The Cornell COVID-19 Testing Laboratory: A Model to High-Capacity Testing Hubs for Infectious Disease Emergency Response and Preparedness

Abstract

The unprecedented COVID-19 pandemic posed major challenges to local, regional, and global economies and health systems, and fast clinical diagnostic workflows were urgently needed to contain the spread of SARS-CoV-2. Here, we describe the platform and workflow established at the Cornell COVID-19 Testing Laboratory (CCTL) for the high-throughput testing of clinical samples from the university and the surrounding community. This workflow enabled efficient and rapid detection and the successful control of SARS-CoV-2 infection on campus and its surrounding communities. Our cost-effective and fully automated workflow enabled the testing of over 8000 pooled samples per day and provided results for over 2 million samples. The automation of time- and effort-intensive sample processing steps such as accessioning and pooling increased laboratory efficiency. Customized software applications were developed to track and store samples, deconvolute positive pools, track and report results, and for workflow integration from sample receipt to result reporting. Additionally, quality control dashboards and turnaround-time tracking applications were built to monitor assay and laboratory performance. As infectious disease outbreaks pose a constant threat to both human and animal health, the highly effective workflow implemented at CCTL could be modeled to establish regional high-capacity testing hubs for infectious disease preparedness and emergency response.

The role of veterinary diagnostic laboratories during COVID-19 response in the United States

“…[16] Result reporting for pooled samples had a median turnaround time of 4 hours and 46 minutes, although positive pools had a median turn-around time of 22 hours and 19 minutes. [16] Samples that were not pooled (and tested individually) had a median turn-around time of 3 hours and 56 minutes. [16] Although logistically more complicated, pooling increased efficiency, enabling rapid test result communication, which ultimately improved the effectiveness of intervention among positive cases.…”

“…The well position within the 96-well plate and the sample position in storage racks were retained and managed through a custom software application (COVID-19 Receiving App). [16] Three wells were left as controls. [16] In forty-five minutes, 465 samples were pooled into 93 wells of the 96-well plate.…”

“…[16] Three wells were left as controls. [16] In forty-five minutes, 465 samples were pooled into 93 wells of the 96-well plate. [16] If any pools tested positive, deconvolution took place and samples were tested individually.…”

“…[16] In forty-five minutes, 465 samples were pooled into 93 wells of the 96-well plate. [16] If any pools tested positive, deconvolution took place and samples were tested individually. [16] Result reporting for pooled samples had a median turnaround time of 4 hours and 46 minutes, although positive pools had a median turn-around time of 22 hours and 19 minutes.…”

“…[16] If any pools tested positive, deconvolution took place and samples were tested individually. [16] Result reporting for pooled samples had a median turnaround time of 4 hours and 46 minutes, although positive pools had a median turn-around time of 22 hours and 19 minutes. [16] Samples that were not pooled (and tested individually) had a median turn-around time of 3 hours and 56 minutes.…”