Comparison of mechanical homogenization versus enzymatic digestion sample preparation methodologies for SARS-CoV-2 detection in saliva for surveillance of variants of concern on the University of Tennessee campus in early 2021

The SARS-CoV-2 pandemic has profoundly impacted communities across the globe, requiring accurate and accessible diagnostic technologies in support of public health mitigation efforts. As testing has evolved throughout the course of the pandemic, varying sample preparation methodologies have been employed. Herein we perform a comparison of three commercial sample preparation methods: two mechanical homogenization workflows and one enzymatic digestion approach for the detection of SARS-CoV-2 from biomarker genes in 20 human saliva pools. SARS-CoV-2 variants of concern were also identified on the University of Tennessee, Knoxville campus during the spring semester of 2021 utilizing the commercial PerkinElmer PKamp VariantDetect SARS-CoV-2 RT-PCR Assay kit. Two hundred and ten (210) human saliva pools were selected and analyzed for the presence of SARS-CoV-2 variants of concern providing insight into the utility of these various commercial workflows for integration into current public health SARS-CoV-2 surveillance measures. ### Competing Interest Statement Authors Caleb M Proctor, Gabriella L Ryan, and Rodney J Nash are all employed by Omni International Inc, A PerkinElmer Company, which provided some funding and reagents for this work. Author Zachary P Morehouse has a contractor association with Omni International Inc, A PerkinElmer Company. Authors Caleb M Proctor, Zachary P Morehouse, and Rodney J Nash are all named inventors on the patented Omni dPCR method described in this paper, however, they have no financial ownership of the method and do not have any financial incentives for its success or failure. The above authors attest that their relationship with Omni International Inc, A PerkinElmer company has not influenced their work on this project, nor are they receiving any incentive for the publication of this work. Authors Magen R Poindexter, Tingting Xu, Cynthia M Swift, Fadime Kara-Murdoch, and Frank E Löffler have no conflicts of interests to report. ### Funding Statement The authors received no specific funding for this work. All funding for this project was provided from internal funding sources. The University of Tennessee Office of Research and Engagement provided internal funding to support the on campus research efforts while Omni International Inc, A PerkinElmer Company provided resources and internal funding to provide equipment and testing supplies to support this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Not Applicable The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The samples utilized in this study were obtained from the University of Tennessee, Knoxville campus in the Spring 2021 semester. All participants were consented via written and oral consent prior to providing saliva samples. Saliva samples provided for the research in this study were deidentified prior to being handed over to the lab for further use. All research was approved under protocol IBC-20-547-2 approved on July 6 2020 by the UTK institutional review board. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Not Applicable I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Not Applicable I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Not Applicable All data pertaining to this study is presented and available in the manuscript without alterations or restrictions.