Uriu23b - 10.1101/2023.09.07.556636 (#988)

* add uriu23b

* correct IC50 upper limit

* NT50 -> IC50 for mAb potency records

* correct section

* correct IC50 units

* ug/ml -> μg/ml

* correct units

* µg/ml -> ng/ml

* update upper-limit, set ceiling of potency values for IC50

* Autogenerated data updated by HIVDB Bot

---------

Co-authored-by: HIVDB Bot <[email protected]>

tables/articles.csv

@@ -795,5 +795,6 @@ Hu23,10.1021/acscentsci.3c00538,NULL,"Hu, Y",2023,2023-09-18,NULL
 Bruel23,10.1101/2023.05.25.23290512,NULL,"Bruel, T",2023,2023-09-25,NULL
 Yang23b,10.3346/jkms.2023.38.e205,NULL,"Yang, J",2023,2023-09-21,NULL
 Yisimayi23,10.1101/2023.05.01.538516,NULL,"Yisimayi, A",2023,2023-09-29,NULL
+Uriu23b,10.1101/2023.09.07.556636,NULL,"Uriu, K",2023,2023-10-03,NULL
 Ju23,10.1093/nsr/nwad148,NULL,"Ju, B",2023,2023-10-04,NULL
 Sheward23,10.1101/2023.09.02.556033,NULL,"Sheward, D",2023,2023-10-03,NULL

tables/ref_isolate_pairs/uriu23b-pair.csv

@@ -0,0 +1,4 @@
+ref_name,control_iso_nam,iso_name
+Uriu23b,B.1 Spike,BA.2 Spike
+Uriu23b,B.1 Spike,EG.5.1 Spike
+Uriu23b,B.1 Spike,BA.2.86 Spike

tables/rx_antibodies/uriu23b-mab.csv

@@ -0,0 +1,7 @@
+ref_name,rx_name,ab_name
+Uriu23b,Bebtelovimab,Bebtelovimab
+Uriu23b,Sotrovimab,Sotrovimab
+Uriu23b,Cilgavimab,Cilgavimab
+Uriu23b,Tixagevimab,Tixagevimab
+Uriu23b,Evusheld,Cilgavimab
+Uriu23b,Evusheld,Tixagevimab

tables/rx_potency/uriu23b-pot.csv

@@ -0,0 +1,41 @@
+ref_name,rx_name,iso_name,section,assay_name,potency_type,potency,cumulative_count,potency_upper_limit,potency_lower_limit,potency_unit,date_added
+Uriu23b,monovalent_3dose,B.1 Spike,Figure 1F,Pseudovirus (lentivirus),NT50,2002,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_3dose,BA.2 Spike,Figure 1F,Pseudovirus (lentivirus),NT50,446,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_3dose,EG.5.1 Spike,Figure 1F,Pseudovirus (lentivirus),NT50,44,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_3dose,BA.2.86 Spike,Figure 1F,Pseudovirus (lentivirus),NT50,48,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_4dose,B.1 Spike,Figure 1G,Pseudovirus (lentivirus),NT50,3203,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_4dose,BA.2 Spike,Figure 1G,Pseudovirus (lentivirus),NT50,893,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_4dose,EG.5.1 Spike,Figure 1G,Pseudovirus (lentivirus),NT50,55,15,100000,40,NULL,2023-10-03
+Uriu23b,monovalent_4dose,BA.2.86 Spike,Figure 1G,Pseudovirus (lentivirus),NT50,72,15,100000,40,NULL,2023-10-03
+Uriu23b,BA1_bivalent,B.1 Spike,Figure 1H,Pseudovirus (lentivirus),NT50,2031,21,100000,40,NULL,2023-10-03
+Uriu23b,BA1_bivalent,BA.2 Spike,Figure 1H,Pseudovirus (lentivirus),NT50,394,21,100000,40,NULL,2023-10-03
+Uriu23b,BA1_bivalent,EG.5.1 Spike,Figure 1H,Pseudovirus (lentivirus),NT50,41,21,100000,40,NULL,2023-10-03
+Uriu23b,BA1_bivalent,BA.2.86 Spike,Figure 1H,Pseudovirus (lentivirus),NT50,49,21,100000,40,NULL,2023-10-03
+Uriu23b,BA5_bivalent,B.1 Spike,Figure 1I,Pseudovirus (lentivirus),NT50,3813,13,100000,40,NULL,2023-10-03
+Uriu23b,BA5_bivalent,BA.2 Spike,Figure 1I,Pseudovirus (lentivirus),NT50,1008,13,100000,40,NULL,2023-10-03
+Uriu23b,BA5_bivalent,EG.5.1 Spike,Figure 1I,Pseudovirus (lentivirus),NT50,54,13,100000,40,NULL,2023-10-03
+Uriu23b,BA5_bivalent,BA.2.86 Spike,Figure 1I,Pseudovirus (lentivirus),NT50,63,13,100000,40,NULL,2023-10-03
+Uriu23b,XBB_BTI,B.1 Spike,Figure 1K,Pseudovirus (lentivirus),NT50,2724,15,100000,40,NULL,2023-10-03
+Uriu23b,XBB_BTI,BA.2 Spike,Figure 1K,Pseudovirus (lentivirus),NT50,1896,15,100000,40,NULL,2023-10-03
+Uriu23b,XBB_BTI,EG.5.1 Spike,Figure 1K,Pseudovirus (lentivirus),NT50,443,15,100000,40,NULL,2023-10-03
+Uriu23b,XBB_BTI,BA.2.86 Spike,Figure 1K,Pseudovirus (lentivirus),NT50,310,15,100000,40,NULL,2023-10-03
+Uriu23b,Bebtelovimab,B.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,5500,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Sotrovimab,B.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,200000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Cilgavimab,B.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,31000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Tixagevimab,B.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,4600,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Evusheld,B.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,5400,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Bebtelovimab,BA.2 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1400,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Sotrovimab,BA.2 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Cilgavimab,BA.2 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,37000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Tixagevimab,BA.2 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Evusheld,BA.2 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,60000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Bebtelovimab,EG.5.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,775000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Sotrovimab,EG.5.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,532000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Cilgavimab,EG.5.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Tixagevimab,EG.5.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Evusheld,EG.5.1 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Bebtelovimab,BA.2.86 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,775000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Sotrovimab,BA.2.86 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Cilgavimab,BA.2.86 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Tixagevimab,BA.2.86 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03
+Uriu23b,Evusheld,BA.2.86 Spike,Figure 1J,Pseudovirus (lentivirus),IC50,1000000,1,1000000,1,ng/ml,2023-10-03

