Background: The follow-up of COVID-19 recovered patients is especially important to assess their infectivity and/or transmissibility statuses in order to maximize the COVID-19 management and containment. The aim of this study was to determine both total (genomic) and replicative (sub-genomic) SARS-CoV-2 RNA levels in nasal/oropharyngeal swab (NOS) samples from patients at follow-up times after COVID-19 recovering.
Materials/methods: We tested 176 NOS samples of COVID-19 recovered patients who were followed up at the Fondazione Policlinico Universitario A. Gemelli IRCCS in Rome from 21 April to 18 June 2020, according to our COVID-19 care protocol. The RT-PCR tests were performed using the Allplex™ 2019-nCoV and the Quanty COVID-19 assays (for total RNA detection and quantification, respectively) and an in-house assay (for replicative RNA detection).
Results: Of 176 NOS samples studied, 32 (18.2%) tested positive for total RNA, with CT values ranging from 29.3 to 38.8 for E, RdRP, and N genes (9 samples), 32.2 to 39.3 for RdRP and N genes (7 samples) or 35.8 to 39.8 for the N gene (16 samples). Consistently, viral loads ranged from 1.6 × 101 to 1.3 × 104 RNA copies/mL. Interestingly, we found replicative RNA in only one of 32 positive samples based on the presence of E-gene sub-genomic RNA (CT value of 39.1). The CT value (29.3) of E-gene genomic RNA in this sample was the lowest among the CT values of all 9 samples in which the E gene was detected. Testing samples obtained from the 32 patients at the time of COVID-19 diagnosis showed that the CT values ranged from 17.1 to 38.1 for E, RdRP, and N genes. Of note, the mean CT value of E-gene sub-genomic RNA (34.9) in these samples differed of 9.0 ± 2.8 from the mean CT value of E-gene genomic RNA (25.9). Finally, all but one of the 32 patients had positive serology results against SARS-CoV-2.
Conclusions: Our findings show that at least a proportion of COVID-19 recovered patients were still positive for SARS-CoV-2 RNA, despite to a lower extent, and that only a minority of them was likely to have actively replicating virus in the upper respiratory tract.