Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests

Abstract

Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Here we report analysis of 133,816 samples collected at April-September 2020, tested by pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the reality of frequently changing prevalence rate (0.5%-6%). Surprisingly, we observed pooling efficiency and sensitivity that exceed theoretical predictions, which resulted from non-random distribution of positive samples in pools. Overall, the findings strongly support the use of pooling for efficient large high throughput SARS-CoV-2 testing.

Active Surveillance of Asymptomatic, Presymptomatic, and Oligosymptomatic SARS-CoV-2-Infected Individuals in Communities Inhabiting Closed or Semi-closed Institutions

“…On the basis of these results and considering that contagiousness of individuals with Ct ≥ 36 would not impact on COVID-19 epidemiology ( 24 – 26 ), the Ministry of Health of the Province of Buenos Aires decided to apply this methodology to analyze health situation in closed or semi-closed facilities.…”

Group testing as a strategy for COVID-19 epidemiological monitoring and community surveillance

“…The case of a pool of N samples that contains k > 1 positive individual is particularly relevant as pooling may be achieved on individuals living in the same household, as in [ 47 ], or students sharing the same residence hall, as mentionned in [ 61 ]; in these cases, the fact that one individual is infected increases the probability that more individuals in the pool are infected as well. Such correlation has been clinically found to lower the risk of false negative risk, an effect coined hitchhiking in [ 47 ]. In Sec II in S1 Text , we provide estimation for the false-negative rate in pools, we expect to depend on the prevalence among the tested individuals.…”

“…Some individuals may also refuse to comply to the diagnosis tests. In addition, diagnostic tests performed on positive pools may also turn negative [ 47 ]; we see at least 3 possible reasons for such discrepancies: (i) an inherent false-negative risk in diagnostic tests, (ii) a possible time delay between the screening and diagnosis tests (e.g. that could result in positive individuals in the pool turning negative in the diagnostic test) or (iii) the fact that the screening and diagnostic tests may not rely on the same sample collection—with screenings relying on self-collected nasal swabs or saliva collection, while diagnosis tests are most often performed on nasopharyngeal swabs samples with an arguably higher level of sensitivity.…”

An Accurate Model for SARS-CoV-2 Pooled RT-PCR Test Errors

“…RT-PCR testing is a key component in breaking transmission chains and mitigating the COVID-19 pandemic. As such, the need for large-scale testing has resulted in the development of pooling schemes of RT-PCR tests [2, 6, 7, 10, 11]. One such popular scheme is Dorfman pooling [2, 5]: Select N individuals and perform a single RT-PCR test on their combined (“pooled”) samples.…”

“…If the pooled test yields a positive result — test each individual separately. The throughput efficiency of Dorfman pooling has been demonstrated empirically [2]. However, when test error rates are taken into consideration, a sharp increase in false-negative rates can be expected.…”