SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients: a retrospective observational study

  1. Bisakh Bhattacharya
  2. Rohit Kumar
  3. Ved Prakash Meena
  4. Manish Soneja
  5. Amit Singh
  6. Rojaleen Das
  7. Ashit Xess
  8. Nazneen Arif
  9. Saurabh Vig
  10. Vandana Rastogi
  11. Pavan Tiwari
  12. Sushma Bhatnagar
  13. Anant Mohan
  14. Naveet Wig
  15. Lalit Dar

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Abstract

Background: despite being in the 5th month of pandemic, knowledge with respect to viral dynamics, infectivity and RT-PCR positivity continues to evolve.

Aim: to analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients.

Design: it was a retrospective, observational study conducted at COVID facilities under AIIMS, New Delhi.

Methods: patients admitted with laboratory confirmed COVID-19 were eligible for enrolment. Patients with incomplete details, or only single PCR tests were excluded. Data regarding demographic details, comorbidities, treatment received and results of SARS-CoV-2 RT-PCR performed on nasopharyngeal and oropharyngeal swabs, collected at different time points, was retrieved from the hospital records.

Results: a total of 298 patients were included, majority were males (75·8%) with mean age of 39·07 years (0·6–88 years). The mean duration from symptom onset to first positive RT-PCR was 4·7 days (SD 3·67), while that of symptom onset to last positive test was 17·83 days (SD 6·22). Proportions of positive RT-PCR tests were 100%, 49%, 24%, 8·7% and 20·6% in the 1st, 2nd, 3rd, 4th and >4 weeks of illness. A total of 12 symptomatic patients had prolonged positive test results even after 3 weeks of symptom onset. Age > = 60 years was associated with prolonged RT-PCR positivity (statistically significant).

Conclusion: this study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up.

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  1. Version published to 10.1093/femspd/ftaa064
  2. ScreenIT

    SciScore for 10.1101/2020.06.19.20135905: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis: The statistical software STATA v15.1 (STATA corp, LLC, TX, USA) was used for all statistical analysis.
    STATA
    suggested: (Stata, RRID:SCR_012763)

    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:
    Similar findings have also been noted by Xiao et al. in two published studies where they have highlighted the issue of prolonged viral nucleic acid detection.(9,10) Compared to viral isolation, RT-PCR tests have some intrinsic limitations. Firstly, COVID-19 infection cannot be ruled out based on negative RT-PCR results, particularly when highly suspected. False negative results can occur as a result of inadequate specimen or faulty sample collection technique, timing of sample collection, sample storage and processing and viral mutation.(2) Further, detection of nucleic acid doesn’t imply presence of viable virus and therefore PCR positivity doesn’t necessarily relate to infectivity. A recent study by Scola et al. evaluated the correlation between Ct values of RT-PCR and viral isolation in cell culture where they found that patients with positive RT-PCR and Ct values more than 33-34 were not contagious.(11) Further studies on viability of the SARS-CoV-2 virus in respiratory samples are needed to draw a firm conclusion. Association of age, sex, comorbidities, and symptomatology with duration of PCR positivity from 1st PCR or symptom onset was studied and analyzed. There was no statistically significant difference with respect to gender, presence of comorbidities (diabetes and hypertension). However, patients aged 60 years or more had a significantly prolonged duration of RT-PCR positivity since the onset of symptoms as compared to the younger age group. Xu et al. studied the p...

    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

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  3. Version published to 10.1101/2020.06.19.20135905v1 on medRxiv