Comparative evaluation of five rapid PCR platforms for respiratory virus detection

Pieter W Smit; Peter de Man; Henk Brand; Simone Breijer; Mariska van Wijk; Adam Meijer; David S Y Ong

doi:10.1371/journal.pone.0338716

Comparative evaluation of five rapid PCR platforms for respiratory virus detection

Pieter W Smit
, Peter de Man
, Henk Brand
, Simone Breijer
, Mariska van Wijk
, Adam Meijer^*
, David S Y Ong^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

BACKGROUND: The demand for rapid molecular diagnostics for respiratory viruses has increased substantially. Several point-of-care PCR platforms have become available, yet comparative performance data remain limited.

OBJECTIVES: To evaluate the diagnostic accuracy and operational reliability of four rapid PCR platforms for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses (IAV, IBV), and respiratory syncytial virus (RSV), in comparison with the GeneXpert (Cepheid, USA) platform.

METHODS: Nasopharyngeal swabs from patients with respiratory symptoms were tested using the GeneXpert, positive samples were subsequently analysed on four alternative systems: the 30-minute and 1-hour M10 (SD Biosensor, South Korea) assays, FlashDetect™ Flash10 (Coyote Bioscience, China), Vivalytic (Bosch Healthcare Solutions, Germany), and Galaxy Lite (Igenesis, China). Additional lower viral load samples and cultured IAV/ IBV strains were included.

RESULTS: A total of 223 GeneXpert positive samples were prospectively analysed. Flash10 showed 94.6% overall agreement, missing SARS-CoV-2 (n = 4, GeneXpert Cycle threshold (Ct) min-max; 37.7-42.2), IAV (n = 5, 32.8-37.7), and IBV (n = 3, 26.5-36.7). Vivalytic showed 83.0% overall agreement, missing SARS-CoV-2 (n = 16, 30.4-42.2), IAV (n = 9, 26.8-37.7), IBV (n = 9, 27.2-36.7), and RSV (n = 4, 31.5-37.0). Galaxy Lite achieved 88.2% overall agreement but failed in 27.2% of test runs. With a smaller sample size the M10 (30-minute) assay showed 98.6% overall agreement with GeneXpert, missing one SARS-CoV-2 case (Ct 39.7).

CONCLUSION: Among four platforms, the M10 (30-min version) and Flash10 platforms demonstrated the highest agreement rates with the GeneXpert. The variability in performance highlights the importance of independent platform evaluation.

Original language	English
Article number	e0338716
Number of pages	10
Journal	PLoS ONE
Volume	20
Issue number	12
DOIs	https://doi.org/10.1371/journal.pone.0338716
Publication status	Published - 11 Dec 2025

Keywords

COVID-19/diagnosis
Humans
Influenza A virus/genetics
Influenza B virus/genetics
Nasopharynx/virology
Polymerase Chain Reaction/methods
Reproducibility of Results
Respiratory Syncytial Viruses/genetics
SARS-CoV-2/genetics
Sensitivity and Specificity

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Comparative evaluation of five rapid PCR platforms for respiratory virus detectionFinal published version, 347 KBLicence: CC BY

Cite this

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title = "Comparative evaluation of five rapid PCR platforms for respiratory virus detection",

abstract = "BACKGROUND: The demand for rapid molecular diagnostics for respiratory viruses has increased substantially. Several point-of-care PCR platforms have become available, yet comparative performance data remain limited.OBJECTIVES: To evaluate the diagnostic accuracy and operational reliability of four rapid PCR platforms for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses (IAV, IBV), and respiratory syncytial virus (RSV), in comparison with the GeneXpert (Cepheid, USA) platform.METHODS: Nasopharyngeal swabs from patients with respiratory symptoms were tested using the GeneXpert, positive samples were subsequently analysed on four alternative systems: the 30-minute and 1-hour M10 (SD Biosensor, South Korea) assays, FlashDetect{\texttrademark} Flash10 (Coyote Bioscience, China), Vivalytic (Bosch Healthcare Solutions, Germany), and Galaxy Lite (Igenesis, China). Additional lower viral load samples and cultured IAV/ IBV strains were included.RESULTS: A total of 223 GeneXpert positive samples were prospectively analysed. Flash10 showed 94.6\% overall agreement, missing SARS-CoV-2 (n = 4, GeneXpert Cycle threshold (Ct) min-max; 37.7-42.2), IAV (n = 5, 32.8-37.7), and IBV (n = 3, 26.5-36.7). Vivalytic showed 83.0\% overall agreement, missing SARS-CoV-2 (n = 16, 30.4-42.2), IAV (n = 9, 26.8-37.7), IBV (n = 9, 27.2-36.7), and RSV (n = 4, 31.5-37.0). Galaxy Lite achieved 88.2\% overall agreement but failed in 27.2\% of test runs. With a smaller sample size the M10 (30-minute) assay showed 98.6\% overall agreement with GeneXpert, missing one SARS-CoV-2 case (Ct 39.7).CONCLUSION: Among four platforms, the M10 (30-min version) and Flash10 platforms demonstrated the highest agreement rates with the GeneXpert. The variability in performance highlights the importance of independent platform evaluation.",

