881. Saliva-Based, Extraction-Free PCR Testing For The Detection Of Key Respiratory Pathogens

Abstract

Abstract Background Efforts to control and monitor transmissible infectious diseases rely on large-scale screening often impaired by logistically difficult or invasive sample collection. The use of saliva as a non-invasive sample type could alleviate bottlenecks encountered in mass testing strategies. Having extensively demonstrated saliva as a sensitive sample type for SARS-CoV-2 detection, we sought to validate the approach for other common upper respiratory tract pathogens. Methods We modified our RNA-extraction-free SARS-CoV-2 PCR test for multiplexed detection of four additional respiratory viruses (“SalivaDirect+”): influenza A/B, RSV, and hMPV, and singleplex detection of pneumococcus. Stability of detection was tested after storage of saliva from pathogen-positive patients at +4°C, room temperature (∼19°C) and 30°C for 72 hours. De-identified saliva samples were collected from consenting adults ≥ 18 years of age with respiratory symptoms, requiring nasopharyngeal-swab based SARS-CoV-2 testing at Yale Health, New Haven, CT, USA. Saliva samples from individuals testing nasopharyngeal-swab negative for SARS-CoV-2 at the clinical laboratory were stored at -80°C until further processing in the research laboratory. Results We confirmed the limit of assay detection at 4 copies/µl for each target. We confirmed pathogen detection remained stable at +4°C, room temperature and 30°C for up to 72 hours. From the symptomatic testing site, 804 nasopharyngeal swabs tested negative for SARS-CoV-2; their paired saliva samples were tested with the SalivaDirect+ assay. Of those, 17 (2.1%) tested positive for one of the viruses targeted (influenza A, n=7; RSV, n=4; hMPV, n=6). No samples tested positive for influenza B. For influenza A and RSV, detection by SalivaDirect+ was comparable to testing following RNA extraction but detection of hMPV was less sensitive, even following assay modifications. In singleplex testing, 87 (10.8%) samples tested positive for pneumococcus. Conclusion We expanded a low-cost, open-source saliva-based PCR test for detection of other common respiratory pathogens. By testing saliva samples from symptomatic, SARS-CoV-2-negative adults, we detected common respiratory viruses which were otherwise missed in testing focused solely on SARS-CoV-2. Disclosures Anne L. Wyllie, PhD, Co-Diagnostics: Board Member|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support