Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19

Abstract

ABSTRACT Background The detection of SARS-CoV-2 by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR. Here we review our experience using SARS-CoV-2 culture to determine infectivity and safe de-isolation of COVID-19 patients. Methods 195 patients with diverse severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and ICU [n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was documented, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) values of the day four PCR (Ct culture ) and the PCR of the original clinical sample (Ct sample ) were compared, and positive cultures were defined as a Ct sample - Ct culture value of ≥3. Findings Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ct sample values <32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18 days). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0.001) and ICU patients (p<0.0001) compared with outpatients, and in samples with lower Ct sample values. Conclusion SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.