tables/subject_infections/uriu23b-inf.csv

@@ -0,0 +1,2 @@
+ref_name,subject_name,infection_date_cmp,infection_date,infected_var_name,location,immune_status,severity,section
+Uriu23b,XBB_BTI,~,2023-07-15,Omicron_XBB.1.5_or_XBB.1.9_or_XBB.1.16,Japan,NULL,NULL,NULL

tables/subject_mixed.csv

@@ -28,4 +28,7 @@ Branche23,bivalent_BA1_booster_w_wo_inf,FALSE,FALSE,TRUE,FALSE
 Branche23,bivalent_BA4/5_booster_w_wo_inf,FALSE,FALSE,TRUE,FALSE
 Nair23,Vaccinee,TRUE,FALSE,FALSE,FALSE
 Yang23b,TIX_CIL_1dose,TRUE,TRUE,TRUE,FALSE
+Uriu23b,BA1_bivalent,FALSE,FALSE,TRUE,FALSE
+Uriu23b,BA5_bivalent,TRUE,TRUE,TRUE,FALSE
+Uriu23b,XBB_BTI,TRUE,TRUE,TRUE,TRUE
 Ju23,BA4or5_BTI_vacc_geq2dose,TRUE,TRUE,FALSE,FALSE

tables/subject_plasma/uriu23b-plasma.csv

@@ -0,0 +1,6 @@
+ref_name,subject_name,rx_name,collection_date_cmp,collection_date,location,cumulative_group,section
+Uriu23b,monovalent_3dose,monovalent_3dose,~,2022-02-18,Japan,monovalent_3dose,NULL
+Uriu23b,monovalent_4dose,monovalent_4dose,~,2022-08-25,Japan,monovalent_4dose,NULL
+Uriu23b,BA1_bivalent,BA1_bivalent,~,2022-10-26,Japan,BA1_bivalent,NULL
+Uriu23b,BA5_bivalent,BA5_bivalent,~,2022-11-22,Japan,BA5_bivalent,NULL
+Uriu23b,XBB_BTI,XBB_BTI,~,2023-08-11,Japan,XBB_BTI,NULL

