Assessment of Sample Pooling for Clinical SARS-CoV-2 Testing

Area of Science:

• Clinical diagnostics
• Virology
• Laboratory automation

Background:

• Clinical laboratories faced significant challenges managing increased sample workloads during the COVID-19 pandemic.
• Existing automation and efficiencies struggled to meet demand, prompting exploration of new strategies like sample pooling.

Purpose of the Study:

• To evaluate the detection rates of weakly positive samples in pooled specimens.
• To assess the frequency of weakly positive samples during the COVID-19 pandemic.
• To consider the broader impact of sample pooling on laboratory workflows.

Main Methods:

• Detection rates were assessed in five- and nine-sample pools containing weakly positive specimens (Cq ≥ 33).
• Frequencies of weakly positive samples (Cq > 31) were reviewed throughout the pandemic.
• The impact of pooling on laboratory processes like accessioning and data management was considered.

Main Results:

• Weakly positive samples were detected in 95% of five-sample pools and 87% of nine-sample pools.
• The proportion of positive samples with very low viral loads (weakly positive) peaked in June, comprising 29% to over 80% of samples.
• Pooling may complicate, rather than streamline, other laboratory operations such as data management and billing.

Conclusions:

• Sample pooling is a potential strategy to increase testing capacity but carries a risk of reduced sensitivity for low-concentration viral targets.
• The prevalence of weakly positive samples necessitates careful consideration of pooling's impact on diagnostic accuracy.
• A comprehensive assessment of the entire laboratory workflow is essential to determine the true utility of sample pooling strategies.