Effective bubble-based testing for SARS-CoV-2 using swab-pooling

Abstract

Objectives

Despite the success in developing COVID-19 vaccines, containment of the disease is obstructed worldwide by vaccine production bottlenecks, logistics hurdles, refusal to be vaccinated, transmission through unvaccinated children, and the appearance of new viral variants. This underscores the need for effective strategies for identifying carriers/patients which was the main aim of this study.

Methods

We present a bubble-based PCR testing approach using swab-pooling into lysis buffer. A bubble is a cluster of people who can be periodically tested for SARS-CoV-2 by swab-pooling. A positive test of a pool mandates quarantining each of its members, who are then individually tested while in isolation, to identify the carrier(s) for further epidemiological contact tracing.

Results

We tested an overall sample of 25,831 individuals, divided into 1273 bubbles, with an average size of 20.3±7.7 swabs/test-tube, getting for all pools (≤37 swabs/pool) a specificity of 97.5% (lower bound 96.6%) and a sensitivity of 86.3% (lower bound 78.2%), and a post-hoc analyzed sensitivity of 94.6% (lower bound 86.7%) and a specificity of 97.2% (lower bound 96.2%) in pools with ≤25 swabs, relative to individual testing.

Conclusions

This approach offers significant scale-up in sampling and testing throughput, savings in testing cost, while not reducing sensitivity and not affecting the standard PCR testing laboratory routine. It can be used in school classes, airplanes, hospitals, military units and workplaces, and may be applicable to future pandemics.

Graphical abstract