Genomic monitoring unveils a high prevalence of SARS-CoV-2 Omicron variant in vaccine breakthrough cases

  1. Gúbio Soares Campos
  2. Marta Giovanetti
  3. Laise de Moraes
  4. Helena Souza da Hora
  5. Keila Oliveira Motta de Alcantara
  6. Silvia Ines Sardi

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Abstract

Genome sequencing proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by SARS-CoV-2, i.e., coronavirus disease (COVID-19). Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern (VOCs). To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different VOCs in these cases. Nasopharyngeal swabs from infected (symptomatic and asymptomatic), fully vaccinated individuals (n=29) who were of varying age and had RT-qPCR Ct values of ≤30 were subjected to viral sequencing using Nanopore technology. Our analysis revealed that the Omicron variant was found in 99% of cases and that only one case was due to the Delta variant. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of VOCs not neutralized by the vaccines.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.16.22271059: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethics statement: This research was reviewed and approved by the Ethical Committee of the Federal University of Bahia (CAAE 30687320.9.0000.5662), and informed consent of all participating subjects or their legal guardians have been obtained.
    Consent: Ethics statement: This research was reviewed and approved by the Ethical Committee of the Federal University of Bahia (CAAE 30687320.9.0000.5662), and informed consent of all participating subjects or their legal guardians have been obtained.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The consensus sequences were then masked with “N” at regions with coverage depth <20, and the variant candidates were incorporated into the consensus genome using BCFtools v.1.10.212.
    BCFtools
    suggested: (SAMtools/BCFtools, RRID:SCR_005227)
    The alignment statistics were calculated with SAMtools v.
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    One limitation of our work is not knowing the level of protective immunity of those who are currently vaccinated; however, even with three doses, there have been cases of viral infection. Dose reinforcements in countries such as England and Israel with a four-dose regimen raise doubts as to whether they will solve the situation of viral recrudescence for new VOCs in circulation22,23. It is important to acknowledge the limitations of these vaccines and to urgently develop new vaccines to emergent VOCs, as is the case of the vaccine for Influenza; going through new doses of the same vaccines is “more of the same”. Measures to control the use of face masks, social distancing, and crowd avoidance continue to be effective, but these need to be combined with new immunogens that prevent viral infection (an elementary concept for the approval of vaccines for widespread use).

    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

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  2. Version published to 10.1101/2022.02.16.22271059 on medRxiv