Detection of SARS-CoV-2 in saliva using tailed amplicon sequencing

  1. Aaron Garoutte
  2. Tasha M. Santiago-Rodriguez
  3. Heather L. Fehling
  4. Rafal Iwasiow

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Abstract

The most recent virus from the Coronaviridae family infecting humans, SARS-CoV-2, has resulted in a global pandemic. As part of the surveillance efforts, SARS-CoV-2 genomes are increasingly being made publicly available. Methods that include both short- and long-read sequencing have been used to elucidate SARS-CoV-2 genomes; however, many of these untargeted approaches may require deeper sequencing for greater genome coverage. For this reason, sequence capture or amplicon-based approaches for SARS-CoV-2 genome sequencing have been developed. The present study evaluated a modified sequence capture approach, namely, tailed amplicon sequencing, to determine SARS-CoV-2 near complete genome sequences from the saliva of infected individuals. Particularly, the suitability of saliva samples stored at room temperature using OMNIgene ® •ORAL OME-505 was evaluated. The tailed amplicon sequencing approach poses the additional advantage of being a cost-effective method for library preparation. Different known SARS-CoV-2 variants were identified across the infected subjects, with an average of > 99.4% genome coverage. This methodology also enabled robust genomic surveillance using phylogenetic analyses. The present study supports the suitability of saliva stored at room temperature using collection devices for SARS-CoV-2 variant detection. Importantly, the present study supports the use of tailed amplicon sequencing approaches as an alternative, cost-effective method for SARS-CoV-2 detection in saliva for genomic surveillance.

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  1. ScreenIT

    SciScore for 10.1101/2021.05.19.21257217: (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.
    RandomizationAt a later point, one to fifteen days post diagnosis, eight randomly selected samples from a pool of samples which had previously tested positive for SARS-CoV-2 by the CRL Rapid Response™ COVID-19 Test were selected to be sequenced.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    After sequencing, the paired ends were joined using PANDAseq (Masella et al.,
    PANDAseq
    suggested: (PANDAseq, RRID:SCR_002705)
    Unaligned reads were aligned to Wuhan-Hu-1 SARS-CoV-2 genome (MN908947.3) using BWA (Li and Durbin, 2010; Wu et al., 2020).
    BWA
    suggested: (BWA, RRID:SCR_010910)

    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: 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

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  2. Version published to 10.1101/2021.05.19.21257217v1 on medRxiv