{"id":"W3092684668","doi":"10.3390/v12101164","title":"Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism","year":2020,"lang":"en","type":"article","venue":"Viruses","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":70,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Medical Research Council; U.S. Food and Drug Administration; Hamilton Health Sciences Foundation; King Fahad Medical City; Biotechnology and Biological Sciences Research Council; Public Health England; National Institute for Health and Care Research; National Institute for Health Research Health Protection Research Unit; University of Liverpool; Wellcome Trust","keywords":"Amplicon; Biology; Genome; Minion; Virology; Genetics; Coronavirus; DNA sequencing; Computational biology; Polymerase chain reaction; Gene; Nanopore sequencing; Coronavirus disease 2019 (COVID-19); Medicine; Disease; Infectious disease (medical specialty)","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":[0.0003404194,0.0004193554,0.0003780696,0.0007575275,0.0002019584,0.0003727736,0.0002413262,0.0004154861,0.0007828958],"category_scores_gemma":[0.0009096903,0.0002924527,0.0003987525,0.0004550572,0.0002164326,0.0001681506,0.000304778,0.0003754461,0.0004497045],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002186722,"about_ca_system_score_gemma":0.0002201968,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001234859,"about_ca_topic_score_gemma":0.002932803,"domain_scores_codex":[0.9994746,0.00007443915,0.00005178252,0.0001571824,0.0001752915,0.00006670481],"domain_scores_gemma":[0.9996891,0.00008750104,0.00005835094,0.00002748193,0.0001020237,0.0000354797],"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":[0.0005484094,0.00009258038,0.05140904,0.0001629477,0.00006218398,0.001247629,0.0008572061,0.0004230987,0.931011,0.0001212175,0.0002879892,0.01377677],"study_design_scores_gemma":[0.00004874926,0.001326122,0.3526917,0.0001117415,0.0002199361,0.006233056,0.001270389,0.01363824,0.6162279,0.0003194014,0.007867165,0.0000454991],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9845518,0.0006781793,0.0112028,0.00007767676,0.00003383377,0.0001895299,0.001610744,0.000159799,0.001495772],"genre_scores_gemma":[0.9659481,0.0006533494,0.02826184,0.000296432,0.00001832882,0.00014936,0.003117388,0.00006803198,0.001487294],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001234859,"threshold_uncertainty_score":0.002619088,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.09573910230631716,"score_gpt":0.3344596861896819,"score_spread":0.2387205838833648,"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."}}