the ID Now Influenza A & B 2, Cobas Influenza A/B, and Xpert Xpress Flu Point-of-Care Nucleic Acid Amplification Tests for Influenza A/B Virus Detection in Children

Diagnostic accuracy of Savanna RVP4 (QuidelOrtho) for the detection of Influenza A virus, RSV, and SARS-CoV-2

Seasonal increase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV) require rapid diagnostic test methods for the management of respiratory tract infections. In this study, we compared the diagnostic accuracy of Savanna RVP4 (RVP4, QuidelOrtho) with Xpert Xpress Plus SARS-CoV-2/Flu/RSV (Xpert, Cepheid). Nasopharyngeal swabs from patients treated at a tertiary care hospital (Germany) were tested for SARS-CoV-2, Flu A/B, and RSV by RVP4 to assess diagnostic accuracy (reference standard: Xpert). The intra and inter assay precision of Ct-values was assessed by repeated test in triplicates (on day 1) and duplicates (days 2-3). All patients with a physician's order for a multiplex test for SARS-CoV-2, Flu, and RSV test were included. Duplicate swabs from the same patient, samples with a total volume ≤1 mL, or inappropriate shipment/storage were excluded. In total, 229 swabs were included between September 2023 and February 2024. The concordance between both tests was 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.6% (RSV). Flu B was not detected by both tests. The RVP4 test had a sensitivity of 85%-95% and a specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV. The intra and inter assay precision of Ct-values from RVP4 was 3% and 2% (SARS-CoV-2), 5% and 4% (Flu A), and 0% and 3% (RSV), respectively. The Savanna RVP4 has a favorable diagnostic accuracy for the detection of SARS-CoV-2, Flu A, and RSV.

IMPORTANCE

We assessed the diagnostic accuracy of a new point-of-care test for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A/B (Flu A/B), and respiratory syncytial virus (RSV). The new test has a concordance with the reference standard of 96.5% (SARS-CoV-2), 98.7% (Flu A), and 99.1% (RSV). The sensitivity of 85%-95% and specificity of 100% for the detection of SARS-CoV-2, Flu A, and RSV is comparable with similar nucleic acid amplification-based point of care tests but at lower costs.

Home and Clinical Laboratory Improvement Amendments-Waived Testing for Infectious Diseases-How Do These Fit in the Testing Landscape?

Though testing for infectious diseases has long been performed in traditional clincial laboratory settings, more widespread availability of waived testing is expanding accessibility of patients to rapid test results. This is being further expanded to home testing. Nevertheless, with this greater democratization and availability of clinical testing there are important limitations that need to be balanced. In this article, we review the current test landscape for infectious diseases waived testing and opportunities for assuring optimal quality testing.

Gargle sample is an effective option in a novel fully automated molecular point-of-care test for influenza: a multicenter study

BACKGROUND

We conducted a multicenter study to evaluate the performance of a novel fully automated molecular point-of-care test using transcription-reverse transcription concerted reaction that can detect influenza A and B within 15 min in nasopharyngeal swabs and gargle samples (TRCsatFLU).

METHODS

Patients who visited or were hospitalized at eight clinics and hospitals with influenza-like illnesses between December 2019 and March 2020 participated in this study. We collected nasopharyngeal swabs from all patients and gargle samples from patients whom the physician judged fit to perform gargling. The result of TRCsatFLU was compared to a conventional reverse transcription-polymerase chain reaction (RT-PCR). If the results of TRCsatFLU and conventional RT-PCR were different, the samples were analyzed by sequencing.

