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, vaccine refusal, 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, obtaining 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.

Discussion: This approach offers a significant scale-up in sampling and testing throughput and savings in testing cost, without reducing sensitivity or 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.

Keywords: Bubble; COVID-19; Capsule; Corona testing; Pool testing; SARS-CoV-2; Swab pooling.

Graphical abstract

Fig. 1

Outline of the bubble-based swab-pooling concept. (A) individuals in a workplace or a school are divided into bubbles, with each individual in a bubble (six in this example) tested with two swabs: one is placed in the swab-pool test tube and the second in an individual tube. Black person image, healthy individual; red image, SARS-CoV-2–infected individual, whose swab is coloured red. (B) Swab-pool A and swab-pool C are PCR negative, and therefore all individuals belonging to bubbles A and C are regarded as negative. Swab-pool B gave a positive PCR result, and therefore each individual belonging to swab-pool B is being isolated. (C) The individual test tubes for swab-pool B members are individually PCR tested to identify the SARS-CoV-2–positive individual. This is followed by contact tracing.

Fig. 2

Association of pool size to estimated sensitivity and comparison of Ct values of pool versus expected values from individual Ct. (A) Sensitivity as a function of pool size, as estimated by the logistic regression (solid line), with pointwise 95% lower confidence bounds for sensitivity (dashed line). (B) Comparison of the pooled Ct value to the expected Ct for the pool, computed from the Ct results for the individuals in the pool and adjusting for the extra dilution in the pooled sample. The 69 pools for which the pool gave a positive numerical result and positive individuals were identified are plotted along the line Y = X (black dots). The 11 pools that were negative but included positive individuals are represented by blue dots parallel to the X axis (i.e. a false negative pool). The 30 pools that were positive but included no positive individuals appear as blue dots parallel to the Y axis (i.e. a false positive pool).