Pooled RT-qPCR testing for SARS-CoV-2 surveillance in schools - a cluster randomised trial

Abstract

Background The extent to which children and adolescents contribute to SARS-CoV-2 transmission remains not fully understood. Novel high-capacity testing methods may provide real-time epidemiological data in educational settings helping to establish a rational approach to prevent and minimize SARS-CoV-2 transmission. We investigated whether pooling of samples for SARS-CoV-2 detection by RT-qPCR is a sensitive and feasible high-capacity diagnostic strategy for surveillance of SARS-CoV-2 infections in schools. Methods In this study, students and school staff of 14 educational facilities in Germany were tested sequentially between November 9 and December 23, 2020, two or three times per week for at least three consecutive weeks. Participants were randomized for evaluation of two different age adjusted swab sampling methods (oropharyngeal swabs or buccal swabs compared to saliva swabs using a ‘lolli method’). Swabs were collected and pooled for SARS-CoV-2 RT-qPCR. Individuals of positive pooled tests were retested by RT-qPCR the same or the following day. Positive individuals were quarantined while the SARS-CoV-2 negative individuals remained in class with continued pooled RT-qPCR surveillance. The study is registered with the German Clinical Trials register (registration number: DRKS00023911). Findings 5,537 individuals were eligible and 3970 participants were enroled and included in the analysis. In students, a total of 21,978 swabs were taken and combined in 2218 pooled RT-qPCR tests. We detected 41 positive pooled tests (1·8%) leading to 36 SARS-CoV-2 cases among students which could be identified by individual re-testing. The cumulative 3-week incidence for primary schools was 564/100,000 (6/1064, additionally 1 infection detected in week 4) and 1249/100,000 (29/2322) for secondary schools. In secondary schools, there was no difference in the number of SARS-CoV-2 positive students identified from pooled oropharyngeal swabs compared to those identified from pooled saliva samples (lolli method) (14 vs. 15 cases; 1·3% vs. 1·3%; OR 1.1; 95%-CI 0·5–2·5). A single secondary school accounted for 17 of 36 cases (47%) indicating a high burden of asymptomatic prevalent SARS-CoV-2 cases in the respective school and community. Interpretation In educational settings, SARS-CoV-2 screening by RT-qPCR-based pooled testing with easily obtainable saliva samples is a feasible method to detect incident cases and observe transmission dynamics. Funding Federal Ministry of education and research (BMBF; Project B-FAST in “NaFoUniMedCovid19”; registration number: 01KX2021).

Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda

“…As a vast majority of people with COVID-19 remain asymptomatic (Dhama et al, 2020), large scale screening using pooled sample strategy may be employed in settings such as schools, the community and other high volume testing settings to rapidly identify cases and limit transmission of SARS-CoV-2 (Joachim et al, 2021).…”

“…Pooled sample testing for SARS-CoV-2 has been shown to be feasible to detect incident cases of COVID-19 and determine transmission dynamics in communities and schools (Joachim et al, 2021). The strategy has been found to be cost effective compared to individual testing (Abdalhamid et al, 2020).…”

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“…Other screening testing methods such as molecular-based pool testing, which involves RT-PCR testing of pooled samples and so-called deconvolution testing of individuals belonging to pools tested positive, are currently under investigation [71][72][73] and may complement mere antigen testing, in particular in low prevalence settings. Additionally, novel tests, for example, lateral flow tests based on clustered regularly interspaced short palindromic repeat (CRISPR), hold great promise for a highly sensitive direct detection of SARS-CoV-2 74 but have yet to gain market access and demonstrate their value.…”

Triple-Probe DNA Framework-Based Transistor for SARS-CoV-2 10-in-1 Pooled Testing

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