RESULTS

We evaluated 233 nasopharyngeal swabs and 213 gargle samples from 244 patients. The average age of the patients was 39.3 ± 21.2. Of the patients, 68.9% visited a hospital within 24 h of symptom onset. The most common symptoms were fever (93.0%), fatigue (79.5%), and nasal discharge (64.8%). All patients in whom the gargle sample was not collected were children. Influenza A or B was detected in 98 and 99 patients in nasopharyngeal swabs and gargle samples using TRCsatFLU, respectively. Four and five patients in nasopharyngeal swabs and gargle samples, respectively, with different TRCsatFLU and conventional RT-PCR results. Influenza A or B was detected using sequencing in all samples with different results. Based on the combined conventional RT-PCR and sequencing results, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of TRCsatFLU for influenza detection in nasopharyngeal swabs were 0.990, 1.000, 1.000, and 0.993, respectively. In the gargle samples, the sensitivity, specificity, PPV, and NPV of the TRCsatFLU for detecting influenza were 0.971, 1.000, 1.000, and 0.974, respectively.

CONCLUSIONS

The TRCsatFLU showed great sensitivity and specificity for the detection of influenza in nasopharyngeal swabs and gargle samples.

TRIAL REGISTRATION

This study was registered in the UMIN Clinical Trials Registry (reference number: UMIN000038276) on October 11, 2019. Before sample collection, written informed consent for the participation and publication of this study was obtained from all participants.

A narrative review of nine commercial point of care influenza tests: an overview of methods, benefits, and drawbacks to rapid influenza diagnostic testing

CONTEXT

Rapid influenza diagnostic tests (RIDTs) are becoming increasingly accurate, available, and reliable as the first line of testing when suspecting influenza infections, although the global burden of influenza infections remains high. Rapid diagnosis of influenza infections has been shown to reduce improper or delayed treatment and to increase access to diagnostic measures in public health, primary care, and hospital-based settings.

OBJECTIVES

As the use of RIDTs continues to expand in all healthcare settings, there is a multitude of molecular techniques being employed by these various testing platforms. With this in mind, we compare the sensitivity, specificity, and time to diagnosis for nine highly utilized commercial RIDTs.

METHODS

Nine commercially available RIDTs were identified from the US Centers for Disease Control and Prevention (CDC) website, which were also referenced on PubMed by name within the title or abstract of peer-reviewed publications examining the sensitivity and specificity of each test against a minimum of three influenza A virus (IAV) strains as well as seasonal influenza B virus (IBV). Data from the peer-reviewed publications and manufacturers' websites were combined to discuss the sensitivity, specify, and time to diagnosis associated with each RIDT.

RESULTS

The sensitivity and specificity across the examined RIDTs were greater than 85.0% for both IAV and IBV across all platforms, with the reverse transcriptase-polymerase chain reaction (RT-PCR) assays maintaining sensitivity and specificity greater than 95.0% for all viruses tested. However, the RT-PCR platforms were the longest in time to diagnosis when compared to the other molecular methods utilized in the examined RIDTs.

CONCLUSIONS

Herein, we discussed the benefits and limitations of nine commercially available RIDTs and the molecular techniques upon which they are based, showing the relative accuracy and speed of each test for IAV and IBV detection as reported by the peer-reviewed literature and commercial manufacturers.

Comparing the cobas Influenza A/B Nucleic acid test for use on the cobas Liat System (Liat) with rapid antigen tests for clinical management of Japanese patients at the point of care

Background

Rapid diagnosis of influenza is critical in preventing the spread of infection and ensuring patients quickly receive antiviral medication to reduce the severity and duration of influenza symptoms, whilst controlling the spread of the causative virus. In Japan patients are often administered anti-influenza medication following a positive rapid antigen detection test (RADT) result. However, the sensitivity of RADTs can lead to false negative results. The cobas^® Influenza A/B Nucleic acid test for use on the cobas Liat^® System (Liat) is a molecular point-of-care method that can provide a more sensitive alternative to RADTs for rapid influenza diagnosis and treatment.

Methods

In this prospective multicenter study, diagnostic performance of the Liat test was compared with RADTs in patients presenting with influenza-like-illness. Test performance was also assessed by time since symptom onset.

