Implementation of a Rural Community Diagnostic Testing Strategy for SARS-CoV-2 in Upstate South Carolina

Abstract

By developing a partnership amongst a public university lab, local city government officials and community healthcare providers, we established a drive-through COVID-19 testing site aiming to improve access to SARS-CoV-2 testing in rural Upstate South Carolina. We collected information on symptoms and known exposures of individuals seeking testing to determine the number of pre- or asymptomatic individuals. We completed 71,102 SARS-CoV-2 tests in the community between December 2020-December 2021 and reported 91.49% of results within 24 h. We successfully identified 5,244 positive tests; 73.36% of these tests originated from individuals who did not report symptoms. Finally, we identified high transmission levels during two major surges and compared test positivity rates of the local and regional communities. Importantly, the local community had significantly lower test positivity rates than the regional community throughout 2021 (p < 0.001). While both communities reached peak case load and test positivity near the same time, the local community returned to moderate transmission as indicated by positivity 4 weeks before the regional community. Our university lab facilitated easy testing with fast turnaround times, which encouraged voluntary testing and helped identify a large number of non-symptomatic cases. Finding the balance of simplicity, accessibility, and community trust was vital to the success of our widespread community testing program for SARS-CoV-2.

SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva

“…To evaluate the relative viral load of the variants of concern (VOC) found in upstate South Carolina (Alpha, Gamma, and Delta), we compared the Ct values from saliva samples from the SARS-CoV-2 testing lab at Clemson University, which also provides free testing for the surrounding community [ 21 , 22 ]. University surveillance testing is mandatory for students and employees on a weekly or bi-weekly schedule regardless of vaccination status [ 23 ].…”

Predicting COVID-19 Infected Individuals in a Defined Population from Wastewater RNA Data

“…The TigerSaliva multiplex RT-qPCR test targets the N gene of SARS-CoV2 for diagnosis; it is a version of the EUA-approved SalivaDirect protocol . Details of the methods are available elsewhere. − Briefly, saliva is heat treated to 95 °C for 30 min. Then, 2 μL of sample are loaded using open-source sample handlers (Opentrons OT-2) into prepared plates with enzyme mix (New England Biolabs M3006B, M3002B), primers, and probes.…”

Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites

“…To address these limitations, our lab implemented a simple VOC screening method following our established saliva-based SARS-CoV-2 testing procedure ( 35 ). We perform weekly surveillance testing of the entire population at Clemson University ( 25 ) and provide free testing to the surrounding community ( 24 ), which allows for real-time monitoring of current and future VOCs.…”

“…We performed all six assays in duplicate on sequenced saliva samples ( n = 125) that had greater than 95% non-N genome coverage to validate assay parameters. Saliva samples from the university SARS-CoV-2 surveillance program ( 24 , 25 ) were heat-treated to extract viral RNA and confirmed to be SARS-CoV-2 positive via RT-qPCR ( 35 ). Due to extended storage time at −80°C for some positive samples, sample validity was determined using N1 Ct values to account for possible degradation.…”

“…Saliva samples provide many benefits, such as room temperature storage ( 21 ), simple self-collection of samples ( 22 ), and heat-based RNA extraction ( 23 ). Furthermore, these advantages have led to its use for many community surveillance programs aimed at testing non-hospitalized patients ( 24 – 28 ). Thus, saliva-based testing warrants examination as a SARS-CoV-2 VOC detection strategy.…”