Automated collection of pathogen-specific diagnostic data for real-time syndromic epidemiological studies

Lindsay Meyers; Christine C. Ginocchio; Aimie N. Faucett; Frederick S. Nolte; Per H. Gesteland; Amy Leber; Diane Janowiak; Virginia Donovan; Jennifer Dien Bard; Silvia Spitzer; Kathleen A. Stellrecht; Hossein Salimnia; Rangaraj Selvarangan; Stefan Juretschko; Judy A. Daly; Jeremy C. Wallentine; Kristy Lindsey; Franklin Moore; Sharon L. Reed; Maria Aguero-Rosenfeld; Paul D. Fey; Gregory A. Storch; Steve J. Melnick; Christine C. Robinson; Jennifer F. Meredith; Camille V. Cook; Robert K. Nelson; Jay D. Jones; Samuel V. Scarpino; Benjamin M. Althouse; Kirk M. Ririe; Bradley A. Malin; Mark A. Poritz

All sites submitted the Trend project for review by their local Institutional Review Board (IRB); all but one of the 20 IRBs deemed the project "exempt" because of the absence of PHI export. 180 Thus the security requirements for the database and the controls necessary for storage and transport of de-identified data are significantly reduced. The detection counts and pathogen detection rates derived from the Trend data set for each 225 organism in the FilmArray RP are shown in Figure 2 . Other views of these data, including The pathogens' seasonal variability measured by percent detection can be classified into at least three groups. Group 1: The majority of organisms follow the classical "respiratory" season 240 (October through March) and increase by more than 10-fold above their baseline detection rate ( Figure 2C ). These include the CoVs, Flu A, Flu B, hMPV, the PIVs, and RSV (PIV3 is a slight exception to this rule in that it peaks in the summer months, and has a winter peak that is only detected regionally (data not shown)). Within this group, all but five viruses demonstrate significant biennial fluctuations; Flu B, hMPV, OC43, and PIV3 and RSV experience relatively 245 consistent annual peaks. Group 2: HRV/EV is in a class by itself in that it is detected in a high percentage of tests over time, (minimum of 10% in winter) and experiences moderate peaks of two to three fold outside the respiratory season baseline, in the early fall and spring ( Figure 2D ). The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/157156 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/157156 doi: bioRxiv preprint All rights reserved. No reuse allowed without permission.