tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2021 Jun 11;8(7)
fab310.
doi: 10.1093/ofid/ofab310. eCollection 2021 Jul.
SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples
Renu Verma[SUP] 1 [/SUP], Eugene Kim[SUP] 1 [/SUP], Giovanny Joel Martínez-Colón[SUP] 1 [/SUP], Prasanna Jagannathan[SUP] 1 [/SUP], Arjun Rustagi[SUP] 1 [/SUP], Julie Parsonnet[SUP] 1 2 [/SUP], Hector Bonilla[SUP] 1 [/SUP], Chaitan Khosla[SUP] 3 [/SUP], Marisa Holubar[SUP] 1 [/SUP], Aruna Subramanian[SUP] 1 [/SUP], Upinder Singh[SUP] 1 4 [/SUP], Yvonne Maldonado[SUP] 5 [/SUP], Catherine A Blish[SUP] 1 [/SUP], Jason R Andrews[SUP] 1 [/SUP]
Affiliations
Abstract
Background: Given the persistence of viral RNA in clinically recovered coronavirus disease 2019 (COVID-19) patients, subgenomic RNAs (sgRNAs) have been reported as potential molecular viability markers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples.
Methods: We analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of peginterferon Lambda-1a (Lambda; n = 177) and favipiravir (n = 359). Nasal swabs were collected at 3 time points in the Lambda (days 1, 4, and 6) and favipiravir (days 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by quantitative reverse transcription polymerase chain reaction. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549[SUP]ACE2+[/SUP] cells infected with SARS-CoV-2, following treatment with remdesivir or dimethylsulfoxide control.
Results: At 6 days in the Lambda trial and 10 days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (marginal R [SUP]2[/SUP] = 0.83), and the rate of increase did not differ significantly in the Lambda trial (1.36 cycles/d vs 1.36 cycles/d; P = .97) or the favipiravir trial (1.03 cycles/d vs 0.94 cycles/d; P = .26). From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2-infected A549[SUP]ACE2+[/SUP] cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA.
Conclusions: In clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.
Keywords: COVID-19; SARS-CoV-2; cohort; infectiousness; subgenomic RNA.
. 2021 Jun 11;8(7)
fab310.doi: 10.1093/ofid/ofab310. eCollection 2021 Jul.
SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples
Renu Verma[SUP] 1 [/SUP], Eugene Kim[SUP] 1 [/SUP], Giovanny Joel Martínez-Colón[SUP] 1 [/SUP], Prasanna Jagannathan[SUP] 1 [/SUP], Arjun Rustagi[SUP] 1 [/SUP], Julie Parsonnet[SUP] 1 2 [/SUP], Hector Bonilla[SUP] 1 [/SUP], Chaitan Khosla[SUP] 3 [/SUP], Marisa Holubar[SUP] 1 [/SUP], Aruna Subramanian[SUP] 1 [/SUP], Upinder Singh[SUP] 1 4 [/SUP], Yvonne Maldonado[SUP] 5 [/SUP], Catherine A Blish[SUP] 1 [/SUP], Jason R Andrews[SUP] 1 [/SUP]
Affiliations
- PMID: 34295944
- PMCID: PMC8291522
- DOI: 10.1093/ofid/ofab310
Abstract
Background: Given the persistence of viral RNA in clinically recovered coronavirus disease 2019 (COVID-19) patients, subgenomic RNAs (sgRNAs) have been reported as potential molecular viability markers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples.
Methods: We analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of peginterferon Lambda-1a (Lambda; n = 177) and favipiravir (n = 359). Nasal swabs were collected at 3 time points in the Lambda (days 1, 4, and 6) and favipiravir (days 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by quantitative reverse transcription polymerase chain reaction. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549[SUP]ACE2+[/SUP] cells infected with SARS-CoV-2, following treatment with remdesivir or dimethylsulfoxide control.
Results: At 6 days in the Lambda trial and 10 days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (marginal R [SUP]2[/SUP] = 0.83), and the rate of increase did not differ significantly in the Lambda trial (1.36 cycles/d vs 1.36 cycles/d; P = .97) or the favipiravir trial (1.03 cycles/d vs 0.94 cycles/d; P = .26). From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2-infected A549[SUP]ACE2+[/SUP] cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA.
Conclusions: In clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.
Keywords: COVID-19; SARS-CoV-2; cohort; infectiousness; subgenomic RNA.