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

Abstract

Abstract 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 stRT-PCR and 5.95% in the 2 ndRT-PCR. All sgRNA-positive samples had >4log10RNAcopies/1000cells, while samples with ≤1log10 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.