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Yisimayi23 - 10.1101/2023.05.01.538516 #907 #986

Merged
merged 28 commits into from
Oct 3, 2023
Merged

Yisimayi23 - 10.1101/2023.05.01.538516 #907 #986

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85b52cf
init yisimayi23
shegocaga Jun 30, 2023
ef2ee86
annotate rx_potency
shegocaga Jun 30, 2023
1eac807
update annotations
shegocaga Jun 30, 2023
69176c7
group 1A, 1B
shegocaga Jun 30, 2023
cc051e4
add yisimayi23-pot
shegocaga Sep 11, 2023
61b1a9a
init yisimayi23
shegocaga Jun 30, 2023
f77b042
annotate rx_potency
shegocaga Jun 30, 2023
971597e
update annotations
shegocaga Jun 30, 2023
cd7eb33
group 1A, 1B
shegocaga Jun 30, 2023
485e6c3
add yisimayi23-pot
shegocaga Sep 11, 2023
04ad075
update potency
shegocaga Sep 28, 2023
7c79a7f
complete potency
shegocaga Sep 28, 2023
2a2ca88
add yisimayi23
shegocaga Sep 30, 2023
fa9ed8e
Merge branch 'yisimayi23' of github.com:zachandfox/covid-drdb-payload…
shegocaga Sep 30, 2023
c8752fc
update treatments
shegocaga Oct 2, 2023
6886d78
correct treatments
shegocaga Oct 2, 2023
7e07311
Merge branch 'master' into yisimayi23
shegocaga Oct 2, 2023
ea1a27c
correct yisimayi23-mab.csv
shegocaga Oct 2, 2023
b096ada
update vaccines.csv
shegocaga Oct 2, 2023
80053b4
clarify subject names
shegocaga Oct 3, 2023
6c989a7
add to subjects.csv
shegocaga Oct 3, 2023
e715f1a
drop duplicate potency
shegocaga Oct 3, 2023
27882b5
add missing subject
shegocaga Oct 3, 2023
4011e1c
correct isolates
shegocaga Oct 3, 2023
dfa7e03
Add missing vaccine combinations
shegocaga Oct 3, 2023
7682b8f
move un-paired records to excluded
shegocaga Oct 3, 2023
d2f830f
Autogenerated data updated by HIVDB Bot
hivdb-bot Oct 3, 2023
15b817c
correct date_added
shegocaga Oct 3, 2023
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7 changes: 7 additions & 0 deletions excluded/rx_plasma/yisimayi23-plasma.csv
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ref_name,subject_name,rx_name,collection_date_cmp,collection_date,location,cumulative_group,section
Yisimayi23,BA5_spike_mRNA_1ug_2x_mouse,BA5_spike_mRNA_1ug_2x_mouse,~,2022-09-22,China,BA5_spike_mRNA_1ug_2x_mouse,NULL
Yisimayi23,BQ11_spike_mRNA_1ug_2x_mouse,BQ11_spike_mRNA_1ug_2x_mouse,~,2022-09-22,China,BQ11_spike_mRNA_1ug_2x_mouse,NULL
Yisimayi23,XBB_spike_mRNA_1ug_2x_mouse,XBB_spike_mRNA_1ug_2x_mouse,~,2022-09-22,China,XBB_spike_mRNA_1ug_2x_mouse,NULL
Yisimayi23,BA5_spike_mRNA_10ug_2x_mouse,BA5_spike_mRNA_10ug_2x_mouse,~,2022-09-22,China,BA5_spike_mRNA_10ug_2x_mouse,NULL
Yisimayi23,BQ11_spike_mRNA_10ug_2x_mouse,BQ11_spike_mRNA_10ug_2x_mouse,~,2022-09-22,China,BQ11_spike_mRNA_10ug_2x_mouse,NULL
Yisimayi23,XBB_spike_mRNA_10ug_2x_mouse,XBB_spike_mRNA_10ug_2x_mouse,~,2022-09-22,China,XBB_spike_mRNA_10ug_2x_mouse,NULL
13 changes: 13 additions & 0 deletions excluded/rx_potency/yisimayi23-pot.csv
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ref_name,rx_name,iso_name,section,assay_name,potency_type,potency,cumulative_count,potency_upper_limit,potency_lower_limit,potency_unit,date_added
Yisimayi23,BA5_spike_mRNA_1ug_2x_mouse,BA.4/5 Spike,Figure 1E,Pseudovirus (VSV),NT50,30018,10,1000000,30,NULL,2023-09-28
Yisimayi23,BQ11_spike_mRNA_1ug_2x_mouse,BQ.1.1 Spike,Figure 1E,Pseudovirus (VSV),NT50,17683,10,1000000,30,NULL,2023-09-28
Yisimayi23,XBB_spike_mRNA_1ug_2x_mouse,XBB Spike,Figure 1E,Pseudovirus (VSV),NT50,8992,10,1000000,30,NULL,2023-09-28
Yisimayi23,BA5_spike_mRNA_10ug_2x_mouse,BA.4/5 Spike,Figure 1E,Pseudovirus (VSV),NT50,52730,10,1000000,30,NULL,2023-09-28
Yisimayi23,BQ11_spike_mRNA_10ug_2x_mouse,BQ.1.1 Spike,Figure 1E,Pseudovirus (VSV),NT50,35633,10,1000000,30,NULL,2023-09-28
