Repurposing a SARS-CoV-2 surveillance program for infectious respiratory diseases in a university setting

Abstract

Standard multiplex RT-qPCR diagnostic tests use nasopharyngeal swabs to simultaneously detect a variety of infections, but commercially available kits can be expensive and have limited throughput. Previously, we clinically validated a saliva-based RT-qPCR diagnostic test for SARS-CoV-2 to provide low-cost testing with high throughput and low turnaround time on a university campus. Here, we developed a respiratory diagnostic panel to detect SARS-CoV-2, influenza A and B within a single saliva sample. When compared to clinical results, our assay demonstrated 93.5% accuracy for influenza A samples (43/46 concordant results) with no effect on SARS-CoV-2 accuracy or limit of detection. In addition, our assay can detect simulated coinfections at varying virus concentrations generated from synthetic RNA controls. We also confirmed the stability of influenza A in saliva at room temperature for up to 5 days. The cost of the assay is lower than standard nasopharyngeal swab respiratory panel tests as saliva collection does not require specialized swabs or trained clinical personnel. By repurposing the lab infrastructure developed for the COVID-19 pandemic, our multiplex assay can be used to provide expanded access to respiratory disease diagnostics, especially for community, school, or university testing applications where saliva testing was effectively utilized during the COVID-19 pandemic.

Keywords: SARS-CoV-2; flu; influenza; saliva; surveillance testing; virus.

Figure 1

Representative curves of synthetic viral RNA mixtures. Synthetic positive controls 192 for each virus were mixed to evaluate assay performance in the presence of two viruses. 193 representative curves are shown for each combination.

Figure 2

Stability of influenza A in saliva at room temperature. Influenza A is stable in saliva samples at room temperature (~20°C) for 5 days without addition of any stabilization buffers. Ct values increased slightly at days 3 and 5 but remained within detectable limits (Ct < 30).