Clinical, Virological, Immunological, and Genomic Characterization of Asymptomatic and Symptomatic Cases With SARS-CoV-2 Infection in India

  1. Sanchari Chatterjee
  2. Ankita Datey
  3. Soumya Sengupta
  4. Arup Ghosh
  5. Atimukta Jha
  6. Safal Walia
  7. Sharad Singh
  8. Sandhya Suranjika
  9. Gargee Bhattacharya
  10. Eshna Laha
  11. Supriya Suman Keshry
  12. Amrita Ray
  13. Sweta Smita Pani
  14. Amol Ratnakar Suryawanshi
  15. Rupesh Dash
  16. Shantibhusan Senapati
  17. Tushar K. Beuria
  18. Gulam Hussain Syed
  19. Punit Prasad
  20. Sunil Kumar Raghav
  21. Satish Devadas
  22. Rajeeb K. Swain
  23. Soma Chattopadhyay
  24. Ajay Parida

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Abstract

The current global pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to the investigation with clinical, biochemical, immunological, and genomic characterization from patients to understand the pathophysiology of viral infection.

Methods

Samples were collected from six asymptomatic and six symptomatic SARS-CoV-2-confirmed hospitalized patients in Bhubaneswar, Odisha, India. Clinical details, biochemical parameters, and treatment regimen were collected from a hospital; viral load was determined by RT-PCR; and the levels of cytokines and circulating antibodies in plasma were assessed by Bio-Plex and isotyping, respectively. In addition, whole-genome sequencing of viral strains and mutational analysis were carried out.

Results

Analysis of the biochemical parameters highlighted the increased levels of C-reactive protein (CRP), lactate dehydrogenase (LDH), serum SGPT, serum SGOT, and ferritin in symptomatic patients. Symptomatic patients were mostly with one or more comorbidities, especially type 2 diabetes (66.6%). The virological estimation revealed that there was no significant difference in viral load of oropharyngeal (OP) samples between the two groups. On the other hand, viral load was higher in plasma and serum samples of symptomatic patients, and they develop sufficient amounts of antibodies (IgG, IgM, and IgA). The levels of seven cytokines (IL-6, IL-1α, IP-10, IL-8, IL-10, IFN-α2, IL-15) were found to be highly elevated in symptomatic patients, while three cytokines (soluble CD40L, GRO, and MDC) were remarkably higher in asymptomatic patients. The whole-genome sequence analysis revealed that the current isolates were clustered with 19B, 20A, and 20B clades; however, 11 additional changes in Orf1ab, spike, Orf3a, Orf8, and nucleocapsid proteins were acquired. The D614G mutation in spike protein is linked with higher virus replication efficiency and severe SARS-CoV-2 infection as three patients had higher viral load, and among them, two patients with this mutation passed away.

Conclusions

This is the first comprehensive study of SARS-CoV-2 patients from India. This will contribute to a better understanding of the pathophysiology of SARS-CoV-2 infection and thereby advance the implementation of effective disease control strategies.

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  1. Version published to 10.3389/fcimb.2021.725035
  2. ScreenIT

    SciScore for 10.1101/2021.05.21.21257211: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The designed study was approved by Institutional ethics committee and the signed consent forms were taken from the concerned patients.
    Consent: The designed study was approved by Institutional ethics committee and the signed consent forms were taken from the concerned patients.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    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:
    Previous reports have shown significant difference in the expression levels of MCP-3, IL-1β, IL-17A, IL-12 p70, eotaxin and TNF, while in current study there was no significant difference observed as small sample size was a limitation(18). Symptomatic patients showed higher levels of IgE, IgG2, IgG3 and IgG1 serotypes, as compared to asymptomatic patients. IgE has already been reported to be high in COVID-19 patients particularly those with Type II Diabetes. Out of 6 symptomatic patients in this study, 4 were suffering from type II Diabetes and had enhanced IgE levels (22,27). Overall increase in IgG1, IgG2 and IgG3 responses in symptomatic patients explains the increase in inflammatory immune responses(22). Since IgE was high in these patients there was no significant difference in IgG4 level as they compete for fixation sites in basophils and mast cells (28). There was no difference in IgM and IgA levels of the two groups suggesting that patients were at early stage of infection, as peak of virus specific IgM is developed approximately 14–28 days after the onset of symptoms (29). The whole genome sequencing and phylogenetic analysis revealed that the current isolates were clustered in 19B, 20A and 20B clades, however there were several additional unique mutations in different genes as compared to the Wuhan strain. Surprisingly, most of the changes were observed in Orf1ab region. In India, these three clades were predominant in the months from May to July, 2020 (30). It was ...

    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.

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

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  3. Version published to 10.1101/2021.05.21.21257211v1 on medRxiv