Evaluation of pooled sample analysis strategy in expediting case detection in areas with emerging outbreaks of COVID-19: A pilot study

Abstract

Timely diagnosis of COVID-19 infected individuals and their prompt isolation are essential for controlling the transmission of SARS-CoV-2. Though quantitative reverse transcriptase PCR (qRT-PCR) is the method of choice for COVID-19 diagnostics, the resource-intensive and time-consuming nature of the technique impairs its wide applicability in resource-constrained settings and calls for novel strategies to meet the ever-growing demand for more testing. In this context, a pooled sample testing strategy was evaluated in the setting of emerging disease outbreak in 3 central Indian districts to assess if the cost of the test and turnaround time could be reduced without compromising its diagnostic characteristics and thus lead to early containment of the outbreak. From 545 nasopharyngeal and oropharyngeal samples received from the three emerging districts, a total of 109 pools were created with 5 consecutive samples in each pool. The diagnostic performance of qRT-PCR on pooled sample was compared with that of individual samples in a blinded manner. While pooling reduced the cost of diagnosis by 68% and the laboratory processing time by 66%, 5 of the 109 pools showed discordant results when compared with induvial samples. Four pools which tested negative contained 1 positive sample and 1 pool which was positive did not show any positive sample on deconvolution. Presence of a single infected sample with Ct value of 34 or higher, in a pool of 5, was likely to be missed in pooled sample analysis. At the reported point prevalence of 4.8% in this study, the negative predictive value of qRT-PCR on pooled samples was around 96% suggesting that the adoption of this strategy as an effective screening tool for COVID-19 needs to be carefully evaluated.

A robust pooled testing approach to expand COVID-19 screening capacity

“…[ 17 ] shows a similar result for pools of size 30. In addition, several other studies find no loss of sensitivity for smaller pools, e.g., [ 18 – 20 ] use pool sizes of 5, 8, and 10, respectively. Not surprisingly [ 21 , 22 ], show that the dilution effect is more pronounced when the infected specimens in the pool have low viral loads; the window period analysis in [ 21 ] indicates that the low viral load typically occurs for specimens that are collected either too early or too late after infection.…”

Fighting COVID-19 with Flexible Testing: Models and Insights

“…On the other hand, the NPVs of pooled testing are initially lower than those of individual testing, but they quickly increase and become higher than those of individual testing ( Figure 2G) when the prevalence rate under pooled testing is significantly lower than that under individual testing ( Figure 2B). However, research that assumes a fixed prevalence shows that pooled testing always leads to lower NPVs than those of individual testing 21 . Test sensitivity and specificity affect epidemic dynamics differently under different testing strategies, as shown in Figure 5.…”

SARS-CoV-2 RNA detection using pooling of self-collected samples: Simple protocol may foster asymptomatic surveillance

“…Cumulative data since early in the epidemic have suggested that a window of about a week or two, starting 1-2 days before symptoms, a period associated to high viremia in the airways, is responsible for much of the transmission (He 2020). A major deterrent to surveillance is the fact that asymptomatic individuals, along with pre symptomatic cases, are responsible for many infections (reviewed by Huff & Singh, 2020). Association of transmission to higher viremia levels (La Scola 2020, Larremore 2020) suggests that even tests less sensible than the current real-time PCR (rt-qPCR) tests may be useful to curb transmission.…”

“…We introduced a voluntary throat wash plus saliva collection, offered to asymptomatic individuals from different areas of the institute, and tested the feasibility of using samples pooling (Abdalhamid 2020, Singh 2020, Yelin 2020) to minimize reagents and equipment use.…”