{"id":"W4415397596","doi":"10.1371/journal.pone.0333093","title":"Investigating the evolutionary dynamics and mutational pattern of SARS-CoV-2 spike gene on selected SARS-CoV-2 variants","year":2025,"lang":"en","type":"article","venue":"PLoS ONE","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi di Firenze; Università degli Studi di Perugia; Università di Pisa; Università degli Studi di Verona; Institute of Genetics; Università degli Studi di Firenze; Università degli Studi G. d'Annunzio Chieti - Pescara; Università degli Studi di Palermo; Università di Catania; Università degli Studi di Siena","keywords":"Phylogenetic tree; Phylogenetic network; Gene; Viral evolution; Phylogenetics; Evolutionary dynamics; Mutation; Molecular evolution; Selection (genetic algorithm); Negative selection","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000572754,0.0002591755,0.0003791684,0.001071301,0.0003573353,0.0004475807,0.0002100362,0.0002494731,0.0007298354],"category_scores_gemma":[0.0009067001,0.00009688749,0.0005813058,0.001483975,0.0001272968,0.000315951,0.0003453882,0.0003398235,0.0002399837],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003304897,"about_ca_system_score_gemma":0.0003026729,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004060238,"about_ca_topic_score_gemma":0.005366981,"domain_scores_codex":[0.9996481,0.00006562807,0.00001923049,0.0001538925,0.00006544076,0.00004775509],"domain_scores_gemma":[0.9997553,0.0000770296,0.00005336916,0.00002517614,0.00005991198,0.00002912829],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0006139154,0.0001420275,0.654969,0.0002738128,0.0003464624,0.000893496,0.001030087,0.02007375,0.2421503,0.001060482,0.001287935,0.07715871],"study_design_scores_gemma":[0.0000133051,0.0002343318,0.8821576,0.0000541783,0.0001882171,0.0007698062,0.0009555071,0.08287149,0.02443342,0.0009929739,0.007274153,0.0000551069],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9927043,0.0002281366,0.004770065,0.0000362603,0.000005025751,0.00001327166,0.001638903,0.00003912598,0.0005650655],"genre_scores_gemma":[0.975771,0.0002570041,0.01444111,0.00003592273,0.000006831466,0.00003122638,0.008921904,0.0000464572,0.0004884215],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.004060238,"threshold_uncertainty_score":0.008073211,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07098747024566042,"score_gpt":0.3263263531423141,"score_spread":0.2553388828966536,"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."}}