Surveillance genome sequencing reveals multiple SARS‐CoV‐2 variants circulating in central Texas, USA, with a predominance of delta variant and review of vaccine breakthrough cases

  1. Manohar B. Mutnal
  2. Shelby Johnson
  3. Nada Mohamed
  4. Rasha Abddelgader
  5. Linden Morales
  6. Marcus Volz
  7. Kimberly Walker
  8. Alejandro C. Arroliga
  9. Arundhati Rao

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Abstract

As surges in the COVID‐19 pandemic have continued worldwide, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has mutated, spawning several new variants, and impacting, to various degrees, transmission, disease severity, diagnostics, therapeutics, and natural and vaccine‐induced immunity. Baylor Scott & White Health has implemented, along with laboratory diagnosis, SARS‐CoV‐2 sequencing to identify variants in its geographical service area. We analyzed virus sequencing results of specimens collected across Central Texas and found dramatic changes in variant distribution in the first half of 2021. The alpha variant (B 1.1.7) became predominant at week 13 and continued dominance until week 25. A growth rate of 1.20 ( R 2  = 0.92) for the first 15 weeks was noted and this growth gradually declined to −0.55 ( R 2  = 0.99) for the final 13 weeks. Currently, B.1.1.7 is being displaced with B.1.617.2 at a 0.58 growth rate ( R 2  = 0.97). We also investigated vaccine breakthrough cases (VBCs) within our healthcare system and present clinical data on 28 symptomatic patients.

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  1. Version published to 10.1002/jmv.27373
  2. ScreenIT

    SciScore for 10.1101/2021.08.06.21261727: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: This study was reviewed and approved by the Baylor Scott and White Research Institute Institutional Review board (IRB # 021-144) with a waiver of the requirement of informed consent for the use of residual specimens for sequencing and epidemiological studies.
    Consent: This study was reviewed and approved by the Baylor Scott and White Research Institute Institutional Review board (IRB # 021-144) with a waiver of the requirement of informed consent for the use of residual specimens for sequencing and epidemiological studies.
    Sex as a biological variablenot detected.
    RandomizationWe randomly selected 1% of the positive specimens for sequencing when positivity rates were higher than 5% and all positive specimens when positivity rates were <5%, to identify the variants in circulation.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Data was analyzed using the Illumina BaseSpace application/bioinformatics pipeline, DRAGEN COVID Lineage v3.5.1.
    BaseSpace
    suggested: (BaseSpace, RRID:SCR_011881)

    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:
    A second limitation that must be kept in mind when interpreting the results reported here is that, while clinical manifestation data for the 28 vaccine breakthrough cases for which sequencing was possible are presented by vaccine brand they cannot support comparisons of effectiveness between the brands, as there was unequal distribution of vaccine brands in the Central Texas community. In conclusion, our results show that, in early 2021, Central Texas experienced a rapid growth of the alpha (B.1.1.7) variant, which then maintained dominance for several weeks, but towards the end of the study period (June/July 2021) was itself rapidly displaced by the delta (B.617.2) variant. Examination of vaccine breakthrough infections showed small numbers overall and with each of these variants, with the distribution of the variants among breakthrough cases following a similar pattern to the distribution in the overall COVID-19 cases in our study population. Continued monitoring is needed, both to assess the longer-term impact of the delta (B.1.617.2) variant’s dominance on risk for vaccine breakthrough infections, and to identify any new variants, or variants altering the distribution in circulating strains, that might impact risks for disease and/or effectiveness of vaccines and therapeutics. Lastly, the findings in this report are subject to at least two limitations. First, the number of reported COVID-19 vaccine breakthrough cases is likely a substantial undercount of all SARS-CoV-2 in...

    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.

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  3. Version published to 10.1101/2021.08.06.21261727v1 on medRxiv