Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities

Abstract

Background: The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community.

Methods: We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis.

Findings: From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems.

Interpretation: By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty.

Funding: Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.

Keywords: Asymptomatic infections; K-12 schools; Pooled surveillance testing; SARS-CoV-2.

Fig. 1

Flow diagram of the process from specimen collection to testing and result analysis.

Fig. 2

A graph of a quantitative RT-PCR amplification from a positive pooled sample (24 samples) with a Ct value of 37.02, 36.37 and 36.04 for the N gene, ORF1ab and S gene targets, respectively. Each line indicates the amplification curve for one replicate.

Fig. 3

Ct value comparisons between pooled and individual samples. Twenty randomly selected positive samples were analyzed and Ct values compared between a pool of 24 samples and a single sample. The dashed lines connect the dots that indicate the Ct values of individual samples (higher) to the corresponding pools (lower).

Fig. 4

Trend of saliva-based pooled testing positivity in 109 K-12 schools and universities for a five-month period. Peaks of positive cases (individual samples) were observed in dates following October 31, 2020 (Halloween) and December 31st, 2020 (New Year's Eve). The green bar lines indicate the number of positive individual samples, and the red curve is an estimation of the trend. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 5

A graph of the aggregated positivity rate and aggregated number of tests done between the 3 schools we have tested most frequently in New York County, New York. The bar lines indicate the total number of tests done, and the red line indicates the percentage of positive test results from the total tests performed on a given date. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 6

A graph of the aggregated positivity rate and aggregated number of tests performed between the 3 schools we have tested most frequently in Atlanta, Georgia. The bar lines indicate the number of total tests done, and the red line indicates the percentage of positive test results obtained. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)