A pooled testing strategy for identifying SARS-CoV-2 at low prevalence

Leon Mutesa, Pacifique Ndishimye, Yvan Butera, Jacob Souopgui, Annette Uwineza, Robert Rutayisire, Ella Larissa Ndoricimpaye, Emile Musoni, Nadine Rujeni, Thierry Nyatanyi, Edouard Ntagwabira, Muhammed Semakula, Clarisse Musanabaganwa, Daniel Nyamwasa, Maurice Ndashimye, Eva Ujeneza, Ivan Emile Mwikarago, Claude Mambo Muvunyi, Jean Baptiste Mazarati, Sabin NsanzimanaNeil Turok, Wilfred Ndifon

Research output: Contribution to journalArticlepeer-review

Abstract

Suppressing SARS-CoV-2 will likely require the rapid identifcation and isolation of infected individuals on an ongoing basis. Reverse transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, making regular testing of every individual expensive. The costs are a challenge for all countries and particularly for developing countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups [1-7]. A balance must be struck between increasing the group size and retaining test sensitivity, since sample dilution increases the likelihood of false negatives for individuals
with low viral load in the sampled region at the time of the test [8]. Likewise, minimising the number of tests to reduce costs must be balanced against minimising the time testing takes to reduce the spread of infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifes infected individuals
in a small number of tests and rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof of concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (cf. 30-fold to 48-fold dilution in Refs. [9-11]). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor which, furthermore, increases as
the prevalence falls. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to closely and continually monitor infection in a population, along with rapid and effective isolation of infected people, provides a promising pathway to the longterm control of COVID-19.
Original languageEnglish
JournalNature
DOIs
Publication statusPublished - 21 Oct 2020

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