The Epidemiology of Hundreds of Individuals Infected with Omicron BA.1 in Middle-Eastern Jordan

  1. Rima Hajjo
  2. Mahmoud M. AbuAlSamen
  3. Hamed M. Alzoubi
  4. Raeda Alqutob

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Abstract

In less than two months of its detection in Jordan, lineage B.1.1.529 recognized as Omicron, is constituting 55% of all confirmed coronavirus disease of 2019 (COVID-19) infections causing a rise in the daily cases in the country. Herein, we report on 500 cases, among the first identified Omicron infections in Jordan. We also report on the genomic diversity of 25 Omicron viruses identified in nasopharyngeal swabs from Jordan. Our results indicated that 96% of study participants were vaccinated who had asymptomatic, mild or moderate disease. One unvaccinated individual developed severe disease. The median age of Omicron cases was 30 years, and most frequent disease symptoms were: fever, coughing, sore throat, runny nose, general fatigue and muscle/joint pain. Viral genomic analysis results revealed that the BA.1 is the dominant Omicron sublineage in Jordan, with 45 to 58 total mutations. We identified a few amino acid modifications that could impact the accuracy of some polymerase chain reaction (PCR) tests. In summary, infections caused by BA.1 seem milder than earlier infections. However, it is unknown whether this change is due to alterations in the immunity landscape of the infected population or is the result of viral genetic mutations that reduced viral virulence. Hence, comparing similar studies from different countries is likely to give us a get a better understanding of this variant, its behavior and the impact on disease characteristics.

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  1. Version published to 10.1101/2022.01.23.22269442v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2022.01.23.22269442: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: This study was approved by Al-Zaytoonah University Ethics Committee (IRB number: 29/11/2021-2022) and was conducted in accordance with the Declaration of Helsinki. 2.2. Sequencing Data: Sequencing specimens were collected using original nasopharyngeal swabs.
    IRB: This study was approved by Al-Zaytoonah University Ethics Committee (IRB number: 29/11/2021-2022) and was conducted in accordance with the Declaration of Helsinki. 2.2. Sequencing Data: Sequencing specimens were collected using original nasopharyngeal swabs.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All statistics and analysis of proportions were performed in Microsoft® Excel for Mac version 16.57.
    Microsoft® Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    Additional sequencing details are available on GISAID and GitHub: (https://github.com/rhajjo/JCDC_OmicronData). 2.3. Clade and Lineage Assignment: Nextclade in Bioconda version 1.9.0.0(6) has been used to identify mutations in comparison with SARS-CoV-2 reference sequence (WIV04/MN996528.1).
    Bioconda
    suggested: (BioConda, RRID:SCR_018316)

    Results from OddPub: Thank you for sharing your code and data.

    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.

    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.

  3. Version published to 10.1101/2022.01.23.22269442v1 on medRxiv