Persistent SARS-CoV-2 RNA Shedding Without Evidence of Infectiousness: A Cohort Study of Individuals With COVID-19

Abstract

Background To better understand SARS-CoV-2 shedding duration and infectivity, we estimated SARS-CoV-2 RNA shedding duration, described characteristics associated with viral RNA shedding resolution1, and determined if replication-competent viruses could be recovered ≥10 days after symptom onset among individuals with mild to moderate COVID-19. Methods We collected serial nasopharyngeal specimens at various time points from 109 individuals with rRT-PCR-confirmed COVID-19 in Utah and Wisconsin. We calculated probability of viral RNA shedding resolution using the Kaplan-Meier estimator and evaluated characteristics associated with shedding resolution using Cox proportional hazards regression. We attempted viral culture for 35 rRT-PCR-positive nasopharyngeal specimens collected ≥10 days after symptom onset. Results The likelihood of viral RNA shedding resolution at 10 days after symptom onset was approximately 3%. Time to shedding resolution was shorter among participants aged <18 years (adjusted hazards ratio [aHR]: 3.01; 95% CI: 1.6–5.6) and longer among those aged ≥50 years (aHR: 0.50; 95% CI: 0.3–0.9) compared to participants aged 18–49 years. No replication-competent viruses were recovered. Conclusions Although most patients were positive for SARS-CoV-2 for ≥10 days after symptom onset, our findings suggest that individuals with mild to moderate COVID-19 are unlikely to be infectious ≥10 days after symptom onset.

Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants

“…This was expected as in most cases, viral RNA is detectable by swab of the nasopharyngeal cavity (NP-swab) 2-3 days before onset of symptoms (pre-symptomatic), but rapidly disappears within 5 days after clinical symptom onset 17,33-36 . The genome copy numbers reported here are consistent with a report of 35 RT-QPCR positive specimens that were collected at >10 days after symptom onset, and that failed to yield infectious virus upon culture 25,37,38 . Control experiments established that complete genome coverage and confident SNV detection was possible down to a limit of 7 pfu/ml; however, it is possible that persistent intra-host replication predominanty leads to the accumulation of fragmented viral genomes or debilitated viral particles with low transmission potential as the intra-host selection pressures differ from the selection pressures that lead to increased transmissibility between hosts.…”

Detection of SARS-CoV-2 infection in asymptomatic populations using the DiaSorin molecular Simplexa and Roche Cobas EUA assays

“…There is a possibility with these high Ct specimens, that patients are shedding inactive fragments of viral RNA and that the positive test result is not indicative of active viral replication. This has been previously described in patients 10 days post infection with positive RT-PCR samples but negative viral cultures ( Owusu et al, 2021 ). In addition, according to the Roche IFU the Ct values of these samples are higher than the average Ct values at LOD for both assay targets.…”

Are Posterior Oropharyngeal Saliva Specimens an Acceptable Alternative to Nasopharyngeal Sampling for the Monitoring of SARS-CoV-2 in Primary-Care Settings?

“…Despite this, the concordance between the results for these two kinds of samples did not vary significantly according to the time lapse between collection and symptom onset. We sought to limit this important methodological bias by including only individuals with symptom onset ≤9 days, because the sensitivity of RT–qPCR is >70% within this time range for NPS and because in mild cases shedding of replication-competent virus appears to be rare ≥10 days after onset of symptoms [ 11 , 12 , 24 ]. Moreover, previous studies showed that the sensitivity of saliva testing increased to 90% in individuals with symptoms of <9 days duration [ 9 , 10 ].…”