{"doi":"10.1101/2021.10.22.21265255","title":"Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes","abstract":"ABSTRACT Amplicon-based sequencing methods have been central in characterizing the diversity, transmission and evolution of SARS-CoV-2, but need to be rigorously assessed for clinical utility. Here, we validated the Swift Biosciences’ SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens with a 95% limit of detection of ≥ 40.08 SARS-CoV-2 copies/PCR reaction. Breadth of genome recovery was evaluated across a range of Ct values (11.3 – 36.7, median 21.6). Out of 428 positive samples, 406 (94.9%) generated genomes with < 10% Ns, with a mean genome coverage of 13,545X ± SD 8,382X. No genomes were recovered from PCR-negative specimens (n = 30), or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared to whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R 2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.","journal":"medRxiv","year":2021,"id":221898,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9428,"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":294603,"name":"Michelle J. Lin","orcid":"0000-0002-6925-9948","position":1,"is_corresponding":false},{"id":233053,"name":"Hong Xie","orcid":"0000-0001-6610-0723","position":2,"is_corresponding":false},{"id":804336,"name":"Margaret G. Mills","orcid":"0000-0002-0493-9408","position":3,"is_corresponding":false},{"id":667489,"name":"Shah A. Mohamed Bakhash","orcid":"0000-0003-3170-0862","position":4,"is_corresponding":false},{"id":608594,"name":"Vinod P. Gaur","orcid":null,"position":5,"is_corresponding":false},{"id":667491,"name":"Robert Livingston","orcid":"0000-0002-7424-2956","position":6,"is_corresponding":false},{"id":668455,"name":"Jared Castor","orcid":null,"position":7,"is_corresponding":false},{"id":109794,"name":"Emily A. Bruce","orcid":"0000-0001-8391-370X","position":8,"is_corresponding":false},{"id":109810,"name":"Jason Botten","orcid":"0000-0001-6839-0306","position":9,"is_corresponding":false},{"id":301546,"name":"Meei‐Li Huang","orcid":"0000-0003-2058-2776","position":10,"is_corresponding":false},{"id":108343,"name":"Keith R. Jerome","orcid":"0000-0002-8212-3789","position":11,"is_corresponding":false},{"id":108342,"name":"Alexander L. Greninger","orcid":"0000-0002-7443-0527","position":12,"is_corresponding":false},{"id":71689,"name":"Pavitra Roychoudhury","orcid":"0000-0002-4567-8232","position":13,"is_corresponding":false},{"id":233054,"name":"Lasata Shrestha","orcid":"0000-0002-9760-7348","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":null,"created_at":"2026-07-18T23:53:59.302331Z","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":[]}