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

Abstract

BACKGROUND: The detection of SARS-CoV-2 RNA 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. METHODS: One hundred and ninety-five patients with varying severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and critically unwell patients admitted to the intensive care unit [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 observed, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) of the day four PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined where Ctsample - Ctculture was ?3. FINDINGS: Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ctsample ?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). 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 respectively, and in samples with lower Ctsample. CONCLUSION: SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols.