Genomic and Virological Characterization of SARS-CoV-2 Variants in a Subset of Unvaccinated and Vaccinated U.S. Military Personnel

  1. Darci R. Smith
  2. Christopher Singh
  3. Jennetta Green
  4. Matthew R. Lueder
  5. Catherine E. Arnold
  6. Logan J. Voegtly
  7. Kyle A. Long
  8. Gregory K. Rice
  9. Andrea E. Luquette
  10. Haven L. Miner
  11. Lindsay Glang
  12. Andrew J. Bennett
  13. Robin H. Miller
  14. Francisco Malagon
  15. Regina Z. Cer
  16. Kimberly A. Bishop-Lilly

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Abstract

The emergence of SARS-CoV-2 variants complicates efforts to control the COVID-19 pandemic. Increasing genomic surveillance of SARS-CoV-2 is imperative for early detection of emerging variants, to trace the movement of variants, and to monitor effectiveness of countermeasures. Additionally, determining the amount of viable virus present in clinical samples is helpful to better understand the impact these variants have on viral shedding. In this study, we analyzed nasal swab samples collected between March 2020 and early November 2021 from a cohort of United States (U.S.) military personnel and healthcare system beneficiaries stationed worldwide as a part of the Defense Health Agency's (DHA) Global Emerging Infections Surveillance (GEIS) program. SARS-CoV-2 quantitative real time reverse-transcription PCR (qRT-PCR) positive samples were characterized by next-generation sequencing and a subset was analyzed for isolation and quantification of viable virus. Not surprisingly, we found that the Delta variant is the predominant strain circulating among U.S. military personnel beginning in July 2021 and primarily represents cases of vaccine breakthrough infections (VBIs). Among VBIs, we found a 50-fold increase in viable virus in nasal swab samples from Delta variant cases when compared to cases involving other variants. Notably, we found a 40-fold increase in viable virus in nasal swab samples from VBIs involving Delta as compared to unvaccinated personnel infected with other variants prior to the availability of approved vaccines. This study provides important insight about the genomic and virological characterization of SARS-CoV-2 isolates from a unique study population with a global presence.

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  1. Version published to 10.3389/fmed.2021.836658
  2. ScreenIT

    SciScore for 10.1101/2021.12.16.21267862: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    6) Virus culture: Patient samples were cultured for SARS-CoV-2 using a standard plaque assay on Vero E6 cells expressing TMPRSS2 [4] in six-well plates and a cytopathic effect (CPE) assay on Vero E6/TMPRSS2 cells in T25 cm2 flasks.
    Vero E6
    suggested: None
    Vero E6/TMPRSS2
    suggested: None
    Software and Algorithms
    SentencesResources
    Once a high quality consensus genome was obtained, Single Nucleotide Variants (SNVs) were determined using SAMtools mpileup (20) and iVar (Intrahost variant analysis of replicates) (21) using a minimum frequency of 0.3 and a minimum read depth of 10 (22).(23-25) Lineage information was derived using Pangolin (
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Statistical analysis: Statistical analysis was performed using GraphPad Prism.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    Their results indicate that determining viral load by RNA levels in clinical samples may have limitations and assays for viable virus should be included for emerging variants. Additionally, they detected six times as much infectious virus for the same amount of RNA for Delta variant samples compared to Alpha variant samples. Our results are similar where we found that the Delta variant cases shed viable virus at higher levels. Similar levels of virus were detected from unvaccinated personnel with non-Delta infections prior to the availability of vaccines granted EUA and FDA approval compared to VBI due to other variants besides Delta. In contrast, 50-fold more infectious virus was detected in samples from VBI due to Delta compared to VBIs with other variants. When we analyzed our results by vaccine manufacturer, we continued to detect significantly higher levels of infectious virus in samples from individuals who received the Pfizer and Johnson & Johnson vaccines and experienced a VBI due to Delta when compared to the unvaccinated personnel with non-Delta infections. Interestingly, VBI associated with the Delta variant that received the Moderna vaccine was not statistically significant when compared to the unvaccinated group. This may be a reflection of the limited number of samples in our analyses. Another limitation of our study is the lack of access to metadata for the clinical specimens, which affects our interpretation of the results by differences in age, pre-existing c...

    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 10.1101/2021.12.16.21267862 on medRxiv