keywords = "COVID-19/diagnosis, Humans, Influenza A virus/genetics, Influenza B virus/genetics, Nasopharynx/virology, Polymerase Chain Reaction/methods, Reproducibility of Results, Respiratory Syncytial Viruses/genetics, SARS-CoV-2/genetics, Sensitivity and Specificity",

author = "Smit, \{Pieter W\} and Man, \{Peter de\} and Henk Brand and Simone Breijer and Wijk, \{Mariska van\} and Adam Meijer and Ong, \{David S Y\}",

note = "Publisher Copyright: {\textcopyright} 2025 Smit et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2025",

month = dec,

day = "11",

doi = "10.1371/journal.pone.0338716",

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AU - Smit, Pieter W

AU - Man, Peter de

AU - Brand, Henk

AU - Breijer, Simone

AU - Wijk, Mariska van

AU - Meijer, Adam

AU - Ong, David S Y

N1 - Publisher Copyright: © 2025 Smit et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2025/12/11

Y1 - 2025/12/11

N2 - BACKGROUND: The demand for rapid molecular diagnostics for respiratory viruses has increased substantially. Several point-of-care PCR platforms have become available, yet comparative performance data remain limited.OBJECTIVES: To evaluate the diagnostic accuracy and operational reliability of four rapid PCR platforms for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses (IAV, IBV), and respiratory syncytial virus (RSV), in comparison with the GeneXpert (Cepheid, USA) platform.METHODS: Nasopharyngeal swabs from patients with respiratory symptoms were tested using the GeneXpert, positive samples were subsequently analysed on four alternative systems: the 30-minute and 1-hour M10 (SD Biosensor, South Korea) assays, FlashDetect™ Flash10 (Coyote Bioscience, China), Vivalytic (Bosch Healthcare Solutions, Germany), and Galaxy Lite (Igenesis, China). Additional lower viral load samples and cultured IAV/ IBV strains were included.RESULTS: A total of 223 GeneXpert positive samples were prospectively analysed. Flash10 showed 94.6% overall agreement, missing SARS-CoV-2 (n = 4, GeneXpert Cycle threshold (Ct) min-max; 37.7-42.2), IAV (n = 5, 32.8-37.7), and IBV (n = 3, 26.5-36.7). Vivalytic showed 83.0% overall agreement, missing SARS-CoV-2 (n = 16, 30.4-42.2), IAV (n = 9, 26.8-37.7), IBV (n = 9, 27.2-36.7), and RSV (n = 4, 31.5-37.0). Galaxy Lite achieved 88.2% overall agreement but failed in 27.2% of test runs. With a smaller sample size the M10 (30-minute) assay showed 98.6% overall agreement with GeneXpert, missing one SARS-CoV-2 case (Ct 39.7).CONCLUSION: Among four platforms, the M10 (30-min version) and Flash10 platforms demonstrated the highest agreement rates with the GeneXpert. The variability in performance highlights the importance of independent platform evaluation.

AB - BACKGROUND: The demand for rapid molecular diagnostics for respiratory viruses has increased substantially. Several point-of-care PCR platforms have become available, yet comparative performance data remain limited.OBJECTIVES: To evaluate the diagnostic accuracy and operational reliability of four rapid PCR platforms for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A and B viruses (IAV, IBV), and respiratory syncytial virus (RSV), in comparison with the GeneXpert (Cepheid, USA) platform.METHODS: Nasopharyngeal swabs from patients with respiratory symptoms were tested using the GeneXpert, positive samples were subsequently analysed on four alternative systems: the 30-minute and 1-hour M10 (SD Biosensor, South Korea) assays, FlashDetect™ Flash10 (Coyote Bioscience, China), Vivalytic (Bosch Healthcare Solutions, Germany), and Galaxy Lite (Igenesis, China). Additional lower viral load samples and cultured IAV/ IBV strains were included.RESULTS: A total of 223 GeneXpert positive samples were prospectively analysed. Flash10 showed 94.6% overall agreement, missing SARS-CoV-2 (n = 4, GeneXpert Cycle threshold (Ct) min-max; 37.7-42.2), IAV (n = 5, 32.8-37.7), and IBV (n = 3, 26.5-36.7). Vivalytic showed 83.0% overall agreement, missing SARS-CoV-2 (n = 16, 30.4-42.2), IAV (n = 9, 26.8-37.7), IBV (n = 9, 27.2-36.7), and RSV (n = 4, 31.5-37.0). Galaxy Lite achieved 88.2% overall agreement but failed in 27.2% of test runs. With a smaller sample size the M10 (30-minute) assay showed 98.6% overall agreement with GeneXpert, missing one SARS-CoV-2 case (Ct 39.7).CONCLUSION: Among four platforms, the M10 (30-min version) and Flash10 platforms demonstrated the highest agreement rates with the GeneXpert. The variability in performance highlights the importance of independent platform evaluation.

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KW - Humans

KW - Influenza A virus/genetics

KW - Influenza B virus/genetics

KW - Nasopharynx/virology

KW - Polymerase Chain Reaction/methods

KW - Reproducibility of Results

KW - Respiratory Syncytial Viruses/genetics

KW - SARS-CoV-2/genetics

KW - Sensitivity and Specificity

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DO - 10.1371/journal.pone.0338716

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Comparative evaluation of five rapid PCR platforms for respiratory virus detection

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