{"doi":"10.1093/infdis/jiad164","title":"Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Genomic Variation Associated With Breakthrough Infection in Northern California: A Retrospective Cohort Study","abstract":"BACKGROUND: The association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic variation and breakthrough infection is not well defined among persons with Delta variant SARS-CoV-2 infection. METHODS: In a retrospective cohort, we assessed whether individual nonlineage defining mutations and overall genomic variation (including low-frequency alleles) were associated with breakthrough infection, defined as SARS-CoV-2 infection after coronavirus disease 2019 primary vaccine series. We identified all nonsynonymous single-nucleotide polymorphisms, insertions, and deletions in SARS-CoV-2 genomes with ≥5% allelic frequency and population frequency of ≥5% and ≤95%. Using Poisson regression, we assessed the association with breakthrough infection for each individual mutation and a viral genomic risk score. RESULTS: Thirty-six mutations met our inclusion criteria. Among 12 744 persons infected with Delta variant SARS-CoV-2, 5949 (47%) were vaccinated and 6795 (53%) were unvaccinated. Viruses with a viral genomic risk score in the highest quintile were 9% more likely to be associated with breakthrough infection than viruses in the lowest quintile, but including the risk score improved overall predictive model performance (measured by C statistic) by only +0.0006. CONCLUSIONS: Genomic variation within SARS-CoV-2 Delta variant was weakly associated with breakthrough infection, but several potential nonlineage defining mutations were identified that might contribute to immune evasion by SARS-CoV-2.","journal":"The Journal of Infectious Diseases","year":2023,"id":381895,"datarank":0.20794415416798362,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.0,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9595,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":578554,"name":"Joshua R. Nugent","orcid":"0000-0002-4479-9673","position":1,"is_corresponding":false},{"id":1148186,"name":"Mariah S. Wood","orcid":null,"position":2,"is_corresponding":false},{"id":1147796,"name":"Liyan Liu","orcid":"0000-0001-5841-4351","position":3,"is_corresponding":false},{"id":919907,"name":"Teal Bullick","orcid":"0000-0001-9043-6155","position":4,"is_corresponding":false},{"id":234548,"name":"Jeffrey M. Schapiro","orcid":null,"position":5,"is_corresponding":false},{"id":1147797,"name":"Phacharee Arunleung","orcid":"0000-0002-2446-4227","position":6,"is_corresponding":false},{"id":1018537,"name":"Christina Morales","orcid":"0000-0001-5813-7219","position":7,"is_corresponding":false},{"id":1147798,"name":"Laura B. Amsden","orcid":"0000-0003-1178-2792","position":8,"is_corresponding":false},{"id":1147799,"name":"Crystal A. Hsiao","orcid":"0000-0003-0806-2671","position":9,"is_corresponding":false},{"id":104243,"name":"Debra A. Wadford","orcid":"0000-0002-8630-427X","position":10,"is_corresponding":false},{"id":234937,"name":"Shua J. Chai","orcid":"0000-0003-2048-2871","position":11,"is_corresponding":false},{"id":234314,"name":"Arthur Reingold","orcid":null,"position":12,"is_corresponding":false},{"id":273395,"name":"Stacia K. Wyman","orcid":"0000-0002-8937-8397","position":13,"is_corresponding":false},{"id":636517,"name":"Jacek Skarbinski","orcid":"0000-0003-1630-5733","position":0,"is_corresponding":true}],"reference_count":21,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:17:12.933204Z","pmid":"37195913","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":[]}