key: cord-1036639-bw2y5lpi authors: Choudhuri, J.; Carter, J.; Nelson, R.; Skalina, K.; Osterbur-Badhey, M.; Johnson, A.; Goldstein, D. Y.; Paroder, M.; Szymanski, J. title: SARS-CoV-2 PCR cycle threshold at hospital admission associated with Patient Mortality date: 2020-09-20 journal: nan DOI: 10.1101/2020.09.16.20195941 sha: 81dfa3697b57a5ec72b8d846b2e0a507ea1e5d10 doc_id: 1036639 cord_uid: bw2y5lpi Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cycle threshold (Ct) has been suggested as an approximate measure of initial viral burden. The relationship of initial Ct at hospitalization and patient mortality has not been thoroughly investigated. Methods and findings We conducted a retrospective study of all SARS-CoV-2 positive, hospitalized patients from 3/26/2020 to 8/5/2020 who had SARS CoV-2 Ct data within 48 hours of admission (n=1044). Only patients with complete survival data discharged (n=774) or died in hospital (n=270), were included in our analysis. Laboratory, demographic, and clinical data were extracted from electronic medical records. Multivariable logistic regression was applied to examine the relationship of patient mortality with Ct values while adjusting for established risk factors. Ct values were analyzed both as continuous variables and subdivided into quartiles to better illustrate their relationship with outcomes, and other covariates. Cumulative incidence curves were created to assess whether there was a survival difference in the setting of the competing risks of death versus patient discharge. In this cohort the mean Ct at admission was higher for survivors (28.6, SD=5.8) compared to non-survivors (24.8, SD=6.0, P<0.001). Patients with a lower Ct value on admission were found to have a higher odds ratio (0.91, CI 0.89-0.94, p<0.001) of in hospital mortality after adjusting for age, gender, body mass index (BMI) and history of hypertension and diabetes. Patients with Ct values in 3rd Quartile (Ct 27.4-32.8) and 4th Quartile (Ct >32.9) have a lower odds of in-hospital death (P<0.001) in comparison to the 1st Quartile. On comparing between Ct quartiles, the mortality, BMI and glomerular filtration rate (GFR) were significantly different (p<0.05) between the groups. The cumulative incidence of all-cause mortality and discharge was found to differ between Ct quartiles (Grays Test P<0.001 for both.) Conclusion: SARS-CoV-2 Ct at admission was found to be an independent predictor of in patient mortality. However, further study is needed on how to best clinically utilize such information given the result variation due to specimen quality, phase of disease, and the limited discriminative ability of the test. ( c o r r e l a t i o n b e t w e e n v a r i a b l e s w a s a s s e s s e d u s i n g t h e K e n d a l l r a n k c o r r e l a t i o n m e t h o d d u e t o n o n -122 p a r a m e t r i c d a t a . T h e r e l a t i o n s h i p b e t w e e n i n -h o s p i t a l m o r t a l i t y , c y c l e q u a r t i l e , c l i n i c a l r i s k f a c t o CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this this version posted September 20, 2020. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. c u t p o i n t d e t e r m i n e d u s i n g Y o u d e n ' s i n d e x . T h e c u t p o i n t w h i c h m a x i m i z e d Y o u d e n ' s s t a t i s t i c w a s f o u n d 169 t o b e 2 6 ( C I 2 6 -2 7 ) . A t t h i s c u t p o i n t , t h e t e s t i n g s e t ( o u t -o f -b a g ) s e n s i t i v i t y w a s f o u n d t o b e 0 . 6 5 ( C I 0 CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020 . . https://doi.org/10.1101 . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. . https://doi.org/10. 1101 Page | 21 nd . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. . CC-BY-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) preprint The copyright holder for this this version posted September 20, 2020. . 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