{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001482505,0.0002073688,0.0002298913,0.0006531719,0.0002257189,0.0003101149,0.00009394062,0.0001981215,0.001022352],"category_scores_gemma":[0.0004274698,0.00008455184,0.0002428331,0.0006392048,0.0001330919,0.0001538658,0.0001300448,0.000192547,0.00034732],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002265331,"about_ca_system_score_gemma":0.0002956768,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005309485,"about_ca_topic_score_gemma":0.0155017,"domain_scores_codex":[0.9999158,0.00001251306,0.000005499174,0.00002793292,0.00002266536,0.00001562314],"domain_scores_gemma":[0.999815,0.00004315062,0.00006163006,0.00001461096,0.00003854306,0.0000270918],"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":[0.0005119169,0.00006299751,0.4544449,0.0001434374,0.0001317162,0.0006289735,0.0002233367,0.002574849,0.5085912,0.0003044922,0.0004541197,0.03192794],"study_design_scores_gemma":[0.00001354157,0.0001921656,0.9563529,0.00003403489,0.0000873992,0.001185288,0.0002921802,0.01458047,0.02372214,0.0004214317,0.003101022,0.0000175041],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9960891,0.0002568919,0.001639182,0.0000376732,0.000004620479,0.000009263152,0.001222607,0.00003956817,0.0007010323],"genre_scores_gemma":[0.9938426,0.0001272235,0.002783771,0.00003714313,0.000004548751,0.000006664669,0.002864531,0.000009193306,0.0003243754],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005309485,"threshold_uncertainty_score":0.01055717,"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."}}