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SARS-CoV-2 Viral dynamics

Cite this dataset

Alamri, Maha (2022). SARS-CoV-2 Viral dynamics [Dataset]. Dryad.


Background: Cases of undiagnosed pneumonia have emerged, and sequencing of respiratory samples indicated the presence of SARS-CoV-2 causing COVID-19. Patients with higher viral load and lower Ct values tend to have progressive disease and severe lung injury. The objective of this study is to describe the clinical manifestation and disease outcomes of COVID-19 patients in relation to their Ct values.

Methods: A retrospective, single-center observational study was performed, including patients admitted to King Faisal Specialist Hospital and Research Centre (KFSH&RC) Riyadh in one month in 2020 and have a confirmed diagnosis of COVID-19. The Ct value was identified to determine the viral load. All patients were treated according to KFSH&RC guidelines. Patients were divided into HCQ/AZI and non HCQ/AZI treated groups.

Results: There were many days where Ct values were not available. An attempt at imputing information for missing Ct values was made using logic. The logic leads to an ordinal Ct score 1, 2, 3, or 4. As a result, complete Ct score profiles were available. There was no evidence of statistically significant difference between the two groups in regard to clinical severity, duration to negative test, or changes in Ct values. 

Conclusion: There is little knowledge known to the time profile of Ct values and their relation to disease course of COVID-19. This study provides insight on how Ct values might be used to determine treatment efficacy. As it might be difficult to obtain Ct values at all times, this study provides an imputation method that may be used with conservative statistical assumptions for analyses of Ct profiles. 


A retrospective, single-center observational study was undertaken and included all patients who were admitted to KFSH&RC-Riyadh in one month in 2020 and had a confirmed diagnosis of COVID-19 based on a positive PCR taken from a respiratory sample.  The study was approved by the policies and guidelines for clinical research at KFSH&RC and the KFSH&RC-Riyadh Institutional Review Board (IRB) with a RAC number RAC # 2201054. As this is a retrospective study, consent to participate from patients was waived by the IRB.

All but two patients were followed for a total duration of 14 days after the initial diagnosis. Repeat PCR results were sought during data abstraction for days 3, 7, 10, and 14. The Ct value was identified on the obtained samples. All patients were treated according to KFSH&RC treatment guidelines (as detailed below).

Epidemiological, demographic, clinical, laboratory, treatment administered, and outcome of the disease data were obtained from the patient’s electronic medical records. All data were entered in a password-protected database developed using the Research Electronic Data Capture (REDCap) version 9.4 software. The Ct values on admission and follow-up samples were obtained from the microbiology laboratory. As hydroxychloroquine (HCQ) and azithromycin (AZI) were one of the commonly used regimens for treatment, we divided our cohort into HCQ/AZI and non-HCQ/AZI treated groups.

Usage notes

NA is a non-available value.