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Objective:We present the National Prion Disease Pathology Surveillance Center’s (NPDPSC) experience using cerebrospinal fluid (CSF) real time quaking induced conversion (RT-QuIC) as a diagnostic test, examine factors associated with false negative RT-QuIC results, and investigate RT-QuIC’s impact on prion disease surveillance.Methods:Between May 2015-April 2018, the NPDPSC received 10,498 CSF specimens that were included in the study. Sensitivity and specificity analyses were performed using 567 autopsy verified cases. Prion disease type, demographic characteristics, specimen color, and time variables were examined for association with RT-QuIC results. The effect of including positive RT-QuIC cases in prion disease surveillance was examined.Results:The diagnostic sensitivity and specificity of RT-QuIC across all prion diseases was 90.3% and 98.5%, respectively. Diagnostic sensitivity was lower for fatal familial insomnia, Gerstmann-Sträussler-Scheinker disease, sporadic fatal insomnia, variably protease sensitive prionopathy, and the VV1 and MM2 subtypes of sCJD. Individuals with prion disease and negative RT-QuIC results were younger, had elevated tau levels, and non-elevated 14-3-3 levels compared to RT-QuIC positive cases. Sensitivity was high throughout the disease course. Some cases that initially tested RT-QuIC negative had a subsequent specimen test positive. Including positive RT-QuIC cases in surveillance statistics increased laboratory-based case ascertainment of prion disease by 90% over autopsy alone.Conclusions:RT-QuIC has high sensitivity and specificity for diagnosing prion diseases. Sensitivity limitations are associated with prion disease type, age, and related CSF diagnostic results. RT-QuIC greatly improves laboratory-based prion disease ascertainment for surveillance purposes.Classification of Evidence:This study provides Class III evidence that 2nd generation real time quaking-induced conversion (RT-QuIC) identifies prion disease with sensitivity of 90.3% and specificity of 98.5%, among patients being screened for these diseases due to concerning symptoms.

Background: The ongoing COVID-19 pandemic has resulted in shortages in nasopharyngeal swabs (NPS) and viral transport media, necessitating the search for alternate diagnostic specimens, such as saliva. We directly compared matched saliva and NPS specimens from symptomatic patients suspected of having COVID-19. Methods: An enhanced saliva specimen (ie strong sniff, elicited cough, and collection of saliva/secretions) was collected without transport media prior to NPS from 224 patients with symptoms deemed consistent with COVID-19. Both specimens were tested with the CDC 2019 nCoV Real-Time RT-PCR Diagnostic Panel (4 February 2020 version), with the NPS result used as the reference standard. Results: Of the 216 patients included in the final analysis, there was a 100% Positive Percent Agreement (38/38 positive specimens) and 99.4% Negative Percent Agreement (177/178 negative specimens). The one discrepant specimen had the presence of SARS-CoV-2 confirmed in the saliva specimen using an alternate FDA EUA assay. The overall mean difference in crossing threshold (Ct) values for the positive NPS and saliva specimens was -3.61 (95% C.I. -5.78 to -1.44, p = 0.002). Conclusion: An enhanced saliva specimen performed as well as NPS for the qualitative detection of SARS-CoV-2 in symptomatic patients, albeit the overall mean viral load in saliva was lower.

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22The SARS-CoV-2 pandemic has brought a new wave of challenges to health care, particularly in 23 the area of rapid diagnostic test development and implementation. Acute diagnosis of infection is critically dependent on detection of SARS-CoV-2 RNA from clinical specimens (e.g. 25 nasopharyngeal swabs). While laboratory-developed testing for SARS-CoV-2 is an essential 26 component of diagnostic testing for this virus, the majority of clinical microbiology laboratories 27 are dependent on commercially available SARS-CoV-2 molecular assays. In contrast to assays 28 approved or cleared by the Food and Drug Administration for in vitro diagnostic use, assays for 29 the detection of SARS-CoV-2 nucleic acids have Emergency Use Authorization (EUA) from the 30 FDA. Outside of highly specialized academic and commercial laboratory settings, clinical 31 microbiology laboratories are likely unfamiliar with EUA classification and thus assay 32verification can be daunting. Further compounding anxiety for laboratories are major issues with 33 supply chain that are dramatically affecting the availability of test reagents and requiring 34 laboratories to implement multiple commercial EUA tests. Here, we describe guidance for the 35 verification of assays with EUA for the detection of SARS-CoV-2 nucleic acid from clinical 36 specimens. 37 38 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from The coronavirus disease (COVID-19) pandemic due to SARS-CoV-2-associated 39 respiratory tract illness has created unprecedented demand for diagnostic testing. Infection with 40 SARS-CoV-2 leads to a range of outcomes from asymptomatic infection to mild and moderate 41 symptoms including fever and cough to the requirement of intensive respiratory support and 42 death. According to the Johns Hopkins University COVID-19 Dashboard, as of May 6, 2020, 43 there are over 3.7 million confirmed cases of COVID-19 and more than 258,000 deaths 44 worldwide, with the U.S. representing the country with the largest number of reported cases and 45 deaths to date. Unfortunately, many cases are likely to have gone undocumented because testing 46resources have been limited such that testing has been predominantly restricted to the most at-47 risk individuals. As more resources are produced and more testing is implemented, less acute 48 cases of COVID-19 should be able to be tested and identified. 49The slow implementation of testing and the lack of testing capacity has repeatedly made 50 headlines. Initial problems with the CDC test led to delayed deployment to public health labs and 51 restricted testing to the CDC for several weeks. Further delaying implementation of testing was 52 the requirement for laboratory-developed tests (LDTs) to be submitted for U.S Federal Drug 53 Administration (FDA) Emergency Use Authorization (EUA) review (discussed below) and 54 shortages of collection devices, extraction kits, mastermix and other commercial reagents. 55Additionally, commercial manufacturers of diagnostic devices took several additional weeks to 56 devel...

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