Two-Stage Hierarchical Group Testing Strategy to Increase SARS-CoV-2 Testing Capacity at an Institution of Higher Education

Abstract

Population testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is necessary owing to the potential for viral transmission from asymptomatic cases, yet scarcity of reagents and equipment has increased the cost-prohibitive implementation of screening campaigns at institutions of higher education. Significant analytical sensitivities of nucleic acid amplification methods permit sample pooling to increase testing capacity. Statistical models compared optimal testing configuration for pools of 3, 5, and 10 samples. Assessment of pooling using the TaqPath COVID-19 Combo Kit multiplex assay ( ORF1ab , N , and S gene targets) involved a limit of detection (LOD) study, matrix effect study, and clinical comparison of neat to pooled sample. An LOD of 135.02 ( ORF1ab ; CI.95: 117.21-155.52), 373.92 ( N ; CI.95: 257.05-437.64), and 1001.32 ( S ; CI.95: 896.62-1118.33) gce per milliliter was resolved. Seventy-two randomly selected samples demonstrated slight suppression due to negative sample matrix. Resulting mean cycle threshold (CT) shifts were 2.09 ( ORF1ab ), 1.76 ( N ), and 2.31 ( S ) for the 3-pool, 2.83 ( ORF1ab ), 2.45 ( N ), and 3.24 ( S ) for the 5-pool, and 3.99 ( ORF1ab ), 3.46 ( N ), and 4.07 ( S ) for the 10-pool. Despite quantitative sensitivity loss trend, the qualitative result was unaffected in each pool. According to the range of disease prevalence observed at the testing site (0.03-7.32%), a pool of five samples was deemed an optimal and cost-effective option for monitoring the Northeastern University community.

Epidemiological Interactions of Influenza and SARS-CoV-2 within a University Population During Omicron B.1.1.529 Outbreak

“…1B-C). With news of the rapidly spreading Omicron (B.1.1.529) variant, samples reactive for SARS-CoV-2 were crossed referenced on the TaqPath™ COVID-19 Combo Kit, whose RT-qPCR targets permit proxy identification via S-gene target failure (SGTF) [3]. Retrospective analysis indicated a demonstrable suppression of influenza cases with the surge in Omicron B.1.1.529 (Fig.…”

“…Our lab, the Life Sciences Testing Center (Burlington, MA), has performed SARS-CoV-2 molecular diagnostics for the Northeastern University population since August 2020 using the TaqPath™ COVID-19 Combo kit (Thermo Fisher Scientific, CAT#: A47814). As previously reported, collection of anterior nare swabs was conducted at facilities designated for either symptomatic or non-symptomatic individuals [3]. Individuals were directed to submit a sample at the symptomatic site based on whether they were experiencing COVID-19-related symptoms or were close contacts of a COVID-19 case.…”

Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations

“…The study was conducted at the Northeastern University COVID-19 response laboratory, the Life Sciences Testing Center (LSTC; Burlington, MA, USA), which performs population testing for university affiliates. Students on campus are required to test every three days while staff and faculty on campus test twice a week [8]. Affiliates attending campus are required to complete an online daily wellness survey that identifies whether they have experienced COVID-19 related symptoms or have been in close contact with a positive COVID-19 case in the past 24 hours.…”

“…Temperature checks and general symptom screening were performed by trained personnel on the subjects at both sites to determine presence or absence of symptoms. Anterior nasal swabs (polyester) are collected in 3-mL BD Vacutainer1 (cat: 366703; without additives, Mississauga, ON, Canada) tubes and transported dry to the LSTC facility [8]. Upon logging into the laboratory information system (Harvest™; Orchard Software Corporation, Carmel, IN), 3 mL of viral transport media (cat: VR2019-1L; Redoxica, Little Rock, AR) is added and the sample is shaken at 1 x g rpm for 5 minutes [8].…”

“…Anterior nasal swabs (polyester) are collected in 3-mL BD Vacutainer1 (cat: 366703; without additives, Mississauga, ON, Canada) tubes and transported dry to the LSTC facility [8]. Upon logging into the laboratory information system (Harvest™; Orchard Software Corporation, Carmel, IN), 3 mL of viral transport media (cat: VR2019-1L; Redoxica, Little Rock, AR) is added and the sample is shaken at 1 x g rpm for 5 minutes [8]. Processed specimens are stable for <72 hours at 2-8˚C.…”