Viral culture confirmed SARS-CoV-2 subgenomic RNA value as a good surrogate marker of infectivity.

Determining SARS-CoV-2 viral infectivity is crucial for patient clinical assessment and isolation decisions. We assessed subgenomic RNA (sgRNA) as a surrogate marker of SARS-CoV-2 infectivity in SARS-CoV-2-positive RT-PCR respiratory samples (n=105) by comparison with viral culture as the reference standard for virus replication. sgRNA and viral isolation results were concordant in 99/105 cases (94%) indicating highly significant agreement between the two techniques (Cohen's kappa coefficient 0.88, 95% CI 0.78-0.97, p<0.001). sgRNA RT-PCR showed a sensitivity of 97% and a positive predictive value of 94% to detect replication-competent virus, further supporting sgRNA as a surrogate marker of SARS-CoV-2 infectivity. sgRNA RT-PCR is an accurate, rapid and affordable technique that can overcome culture and Ct value limitations and can be routinely implemented in hospital laboratories to detect viral infectivity, which is essential to optimize patient monitoring, the efficacy of treatments/vaccines, work reincorporation policies and for safely shortening isolation precautions.