{"id":"W4408913977","doi":"10.1101/2025.03.25.645210","title":"Long-Term Intra-Host Evolution of SARS-CoV-2 in an Immunocompromised Patient: Recombination and Within-Host Mutations Driving Viral Adaptation","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Nautical Research Society","funders":"","keywords":"Host (biology); Adaptation (eye); Term (time); Host adaptation; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Recombination; Coronavirus disease 2019 (COVID-19); Biology; Virology; Viral evolution; Mutation; Evolutionary biology; Genetics; Gene; Medicine; Genome; Neuroscience; Infectious disease (medical specialty); Disease","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001486921,0.0004041285,0.0004032947,0.0002862323,0.000782426,0.0005068274,0.0001834311,0.0009616493,0.0008040522],"category_scores_gemma":[0.0005963728,0.0002429385,0.0003713594,0.0002205346,0.0003538133,0.0003424008,0.0002975673,0.0008992172,0.0002733125],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003378518,"about_ca_system_score_gemma":0.0001649437,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007631555,"about_ca_topic_score_gemma":0.0007393189,"domain_scores_codex":[0.9998782,0.00001747063,0.00001051336,0.00003952375,0.00001477196,0.00003953604],"domain_scores_gemma":[0.999751,0.00006489355,0.000050903,0.00001656348,0.00001358754,0.0001029857],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"case_report","study_design_gemma":"observational","study_design_scores_codex":[0.001462467,0.0007223453,0.3403417,0.00004557932,0.00005462054,0.5869975,0.002237565,0.0009071968,0.05653591,0.0004905125,0.0003183172,0.009886146],"study_design_scores_gemma":[0.0001009426,0.004750077,0.3029632,0.00003143843,0.00009583202,0.6735967,0.00144093,0.004287224,0.01066522,0.0004187911,0.001592496,0.00005711726],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9994256,0.00005998872,0.00009353218,0.00006598093,0.000003413401,0.000004712066,0.00001630942,0.000003580561,0.0003268123],"genre_scores_gemma":[0.9996583,0.00003681309,0.0000822483,0.00005986808,0.00001252269,0.00000130075,0.00001855899,0.000002692406,0.0001275917],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0009616493,"threshold_uncertainty_score":0.002689898,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02588574240984989,"score_gpt":0.2934055356682966,"score_spread":0.2675197932584468,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}