• Detection and kinetics of subgenomic SARS-CoV-2 RNA viral load in longitudinal diagnostic RNA positive samples.

      Deming, Meagan E; Dong, Tracy Q; Agrawal, Vaidehi; Mills, Margaret G; Huang, Meei-Li W; Greninger, Alexander L; Jerome, Keith R; Wener, Mark H; Paasche-Orlow, Michael K; Kissinger, Patricia; et al. (Oxford University Press, 2022-02-12)
      While detection of SARS-CoV-2 by diagnostic RT-PCR is highly sensitive for viral RNA, the nucleic acid amplification of subgenomic RNAs (sgRNA) that are the product of viral replication may more accurately identify replication. We characterized the diagnostic RT-PCR and sgRNA detection from nasal swabs collected daily by participants in post exposure prophylaxis or treatment studies for SARS-CoV-2. Among 1932 RT-PCR-positive swabs with sgRNA tests, 40% (767) had detectable sgRNA. Above a diagnostic PCR viral load threshold of 5.1 log10 copies/mL, 96% of samples had detectable sgRNA with viral loads that followed a linear trend. The trajectories of diagnostic and sgRNA viral loads differed, with 80% peaking on the same day but duration of sgRNA detection being shorter (8 versus 14 days). With a large sample of daily swabs we provide comparative sgRNA kinetics and a diagnostic PCR threshold that correlates with replicating virus independent of symptoms or duration of illness.