{"id":"W4414029224","doi":"10.1101/2025.09.01.673077","title":"Viral evolution during primary infection in immunocompromised hosts","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":"Université de Montréal","funders":"","keywords":"Primary (astronomy); Virology; Viral evolution; Viral infection; Human immunodeficiency virus (HIV); Biology; Immunology; Virus; Genetics; Genome; Gene","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":[0.0001634421,0.0001763537,0.0002504147,0.0001997701,0.0001759407,0.0003824177,0.0001117145,0.0002748671,0.002803489],"category_scores_gemma":[0.0003507979,0.00007226716,0.0001292759,0.0001055737,0.0001963971,0.0001734667,0.0002556147,0.0004346865,0.0003503659],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002346042,"about_ca_system_score_gemma":0.00009224249,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001979878,"about_ca_topic_score_gemma":0.0001644553,"domain_scores_codex":[0.9998662,0.00002859164,0.000007772449,0.00003891416,0.00002218519,0.00003629822],"domain_scores_gemma":[0.9997025,0.00008632844,0.00009156215,0.00003007812,0.00001591789,0.00007351699],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0008472036,0.0001213788,0.01546373,0.00005402097,0.00002212154,0.0008709683,0.0001152065,0.0007452644,0.9753283,0.0005782153,0.0001791072,0.005674517],"study_design_scores_gemma":[0.0001302441,0.004224362,0.2881696,0.00005069856,0.00009380191,0.01230591,0.0006188778,0.01042191,0.6731089,0.003090219,0.007724034,0.00006149703],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980118,0.0004342965,0.0005711685,0.0000381657,0.000008717102,0.000005474056,0.0001031428,0.00001329298,0.0008138455],"genre_scores_gemma":[0.9985083,0.0001544611,0.0004844886,0.00003128645,0.000008035684,0.000006608259,0.0001146539,0.000006049529,0.0006861294],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002803489,"threshold_uncertainty_score":0.009378552,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01422740314406222,"score_gpt":0.2693266249988345,"score_spread":0.2550992218547723,"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."}}