A Regional Pooling Intervention in a High-Throughput COVID-19 Diagnostic Laboratory to Enhance Throughput, Save Resources and Time Over a Period of 6 Months

Abstract

An effective and rapid diagnosis has great importance in tackling the ongoing COVID-19 pandemic through isolation of the infected individuals to curb the transmission and initiation of specialized treatment for the disease. It has been proven that enhanced testing capacities contribute to efficiently curbing SARS-CoV-2 transmission during the initial phases of the outbreaks. RT-qPCR is considered a gold standard for the diagnosis of COVID-19. However, in resource-limited countries expenses for molecular diagnosis limits the diagnostic capacities. Here, we present interventions of two pooling strategies as 5 sample pooling (P-5) and 10 sample pooling (P-10) in a high-throughput COVID-19 diagnostic laboratory to enhance throughput and save resources and time over a period of 6 months. The diagnostic capacity was scaled-up 2.15-folds in P-5 and 1.8-fold in P-10, reagents (toward RNA extraction and RT-qPCR) were preserved at 75.24% in P-5 and 86.21% in P-10, and time saved was 6,290.93 h in P-5 and 3147.3 h in P-10.

Keywords: COVID-19; RT-qPCR–real-time quantitative polymerase chain reaction; SARS-CoV-2; high-throughput diagnosis; pooling interventions.

FIGURE 1

The average Ct for viral targets in deconvoluted (unpool) samples and in pools (P-5 and P-10 strategy) which resulted in only one positive specimen in deconvolution.

FIGURE 2

Distribution of Ct values for viral target in pools and deconvoluted samples with only one positive sample in deconvolution. (A) Distribution of Ct values (≥30) in the P-5 testing strategy. (B) Distribution of Ct values in (<30) in P-5 testing strategy. (C) Distribution of Ct values (≥30) in P-10 testing strategy. (D) Distribution of Ct values in (<30) in P-10 testing strategy. Blue and orange color markers indicate Ct of viral targets in pools and in deconvoluted samples, respectively.

FIGURE 3

Time saved in pooling strategies. (A) Percent time saved during pooling strategies (combined of P-5 and P-10). The dark color column represents time consumed and the light color column represents time saved. (B) Comparison of percent time saved in P-5 and P-10 testing strategies. (C) Time saved in hours during different areas of testing including aliquoting, RNA extraction, and PCR during the P-5 testing strategy. (D) Time saved in hours during different areas of testing including aliquoting, RNA extraction and PCR during P-10 testing strategy. The dark color column and area under the dash line indicate the consumed and saved time in different areas of the testing protocol due to pooling strategies.

FIGURE 4

Representation of resources consumed and saved during pooling strategies. Dash type trend line and dark color trend line indicate the percentage of lab positivity and the positivity rate in pooling during the testing period, respectively. Y-axis indicates reactions saved in numbers and positivity rate in percentage.