Assessment of sample pooling for clinical SARS-CoV-2 testing

Abstract

Accommodating large increases in sample workloads has presented one of the biggest challenges to clinical laboratories during the COVID-19 pandemic. Despite the implementation of new automated detection systems, and previous efficiencies such as barcoding, electronic data transfer and extensive robotics, throughput capacities have struggled to meet the demand. Sample pooling has been suggested as an additional strategy to further address this need. The greatest concern with this approach in a clinical setting is the potential for reduced sensitivity, particularly the risk of false negative results when weak positive samples are pooled. To investigate this possibility, detection rates in pooled samples were evaluated, with extensive assessment of pools containing weak positive specimens. Additionally, the frequency of occurrence of weak positive samples across ten weeks of the pandemic were reviewed. Weak positive specimens were detected in all five-sample pools but failed to be detected in four of the 24 nine-sample pools tested. Weak positive samples comprised an average 16.5% of the positive specimens tested during the pandemic thus far, slightly increasing in frequency during later weeks. Other aspects of the testing process should be considered, however, such as accessioning and reporting, which are not streamlined and may be complicated by pooling procedures. Therefore, the impact on the entire laboratory process needs to be carefully assessed prior to implementing such a strategy.

Considerations for Pooled Testing of Employees for SARS-CoV-2

“…The utility of pooled testing to identify individuals infected with SARS-Cov-2 has been demonstrated. 20 - 22 , 25 , 31 , 33 , 42 , 48 , 60 Because samples are diluted when pooled, proportionally less viral genetic material is available for detection, resulting in a greater likelihood of false negatives, 38 which can vary by method. 8 However, a number of studies indicate that a weakly positive sample within the limit of detection of the assay can be identified in pooled studies.…”

“…Pooled testing can be a complex effort to manage. 42 , 73 There are numerous technical hurdles to overcome. 24 The timing and coordination needed to pool specimens and track individuals requires planning and resources.…”

“…80 Without adequate and appropriate coordination, pooled testing can result in slow response time, which could impact the isolation of positive cases and quarantining of contacts. 26 , 42 , 73 However, when prevalence of infection is low, there will be a need for fewer follow-up tests and pooled testing can yield results relatively quickly. Key in the management of pooled testing is informing employees of pooled and individual test results, maintaining the confidentiality of the test results, then using the results to make decisions about whether the employee can work or will need isolation.…”

Modelling pool testing for SARS-CoV-2: addressing heterogeneity in populations

“…However, since the pooling of specimens might reduce the test sensitivity due to pooling dilution, the optimal group sizes should be thoughtfully estimated [26,27]. In addition, it is crucial to establish guidelines for efficient and accurate pooling algorithms that will ensure maximum throughput of the strategy when implemented in the clinical context [28].…”

“…Moreover, the viral load might play a decisive role in the sensitivity of the pooled samples [24], and targeting two genes of SARS-CoV-2 might increase the efficiency of the detection of positive samples in minipools of 5–10 samples [25]. However, since the pooling of specimens might reduce the test sensitivity due to pooling dilution, the optimal group sizes should be thoughtfully estimated [26, 27]. In addition, it is crucial to establish guidelines for efficient and accurate pooling algorithms that will ensure maximum throughput of the strategy when implemented in the clinical context [28].…”