SARS-CoV-2 normalized viral loads and subgenomic RNA detection as tools for improving clinical decision-making and work reincorporation

Santos Bravo, Marta; Nicolás, David; Berengua, Carla; Fernandez, Mariana; Hurtado, Juan Carlos; Tortajada, Marta; Barroso, Sonia; Vilella, Anna; Mosquera, Mar; Vila, Jordi; Marcos, María Angeles

BACKGROUND: SARS-CoV-2 RT-PCR provides a highly variable cycle-threshold (Ct) value that cannot distinguish viral infectivity. Subgenomic RNA (sgRNA) has been used to monitor active replication. Given the importance of long RT-PCR positivity and the need for work reincorporation and discontinuing isolation, we studied the functionality of normalized viral loads (NVL) for patient monitoring and sgRNA for viral infectivity detection. METHODS: NVL measured through the Nucleocapsid and RNA-dependent-RNA-polymerase genes and sgRNA RT-PCRs were performed in 2 consecutive swabs from 84 health-care workers. RESULTS: NVL provided similar and accurate quantities of both genes of SARS-CoV-2 at two different time-points of infection, overcoming Ct-value and swab collection variability. Among SARS-CoV-2-positive samples, 51.19% were sgRNA-positive in the 1 (st)RT-PCR and 5.95% in the 2 (nd)RT-PCR. All sgRNA-positive samples had >4log(10)RNAcopies/1000cells, while samples with ≤1log(10) NVL were sgRNA-negative. Although NVL were positive until 29 days after symptom onset, 84.1% of sgRNA-positive samples were from the first 7 days, which correlated with viral culture viability. Multivariate analyses showed that sgRNA, NVL and days of symptoms were significantly associated (p<0.001) CONCLUSIONS: NVL and sgRNA are two rapid accessible techniques that could be easily implemented in routine hospital practice providing a useful proxy for viral infectivity and COVID-19 patient follow-up.