{"doi":"10.1101/2021.04.26.21256131","title":"SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples","abstract":"Abstract Background Given the persistence of viral RNA in clinically recovered COVID-19 patients, subgenomic RNAs (sgRNA) have been reported as potential molecular viability markers for 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 three time points in the Lambda (Day 1, 4 and 6) and favipiravir (Day 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by RT-qPCR. To investigate the decay kinetics in vitro , we measured gRNA and sgRNA in A549 ACE2+ cells infected with SARS-CoV-2, following treatment with remdesivir or DMSO control. Results At six days in the Lambda trial and ten 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 (Pearson’s r=0.87) and the rate of increase did not differ significantly in Lambda (1.36 cycles/day vs 1.36 cycles/day; p = 0.97) or favipiravir (1.03 cycles/day vs 0.94 cycles/day; p=0.26) trials. 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 ACE2+ 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. Summary We observed prolonged detection of subgenomic RNA in nasal swabs and equivalent decay rates to genomic RNA in both longitudinal nasal swabs and in remdesivir-treated A549 ACE2+ cells infected with SARS-CoV-2. Taken together, these findings suggest that subgenomic RNA from SARS-CoV-2 is comparably stable to genomic RNA and that its detection is therefore not a more reliable indicator of replicating virus.","journal":"medRxiv","year":2021,"id":224087,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.7451,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":825846,"name":"Eugene Kim","orcid":"0000-0003-3409-4124","position":1,"is_corresponding":false},{"id":105415,"name":"Giovanny J. Martínez-Colón","orcid":"0000-0001-6792-8004","position":2,"is_corresponding":false},{"id":233149,"name":"Prasanna Jagannathan","orcid":"0000-0001-6305-758X","position":3,"is_corresponding":false},{"id":105412,"name":"Arjun Rustagi","orcid":"0000-0002-6921-1012","position":4,"is_corresponding":false},{"id":231939,"name":"Julie Parsonnet","orcid":"0000-0001-7342-5366","position":5,"is_corresponding":false},{"id":264385,"name":"Hector Bonilla","orcid":"0000-0002-0513-8733","position":6,"is_corresponding":false},{"id":430078,"name":"Chaitan Khosla","orcid":"0000-0001-6529-495X","position":7,"is_corresponding":false},{"id":401878,"name":"Marisa Holubar","orcid":"0000-0002-7585-1809","position":8,"is_corresponding":false},{"id":105422,"name":"Aruna Subramanian","orcid":"0000-0002-1373-6768","position":9,"is_corresponding":false},{"id":233142,"name":"Upinder Singh","orcid":"0000-0003-0630-0306","position":10,"is_corresponding":false},{"id":50477,"name":"Yvonne Maldonado","orcid":"0000-0002-5664-5583","position":11,"is_corresponding":false},{"id":52017,"name":"Catherine A. Blish","orcid":"0000-0001-6946-7627","position":12,"is_corresponding":false},{"id":231886,"name":"Jason R. Andrews","orcid":"0000-0002-5967-251X","position":13,"is_corresponding":false},{"id":681785,"name":"Renu Verma","orcid":"0000-0003-1277-8824","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-18T23:54:14.760456Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}