{"doi":"10.1093/ajcp/aqab212","title":"High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants","abstract":"OBJECTIVES: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure. METHODS: We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription-polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants. RESULTS: The median turnaround for genotyping was 2 days using the high-throughput RT-PCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach. CONCLUSIONS: These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.","journal":"American Journal of Clinical Pathology","year":2021,"id":211461,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9618,"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":800944,"name":"Xiao Song","orcid":"0000-0003-1546-3094","position":1,"is_corresponding":false},{"id":801350,"name":"Cameron Norris","orcid":null,"position":2,"is_corresponding":false},{"id":800945,"name":"Mehul Jani","orcid":"0000-0002-2486-5696","position":3,"is_corresponding":false},{"id":800946,"name":"David Alouani","orcid":"0000-0002-8539-2562","position":4,"is_corresponding":false},{"id":801351,"name":"Maureen Atchley","orcid":null,"position":5,"is_corresponding":false},{"id":800947,"name":"Lisa M. Stempak","orcid":"0000-0001-8314-7638","position":6,"is_corresponding":false},{"id":800948,"name":"Sarah Cherian","orcid":"0009-0006-4292-1651","position":7,"is_corresponding":false},{"id":800949,"name":"Christine Schmotzer","orcid":"0000-0002-7235-8728","position":8,"is_corresponding":false},{"id":800950,"name":"Navid Sadri","orcid":"0000-0001-5051-717X","position":9,"is_corresponding":false},{"id":697701,"name":"Zita Hubler","orcid":"0000-0003-0991-6229","position":0,"is_corresponding":true}],"reference_count":23,"raw_metadata":null,"created_at":"2026-07-18T23:52:20.112538Z","pmid":"34999740","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":[]}