Results

Of 419 patients enrolled, 413 were evaluable for all designated tests. Most patients had type-A infection, and only one patient had influenza type B. In 413 patients, the sensitivity and specificity (95% CI) of the Liat test were 99.5% (97.2–99.9%) and 99.5% (97.4–99.9%), respectively, and were 79.7% (73.5–84.7%) and 95.4% (91.7–97.5%) for RADTs. For patients tested <12 hours from symptom onset, the Liat test had significantly higher sensitivity than RADTs (p<0.0001).

Conclusion

Overall, compared with standard of care RADTs, the Liat test was more sensitive and specific in children and adults, particularly in the early stages of infection. Greater sensitivity can enable earlier diagnosis and may better inform appropriate antiviral treatment decisions.

Evaluation of Four Fully Integrated Molecular Assays for the Detection of Respiratory Viruses during the Co-Circulation of SARS-CoV-2, Influenza and RSV

Background: The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B 2. Methods: The study was conducted in two parts: (i) the Idylla™ assays were assessed using a collection of nasopharyngeal swabs which were positive for various respiratory viruses. (ii) The performances of the four assays were assessed prospectively: all of the symptomatic patients admitted to the emergency department from 10 to 21 December were enrolled. Results: (i) All of the SARS-CoV-2 false negatives with the Idylla™ assays had a Ct value greater than 30 with the reference RT-PCR. No cross-reactivity was identified. (ii) Overall, 218 patients were enrolled. The respective prevalences of SARS-CoV-2, influenza A, and RSV were 19.8%, 4.8%, and 3.2%. All of the assays were 100% specific. The sensitivity of SARS-CoV-2 detection was 97.7%, 82.5%, and 86.3% for the Idylla™ SARS-CoV2, the Idylla™ SARS-CoV2/Flu/RSV, and the ID NOW COVID-19, respectively. For influenza A, it was 90.0% for the Idylla™ SARS-CoV2/Flu/RSV and 80.0% for the ID NOW Influenza. Discussion. All of the assays are suitable for testing patients with respiratory symptoms. False negatives should be considered, and the test should be repeated regarding the context.

Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses

As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification

Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.

Comparison of rapid molecular testing methods for detecting respiratory viruses in emergency care: a prospective study

BACKGROUND

Respiratory tract infections (RTIs) caused by contagious viruses are common among patients presenting to the emergency department (ED). Early detection of these viruses can help prevent nosocomial transmission.

AIM

To investigate the efficacy of three rapid molecular methods, namely FilmArray^® Pneumonia Panel plus (FAP plus), ID NOW^™ Influenza A and B 2 (ID NOW2) point-of-care test, and an in-house real-time polymerase chain reaction (RT-PCR) test, to identify patients with viral RTIs requiring isolation in an emergency setting.

METHODS

We included a FilmArray^® Pneumonia Panel plus in the initial workup of patients with suspected RTIs during a flu season. The RT-PCR and the influenza point-of-care test were performed as part of routine diagnostics, on demand from the treating physicians. We compared viral detections and compared time to positive test results for each method.

FINDINGS

The FAP plus significantly reduced the turnaround time and was able to identify 95% patients with potential contagious viral RTI. Routine diagnostics ordered by the treating physician had a turnaround time of a median 22 h and detected 87% of patients with potential contagious viral RTI. In patients that had all three tests, the ID NOW2 detected 62% of patients with influenza.

CONCLUSIONS

The FAP plus was able to rapidly and reliably identify patients with potential contagious viral RTIs; its use was feasible in the ED setting. Failing to test patients with viral RTI and using tests with long turnaround time may lead to nosocomial transmission of viral infections and adverse patient outcomes.

Prospective evaluation of ID NOW COVID-19 assay used as point-of-care test in an emergency department

BACKGROUND

Rapid testing for COVID-19 has been clearly identified as an essential component of the strategy to control the SARS-CoV-2 epidemic, worldwide. The ID NOW COVID-19 assay is a simple, user-friendly, rapid molecular biology test based on nicking and extension amplification reaction (NEAR).

OBJECTIVES

The aim of this study was to evaluate the ID NOW COVID-19 assay when used as a point-of-care test (POCT) in our Emergency Department (ED).

