Evaluation of Seegene Allplex Respiratory Panel 1 kit for the detection of influenza virus and human respiratory syncytial virus

Gimferrer, Laura; Andrés, Cristina; Rando, Ariadna; Piñana, María; Codina, María Gema; Martín, María del Carmen; Fuentes, Francisco; Rubio, Susana; Alcubilla, Pilar; Pumarola, Tomás; Antón, Andrés

doi:10.1016/j.jcv.2018.05.006

Cited by 15 publications

(17 citation statements)

References 11 publications

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“…A study comparing Allplex RP1 assay with ProdesseProFlu+ and ProFAST+ (Hologic, Madison, WI, USA), and GeneXpert Flu/RSV XC (Cepheid, USA) for IV and RSV detection, found accuracy of 95, 91, and 96% and sensitivity of 94, 88, and 95%, respectively. The three assays showed a 100% specificity and positive predictive value (PPV), while the negative predictive values (NPV) were 84, 73, and 86% for Allplex RP1, Prodesse and GeneXpert, respectively (Gimferrer et al, 2018).…”

Section: What Is the Efficiency Of Multiplex Platforms In The Identifmentioning

confidence: 99%

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

Esposito

Mencacci

Cenci

et al. 2019

Front. Cell. Infect. Microbiol.

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

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Section: What Is the Efficiency Of Multiplex Platforms In The Identifmentioning

confidence: 99%

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

Esposito

Mencacci

Cenci

et al. 2019

Front. Cell. Infect. Microbiol.

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“…Several multiplexed respiratory assays with CE-IVD approval are currently available on the market. Among them, Allplex respiratory assays have shown good performance and reliable results [15][16][17]. The recently-developed Panther Fusion System is a fully automated randomaccess testing system that has shown comparable results with those obtained with the eSensor RVP (eSensor; Genmark Dx, Carlsbad, CA) and Lyra (Quidel, San Diego, CA) respiratory assays [13].…”

Section: Discussionmentioning

confidence: 99%

“…The purpose of this study was to compare these two commercial products (Panther Fusion assay and Allplex respiratory panels) for the detection of influenza A (Flu A), influenza B (Flu B), RSV, parainfluenza virus (PIV), human metapneumovirus (hMPV), rhinovirus (RV) and adenovirus (AdV), using a single patient sample. Both assays consist of three multiplex realtime PCR (rRT-PCR) panels, and have recently shown good performance in the detection of a battery of respiratory viruses [13][14][15][16][17], but to date they have not been compared to each other.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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

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“…Demographic information, medical history and outcome information were collected. Respiratory specimens were used for the detection of influenza viruses [ 27 ] and SARS-CoV-2 envelop (E) and ORF1ab genes [ 28 ] based rRT-PCR assays.…”

Section: Methodsmentioning

confidence: 99%

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

Alosaimi

Naeem

Alghoribi

et al. 2021

Viruses

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In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

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Evaluation of Seegene Allplex Respiratory Panel 1 kit for the detection of influenza virus and human respiratory syncytial virus

Abstract: In this study, Seegene's Allplex RP1 assay showed to be highly sensitive, specific, and suitable for detection of FLUV and HRSV, including FLUAV subtyping. In addition, it is also a hands-on-time saving assay due to the automated nucleic acid extraction and PCR setup.

Cited by 15 publications

References 11 publications

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

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

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

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

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