BACKGROUND: Previous studies demonstrated that SARS-CoV-2 RNA can be detected for weeks after infection . The significance of this finding is unclear and, in most patients, does not represent active infection . Detection of subgenomic RNA has been proposed to represent productive infection and may be a useful marker for monitoring infectivity .
METHODS: We used RT-qPCR to quantify total and subgenomic nucleocapsid (sgN) and envelope (sgE) transcripts in 185 SARS-CoV-2 positive nasopharyngeal swab samples collected on hospital admission and to relate to symptom duration .
RESULTS: We find that all transcripts decline at the same rate; however, sgE becomes undetectable before other transcripts . The median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN . There is a linear decline in subgenomic compared to total RNA suggesting subgenomic transcript copy number is dependent on copy number of total transcripts . The mean difference between total and sgN is 16-fold and the mean difference between total and sgE is 137-fold . This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number .
CONCLUSIONS: Subgenomic RNA may be no more useful in determining infectivity than a copy number threshold determined for total RNA.