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Modelling pool testing for SARS-CoV-2: addressing heterogeneity in populations

Published online by Cambridge University Press:  28 December 2020

Javier Fernández-Salinas*
Affiliation:
Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
Diego Aragón-Caqueo
Affiliation:
Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
Gonzalo Valdés
Affiliation:
Departamento de Ingeniería Industrial y de Sistemas, Universidad de Tarapacá, Casilla 7D, Arica, Chile
David Laroze
Affiliation:
Instituto de Alta Investigación, CEDENNA, Universidad de Tarapacá, Casilla 7D, Arica, Chile
*
Author for correspondence: Javier Fernández-Salinas, E-mail: javier.fernandez@alumnos.uv.cl
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Abstract

Amplifying the testing capacity and making better use of testing resources is a crucial measure when fighting any pandemic. A pooled testing strategy for SARS-CoV-2 has theoretically been shown to increase the testing capacity of a country, especially when applied in low prevalence settings. Experimental studies have shown that the sensitivity of reverse transcription-polymerase chain reaction is not affected when implemented in small groups. Previous models estimated the optimum group size as a function of the historical prevalence; however, this implies a homogeneous distribution of the disease within the population. This study aimed to explore whether separating individuals by age groups when pooling samples results in any further savings on test kits or affects the optimum group size estimation compared to Dorfman's pooling, based on historical prevalence. For this evaluation, age groups of interest were defined as 0–19 years, 20–59 years and over 60 years old. Generalisation of Dorfman's pooling was performed by adding statistical weight to the age groups based on the number of confirmed cases and tests performed in the segment. The findings showed that when the pooling samples are based on age groups, there is a decrease in the number of tests per subject needed to diagnose one subject. Although this decrease is minuscule, it might account for considerable savings when applied on a large scale. In addition, the savings are considerably higher in settings where there is a high standard deviation among the positivity rate of the age segments of the general population.

Information

Type
Original Paper
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press
Figure 0

Table 1. Different ɛ and γ values obtained in specific scenarios

Figure 1

Fig. 1. z as a function of n for different prevalences (x) ranging from 0.05 to 0.4 for the particular case of New South Wales state, Australia. Horizontal axis: group size of a pooled sample (n). Vertical axis: number of tests per subject needed to diagnose one subject (z). Different colours represent different prevalences. Input: ɛ1 = 0.101, ɛ2 = 0.691, ɛ3 = 0.208, γ1 = 0.396, γ2 = 0.941 and γ3 = 1.489.

Figure 2

Table 2. Summary of the main findings for n and z from varying γ2 across different scenarios

Figure 3

Fig. 2. (a) Optimum z as a function of σ for different prevalences colour-coded, from 0.05 to 0.3. Horizontal axis: heterogeneity of the population (σ). Vertical axis: optimum number of tests needed to diagnose one subject (z) based on the optimum group size previously calculated. (b) Relative percentage decrease of the optimum z as a function of σ with respect to the optimum z estimated for σ = 0 expressed in logarithmic form. Horizontal axis: heterogeneity of the population (σ). Vertical axis: percentage decrease of the optimum z as a function of σ with respect to the optimum z estimated for σ = 0.

Figure 4

Table 3. Coefficients a0, a1, a2 and b to estimate z and PDz as a function of σ at different prevalence settings

Figure 5

Table 4. Comparison of the pooled strategies mentioned