A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples.

At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.

Implementing Pool-Based Surveillance Testing for SARS-CoV-2 at the Army Public Health Center Laboratory and across the Army Public Health Laboratory Enterprise.

With limited clinical resources, burgeoning testing requests from Army and other Service units to clinical laboratories, and the continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) throughout the military population, the Army Public Health Laboratory (APHL) Enterprise was tasked to establish surveillance testing capabilities for active duty military populations in an expedient manner. Following a proof-of-concept study conducted by Public Health Command-Pacific, Public Health Command-Europe was the first public health laboratory to offer the capability to assess for SARS-CoV-2 in pooled samples, followed closely by the Army Public Health Center (APHC) at Aberdeen Proving Grounds, MD, paralleling the spread of the SARS-CoV-2 virus from China to Europe to the continental US. The APHLs have selected pool sizes of up to 10 samples per pool based on the best evidence available at the time of method development and validation. Real-Time quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) assays using RNA extracts from pooled nasopharyngeal swabs preserved in viral transport media were selected to assess the presence of SARS-CoV-2. The rapid development of initial surveillance testing capabilities depended on existing equipment in each laboratory, with a plan to implement full operational capability using additional staff and common high-throughput platforms. APHL Enterprise has successfully used existing resources to begin to address the changing and complex needs for COVID-19 testing within the Army population. Successful implementation of pooled surveillance testing at the APHC Laboratory has enabled more than 8,600 Soldiers to avoid clinical testing to date. The APHC Laboratory alone has tested over 10,000 samples and prevented approximately 8,600 soldiers from seeking testing with clinical diagnostic assays.

Reduced expression of ribosomal proteins relieves microRNA-mediated repression.

MicroRNAs (miRNAs) regulate physiological and pathological processes by inducing posttranscriptional repression of target messenger RNAs (mRNAs) via incompletely understood mechanisms. To discover factors required for human miRNA activity, we performed an RNAi screen using a reporter cell line of miRNA-mediated repression of translation initiation. We report that reduced expression of ribosomal protein genes (RPGs) dissociated miRNA complexes from target mRNAs, leading to increased polysome association, translation, and stability of miRNA-targeted mRNAs relative to untargeted mRNAs. RNA sequencing of polysomes indicated substantial overlap in sets of genes exhibiting increased or decreased polysomal association after Argonaute or RPG knockdowns, suggesting similarity in affected pathways. miRNA profiling of monosomes and polysomes demonstrated that miRNAs cosediment with ribosomes. RPG knockdowns decreased miRNAs in monosomes and increased their target mRNAs in polysomes. Our data show that most miRNAs repress translation and that the levels of RPGs modulate miRNA-mediated repression of translation initiation.