tables/subject_vaccines/uriu23b-vacc.csv

@@ -0,0 +1,22 @@
+ref_name,subject_name,vaccination_date_cmp,vaccination_date,vaccine_name,dosage,location,section
+Uriu23b,monovalent_3dose,~,2021-04-09,BNT162b2,1,Japan,NULL
+Uriu23b,monovalent_3dose,~,2021-04-30,BNT162b2,2,Japan,NULL
+Uriu23b,monovalent_3dose,~,2022-01-24,BNT162b2,3,Japan,NULL
+Uriu23b,monovalent_4dose,~,2021-05-12,BNT162b2,1,Japan,NULL
+Uriu23b,monovalent_4dose,~,2021-06-04,BNT162b2,2,Japan,NULL
+Uriu23b,monovalent_4dose,~,2022-01-28,BNT162b2,3,Japan,NULL
+Uriu23b,monovalent_4dose,~,2022-08-02,BNT162b2,4,Japan,NULL
+Uriu23b,BA1_bivalent,~,2021-08-06,BNT162b2,1,Japan,NULL
+Uriu23b,BA1_bivalent,~,2021-09-08,BNT162b2,2,Japan,NULL
+Uriu23b,BA1_bivalent,~,2022-04-11,BNT162b2,3,Japan,NULL
+Uriu23b,BA1_bivalent,~,2022-10-02,BNT162b2_BA.1_bivalent,4,Japan,NULL
+Uriu23b,BA5_bivalent,~,2021-08-23,BNT162b2,1,Japan,NULL
+Uriu23b,BA5_bivalent,~,2021-09-17,BNT162b2,2,Japan,NULL
+Uriu23b,BA5_bivalent,~,2022-03-29,BNT162b2,3,Japan,NULL
+Uriu23b,BA5_bivalent,~,2022-10-28,BNT162b2_BA.1_bivalent,4,Japan,NULL
+Uriu23b,BA5_bivalent,~,2022-11-01,BNT162b2_BA.1_bivalent,5,Japan,NULL
+Uriu23b,XBB_BTI,~,2021-08-18,BNT162b2 or mRNA-1273,1,Japan,NULL
+Uriu23b,XBB_BTI,~,2021-09-04,BNT162b2 or mRNA-1273,2,Japan,NULL
+Uriu23b,XBB_BTI,~,2022-04-16,BNT162b2 or mRNA-1273,3,Japan,NULL
+Uriu23b,XBB_BTI,~,2022-08-22,BNT162b2 or mRNA-1273,4,Japan,NULL
+Uriu23b,XBB_BTI,~,2023-01-08,BNT162b2 or mRNA-1273,5,Japan,NULL

tables/subjects.csv

@@ -4451,6 +4451,11 @@ Uriu23,BA5_inf__P451,Human,NULL,1
 Uriu23,BA5_inf__P455,Human,NULL,1
 Uriu23,BA5_inf__P456,Human,NULL,1
 Uriu23,BA5_inf__P464,Human,NULL,1
+Uriu23b,BA1_bivalent,Human,NULL,1
+Uriu23b,BA5_bivalent,Human,NULL,1
+Uriu23b,XBB_BTI,Human,NULL,1
+Uriu23b,monovalent_3dose,Human,NULL,1
+Uriu23b,monovalent_4dose,Human,NULL,1
 Vacharathit21,CP_2020,Human,NULL,30
 Vacharathit21,CP_2021,Human,NULL,30
 Vacharathit21,CoronaVac,Human,NULL,60

tables/treatments.csv

@@ -6863,6 +6863,11 @@ Uraki23,Cilgavimab
 Uraki23,Tixagevimab+Cilgavimab
 Uraki23,S309
 Uraki23,Bebtelovimab
+Uriu23b,Bebtelovimab
+Uriu23b,Sotrovimab
+Uriu23b,Cilgavimab
+Uriu23b,Tixagevimab
+Uriu23b,Evusheld
 VanBlargan22,COV2-2196
 VanBlargan22,COV2-2130
 VanBlargan22,COV2-2196+COV2-2130
@@ -29638,6 +29643,11 @@ Uriu23,BA5_inf_13180
 Uriu23,BA5_inf_12912
 Uriu23,BA5_inf_14956
 Uriu23,BA5_inf_15707
+Uriu23b,monovalent_3dose
+Uriu23b,monovalent_4dose
+Uriu23b,BA1_bivalent
+Uriu23b,BA5_bivalent
+Uriu23b,XBB_BTI
 Vacharathit21,CoronaVac_1
 Vacharathit21,CoronaVac_10
 Vacharathit21,CoronaVac_100

tables/variants.csv

@@ -480,3 +480,4 @@ Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N,FALSE,FALSE
 Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P,FALSE,FALSE
 Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P/Y453F,FALSE,FALSE
 Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P/Y453F/N405K,FALSE,FALSE
+Omicron_XBB.1.5_or_XBB.1.9_or_XBB.1.16,FALSE,FALSE