SARS-CoV-2 PCR cycle threshold at hospital admission associated with Patient Mortality

Choudhuri, J.; Carter, J.; Nelson, R.; Skalina, K.; Osterbur-Badhey, M.; Johnson, A.; Goldstein, D. Y.; Paroder, M.; Szymanski, J.

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.