Genomic Surveillance of SARS-CoV-2 in a University Community: Insights Into Tracking Variants, Transmission, and Spread of Gamma (P.1) Variant

  1. Ilinca I Ciubotariu
  2. Jack Dorman
  3. Nicole M Perry
  4. Lev Gorenstein
  5. Jobin J Kattoor
  6. Abebe A Fola
  7. Amy Zine
  8. G Kenitra Hendrix
  9. Rebecca P Wilkes
  10. Andrew Kitchen
  11. Giovanna Carpi

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Abstract

Background

Using a combination of data from routine surveillance, genomic sequencing, and phylogeographic analysis, we tracked the spread and introduction events of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants focusing on a large university community.

Methods

Here, we sequenced and analyzed 677 high-quality SARS-CoV-2 genomes from positive RNA samples collected from Purdue University students, faculty, and staff who tested positive for the virus between January 2021 and May 2021, comprising an average of 32% of weekly cases across the time frame.

Results

Our analysis of circulating SARS-CoV-2 variants over time revealed periods when variants of concern (VOC) Alpha (B.1.1.7) and Iota (B.1.526) reached rapid dominance and documented that VOC Gamma (P.1) was increasing in frequency as campus surveillance was ending. Phylodynamic analysis of Gamma genomes from campus alongside a subsampling of >20 000 previously published P.1 genomes revealed 10 independent introductions of this variant into the Purdue community, predominantly from elsewhere in the United States, with introductions from within the state of Indiana and from Illinois, and possibly Washington and New York, suggesting a degree of domestic spread.

Conclusions

We conclude that a robust and sustained active and passive surveillance program coupled with genomic sequencing during a pandemic offers important insights into the dynamics of pathogen arrival and spread in a campus community and can help guide mitigation measures.

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  1. Version published to 10.1093/ofid/ofac268
  2. ScreenIT

    SciScore for 10.1101/2022.02.25.22271521: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Ethics Statement: The Institutional Review Board from the Purdue University Human Research Protection Program determined that viral genome sequencing of de-identified remnant COVID-19 samples included in this study is not research involving human subjects (IRB-2021-438).
    Human Research Protection Program
    suggested: None
    Collected samples were submitted to the Animal Disease Diagnostic Lab (ADDL) at Purdue University for testing, which performed nucleic acid RT-PCR using the Thermo Fisher TaqPath COVID-19 Combo Kit (Applied Biosystems™, Thermo Fisher Scientific) on a 7500 Fast Real-Time PCR System (Applied Biosystems™, Thermo Fisher Scientific).
    Thermo Fisher TaqPath
    suggested: None
    Bioinformatics processing: High accuracy basecalling were performed with Guppy basecaller version 3.1.5 on MinIT for the sequencing data generated on the MinION, and with Guppy version 4.2.4 for sequencing runs performed on the GridION5X.
    MinION
    suggested: (MinION, RRID:SCR_017985)
    1 sequences using MAFFT with genomic data combined into a single multi FASTA file using custom scripts [35, 36].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Trees were visualized in FigTree v1.4.4 (https://github.com/rambaut/figtree/releases).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    These were complemented by subsequent Bayesian phylogenetic analyses performed in BEAST with a discrete phylogeographic model and Bayesian stochastic search variable selection to determine migration rates between Purdue and other geographic areas represented in our final sample of closely related P.1 genomes.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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:
    This study had some limitations, including the fact that we used two sampling schemes, as one goal was to ensure we were tracking active cases of SGTF for proper case and contact isolation, and the second was to sequence more cases to gain a better understanding of transmission. Moreover, it was not possible to compare our results to other sequencing data within the county or neighboring counties as no data were available on GISAID. Due to inadequacies of SARS-CoV-2 genomic surveillance in many places across the US, our estimates of introductions of Gamma variant to the campus may be biased toward states that had higher sequencing effort and enhanced genomic surveillance. Indeed, there is substantial variation by U.S. state in the number of genomes deposited in the GISAID database (total n=714,368 through June 2021 with assigned U.S. state origin) (Supplementary Table 2). Through June 2021, the median number of total genome sequences deposited for U.S. states was 6910.5, with a mean of 14,287 and with a range of 732 (South Dakota) to 102988 (California). The collection of GISAID P.1 /Gamma genomes available as of July 2021 was also skewed by U.S. state, with a median of 60 P.1 sequences, (range of 3 (South Dakota) to 2035 (Illinois)). However, the correlation between the total number of SARS-CoV-2 sequences with state of origins data through June 2021 in GISAID and state population sizes (U.S. Census Bureau, https://data.census.gov) is substantial (Pearson’s r = 0.91); this m...

    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 10.1101/2022.02.25.22271521 on medRxiv