{"doi":"10.1101/2020.03.20.001008","title":"DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP","abstract":"The ongoing COVID-19 pandemic has caused an unprecedented need for rapid diagnostic testing. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recommend a standard assay that includes an RNA extraction step from a nasopharyngeal (NP) swab followed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) to detect the purified SARS-CoV-2 RNA. The current global shortage of RNA extraction kits has caused a severe bottleneck to COVID-19 testing. We hypothesized that SARS-CoV-2 RNA could be detected from NP samples via a direct RT-qPCR assay that omits the RNA extraction step altogether, and tested this hypothesis on a series of blinded clinical samples. The direct RT-qPCR approach correctly identified 92% of NP samples (n = 155) demonstrated to be positive for SARS-CoV-2 RNA by traditional clinical diagnostic RT-qPCR that included an RNA extraction. Thus, direct RT-qPCR could be a front-line approach to identify the substantial majority of COVID-19 patients, reserving a repeat test with RNA extraction for those individuals with high suspicion of infection but an initial negative result. This strategy would drastically ease supply chokepoints of COVID-19 testing and should be applicable throughout the world.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":118426,"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":83,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9585,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":301546,"name":"Meei‐Li Huang","orcid":"0000-0003-2058-2776","position":1,"is_corresponding":false},{"id":246853,"name":"Garrett A. Perchetti","orcid":"0000-0003-3786-0509","position":2,"is_corresponding":false},{"id":33230,"name":"Scott Tighe","orcid":"0000-0002-3988-0741","position":3,"is_corresponding":false},{"id":246854,"name":"Pheobe Laaguiby","orcid":"0000-0002-4845-6985","position":4,"is_corresponding":false},{"id":551398,"name":"Jessica J. Hoffman","orcid":null,"position":5,"is_corresponding":false},{"id":172380,"name":"Diana L. Gerrard","orcid":null,"position":6,"is_corresponding":false},{"id":551399,"name":"Arun K. Nalla","orcid":null,"position":7,"is_corresponding":false},{"id":248616,"name":"Yulun Wei","orcid":null,"position":8,"is_corresponding":false},{"id":108342,"name":"Alexander L. Greninger","orcid":"0000-0002-7443-0527","position":9,"is_corresponding":false},{"id":246856,"name":"Sean A. Diehl","orcid":"0000-0001-9700-235X","position":10,"is_corresponding":false},{"id":246857,"name":"David J. Shirley","orcid":"0000-0003-4529-0403","position":11,"is_corresponding":false},{"id":246858,"name":"Debra G. B. Leonard","orcid":"0000-0003-1431-4935","position":12,"is_corresponding":false},{"id":246859,"name":"Christopher D. Huston","orcid":"0000-0002-5393-139X","position":13,"is_corresponding":false},{"id":246860,"name":"Beth D. Kirkpatrick","orcid":"0000-0002-7016-7338","position":14,"is_corresponding":false},{"id":246861,"name":"Julie A. Dragon","orcid":"0000-0002-8031-5381","position":15,"is_corresponding":false},{"id":246862,"name":"Jessica W. Crothers","orcid":"0000-0003-4594-5051","position":16,"is_corresponding":false},{"id":108343,"name":"Keith R. Jerome","orcid":"0000-0002-8212-3789","position":17,"is_corresponding":false},{"id":109810,"name":"Jason Botten","orcid":"0000-0001-6839-0306","position":18,"is_corresponding":false},{"id":109794,"name":"Emily A. Bruce","orcid":"0000-0001-8391-370X","position":0,"is_corresponding":true}],"reference_count":6,"raw_metadata":null,"created_at":"2026-07-18T23:13:58.531532Z","pmid":"32511328","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":[]}