{"doi":"10.1093/jalm/jfae095","title":"SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity","abstract":"BACKGROUND: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. METHODS: SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. RESULTS: Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%-65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. CONCLUSIONS: As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.","journal":"The Journal of Applied Laboratory Medicine","year":2024,"id":503047,"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":0.9607,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1352727,"name":"Yunho Shin","orcid":"0009-0001-3934-8544","position":1,"is_corresponding":false},{"id":296618,"name":"Yesun Lee","orcid":null,"position":2,"is_corresponding":false},{"id":242087,"name":"Thomas Fabrizio","orcid":"0000-0002-8960-0728","position":3,"is_corresponding":false},{"id":867715,"name":"Zion Congrave‐Wilson","orcid":"0000-0002-6131-7349","position":4,"is_corresponding":false},{"id":400254,"name":"Wesley A. Cheng","orcid":"0000-0001-9131-8556","position":5,"is_corresponding":false},{"id":294650,"name":"Jaycee Jumarang","orcid":"0000-0002-0123-7718","position":6,"is_corresponding":false},{"id":1113715,"name":"Minjun Kim","orcid":"0009-0006-5755-6837","position":7,"is_corresponding":false},{"id":505623,"name":"Richard Webby","orcid":null,"position":8,"is_corresponding":false},{"id":912509,"name":"Jeffrey M. Bender","orcid":"0000-0001-9768-264X","position":9,"is_corresponding":false},{"id":91739,"name":"Pia S. Pannaraj","orcid":"0000-0002-5208-0933","position":10,"is_corresponding":false},{"id":277268,"name":"Jason S. Chwa","orcid":"0000-0003-0897-4611","position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":null,"created_at":"2026-07-19T02:10:27.781502Z","pmid":"39246012","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":[]}