Nested pool testing strategy for the diagnosis of infectious diseases

Author(s)

Armendariz, Ines ^{[1, 2, 3]} ; Ferrari, Pablo A. ^{[1, 2, 3]} ; Fraiman, Daniel ^[4] ; Martinez, Jose M. ^[5] ; Menzella, Hugo G. ^{[1, 6, 7]} ; Ponce Dawson, Silvina ^{[1, 8, 9]}

Affiliation

^[1] Consejo Nacl Invest Cient & Tecn, C1428EGA, Buenos Aires, DF - Argentina

^[2] FCEN UBA, Dept Matemat, C1428EGA, Buenos Aires, DF - Argentina

^[3] FCEN UBA, IMAS, C1428EGA, Buenos Aires, DF - Argentina

^[4] Univ San Andres, Dept Matemat & Ciencias, B1644BID, Victoria - Argentina

^[5] IMECC UNICAMP, Dept Appl Math, BR-13083859 Campinas - Brazil

^[6] FBIOy FUNR, Dept Technol, S2002LRK, Rosario - Argentina

^[7] FBIOy FUNR, IPROByQ, S2002LRK, Rosario - Argentina

^[8] FCEN UBA, Dept Fis, C1428EGA, Buenos Aires, DF - Argentina

^[9] FCEN UBA, IFIBA, C1428EGA, Buenos Aires, DF - Argentina

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 11, n. 1 SEP 13 2021.
• Web of Science Citations: 0

Abstract

The progress of the SARS-CoV-2 pandemic requires the design of large-scale, cost-effective testing programs. Pooling samples provides a solution if the tests are sensitive enough. In this regard, the use of the gold standard, RT-qPCR, raises some concerns. Recently, droplet digital PCR (ddPCR) was shown to be 10-100 times more sensitive than RT-qPCR, making it more suitable for pooling. Furthermore, ddPCR quantifies the RNA content directly, a feature that, as we show, can be used to identify nonviable samples in pools. Cost-effective strategies require the definition of efficient deconvolution and re-testing procedures. In this paper we analyze the practical implementation of an efficient hierarchical pooling strategy for which we have recently derived the optimal, determining the best ways to proceed when there are impediments for the use of the absolute optimum or when multiple pools are tested simultaneously and there are restrictions on the throughput time. We also show how the ddPCR RNA quantification and the nested nature of the strategy can be combined to perform self-consistency tests for a better identification of infected individuals and nonviable samples. The studies are useful to those considering pool testing for the identification of infected individuals. (AU)

• FAPESP's process: 16/01860-1 - Cutting, packing, lot-sizing, scheduling, routing and location problems and their integration in industrial and logistics settings
• Grantee: Reinaldo Morabito Neto
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 13/07375-0 - CeMEAI - Center for Mathematical Sciences Applied to Industry
• Grantee: Francisco Louzada Neto
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 18/24293-0 - Computational methods in optimization
• Grantee: Sandra Augusta Santos
• Support Opportunities: Research Projects - Thematic Grants