Dynamics of ORF1ab and N Gene among hospitalized COVID-19 positive cohorts: A hospital based retrospective study

  1. Pojul Loying
  2. Vaishali Sarma
  3. Suranjana C. Hazarika
  4. Monjuri Kataki
  5. Dina Raja
  6. Divyashree Medhi
  7. Ridip Dutta
  8. Achu Chena
  9. Divya Daimary
  10. Aakangkhita Choudhury
  11. Lahari Saikia

Reviewed by

Read the full article

Discuss this preprint

Start a discussion What are Sciety discussions?

Listed in

Log in to save this article

Abstract

1.

Objective

The present study hospital based retrospective study aimed at investigating the dynamics of ORF1ab and N gene from hospitalized COVID-19 positive cohorts considering the Ct values of both genes.

Study design and Methodology

Retrospective analyses of Ct values were done from 115 hospitalized COVID-19 positive patients in different time interval. Patients were admitted to the hospital either by RAT or/and RT-PCR and first RT-PCR testing were made after 9 days of incubation followed by testing in every 3 days of interval till negative, subsequently release of the patients.

Results

We have looked into the dynamics of ORF1ab and N gene and found that N gene require longer duration of days with 12.68 (S.D.±3.24) to become negative than ORF1ab with 12.09 (S.D.±2.88) days and it differs significantly (p=0.012; p<0.05). The persistent of N gene found in 46 patients out of 115 (39.65%) to the succeeding reading after 3 days. We have also looked into the mean differences in the between N and ORF1ab genes every readings separately and found that there were no significant differences between the mean Ct value of ORF1ab and N gene except in the day 3 (p=0.015; p<0.05). Further, we have looked into the relationship of age and gender of patients with the duration of positivity; however we did not find any significant role.

Conclusion

In COVID-19 hospital positive cohorts, the persistent of positivity of N gene is significantly for more duration than ORF1ab. As the SARS-CoV-2 is a new virus and study on it is evolving, so, exhaustive study is required on the dynamic of N gene positivity persistent in relation to the other pathophysiological parameters for the management and control of COVID-19.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.11.22.20236240: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIACUC: RT-PCR data were taken for analysis after approval from institutional ethical committee (IEC), GMCH.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    RNA from the processed samples was extracted by using QIAmp Viral RNA Mini Kit (QIAGEN, Germany) following manufacturer guidelines. 3.3. RT-PCR for SARS-CoV-2 detection: One Step Reverse Transcriptase Real Time Polymerase Chain Reaction (RT-PCR) were performed to detect the presence or absence of ORF1ab and N gene using Taqman probe based multicolor Meril COVID-19 One-step RTPCR Kit (Meril Diagnostics, Belgium) in CFX96 Touch Real-Time PCR Detection System RT-PCR platform (Bio-Rad Laboratories, Inc.).
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    All statistical analyses were performed in R (version 4.0.0) and SPSS (version 16.0) software.
    SPSS
    suggested: (SPSS, RRID:SCR_002865)
    The graphical representations were created in R software (version 4.0.0) using GGPLOT2 package.
    GGPLOT2
    suggested: (ggplot2, RRID:SCR_014601)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.11.22.20236240 on medRxiv