Yisimayi23,XBB_spike_mRNA_10ug_2x_mouse,XBB Spike,Figure 1E,Pseudovirus (VSV),NT50,20946,10,1000000,30,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,CH11,Figure 2B,Pseudovirus (VSV),NT50,29,66,1000000,20,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,BQ11,Figure 2B,Pseudovirus (VSV),NT50,93,66,1000000,20,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,XBB,Figure 2B,Pseudovirus (VSV),NT50,29,66,1000000,20,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,XBB15,Figure 2B,Pseudovirus (VSV),NT50,31,66,1000000,20,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,XBB116,Figure 2B,Pseudovirus (VSV),NT50,31,66,1000000,20,NULL,2023-09-28
Yisimayi23,BA5orBF7_BTI,XBB1510,Figure 2B,Pseudovirus (VSV),NT50,23,66,1000000,20,NULL,2023-09-28
13 changes: 13 additions & 0 deletions excluded/subject_vaccines/yisimayi23-vacc.csv
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ref_name,subject_name,vaccination_date_cmp,vaccination_date,vaccine_name,dosage,location,section
Yisimayi23,BA5_spike_mRNA_1ug_2x_mouse,~,2022-09-01,mRNA_BA5,1,China,NULL
Yisimayi23,BA5_spike_mRNA_1ug_2x_mouse,~,2022-09-15,mRNA_BA5,2,China,NULL
Yisimayi23,BQ11_spike_mRNA_1ug_2x_mouse,~,2022-09-01,mRNA_BQ11,1,China,NULL
Yisimayi23,BQ11_spike_mRNA_1ug_2x_mouse,~,2022-09-15,mRNA_BQ11,2,China,NULL
Yisimayi23,XBB_spike_mRNA_1ug_2x_mouse,~,2022-09-01,mRNA_XBB,1,China,NULL
Yisimayi23,XBB_spike_mRNA_1ug_2x_mouse,~,2022-09-15,mRNA_XBB,2,China,NULL
Yisimayi23,BA5_spike_mRNA_10ug_2x_mouse,~,2022-09-01,mRNA_BA5,1,China,NULL
Yisimayi23,BA5_spike_mRNA_10ug_2x_mouse,~,2022-09-15,mRNA_BA5,2,China,NULL
Yisimayi23,BQ11_spike_mRNA_10ug_2x_mouse,~,2022-09-01,mRNA_BQ11,1,China,NULL
Yisimayi23,BQ11_spike_mRNA_10ug_2x_mouse,~,2022-09-15,mRNA_BQ11,2,China,NULL
Yisimayi23,XBB_spike_mRNA_10ug_2x_mouse,~,2022-09-01,mRNA_XBB,1,China,NULL
Yisimayi23,XBB_spike_mRNA_10ug_2x_mouse,~,2022-09-15,mRNA_XBB,2,China,NULL
1,567 changes: 1,567 additions & 0 deletions tables/antibodies.csv
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1 change: 1 addition & 0 deletions tables/articles.csv
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Expand Up @@ -792,3 +792,4 @@ Flynn23,10.1021/acsinfecdis.3c00125,NULL,"Flynn, JM",2023,2023-08-16,NULL
Yang23,10.1101/2023.09.01.555815,NULL,"Yang, S",2023,2023-09-11,NULL
Hu23,10.1021/acscentsci.3c00538,NULL,"Hu, Y",2023,2023-09-18,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
395 changes: 395 additions & 0 deletions tables/isolate_mutations.csv
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9 changes: 9 additions & 0 deletions tables/isolates.csv
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Expand Up @@ -1635,3 +1635,12 @@ EG.5 Spike,Omicron/EG.5,FALSE,NULL,NULL,NULL,TRUE
EG.5.1 Spike,Omicron/EG.5.1,FALSE,NULL,NULL,NULL,TRUE
FL.1.5.1 Spike,Omicron/FL.1.5.1,FALSE,NULL,NULL,NULL,TRUE
Omicron/BN.1 full genome,Omicron/BN.1,FALSE,NULL,NULL,NULL,TRUE
BQ.1.18 Spike,Omicron/BQ.1.18,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5.10 Spike,Omicron/XBB.1.5.10,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y,Omicron/XBB.1.5/K478R/F456L/H505Y,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P+Y453F,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P/Y453F,FALSE,NULL,NULL,NULL,TRUE
XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P+Y453F+N405K,Omicron/XBB.1.5/K478R/F456L/H505Y/R403K/K444T/K440N/A484P/Y453F/N405K,FALSE,NULL,NULL,NULL,TRUE
23 changes: 23 additions & 0 deletions tables/ref_isolate_pairs/yisimayi23-pair.csv
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ref_name,control_iso_name,iso_name
Yisimayi23,S:614G,BA.4/5 Spike
Yisimayi23,S:614G,BQ.1.1 Spike
Yisimayi23,S:614G,XBB Spike
Yisimayi23,S:614G,BA.1 Spike
Yisimayi23,S:614G,BQ.1.18 Spike
Yisimayi23,S:614G,SARS-CoV Spike
Yisimayi23,S:614G,BA.2 Spike
Yisimayi23,S:614G,BF.7 Spike
Yisimayi23,S:614G,CH.1.1 Spike
Yisimayi23,S:614G,XBB.1.5 Spike
Yisimayi23,S:614G,XBB.1.16 Spike
Yisimayi23,S:614G,XBB.1.5.10 Spike
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P+Y453F
Yisimayi23,S:614G,XBB.1.5 Spike:K478R+F456L+H505Y+R403K+K444T+K440N+A484P+Y453F+N405K
Yisimayi23,S:614G,BA.2.75 Spike
Yisimayi23,S:614G,BA.2.75.2 Spike
Yisimayi23,S:614G,BQ.1 Spike
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