Comparative analysis of the outcomes of COVID-19 between patients infected with SARS-CoV-2 Omicron and Delta variants: a retrospective cohort study

  1. Gunadi
  2. Mohamad Saifudin Hakim
  3. Hendra Wibawa
  4. Khanza Adzkia Vujira
  5. Dyah Ayu Puspitarani
  6. Endah Supriyati
  7. Ika Trisnawati
  8. Kristy Iskandar
  9. Riat El Khair
  10. Afiahayati
  11. Siswanto
  12. Yunika Puspadewi
  13. Irene
  14. Sri Handayani Irianingsih
  15. Edwin Widyanto Daniwijaya
  16. Dwi Aris Agung Nugrahaningsih
  17. Gita Christy Gabriela
  18. Esensi Tarian Geometri
  19. Laudria Stella Eryvinka
  20. Fadila Dyah Trie Utami
  21. Edita Mayda Devana
  22. Lanang Aditama
  23. Nathania Christi Putri Kinasih
  24. Verrell Christopher Amadeus
  25. Yekti Hediningsih
  26. Nur Rahmi Ananda
  27. Eggi Arguni
  28. Titik Nuryastuti
  29. Tri Wibawa

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Abstract

Background

The SARS-CoV-2 Omicron variant has replaced the previously dominant Delta variant because of high transmissibility. It is responsible for the current increase in the COVID-19 infectivity rate worldwide. However, studies on the impact of the Omicron variant on the severity of COVID-19 are still limited in developing countries. Here, we compared the outcomes of patients infected with SARS-CoV-2 Omicron and Delta variants and associated with prognostic factors, including age, sex, comorbidities, and smoking.

Methods

We involved 352 patients, 139 with the Omicron variant and 213 with the Delta variant. The whole-genome sequences of SARS-CoV-2 were conducted using the Illumina MiSeq next-generation sequencer.

Results

Ct value and mean age of COVID-19 patients were not significantly different between both groups (Delta: 20.35 ± 4.07 vs . Omicron: 20.62 ± 3.75; p =0.540; and Delta: 36.52 ± 21.24 vs . Omicron: 39.10 ± 21.24; p =0.266, respectively). Patients infected with Omicron and Delta variants showed similar hospitalization ( p =0.433) and mortality rates ( p =0.565). Multivariate analysis showed that older age (≥65 years) had higher risk for hospitalization (OR=3.67 [95% CI=1.22-10.94]; p =0.019) and fatalities (OR=3.93 [95% CI=1.35-11.42]; p =0.012). In addition, patients with cardiovascular disease had higher risk for hospitalization (OR=5.27 [95% CI=1.07-25.97]; p =0.041), whereas patients with diabetes revealed higher risk for fatalities (OR=9.39 [95% CI=3.30-26.72]; p =<0.001).

Conclusions

Our study shows that patients infected with Omicron and Delta variants reveal similar clinical outcomes, including hospitalization and mortality. In addition, our findings further confirm that older age, cardiovascular disease, and diabetes are strong prognostic factors for the outcomes of COVID-19 patients.

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  1. ScreenIT

    SciScore for 10.1101/2022.04.30.22274532: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The Medical and Health Research Ethics Committee of the Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, approved our study (
    Sex as a biological variableSubjects: We used data from 352 patients with COVID-19 from Yogyakarta and Central Java provinces, Indonesia, from May 2021 to February 2022, consisting of 164 males and 188 females.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    dan Pengendalian Penyakit Yogyakarta for whole-genome sequencing using MiSeq Illumina Platform.
    MiSeq
    suggested: (A5-miseq, RRID:SCR_012148)
    We conducted whole-genome sequencing (WGS) of SARS-CoV-2 for all samples with PCR’s Ct value of less than 30.
    WGS
    suggested: None
    The genomes of our samples were assembled and mapped into the reference genome from Wuhan, China (hCoV-19/Wuhan/Hu-1/2019, GenBank accession number: NC_045512.2) using Burrow-Wheeler Aligner (BWA) algorithm embedded in UGENE v.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Firstly, a multiple nucleotide sequence alignment was performed using the MAFFT program version 7 (https://mafft.cbrc.jp/alignment/server/).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    0 (MEGA X) [25] for phylogenetic reconstruction, and followed by tree visualization in FigTree (http://tree.bio.ed.ac.uk/software/FigTree/) to using a Newick tree output from MEGA X.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    We conducted all statistical analyses by the IBM Statistical Package for the Social Sciences (SPSS) version 23 (Chicago, USA).
    Statistical Package for the Social Sciences
    suggested: (SPSS, RRID:SCR_002865)
    SPSS
    suggested: (SPSS, RRID:SCR_002865)

    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:
    Several limitations are noted in our study including design of retrospective study, incomplete data on vaccination and previous infection of COVID-19, data were based on hospital admission, but no data from ICU admission unit and the use of mechanical ventilation, no follow-up data for patients after discharge from hospital, and incomparable sample size between Delta and Omicron variants.

    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.

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

    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 10.1101/2022.04.30.22274532v1 on medRxiv