The evaluation of the utility of the GENECUBE HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol

  1. Asami Naito
  2. Yoshihiko Kiyasu
  3. Yusaku Akashi
  4. Akio Sugiyama
  5. Masashi Michibuchi
  6. Yuto Takeuchi
  7. Shigeyuki Notake
  8. Koji Nakamura
  9. Hiroichi Ishikawa
  10. Hiromichi Suzuki

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Abstract

GENECUBE ® is a rapid molecular identification system, and previous studies demonstrated that GENECUBE ® HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated.

Methods

This prospective comparison between GENECUBE ® HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE ® HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes.

Results

For 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations.

Conclusion

GENECUBE ® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.

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  1. Version published to 10.1371/journal.pone.0262159
  2. ScreenIT

    SciScore for 10.1101/2021.08.23.21262454: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The ethics committee of Tsukuba Medical Center Hospital approved the present study (approval number: 2020-066) for both anterior nasal sampling and positive saliva samples, informed consent was obtained from patients for their participation in the respective part of the current research.
    Consent: The ethics committee of Tsukuba Medical Center Hospital approved the present study (approval number: 2020-066) for both anterior nasal sampling and positive saliva samples, informed consent was obtained from patients for their participation in the respective part of the current research.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Evaluation of the Limit of Detection (LOD) for GENECUBE® HQ SARS-CoV-2 with Nasopharyngeal Samples and Saliva Samples: To evaluate the LOD for GENECUBE® HQ SARS-CoV-2, we made four different concentrations of samples (2500 copies/mL, 1000 copies/mL, 500 copies/mL, 250 copies/mL) with SARS-CoV-2 reference material (AccuPlex™ SARS-CoV-2 Reference Material Kit, SeraCare; SeraCare Life Sciences, Inc., Milford, MA, USA) and matrix (UTM™; three pooled nasopharyngeal samples and two pooled saliva samples).
    SeraCare; SeraCare
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    There are several limitations in this study that should be mentioned. First, the current research was performed at a PCR center in Japan. The influence of LODs of the GENECUBE® evaluation for genetic variants of SARS-CoV-2 was not evaluated in this study. Second, the current evaluated rapid protocol showed excellent performance for the detection of SARS-CoV-2; however, the sample size was insufficient to conclude that the protocol can be used in clinical practice; additional evaluation in studies with large samples is required. Third, the current GENECUBE® examination can analyze only 12 samples at a single run, and the amplification curve is not displayed. The system must be improved for better examination. In conclusion, the GENECUBE® examination with GENECUBE® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a protocol registration statement.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.08.23.21262454v1 on medRxiv