Sample pooling for SARS-CoV-2 RT-PCR screening

Area of Science:

• Clinical Microbiology
• Virology
• Molecular Diagnostics

Background:

• The COVID-19 pandemic necessitated rapid and scalable diagnostic testing.
• Nucleic acid testing is the gold standard for diagnosing COVID-19.
• Optimizing testing workflows is crucial for managing high sample volumes.

Purpose of the Study:

• To assess the effectiveness of pooling samples versus individual analysis for COVID-19 diagnosis.
• To evaluate pooling strategies across diverse commercial platforms for RNA extraction and amplification.
• To determine the impact of sample pooling on diagnostic accuracy and resource utilization.

Main Methods:

• 3519 nasopharyngeal samples were tested individually and in pools (pools of 10 and 9).
• Testing was performed using existing methodologies across nine Spanish clinical microbiology laboratories.
• Commercial platforms for nucleic acid extraction and amplification were utilized.

Main Results:

• Pooling strategies demonstrated high efficiency, potentially saving 2167 PCR tests.
• Sensitivity was 97.10%, specificity 100%, and accuracy 99.80% for pooled testing.
• Minor and major discordances were observed in 22 and 7 pools, respectively; median Ct loss ranged from 2.87 to 3.36.

Conclusions:

• Sample pooling is a highly efficient strategy for SARS-CoV-2 RNA testing.
• The method shows excellent performance across different platforms, with high sensitivity and specificity.
• Pooling effectively reduces the number of tests required while maintaining diagnostic reliability.