Earlier de-isolation of SARS-CoV-2-infected ICU patients using a novel viability PCR: a prospective cohort study

Intensive care unit (ICU) patients with COVID-19 are isolated until two subsequent SARS-CoV-2 PCR tests have become negative. The question is whether the viral RNA detected here represents intact or compromised viral particles. A viability PCR method detects only intact infectious viruses and disregards RNA from incomplete non-infectious viruses or RNA remnants. We hypothesize that the time to a negative PCR is shorter using the viability PCR compared to conventional SARS-CoV-2 PCR. Patients admitted to the ICU in the Maastricht University Medical Center within an ongoing prospective cohort were included, and respiratory samples were collected three times weekly. Samples were aliquoted for viability PCR into two aliquots, one of which was treated with propidium monoazide (PMA) to eliminate incomplete viruses. The PMA-untreated sample corresponded to the traditional SARS-CoV-2 PCR used in routine diagnostics. A mean time difference between viability and conventional PCR was estimated, assuming a negative binomial distribution. One hundred two ICU patients were included in the analysis. The time to a negative PCR test result differed significantly between viability PCR and conventional PCR (Paired Prentice-Wilcoxon test P-value = 0.0001). On average, the first negative viability PCR test result occurred 2.4 days (95% CI 1.5-4.2) before the first negative conventional PCR test result. The application of a viability PCR technique for SARS-CoV-2 provided an earlier indication of the absence of intact virus, suggesting reduced infectivity, potentially enabling earlier de-isolation of ICU patients.

This study demonstrated that, within patients, on average, viability PCR became negative 2.4 days earlier than conventional PCR, indicating that viability PCR could potentially assist in de-isolating patients 2.4 days earlier. Future use of this assay could thus aid in improving routine COVID-19 diagnostics and prognostics related to the timing of de-isolation. Additionally, future development of a similar approach for other respiratory viruses could be of interest.