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Uraki23 - 10.1016/S1473-3099(23)00070-1 #789 (#791)
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* add Uraki23

* add antibodies

* correct vaccines

* correct vaccines

* update subject names

* update rx_names

* Update vaccines

* update plasma collection dates

* update vaccines

* add Uraki23

* add antibodies

* correct vaccines

* correct vaccines

* update subject names

* update rx_names

* Update vaccines

* update plasma collection dates

* update vaccines

* Autogenerated data updated by HIVDB Bot

* Delete covid-drdb-payload

* Autogenerated data updated by HIVDB Bot

* Add Supplemental Figure 2B

* Autogenerated data updated by HIVDB Bot

* update dates

* correct compounds

* Autogenerated data updated by HIVDB Bot

* IC50->EC50

* remove duplicate isolate

* update date_added

* antibodies EC50->IC50

* update subject counts

---------

Co-authored-by: HIVDB Bot <[email protected]>
Co-authored-by: Philip Tzou <[email protected]>
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@shegocaga @hivdb-bot @philiptzou
3 people authored Apr 5, 2023
1 parent 8acd58c commit 9a57288
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Showing 14 changed files with 490 additions and 1 deletion.
17 changes: 17 additions & 0 deletions excluded/rx_antibodies/uraki23-mab.csv
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ref_name,rx_name,ab_name
Uraki23,Remdesivir,Remdesivir
Uraki23,Remdesivir,Remdesivir
Uraki23,Remdesivir,Remdesivir
Uraki23,Remdesivir,Remdesivir
Uraki23,Molnupiravir,Molnupiravir
Uraki23,Molnupiravir,Molnupiravir
Uraki23,Molnupiravir,Molnupiravir
Uraki23,Molnupiravir,Molnupiravir
Uraki23,Nirmatrelvir,Nirmatrelvir
Uraki23,Nirmatrelvir,Nirmatrelvir
Uraki23,Nirmatrelvir,Nirmatrelvir
Uraki23,Nirmatrelvir,Nirmatrelvir
Uraki23,Ensitrelvir,Ensitrelvir
Uraki23,Ensitrelvir,Ensitrelvir
Uraki23,Ensitrelvir,Ensitrelvir
Uraki23,Ensitrelvir,Ensitrelvir
1 change: 1 addition & 0 deletions tables/articles.csv
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Expand Up @@ -758,3 +758,4 @@ Spinicci22,10.1007/s10875-022-01313-6,NULL,"Spinicci, M",2022,2023-03-30,NULL
Han23,NULL,https://www.askgileadmedical.com/docs/conference/Han_SARS-CoV-2%20Replicon%20System%20for%20the%20Phenotypic%20Evaluation%20of%20Nsp%20Gene%20Substitutions@pdf,"Han, D",2023,2023-03-31,NULL
Chaguza23,10.1016/j.xcrm.2023.100943,NULL,"Chaguze, C",2023,2023-03-31,NULL
Fournelle22,10.1101/2022.10.19.512884,NULL,"Fournelle, D",2022,2023-03-31,NULL
Uraki23,10.1016/S1473-3099(23)00070-1,NULL,"Uraki, R",2023,2023-04-05,NULL
76 changes: 76 additions & 0 deletions tables/isolate_mutations.d/uraki23-isomuts.csv
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iso_name,gene,position,amino_acid,count,total
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp1,47,R,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp1,135,R,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,PLpro,24,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,PLpro,489,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,PLpro,1300,D,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp4,264,F,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp4,327,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp4,438,F,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp4,492,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,_3CLpro,132,H,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp6,106,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp6,107,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp6,108,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,RdRP,323,L,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,RdRP,671,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp13,36,P,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp13,392,C,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp14,42,V,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,nsp15,112,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,19,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,24,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,25,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,26,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,27,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,83,A,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,142,D,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,144,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,146,Q,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,183,E,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,213,E,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,252,V,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,339,H,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,346,T,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,368,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,371,F,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,373,P,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,375,F,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,376,A,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,405,N,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,408,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,417,N,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,440,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,445,P,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,446,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,460,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,477,N,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,478,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,484,A,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,486,P,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,490,S,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,498,R,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,501,Y,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,505,H,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,614,G,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,655,Y,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,679,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,681,H,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,764,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,796,Y,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,954,H,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,S,969,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,ORF3a,223,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,E,9,I,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,E,11,A,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,M,19,E,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,M,63,T,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,ORF6,61,L,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,ORF8,8,stop,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,13,L,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,31,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,32,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,33,del,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,203,K,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,204,R,NULL,NULL
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,N,413,R,NULL,NULL
2 changes: 2 additions & 0 deletions tables/isolates.d/uraki23-iso.csv
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iso_name,var_name,site_directed,gisaid_id,genbank_accn,sra_accn,expandable
hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022,Omicron/XBB.1.5,FALSE,16543623,NULL,NULL,TRUE
7 changes: 7 additions & 0 deletions tables/ref_isolate_pairs/uraki23-pair.csv
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ref_name,control_iso_name,iso_name
Uraki23,Wuhan-Hu-1,hCoV-19/Japan/UT-NCD1288-2N/2022
Uraki23,Wuhan-Hu-1,hCoV-19/Japan/TY41-795-P0/2022
Uraki23,Wuhan-Hu-1,hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022
Uraki23,hCoV-19/Japan/UT-NCD1288-2N/2022,Wuhan-Hu-1
Uraki23,hCoV-19/Japan/UT-NCD1288-2N/2022,hCoV-19/Japan/TY41-795-P0/2022
Uraki23,hCoV-19/Japan/UT-NCD1288-2N/2022,hCoV-19/USA/MD-HP40900-PIDYSWHNUB-P2/2022
11 changes: 11 additions & 0 deletions tables/rx_antibodies/uraki23-mab.csv
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ref_name,rx_name,ab_name
Uraki23,Imdevimab,Imdevimab
Uraki23,Casirivimab,Casirivimab
Uraki23,Imdevimab+Casirivimab,Imdevimab
Uraki23,Imdevimab+Casirivimab,Casirivimab
Uraki23,Tixagevimab,Tixagevimab
Uraki23,Cilgavimab,Cilgavimab
Uraki23,Tixagevimab+Cilgavimab,Tixagevimab
Uraki23,Tixagevimab+Cilgavimab,Cilgavimab
Uraki23,S309,Sotrovimab
Uraki23,Bebtelovimab,Bebtelovimab
5 changes: 5 additions & 0 deletions tables/rx_compounds/uraki23-drug.csv
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ref_name,rx_name,drug_name
Uraki23,Remdesivir,Remdesivir
Uraki23,Molnupiravir,Molnupiravir
Uraki23,Nirmatrelvir,Nirmatrelvir
Uraki23,Ensitrelvir,Ensitrelvir
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