TYPE OF STUDY

This prospective study enrolled 395 consecutive patients; paired nasopharyngeal swabs were collected from each study participant. The first swab was tested with the ID NOW COVID-19 assay at the point-of-care by ED nurses. The second swab was diluted in viral transport medium (VTM) and sent to the clinical microbiology department for analysis by both the RT-PCR Simplexa test COVID-19 Direct assay as the study reference method, and the ID NOW COVID-19 assay performed in the laboratory.

RESULTS

Nasopharyngeal swabs directly tested with the ID NOW COVID-19 assay yielded a sensitivity, specificity, PPV and NPV of 98.0%, 97.5%, 96.2% and 98.7%, respectively, in comparison with the RT-PCR study reference assay. When the ID NOW COVID-19 assay was performed in the laboratory using the VTM samples, the sensitivity decreased to 62.5% and the NPV to 79.7%. Three false negative test results were reported with the ID NOW COVID-19 assay when performed using undiluted swabs directly in the ED; these results were obtained from patients with elevated CT values (> 30).

CONCLUSION

We demonstrated that the ID NOW COVID-19 assay, performed as a point of care test in the ED using dry swabs, provides a rapid and reliable alternative to laboratory-based RT-PCR methods.

Performance- and cost-benefit analysis of an influenza point-of-care test compared to laboratory-based multiplex RT-PCR in the emergency department

INTRODUCTION

Influenza poses a heavy burden on emergency departments (ED) and hospital wards. Fast and reliable bedside tests are invaluable in obtaining indications for (cohort) droplet isolation precautions and improving patient flow. We performed a cost-benefit analysis comparing influenza point-of-care testing (POCT) to laboratory-based multiplex ligation-dependent probe amplification.

METHODS

Data of 275 ED presentations between January-April 2019 were analyzed. Patients received both POCT and MLPA to calculate POCT sensitivity and specificity. Costs were calculated for both a POCT and MLPA scenario, including costs for testing, admission, droplet isolation precautions and cleaning.

RESULTS

In our study population, 34 patients (12%) were identified with influenza A. No cases of influenza B were identified. Mean age of the influenza positive patients was 75(18) years and 56% were male. The most common symptoms upon presentation were cough, malaise and fever, with 74%, 56% and 50%, respectively. Compared to MLPA, POCT yielded a sensitivity of 94%, a specificity of 98% and a negative predictive value of 99% for influenza A. Using POCT yielded a cost reduction of €93,26 per patient.

CONCLUSIONS

Influenza POCT is an accurate and cost-beneficial method to differentiate between admission with or without droplet isolation precautions. It can be useful in clinical decision making and reducing pressure on ED and hospital beds in an influenza peak season, by enabling fast patient flow and cohort isolation.

Multiplexed digital polymerase chain reaction as a powerful diagnostic tool

The digital polymerase chain reaction (dPCR) multiplexing method can simultaneously detect and quantify closely related deoxyribonucleic acid sequences in complex mixtures. The dPCR concept is continuously improved by the development of microfluidics and micro- and nanofabrication, and different complex techniques are introduced. In this review, we introduce dPCR techniques based on sample compartmentalization, droplet- and chip-based systems, and their combinations. We then discuss dPCR multiplexing methods in both laboratory research settings and advanced or routine clinical applications. We focus on their strengths and weaknesses with regard to the character of biological samples and to the required precision of such analysis, as well as showing recently published work based on those methods. Finally, we envisage possible future achievements in this field.

