{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003009411,0.0001228462,0.0002598122,0.0002920447,0.00003460742,0.00002298482,0.0001082777,0.00007491316,9.987405e-7],"category_scores_gemma":[0.0002328919,0.00009446056,0.00002148762,0.0003839584,0.0001651007,0.0001636258,0.00003971583,0.0002182296,8.11094e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000173754,"about_ca_system_score_gemma":0.0002350808,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.009845875,"about_ca_topic_score_gemma":0.006534304,"domain_scores_codex":[0.9987584,0.0001592787,0.0003667081,0.0002901435,0.0002712224,0.0001541919],"domain_scores_gemma":[0.9994281,0.0001810397,0.000138626,0.0001775263,0.00004814951,0.00002657222],"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":[0.0008447919,0.00008463302,0.3717106,0.000144023,0.000007966167,0.000007129818,0.002346994,0.000006890065,0.6246303,0.000004703321,4.075494e-7,0.0002115578],"study_design_scores_gemma":[0.002840052,0.0005634996,0.2413635,0.00008765745,0.0000157454,6.92818e-7,0.0007449061,0.001212255,0.7529403,0.00008850983,0.00006480594,0.00007808995],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9975443,0.0001926259,0.0009411258,0.0001953743,0.00001172836,0.001027407,0.000068336,0.00001345382,0.000005599886],"genre_scores_gemma":[0.9905922,0.000007437298,0.00006697854,0.009190924,0.00001515294,0.00009936089,0.00001479095,0.00001303849,5.706746e-8],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1303472,"threshold_uncertainty_score":0.9967477,"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."}}