{"id":"W4392379100","doi":"10.1128/spectrum.03584-23","title":"Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source","year":2024,"lang":"en","type":"article","venue":"Microbiology Spectrum","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba; McMaster University; University of Guelph; Canadian Food Inspection Agency","funders":"Environment and Climate Change Canada; Natural Sciences and Engineering Research Council of Canada; Government of Canada","keywords":"Mink; Biology; Genetics; Lineage (genetic); Adaptation (eye); Major histocompatibility complex; In silico; Odocoileus; Human leukocyte antigen; Immune system; Negative selection; Host adaptation; Single-nucleotide polymorphism; Gene; Epitope; Evolutionary biology; Genome; Zoology; Antigen; Genotype","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005227372,0.0002550404,0.0004200251,0.0002857397,0.0001016877,0.0000378132,0.0004858774,0.0002499207,0.00002535317],"category_scores_gemma":[0.0001310282,0.0001662135,0.0001568838,0.0006121802,0.00053244,0.00003158752,0.0002018301,0.0007337159,0.0001193527],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000190033,"about_ca_system_score_gemma":0.0005442533,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008593726,"about_ca_topic_score_gemma":0.001361759,"domain_scores_codex":[0.9982238,0.0001336626,0.0003534515,0.0005622118,0.0001571083,0.0005697093],"domain_scores_gemma":[0.9990289,0.0002136501,0.00006037736,0.0006000269,0.0000593375,0.00003774079],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001792712,0.00004707909,0.002495959,0.0001031013,0.0001933423,0.000146806,0.001862335,0.000003105149,0.9919145,0.0004330207,0.002563783,0.00005775659],"study_design_scores_gemma":[0.0003568291,0.0005965538,0.0007513465,0.00008671177,0.00005922655,0.0002874994,0.0001492246,0.00006379436,0.8306774,0.0001212694,0.1666993,0.0001508487],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9819049,0.001776006,0.0001475022,0.01421054,0.0003249609,0.0007194926,0.0002001763,0.000156618,0.0005598592],"genre_scores_gemma":[0.9539354,0.000003696492,0.00007826277,0.04539795,0.0002448661,0.00003315119,0.00002528336,0.00004454453,0.0002367807],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1641355,"threshold_uncertainty_score":0.6777992,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04385763729349602,"score_gpt":0.3283171049472425,"score_spread":0.2844594676537465,"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."}}