Comparative practicability and analytical performances of Credo VitaPCR™ Flu A&B and Cepheid Xpert® Xpress Flu/RSV platforms

To compare the practicability (usability and satisfaction) and analytical performances of VitaPCR™ Flu A&B Assay (Credo Diagnostics Biomedical Pte. Ltd., Singapore, Republic of Singapore) and Xpert® Xpress Flu/RSV kit (Cepheid, Sunnyvale, USA), two rapid point-of-care (POC) nucleic acid amplification tests (NAATs) by reference to multiplex RT-PCR for respiratory viruses. Nasopharyngeal swabs (n=117) were collected from patients with influenza-like illness in Paris, France. Thawed specimens were further analyzed with both NAATs. The usability was comparable for both NAATs. Satisfaction questionnaire was better for the VitaPCR™ platform for the short time of test result in 20 minutes. Both NAATs showed comparable sensitivities (VitaPCR^TM: 95.0%; Xpert® Xpress: 97.5%) and specificities (100%) for influenza A/B RNA detection, with excellent reliability and accuracy between both NAATs. Both VitaPCR™ and Xpert® Xpress NAATs can be implemented in hospital setting as POC NAATs to rapidly detect influenza A/B RNA in symptomatic patients.

Multicenter Evaluation of the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV Test

With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from influenza virus and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center.

With the approach of respiratory virus season in the Northern Hemisphere, clinical microbiology and public health laboratories will need rapid diagnostic assays to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from influenza virus and respiratory syncytial virus (RSV) infections for diagnosis and surveillance. In this study, the clinical performance of the Xpert Xpress SARS-CoV-2/Flu/RSV test (Cepheid, Sunnyvale, CA, USA) for nasopharyngeal swab specimens was evaluated in four centers: Johns Hopkins Medical Microbiology Laboratory, Northwell Health Laboratories, NYC Public Health Laboratory, and Los Angeles County/University of Southern California (LAC+USC) Medical Center. A total of 319 nasopharyngeal swab specimens, positive for SARS-CoV-2 (n = 75), influenza A virus (n = 65), influenza B virus (n = 50), or RSV (n = 38) or negative (n = 91) by the standard-of-care nucleic acid amplification tests at each site, were tested using the Cepheid panel test. The overall positive percent agreement for the SARS-CoV-2 target was 98.7% (n = 74/75), and the negative agreement was 100% (n = 91), with all other analytes showing 100% total agreement (n = 153). Standard-of-care tests to which the Cepheid panel was compared included the Cepheid Xpert Xpress SARS-CoV-2, Cepheid Xpert Xpress Flu/RSV, GenMark ePlex respiratory panel, BioFire respiratory panel 2.1 and v1.7, DiaSorin Simplexa COVID-19 Direct, and Hologic Panther Fusion SARS-CoV-2 assays. The Xpert Xpress SARS-CoV-2/Flu/RSV test showed high sensitivity and accuracy for all analytes included in the test. This test will provide a valuable clinical diagnostic and public health solution for detecting and differentiating SARS-CoV-2, influenza A and B virus, and RSV infections during the current respiratory virus season.

Xpert Xpress Flu/RSV: Validation and impact evaluation at a large UK hospital trust

Despite vaccination programs and antivirals, influenza remains a prominent cause of morbidity and mortality. The Xpert Xpress Flu/respiratory syncytial virus (RSV) test is a leading influenza point-of-care test, but its evaluation has been limited to nasopharyngeal samples. In addition, the clinical impacts of Xpress Flu/RSV have not yet been quantified. We evaluated the performance of Xpress Flu/RSV at three locations in a UK Hospital Trust against an existing laboratory assay. Multiple upper respiratory tract sample types were included. In addition, we calculated time saved by Xpert, and the associations between Xpert use and rates of early patient isolation and antiviral prescription as recorded at the time of the laboratory result being telephoned out. A total of 642 patients were included in the diagnostic performance analysis. There were 177 laboratory-confirmed cases of influenza A, 7 influenza B and 86 RSV. For influenza A, sensitivity and specificity were 96.6% (95% confidence interval [CI]: 92.8%-98.8%) and 98.1% (CI: 96.4%-99.1%), respectively. This was sustained across all locations and sample types. The negative predictive value was 98.7% (CI: 97.2%-99.4%). The median amount of time saved was 27.1 h. Xpert use was associated with sixfold higher rates of isolation and threefold higher rates of antiviral prescribing by the time the laboratory result was available. Sensitivity for RSV was lower at 86.0% (95% CI: 76.9%-92.6%). Xpert Xpress Flu/RSV reliably detects influenza A infection and has significant clinical impacts. Cartridge optimization is required to enable accurate multiplexing, including from a range of sample types.

