{"id":"W4389298812","doi":"10.1128/spectrum.02979-23","title":"Targeted amplification-based whole genome sequencing of <i>Monkeypox virus</i> in clinical specimens","year":2023,"lang":"en","type":"article","venue":"Microbiology Spectrum","topic":"Poxvirus research and outbreaks","field":"Immunology and Microbiology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Impact; McMaster University; University of Toronto; Public Health Ontario","funders":"","keywords":"Genome; Biology; Amplicon; Whole genome sequencing; Outbreak; Primer (cosmetics); Metagenomics; Novel virus; DNA sequencing; Phylogenetic tree; Monkeypox; Genetics; Computational biology; Virology; Polymerase chain reaction; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0004400757,0.000403622,0.0004412895,0.0005282406,0.0002948016,0.0007292093,0.0002334697,0.0005572615,0.0007326811],"category_scores_gemma":[0.0009860463,0.0002331937,0.000559077,0.0005386958,0.000286575,0.0002126447,0.0003953741,0.0004234631,0.0005799002],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000246796,"about_ca_system_score_gemma":0.000374942,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001065761,"about_ca_topic_score_gemma":0.001160623,"domain_scores_codex":[0.9993948,0.0001012567,0.00004809427,0.00021935,0.0001646825,0.00007179927],"domain_scores_gemma":[0.9996829,0.00008016796,0.00006248603,0.00004770259,0.00009824266,0.00002857177],"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":[0.0001889722,0.00003942218,0.01792581,0.0002494052,0.00007449292,0.0002885458,0.0002149661,0.0007136043,0.9695902,0.0001041978,0.0003169591,0.01029341],"study_design_scores_gemma":[0.0000606946,0.001352338,0.2394715,0.0002013623,0.0003648244,0.005354398,0.0009159627,0.0148567,0.7195302,0.0006021837,0.01723882,0.0000510337],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"methods","genre_scores_codex":[0.9479802,0.00170711,0.04085131,0.0001640478,0.00005424383,0.0005411931,0.006601877,0.0003516286,0.001748316],"genre_scores_gemma":[0.9357867,0.001027694,0.04890737,0.0003065687,0.00004505729,0.0002876686,0.0125531,0.0001626967,0.0009230876],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.001065761,"threshold_uncertainty_score":0.002451122,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03355892652363702,"score_gpt":0.2960499114148246,"score_spread":0.2624909848911876,"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."}}