A diagnostic decision-making protocol combines a new-generation of serological assay and PCR to fully resolve ambiguity in COVID-19 diagnosis

  1. Hu Cheng
  2. Hao Chen
  3. Yiting Li
  4. Peiyan Zheng
  5. Dayong Gu
  6. Shiping He
  7. Dongli Ma
  8. Ruifang Wang
  9. Jun Han
  10. Zhongxin Lu
  11. Xinyi Xia
  12. Yi Deng
  13. Lan Yang
  14. Wenwen Xu
  15. Shanhui Wu
  16. Cuiying Liang
  17. Hui Wang
  18. Baoqing Sun
  19. Nanshan Zhong
  20. Hongwei Ma

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Abstract

The capacity to accurately diagnosis COVID-19 is essential for effective public health measures to manage the ongoing global pandemic, yet no presently available diagnostic technologies or clinical protocols can achieve full positive predictive value (PPV) and negative predictive value (NPV) performance. Two factors prevent accurate diagnosis: the failure of sampling methods ( e.g ., 40% false negatives from PCR testing of nasopharyngeal swabs) and sampling-time-dependent failures reflecting individual humoral responses of patients (e.g., serological testing outside of the sero-positive stage). Here, we report development of a diagnostic protocol that achieves full PPV and NPV based on a cohort of 500 confirmed COVID-19 cases, and present several discoveries about the sero-conversion dynamics throughout the disease course of COVID-19. The fundamental enabling technology for our study and diagnostic protocol—termed SANE, for Symptom (dpo)-Antibody-Nucleic acid-Epidemiological history—is our development of a peptide-protein hybrid microarray (PPHM) for COVID-19. The peptides comprising PPHM covid-19 were selected based on clinical sample data, and give our technology the unique capacity to monitor a patient’s humoral response throughout the disease course. Among other assay-development related and clinically relevant findings, our use of PPHM covid-19 revealed that 5% of COVID-19 patients are from an “early sero-reversion” subpopulation, thus explaining many of the mis-diagnoses we found in our comparative testing using PCR, CLIA, and PPHM covid-19 . Accordingly, the full SANE protocol incorporates orthogonal technologies to account for these patient variations, and successfully overcomes both the sampling method and sampling time limitations that have previously prevented doctors from achieving unambiguous, accurate diagnosis of COVID-19.

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    SciScore for 10.1101/2020.08.11.20172452: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was approved by the ethics committee of the four hospitals mentioned above (Medical Research Ethics No. 44, 2020).
    Consent: Written informed consent was waived in light of this emerging infectious disease of high clinical relevance.
    RandomizationThree subgroups were randomly selected from the training group.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variable47 - 69 years) and 54.8% were females.

    Table 2: Resources

    No key resources detected.

    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, mainly due to two unexpected discoveries: the fact that peptides may enter into the sero-positive period while RBD is still in its window period, and the aforementioned patient subgroup exhibiting early sero-reversion. The random selection process of serum samples resulted in a pool of primary latitudinal sera (i.e., cross-sectional sera), while longitudinal sera (ideally from clinical trials of vaccine development) is required to catch the sero-conversion and sero-reversion phases. Furthermore, we intend to obtain a significantly larger number of samples to further study the aforementioned small probability events (Table S6). Finally, a field study at a large scale is needed to examine whether the probe combination of PPHMcovid-19 calculated from a relatively small population is valid. Notably, our demonstration that sensitivity and specificity is population depended for whole-protein-based assays but not PPHMcovid-19 can be further confirmed with such work. In conclusion, we completed the training and validation studies of PPHMcovid-19 for diagnosis of COVID-19. Given that PPHM has fixed cut-off values and that selection of apparently universal probes can be achieved with a small initial population, it is clear that PPHM development can be standardized, making it especially suitable for rapidly responding to sudden outbreaks of infectious diseases (26, 27). Moreover, the SANE protocol we demonstrate has the potential to significa...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.08.11.20172452 on medRxiv