Evaluation of a novel rapid TRC assay for the detection of influenza using nasopharyngeal swabs and gargle samples

We evaluated a novel transcription-reverse transcription concerted reaction (TRC) assay that can detect influenza A and B within 15 min using nasopharyngeal swab and gargle samples obtained from patients with influenza-like illness, between January and March 2018 and between January and March 2019. Based on the combined RT-PCR and sequencing results, in the nasal swabs, the sensitivity and specificity of TRC for detecting influenza were calculated as 1.000 and 1.000, respectively. In the gargle samples, the sensitivity and specificity of TRC were 0.946 and 1.000, respectively. The TRC assay showed comparable performance to RT-PCR in the detection of influenza viruses.

Multiplex Molecular Point-of-Care Test for Syndromic Infectious Diseases

Point-of-care (POC) molecular diagnostics for clinical microbiology and virology has primarily focused on the detection of a single pathogen. More recently, it has transitioned into a comprehensive syndromic approach that employs multiplex capabilities, including the simultaneous detection of two or more pathogens. Multiplex POC tests provide higher accuracy to for actionable decisionmaking in critical care, which leads to pathogen-specific treatment and standardized usages of antibiotics that help prevent unnecessary processes. In addition, these tests can be simple enough to operate at the primary care level and in remote settings where there is no laboratory infrastructure. This review focuses on state-of-the-art multiplexed molecular point-of-care tests (POCT) for infectious diseases and efforts to overcome their limitations, especially related to inadequate throughput for the identification of syndromic diseases. We also discuss promising and imperative clinical POC approaches, as well as the possible hurdles of their practical applications as front-line diagnostic tests.

Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza

Influenza virus poses a threat to global health by causing seasonal outbreaks as well as three pandemics in the 20th century. In humans, disease is primarily caused by influenza A and B viruses, while influenza C virus causes mild disease mostly in children. Influenza D is an emerging virus found in cattle and pigs. To mitigate the morbidity and mortality associated with influenza, rapid and accurate diagnostic tests need to be deployed. However, the high genetic diversity displayed by influenza viruses presents a challenge to the development of a robust diagnostic test. Nucleic acid-based tests are more accurate than rapid antigen tests for influenza and are therefore better candidates to be used in both diagnostic and surveillance applications. Here, we review various nucleic acid-based techniques that have been applied towards the detection of influenza viruses in order to evaluate their utility as both diagnostic and surveillance tools. We discuss both traditional as well as novel methods to detect influenza viruses by covering techniques that require nucleic acid amplification or direct detection of viral RNA as well as comparing advantages and limitations for each method. There has been substantial progress in the development of nucleic acid-based sensing techniques for the detection of influenza virus. However, there is still an urgent need for a rapid and reliable influenza diagnostic test that can be used at point-of-care in order to enhance responsiveness to both seasonal and pandemic influenza outbreaks.

Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay

In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.

Clinical performance of the GenMark Dx ePlex respiratory pathogen panels for upper and lower respiratory tract infections

The GenMark Dx ePlex Respiratory Pathogen Panel (RP) is a multiplexed nucleic acid test for the qualitative detection of common viral and a few bacterial causes of respiratory tract infections. The ePlex RP has received FDA clearance for nasopharyngeal swab (NPS) specimens collected in viral transport media. In this study, we evaluated the performance of the ePlex RP panel in comparison to the NxTAG Respiratory Pathogen Panel (NxTAG-RPP) from Luminex in use in our laboratory, not only for NPS but also for bronchoalveolar lavage specimens (BAL). We also evaluated the impact of implementing the ePlex RP on the test turn-around time (TAT). The newest panel from GenMark Dx, the ePlex Respiratory Pathogen Panel 2 (RP2), which added the SARS-CoV-2 target to the RP was also evaluated for NPS. Verification of the performance of the ePlex RP for both NPS and BAL showed 93.3 % and 84.9 % total agreement with the NxTAG-RPP respectively. An overall comparison of the TAT after implementing the ePlex RP as compared to the NxTAG-RPP assay showed an average decrease of almost seven-fold.

