Persistent SARS-CoV-2 replication in severe COVID-19

Background: The diagnosis of SARS-CoV-2 infection is based on viral RNA detection by real-time RT-PCR (rRT-PCR) in respiratory samples. This detection can remain positive for weeks without implying virus viability. Methods: We have performed cell culture to assess viral replication in 106 respiratory samples rRT-PCR positive for SARS-CoV-2 from 105 patients with COVID-19. Fifty were samples from 50 patients with mild forms of COVID-19 who did not require hospital admission. Fifty-six samples were obtained from 55 hospitalized patients with severe pneumonia. Samples were obtained at different time points covering the time from clinical diagnosis to the follow up during hospital care. Results: In 49 samples (49/106, 46.2%) a cytopathic effect (CPE) was detected in cell culture. Our study demonstrates that while in patients with mild COVID-19, viral viability is maintained in fact up to 10 days in patients with severe COVID-19 the virus can remain viable for up to 32 days after the onset of symptoms. Patients with severe COVID-19 as compared with mild cases, presented infective virus in a significantly higher proportion in samples with moderate or low viral load (Ct value > 26): 22/46 (47.8%) versus 7/38 (18.4%), (p <0.01), respectively. Conclusions: Persistent SARS-CoV-2 replication could be demonstrated in severe COVID-19 cases for periods up to 32 days after the onset of symptoms and even at high Ct values. COVID-19 severity is a more determining factor for viral viability than the time elapsed since the onset of symptoms or the Ct value obtained in the RT-PCR assay.