Impact of Rapid Influenza Molecular Testing on Management in Pediatric Acute Care Settings

OBJECTIVES

To measure the impact of rapid influenza real-time qualitative reverse transcriptase polymerase chain reaction (RT-PCR) on patient management in busy pediatric emergency department (ED) and urgent care clinic settings.

STUDY DESIGN

We developed a brief, elective survey that clinicians completed when an influenza RT-PCR order was placed in the ED or urgent care clinic between February 18, 2019, and March 13, 2019. We captured the clinical suspicion for influenza, intended management plans, and actual management plans once influenza RT-PCR results were available.

RESULTS

We evaluated 339 encounters, of which 164 (48.4%) had a positive influenza RT-PCR. Clinical suspicion for influenza was a nonsignificant predictor for influenza PT-PCR positivity (P = .126). After rapid influenza RT-PCR results were available, clinicians changed their original plans in 44.5% of influenza RT-PCR positive vs 92.6% of influenza RT-PCR negative cases (P < .0001). Change in plans for antiviral use was observed in 26% of influenza positive vs 77% of influenza negative cases (P < .0001). A total of 135 antiviral prescriptions were avoided in patients with negative influenza RT-PCR.

CONCLUSIONS

Implementation of a rapid and accurate influenza RT-PCR in the acute care setting is important to systematically diagnose influenza in children and improve outpatient management decisions, because clinical suspicion for influenza is inaccurate. A negative influenza RT-PCR decreases unnecessary antiviral use and has the potential for significant cost savings.

Developments in integrating nucleic acid isothermal amplification and detection systems for point-of-care diagnostics

Early disease detection through point-of-care (POC) testing is vital for quickly treating patients and preventing the spread of harmful pathogens. Disease diagnosis is generally accomplished using quantitative polymerase chain reaction (qPCR) to amplify nucleic acids in patient samples, permitting detection even at low target concentrations. However, qPCR requires expensive equipment, trained personnel, and significant time. These resources are not available in POC settings, driving researchers to instead utilize isothermal amplification, conducted at a single temperature, as an alternative. Common isothermal amplification methods include loop-mediated isothermal amplification, recombinase polymerase amplification, rolling circle amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. There has been a growing interest in combining such amplification methods with POC detection methods to enable the development of diagnostic tests that are well suited for resource-limited settings as well as developed countries performing mass screenings. Exciting developments have been made in the integration of these two research areas due to the significant impact that such approaches can have on healthcare. This review will primarily focus on advances made by North American research groups between 2015 and June 2020, and will emphasize integrated approaches that reduce user steps, reliance on expensive equipment, and the system's time-to-result.

Clinical usefulness of a rapid molecular assay, ID NOW™ influenza A & B 2, in adults

INTRODUCTION

ID NOW™ Influenza A & B 2 (ID NOW 2) is a rapid molecular assay that combines two characteristics, namely the rapidness of rapid antigen detection test (RADT) and the high sensitivity of molecular assay.

METHODS

The clinical performance of ID NOW 2 compared with real-time RT-PCR was evaluated in adults.

RESULTS

The sensitivity of ID NOW 2 over multiple seasons from 2016/2017 to 2019/2020 was 97.3% (95% CI: 90.7-99.7) for Type A, 100% (95% CI: 81.9-100) for Type B, and 97.8% (95% CI: 92.2-99.7) for influenza (Type A + Type B), and it was significantly higher than the sensitivity of RADT, which was 80.0% (95% CI: 69.2-88.4) for Type A, 73.3% (95% CI: 44.9-92.2) for Type B, and 78.9% (95% CI: 69.0-86.8) for influenza. The sensitivity of RADT tended to be lower in patients in the particularly early period, within 12 h from disease onset; however, the sensitivity of ID NOW 2 remained high, increasing the difference between the sensitivity of RADT and ID NOW 2. The viral loads were low within 12 h from onset, and it was considered this affected the sensitivity of RADT due to its low analytical sensitivity. The specificity of ID NOW 2 was 98% or greater in all groups.

CONCLUSIONS

Since ID NOW 2 has a high sensitivity and specificity in adults, it is anticipated to be used in clinical practice, particularly in patients who require early and accurate diagnosis.

Respiratory pathogen diversity and co-infections in rural Zambia

Objectives:

The role of respiratory co-infections in modulating disease severity remains understudied in southern Africa, particularly in rural areas. This study was performed to characterize the spectrum of respiratory pathogens in rural southern Zambia and the prognostic impact of co-infections.

Methods:

Respiratory specimens collected from inpatient and outpatient participants in a viral surveillance program in 2018–2019 were tested for selected viruses and a typical bacteria using the Xpert Xpress Flu/RSV assay and FilmArray Respiratory Panel EZ. Participants were followed for 3–5 weeks to assess their clinical course. Multivariable regression was used to examine the role of co-infections in influencing disease severity.

Results:

A respiratory pathogen was detected in 63.2% of samples from 671 participants who presented with influenza-like illness. Common pathogens identified included influenza virus (18.2% of samples), respiratory syncytial virus (RSV) (11.8%), rhinovirus (26.4%), and coronavirus (6.0%). Overall, 6.4% of participants were co-infected with multiple respiratory pathogens. Compared to mono-infections, co-infections were found not to be associated with severe clinical illness either overall (relative risk (RR) 0.72, 95% confidence interval (CI) 0.39–1.32) or specifically with influenza virus (RR 0.80, 95% CI 0.14–4.46) or RSV infections (RR 0.44, 95% CI 0.17–1.11).

Conclusions:

Respiratory infections in rural southern Zambia were associated with a wide range of viruses. Respiratory co-infections in this population were not associated with clinical severity.

A critical review of point-of-care diagnostic technologies to combat viral pandemics

The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.

PCR past, present and future

PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.

Evaluation of cobas Influenza A/B & RSV Test for Diagnosis of Equine Influenza

A rapid and sensitive diagnostic method is needed to help prevent the spread of equine influenza virus. The cobas Influenza A/B & RSV test for the cobas Liat system (Roche Diagnostics) is based on real-time reverse transcription polymerase chain reaction and is designed to broadly detect influenza A virus RNA within 20 minutes. It detected a broad range of equine influenza virus strains, and detected equine influenza virus RNA from nasal swabs of infected horses at the same level as real-time reverse transcription polymerase chain reaction, although it returned some invalid results (7.7%). This suggests that cobas Influenza A/B & RSV test is highly sensitive to equine influenza virus, but should be improved to reduce the rate of invalid results.

The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond

Infectious diseases, such as the most recent case of coronavirus disease 2019, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfill this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.

Scientific research progress of COVID-19/SARS-CoV-2 in the first five months

A cluster of pneumonia (COVID-19) cases have been found in Wuhan China in late December, 2019, and subsequently, a novel coronavirus with a positive stranded RNA was identified to be the aetiological virus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), which has a phylogenetic similarity to severe acute respiratory syndrome coronavirus (SARS-CoV). SARS-CoV-2 transmits mainly through droplets and close contact and the elder or people with chronic diseases are high-risk population. People affected by SARS-CoV-2 can be asymptomatic, which brings about more difficulties to control the transmission. COVID-19 has become pandemic rapidly after onset, and so far the infected people have been above 2 000 000 and more than 130 000 died worldwide according to COVID-19 situation dashboard of World Health Organization (https://covid19.who.int). Here, we summarized the current known knowledge regarding epidemiological, pathogenesis, pathology, clinical features, comorbidities and treatment of COVID-19/ SARS-CoV-2 as reference for the prevention and control COVID-19.